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\title{\bf Transcription-dependent DNA supercoils determine the 3D organization of dinoflagellate genomes}
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\author[1,,*,$\#$]{Georgi K. Marinov}
\author[3,7,*]{Alexandro E. Trevino}
\author[2,8,*]{Tingting Xiang}
\author[1]{John R. Pringle}
\author[1,6]{Anshul Kundaje}
\author[2]{Arthur R. Grossman}
\author[1,3,4,5,$\#$]{William J. Greenleaf}
\renewcommand\Affilfont{\itshape\small}
\affil[1]{Department of Genetics, Stanford University, Stanford, California 94305, USA}
\affil[2]{Carnegie Institution for Science, Department of Plant Biology, Stanford, California 94305, USA}
\affil[3]{Center for Personal Dynamic Regulomes, Stanford University, Stanford, California 94305, USA}
\affil[4]{Department of Applied Physics, Stanford University, Stanford, California 94305, USA}
\affil[5]{Chan Zuckerberg Biohub, San Francisco, California, USA}
\affil[6]{Department of Computer Science, Stanford University, Stanford, California 94305, USA}
\affil[7]{Department of Bioengineering, Stanford University, Stanford, California 94305, USA}
\affil[8]{Department of  Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223, USA}
\affil[*]{These authors contributed equally to this work}
\affil[$\#$]{Corresponding author}
\date{}

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\begin{abstract}

\noindent {\normalsize \textbf{Dinoflagellate chromosomes represent a unique evolutionary experiment, as they exist in a permanently condensed, liquid crystalline state, are not packaged by histones, and genes are organized into polycistronic arrays, with little transcriptional regulation. We analyze the 3D genome of \textit{Breviolum minutum}, and find large topological domains without chromatin loops, demarcated by convergent gene array boundaries (``dinoTADs’’). Transcriptional inhibition degrades dinoTADs, implicating transcription-induced supercoiling as the primary topological force in dinoflagellates.}
}
\centerline{}
\centerline{}
\end{abstract}

\begin{multicols}{2}

\begin{figure*}[!ht]
\begin{center}
\includegraphics[width=18.5cm]{Fig1-V6.png}
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\caption{
{\bf \textit{B. minutum} genome is physically partitioned into dinoTADs defined by polycistronic gene arrays}. 
(A) Hi-C scaffolding of the \textit{B. minutum} draft genome assembly. 
(B) Inset from (A). KR-normalized 5-kb resolution Hi-C map for pseudochromosome 10. 
(C) Inset from (B). Hi-C loops and stripes are not observed in dinoTADs. 
(D) Scales of chromosome size with dinoTAD number.
(E) Comparison of human and \textit{B. minutum} topological domain sizes.
(F) Hi-C map for pseudochromosome 10 together with forward- and reverse-strand transcript levels and gene arrays. 
(G) Average Hi-C contacts across dinoTAD boundaries.
(H) Average forward- and reverse-strand RNA-seq levels across dinoTAD boundaries.
}
\label{Fig1}
\end{figure*}

Investigations into the 3D organization of genomes have identified multiple mechanisms underlying genome folding\cite{Szabo2019}. Two main forces are thought to drive it -- associations between similar chromatin states determine formation of compartments, a mechanism probably present in most eukaryotes, while constraints on cohesin-mediated loop extrusion, imposed in vertebrates by CTCF, generate topologically associating domains (TADs). 

Three-dimensional genome architecture has functional consequences for gene regulation, organismal development, replication, mutational processes, and others, but how functional activity itself impacts genome organization is still poorly understood. There has also been little exploration of 3D organization across eukaryotes, even though major deviations from conventional eukaryotic norms are known to exist, presenting natural experiments that may reveal deeper underlying organizational principles masked in other lineages.

Dinoflagellates are the most radical such departure. They are a diverse, widespread clade playing major roles in aquatic ecosystems, for example, as symbioints of corals, providing the metabolic basis for reef ecosystems. Dinoflagellates possess numerous highly divergent molecular features\cite{Hackett2004}, including, uniquely among eukaryotes, the loss of nucleosomal packaging of chromatin. Histones are extremely conserved across eukaryotes, were present in their current form already in the Last Eukaryotic Common Ancestor\cite{Postberg2010}, and they and their posttranslational modifications are pivotal to all biochemical processes involving chromatin.

Dinoflagellates are the sole known exception. Their chromosomes exist in a liquid crystalline state, are permanently condensed throughout the cell cycle, and, although highly divergent histone genes are retained in their genomes\cite{Marinov2015}, a combination of virus-derived nucleoproteins and bacterial-derived histone-like proteins have taken over as main packaging components\cite{Jano2017}. Dinoflagellate genomes are often huge (up to $\geq$100 Gbp), genes are organized into polycistronic gene arrays, individual mRNAs are generated through \textit{trans}-splicing, and transcriptional regulation is largely absent. These fascinating features simultaneously pose intriguing questions regarding the adaptation of transcriptional and regulatory mechanisms to the absence of nucleosomes, and provide a unique opportunity to explore the biophysical forces underlying genomic organization in the context of a large eukaryotic genome in which nucleosomes are absent.

We address these questions by studying the 3D genome of the coral symbiont \textit{Breviolum minutum}. We generated multiple Hi-C libraries, including one for cells grown at elevated temperature, obtained $\sim$150--220 million Hi-C contacts for each (Supplementary Table \ref{TableS1}), pooled reads and used them to generate a chromosome-level scaffolding of the previously fragmented \textit{B. minutum} assembly\cite{Shoguchi2013}. We identified 91 major pseudochromosomes ($\geq$ 500 kbp), encompassing $\sim$94\% of the total sequence (Fig. \ref{Fig1}A-B; Supplementary Fig. \ref{FigS1}A), the longest being $\sim$11 Mbp in size, with a median length of 6.7 Mbp (Supplementary Fig. \ref{FigS1}A). At 1-Mbp resolution, they exhibit a bipartite (occasionally tripartite) structure (Supplementary Fig. \ref{FigS2}). 

% This assembly underestimates the total genome size, as the original set of contigs clearly contains a number of collapsed repeats, which is common feature of Hi-C-based genome assemblies (Figure \ref{Fig1}A, lower right). While previous reports suggest the existence of $\sim$20 chromosomes based on microscopy images \cite{Shoguchi2013}, Hi-C analysis strongly suggests the physical separation of a larger number of pseudochromosomes in the nucleus, as does the recent chromosome-level assembly of \textit{F. kawagutii} (another Symbiodiniaceae species) \cite{Li2020}. 

High-resolution maps revealed strong topological domains, $\leq$200--$\geq$2 Mbp in size (Fig. \ref{Fig1}B-E; Supplementary Fig. \ref{FigS3}--\ref{FigS13}). In mammals, TAD boundaries are demarcated by CTCF sites blocking loop extrusion, reflected by chromatin loops and ``stripes''. We find no loop or stripe features in \textit{B. minutum} (Fig. \ref{Fig1}C), suggesting a different mechanism for the formation of dinoflagellate TADs, which we term ``dinoTADs''. DinoTAD number correlates with chromosome size (Fig. \ref{Fig1}D), and they are considerably larger than mammalian TADs (Fig. \ref{Fig1}E).

We then compared Hi-C maps to available annotation features. Remarkably, we find that each dinoTAD corresponds to a pair of divergent gene arrays (Fig. \ref{Fig1}F), and dinoTAD boundaries coincide with convergence between gene arrays (Fig. \ref{Fig1}G-H). 

\begin{figure*}[!ht]
\begin{center}
\includegraphics[width=18.5cm]{Fig3-V5.png}
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\caption{
{\bf Decompaction of dinoTADs upon transcriptional inhibition and the transcription-induced supercoiling model for their formation}. Shown is pseudochromosome 10. 
(A-B) Outline of transcription inhibition time course experiments.
(C) Comparison of cell function, measured by PSII photosythetic efficiency, and cell viability, measured by colony formation (right), between $\alpha$-amanitin-treated and untreated cells. 
(D) KR-normalized Hi-C maps (50-kb resolution) show marked loss of dinoTADs after $\alpha$-amanitin treatment.
(E) Hi-C maps show reduction of insulation at dinoTAD boundaries after triptolide treatment.
(F) Metaplots of Hi-C signal around domain boundaries (50-kb resolution).
(G) Amplification of \textit{TOP2} and \textit{TOP3} topoisomerases in dinoflagellates (based on MMETSP\cite{MMETSP} transcriptome assemblies). 
(H) Transcription-induced supercoiling as driver of dinoflagellate chromatin folding. Transcribing polymerases introduce negative/positive DNA supercoiling behind/ahead of the transcription machinery. Interactions within supercoiled domains could explain the physical association of divergently-oriented arrays. Topological insulation could be driven by supercoiling-related effects, or by specific boundary elements. The exact role of the expanded repertoire of topoisomerases is also currently unclear. 
\label{Fig2}}
\end{center}
\end{figure*}

% Numerous models for dinoflagellate chromosome organization have been suggested since the 1960s, primarily based on electron microscopy. These include proposals that chromosomes are organized as ``toroidal chromonemas'' \cite{Oakley1979}, ``stacks of discs'' \cite{Livolant1978}, ``cored pineapples'' \cite{Levi2008}, or around ``central core fibers'' \cite{Spector1981}. Most of these models imply specific topological constraints maintaining the proposed shapes. 

The correspondence between gene arrays and dinoTADs suggests a role for transcription-dependent DNA supercoiling in the formation of the latter. Transcription inducing self-interacting domains has been previously demonstrated in bacteria\cite{Le2013}, and similar mechanisms have been proposed to explain some topological features in fission yeast\cite{Benedetti2017}. The torque generated by polymerases causes positive/negative supercoiling in front of/behind the transcription bubble; the resulting torsional stress either alters the twist of the double helix or induces superhelical writhe, which in turn can be accommodated through the formation of plectonemes, nucleosome remodeling, or other alterations in DNA structure\cite{Teves2014}. Plectoneme formation over gene arrays is an intuitive explanation for dinoTADs, although other topological constraints might also be involved. 

This model makes a clear prediction -- inhibition of transcription should result in dinoTADs decompaction. We first compared Hi-C maps for cells grown at 34$\,^{\circ}\mathrm{C}$ versus 27$\,^{\circ}\mathrm{C}$, as heat stress could result in general transcription reduction\cite{Levin2016}. While we did not observe dinoTADs disappearance, we did find mild decompaction at 34$\,^{\circ}\mathrm{C}$ (Supplementary Fig. \ref{FigS16}--\ref{FigS18}). 

We then carried out transcription inhibition experiments using $\alpha$-amanitin and triptolide (Fig. \ref{Fig2}A-B). Triptolide quickly blocks transcription initiation by targeting the TFIIH XPB subunit, while $\alpha$-amanitin directly inhibits RNA Polymerase II, but is slow acting\cite{Bensaude2011}. Transcription inhibition conditions for \textit{B. minutum} are not well established; it is also possible that triptolide does not strongly inhibit transcription due to the divergence of dinoflagellate transcription initiation factors\cite{Shoguchi2013}. We therefore assayed multiple time points and doses for each inhibitor (Fig. \ref{Fig2}B). We also found that even high $\alpha$-amanitin doses do not detectably affect photosynthetic efficiency or cell viability relative to controls (Fig. \ref{Fig2}C), excluding cell death as a confounder in our analysis.

Strikingly, $\alpha$-amanitin treatment resulted in a dose-dependent, progressive, near-complete dinoTAD decompaction (Fig. \ref{Fig2}D,F; Supplementary Fig. \ref{FigS33}--\ref{FigS40}). Triptolide treatment did not eliminate topological structures to the same extent, but nevertheless caused ``blurring'' of dinoTADs boundaries (Fig. \ref{Fig2}E-F; Supplementary Figures \ref{FigS36}--\ref{FigS39}). These effects were observed in both technical and biological replicates (Supplementary Fig. \ref{FigS33}--\ref{FigS40}). 

These observations support transcription-induced supercoiling as the primary force driving dinoTAD formation. Examination of dinoflagellate gene repertoires also suggests that they contend with elevated torsional stress, revealing a striking and dinoflagellate-specific expansion of topoisomerase II- and topoisomerase III-like genes (Fig. \ref{Fig1}D; Supplementary Fig. \ref{FigS15}; Supplementary Table \ref{TableS2}), i.e. the genes necessary for relieving torsional stress\cite{Pommier2016}. 

Comparison with self-interacting domains in bacteria or \textit{S. pombe} shows much stronger topological insulation for dinoTADs (Supplementary Fig. \ref{FigS31}) and \ref{FigS32})). Remarkably, no TAD domains are observed in kinetoplastids, the other lineage with long gene arrays and no transcriptional regulation (Supplementary Fig. \ref{FigS30}). 

These differences are readily explained by the unusual dinoflagellate properties. First, neither bacteria nor yeast possess comparably long gene arrays and transcription there is highly nonuniform; less transcription-induced torsional stress is therefore expected. Nucleosome loss is the second, and most salient difference. Single mammalian genes as long as dinoTADs are quite common, yet supercoiling is not apparent in mammalian Hi-C maps, nor is it seen in kinetoplastids (which have conventional chromatin). We therefore hypothesize that plectonemes form in dinoflagellates due to the lack of nucleosomes. In other eukaryotes, interactions between nucleosomes prevent formation of writhe-based structures, requiring more of torsion to be accommodated by changes in twist (Fig. \ref{Fig2}H).

% In summary, we have presented the first map of the physical organization of a dinoflagellate genome using modern molecular tools and have found unexpected links to the functional organization of the genome. The folding of the dinoflagellate genome in 3D space appears to be primarily dependent on transcription, which drives transcription-dependent DNA supercoiling. This model is supported by the co-association of topological domains with the boundaries between divergent gene array pairs, the large expansion of topoisomerase genes in dinoflagellate genomes, and the disappearance of dinoTADs upon exposure to general inhibitors of transcription. As the only known eukaryotes that do not use histones to package DNA, dinoflagellates represent a unique evolutionary experiment that reveals aspects of genome biology that are otherwise masked by nucleosomal chromatin and insulation. This natural experiment also highlights the potential magnitude of transcription-induced supercoiling as a general organizing force for genomes given that transcription-induced torsional stress is present in all organisms.

Numerous open questions remain. How exactly are boundaries between dinoTADs formed mechanistically? Specific boundary elements of markedly different chromatin state could exist; alternatively, they might form purely through torsion-related mechanisms. What exactly role histone genes play is also not clear. Answers to these questions, together with dissecting the specific roles of topoisomerases, will help fully elucidate the interplay between packaging proteins, torsional stress and genome folding in dinoflagellates. 

We also identify transcription-induced torsional stress as a key direction of future studies in eukaryotes generally. The strength of dinoTADs underlines its potency as a topological force. The precise manner by which torsion is accommodated as twist and writhe, as well as its consequences for regulatory protein occupancy, transcriptional activity and other chromatin processes are exciting questions remaining to be unraveled.

\section*{Author contributions}

G.K.M. performed Hi-C experiments. G.K.M and A.E.T. analyzed the data. A.E.T. and T.X. designed and carried out transcription inhibition experiments and cell viability experiments. T.X. carried out \textit{S. minutum} culture and heat stress treatment. W.J.G., A.R.G.. A.K. and J.R.P. supervised the study. G.K.M., A.E.T. and T.X. interpreted data and wrote manuscript with input from all authors. 

\section*{Acknowledgments}

\hl{This work was supported by NIH grants (P50HG007735, RO1 HG008140, U19AI057266 and UM1HG009442 to W.J.G., 1UM1HG009436 to W.J.G. and A.K., 1DP2OD022870-01 and 1U01HG009431 to A.K.), the Rita Allen Foundation (to W.J.G.), the Baxter Foundation Faculty Scholar Grant, and the Human Frontiers Science Program grant RGY006S (to W.J.G).} W.J.G is a Chan Zuckerberg Biohub investigator and acknowledges grants 2017-174468 and 2018-182817 from the Chan Zuckerberg Initiative. Fellowship support provided by the Stanford School of Medicine Dean's Fellowship (G.K.M.), the Siebel Scholars, the Enhancing Diversity in Graduate Education Program and the Weiland Family Fellowship (A.E.T.). This work is also supported by NSF-IOS EDGE Award 1645164 and Carnegie Venture grant 10907 (to T.X. and G.K.M.).

The authors would like to thank Zohar Shipony, Erez Lieberman Aiden, Philip Cleves, and members of the Greenleaf, Kundaje, Pringle and Grossman labs for helpful discussion and suggestions regarding this work.

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\section*{Supplementary Methods}

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Except where otherwise stated, computational analyses were carried out using custom-written Python scripts.

\subsection*{\textit{B. minutum} cell culture}

The clonal axenic \textit{Symbiodinium}/\textit{Breviolum minutum} strain SSB01 was used in all experiments. Stock cultures were grown as previously described\cite{Xiang2013,Xiang2015} in Daigo's IMK medium for marine microalgae (Wako Pure Chemicals) supplemented with casein hydrolysate (IMK+Cas) at 27$\,^{\circ}\mathrm{C}$ at a light intensity of 10 $\mu$mol photons m$^{−2}$ s$^{−1}$ from Philips ALTO II 25-W bulbs on a 12-h-light:12-h-dark cycle. The medium was prepared in artificial seawater (ASW).

\subsection*{Transcription inhibition experiments}

For $\alpha$-amanitin treatment, \textit{Breviolum minutum} cells at a density of $\sim$1 $\times 10^6$ cells/mL were treated with $\alpha$-amanitin (Sigma-Aldrich, Cat \# A2263) at concentrations of 1 $\mu$g/mL (``normal'' dose) and 4 $\mu$g/mL (''high'') dose. 

Samples were harvested at 0, 24, and 48 hours after treatment.

For triptolide treatment, \textit{Breviolum minutum} cells at a density of $\sim$1 $\times 10^6$ cells/mL were treated with triptolide (Sigma-Aldrich, Cat \# T3652) at concentrations of 10 $\mu$M (``normal'' dose) and 40 $\mu$M (''high'') dose.

Samples were harvested fat 0, 8, 24 and 48 hours after treatment.

\subsection*{Cell viability measurements}

\subsubsection*{Photosynthetic activity}

Maximum quantum yields of photosystem II, $Fv/Fm = (Fm - F0)/Fm$ was used to indicate photosynthetic function. S. minutum cultures (approximately $10^6$ cells/mL) were collected and dark adapted for 5 min, and $Fv/Fm$ was determined using a Dual Pam-100 fluorometer (Heinz Walz).

\subsubsection*{Colony formation assay}

Fresh SSB01 cells were sampled at 0, 24 and 48 hours after the treatment of transcription inhibitor $\alpha$-amanitin. For each condition, cell suspensions were diluted 1:5 and 1:10 before plating 1 $\mu$L of each dilution on marine broth (BD) agar plates. Plates were incubated at 27$\,^{\circ}\mathrm{C}$ at a light intensity of 10 $\mu$mol photons m$^{−2}$ s$^{−1}$. Cell numbers on each plate were counted after three weeks.

\subsection*{Hi-C experiments}

The in situ Hi-C procedure used to map 3D genomic interactions in \textit{Symbiodinium} was adapted from previous studies\cite{Rao2014} as follows:

\textit{Symbiodinium minutum} SSBO1 cells were first crosslinked using 37\% formaldehyde (Sigma) at a final concentration of 1\% for 15 minutes at room temperature. Formaldehyde was then quenched using 2.5 M Glycine at a final concentration of 0.25 M. Cells were subsequently centrifuged at 2,000 $g$ for 5 minutes, washed once in 1$\times$ PBS, and stored at -80$\,^{\circ}\mathrm{C}$. 

Cell lysis was initiated by incubation with 250 $\mu$L of cold Hi-C Lysis Buffer (10 mM Tris-HCl pH 8.0, 10 mM NaCl, 0.2\% Igepal CA630) on ice for 15 minutes, followed by centrifugation at 2,500 $g$ for 5 minutes, a wash with 500 $\mu$L of cold Hi-C Lysis Buffer, and centrifugation at 2,500 $g$ for 5 minutes. The pellet was the resuspended in 50 $\mu$L of 0.5\% SDS and incubated at 62$\,^{\circ}\mathrm{C}$ for 10 minutes. SDS was quenched by adding 145 $\mu$L of H$_2$O and 25 $\mu$L of 10\% Triton X-100 and incubating at 37$\,^{\circ}\mathrm{C}$ for 15 minutes.

Restriction digestion was carried out by adding 25 $\mu$L of 10$\times$ NEBuffer 2 and 100 U of the MboI restriction enzyme (NEB, R0147) and incubating for $\geq$2 hours at 37$\,^{\circ}\mathrm{C}$ in a Thermomixer at 900 rpm. The reaction was then incubated at 62$\,^{\circ}\mathrm{C}$ for 20 minutes in order to inactivate the restriction enzyme. 

Fragment ends were filled in by adding 37.5 $\mu$L of 0.4 mM biotin-14-dATP (ThermoFisher Scientific, $\#$ 19524-016), 1.5 $\mu$L each of 10 mM dCTP, dGTP and dTTP, and 8 $\mu$L of 5U/$\mu$L DNA Polymerase I Large (Klenow) Fragment (NEB M0210). The reaction was the incubated at 37$\,^{\circ}\mathrm{C}$ in a Thermomixer at 900 rpm for 45 minutes.

Fragment end ligation was carried out by adding 663 $\mu$L H$_2$O, 120 $\mu$L 10$\times$ NEB T4 DNA ligase buffer (NEB B0202), 100 $\mu$L of 10\% Triton X-100, 12 $\mu$L of 10 mg/mL Bovine Serum Albumin (100$\times$ BSA, NEB), 5 $\mu$L of 400 U/$\mu$L T4 DNA Ligase (NEB M0202), and incubating at room temperature for $\geq$4 hours with rotation. 

Nuclei were then pelleted by centrifugation at 3,500 $g$ for 5 minutes; the pellet was resuspended in 200 $\mu$L ChIP Elution Buffer (1\% SDS, 0.1 M NaHCO$_3$), Proteinase K was added, and incubated at 65$\,^{\circ}\mathrm{C}$ overnight to reverse crosslinks. 

After addition of 600 $\mu$L 1$\times$TE buffer, DNA was sonicated using a Qsonica S-4000 with a 1/16'' tip for 3 minutes, with 10 second pulses at intensity 3.5, and 20 seconds rest between pulses. DNA was then purified using the MinElute PCR Purificaiton Kit (Qiagen $\#$28006), with elution in a total volume of 300 $\mu$L 1$\times$ EB buffer. 

For streptavidin pulldown of biotin-labeled DNA, 150 $\mu$L of 10 mg/mL Dynabeads MyOne Streptavidin T1 beads (Life Technologies, 65602) were separated on a magnetic stand, then washed with 400 $\mu$L of 1$\times$ TWB (Tween Washing Buffer; 5 mM Tris-HCl pH 7.5; 0.5 mM EDTA; 1 M NaCl; 0.05\% Tween 20). The beads were resuspended in 300 $\mu$L of 2$\times$ Binding Buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA; 2 M NaCl), the sonicated DNA was added, and the beads were incubated for $\geq$15 minutes at room temperature on a rotator. After separation on a magnetic stand, the beads were washed with 600 $\mu$L of 1$\times$ TWB, and heated at 55$\,^{\circ}\mathrm{C}$ in a Thermomixer with shaking for 2 minutes. After removal of the supernatant on a magnetic stand, the TWB wash and 55$\,^{\circ}\mathrm{C}$ incubation were repeated. 

Final libraries were prepared on beads using the NEBNext Ultra II DNA Library Prep Kit (NEB, $\#$E7645) as follows. End repair was carried out by resuspending beads in 50 $\mu$L 1$\times$ EB buffer, and adding 3 $\mu$L NEB Ultra End Repair Enzyme and 7 $\mu$L NEB Ultra End Repair Enzyme, followed by incubation at 20$\,^{\circ}\mathrm{C}$ for 30 minutes and then at 65$\,^{\circ}\mathrm{C}$ for 30 minutes. 

Adapters were ligated to DNA fragments by adding 30 $\mu$L Blunt Ligation mix, 1 $\mu$L Ligation Enhancer and 2.5 $\mu$L NEB Adapter, incubating at 20$\,^{\circ}\mathrm{C}$ for 20 minutes, adding 3 $\mu$L USER enzyme, and incubating at 37$\,^{\circ}\mathrm{C}$ for 15 minutes. 

Beads were then separated on a magnetic stand, and washed with 600 $\mu$L TWB for 2 minutes at 55$\,^{\circ}\mathrm{C}$, 1000 rpm in a Thermomixer. After separation on a magnetic stand, beads were washed in 100 $\mu$L 0.1 $\times$ TE buffer, then resuspended in 16 $\mu$L 0.1 $\times$ TE buffer, and heated at 98$\,^{\circ}\mathrm{C}$ for 10 minutes. 

For PCR, 5 $\mu$L of each of the i5 and i7 NEB Next sequencing adapters were added together with 25 $\mu$L 2$\times$ NEB Ultra PCR Mater Mix. PCR was carried out with a 98$\,^{\circ}\mathrm{C}$ incubation for 30 seconds and 12 cycles of 98$\,^{\circ}\mathrm{C}$ for 10 seconds, 65$\,^{\circ}\mathrm{C}$ for 30 seconds, and 72$\,^{\circ}\mathrm{C}$ for 1 minute, followed by incubation at 72$\,^{\circ}\mathrm{C}$ for 5 minutes. 

Beads were separated on a magnetic stand, and the supernatant was cleaned up using 1$\times$ AMPure XP beads. 

Libraries were sequenced in a paired-end format on a Illumina NextSeq instrument using NextSeq 500/550 high output kits (either 2$\times$75 or 2$\times$36 cycles). 

\subsection*{Hi-C data processing and assembly scaffolding}

% Sequencing reads were trimmed down to 36mers and aligned as using Bowtie\cite{Langmead2009} (version 1.0.1) with the following settings: \verb|-v 2| \verb|--k 2| \verb|-m 1| \verb|-t |--best| \verb|--strata|, either as $1 \times $36mers or $2 \times $36mers, depending on the dataset. 

As an initial step, Hi-C sequencing reads from all libraries were trimmed of adapter sequences, pooled together, and processed against the previously published \textit{B. minutum} assembly\cite{Shoguchi2013} using the Juicer pipeline\cite{Durand2016a} for analyzing Hi-C datasets (version 1.8.9 of Juicer Tools). 

The resulting Hi-C matrices were then used as input to the 3D DNA pipeline\cite{Dudchenko2017} for automated scaffolding with the following parameters: \verb|--editor-coarse-resolution| \verb|5000| \verb|--editor-coarse-region| \verb|5000| \verb|--polisher-input-size| \verb|100000| \verb|--polisher-coarse-resolution| \verb|1000| \newline \verb|--polisher-coarse-region| \verb|300000| \newline  \verb|--splitter-input-size| \verb|100000| \newline  \verb|--splitter-coarse-resolution| \verb|5000| \newline \verb|--splitter-coarse-region| \verb|300000| \verb|--sort-output| \verb|--build-gapped-map| \verb|-r 10| \verb|-i 5000|.

Manual correction of obvious assembly and scaffolding errors was then carried out using Juicebox\cite{Durand2016a}.

After finalizing the scaffolding, Hi-C reads were reprocessed against the new assembly using the Juicer pipeline. This was done individually for each library as well as together for the pooled set of reads. 

Data was extracted from the final read matrices using the Juicer suite of tools for Hi-C data analysis.

\subsection*{Identification of Hi-C domains}

Hi-C matrices were first converted to \textit{cool} format using HiCExplorer\cite{Ramirez2018} ``\verb|hicConvertFormat|'' with parameters \verb|--inputFormat| \verb|hic| \verb|--outputFormat| \verb|h5| and default resolutions. Subsequent HiCExplorer commands were carried out at 10 kb, 25 kb, and 50 kb resolutions with similar results. Matrices were normalized using ``\verb|hicNormalize|'' with parameter \verb|--normalize| \verb|smallest|, and corrected using \verb|``hicCorrectMatrix| \verb|correct|'' with parameters \verb|--correctionMethod| \verb|KR|. Hi-C domains were computationally identified using the ``\verb|hicFindTADs|'' from HiCExplorer with parameter \verb|--correctForMultipleTesting| \verb|fdr|.

\subsection*{RNA-seq datasets}

Approximately $5 \times 10^7$ cells were collected by centrifugation at 100 $g$ for 5 minutes at room temperature. Total RNA was extracted and libraries were constructed for RNA-Seq using the TruSeq RNA Library Prep Kit V2 (Illumina, San Diego, CA, USA) according to the manufacturer protocol. All of the raw sequencing reads are available at Sequence Read Archive (SRA) with accession number SRX7258938.

\subsection*{RNA-seq data analysis}

RNA-seq reads were aligned against the corresponding assemblies using the STAR aligner\cite{Dobin2013} (version 2.5.3a) with the following settings: \verb|--limitSjdbInsertNsj| \verb|10000000| \verb|--outFilterMultimapNmax| \verb|50 \verb|--outFilterMismatchNmax| \verb|999| \newline \verb|--outFilterMismatchNoverReadLmax| \verb|0.04| \newline  \verb|--alignIntronMin| \verb|10|  \verb|--alignIntronMax| \verb|1000000|  \verb|--alignMatesGapMax| \verb|1000000|  \verb|--alignSJoverhangMin| \verb|8|  \verb|--alignSJDBoverhangMin| \verb|1|  \verb|--sjdbScore| \verb|1|  \verb|--twopassMode| \verb|Basic|  \verb|--twopass1readsN| \verb|-1|. As available RNA-seq datasets for \textit{B. minutum} are not strand-specific, the strand orientation of the transcriptome was visualized as follows. Aligned reads were first \textit{de novo} assembled into transcripts and quantified at the transcript level using Stringtie\cite{Pertea2015} (version 1.3.3.b); the orientation of splice junctions serves as a reliable guide for the directionality of these transcripts. Open reading frames (ORFs) were identified for each transcript, and transcripts with ORFs shorter than 60 amino acids were filtered out of the transcript set. Strand-specific genomic tracks were then generated by assigning to each basepair covered by at least one exon in that set the sum of the TPM (Transcript Per Million transcripts) values of all transcripts it is included in.

\subsection*{External Hi-C datasets}

Hi-C data for \textit{Trypanosoma brucei} was obtained from GEO accession GSE118764. 

Hi-C data for \textit{Schizosaccharomyces pombe} was obtained from GEO accession GSE57316.

Hi-C data for \textit{Caulobacter vibrioides} CB15 was obtained from GEO accession GSE45966.

\subsection*{Sequence Analysis}

Topoisomerase and other replication-related proteins were identified in annotated MMETSP transcriptome assemblies using HMMER3.0\cite{Eddy2011} and the Pfam 27.0 protein domain database\cite{Finn2014} as previously described\cite{Marinov2015}.

\end{multicols}

\clearpage

% \end{document}

\section*{Supplementary Tables}

\begin{small}
\begin{center}
\begin{longtable}{m{11cm}m{2cm}m{2cm}m{2cm}}
\caption[]{Summary of Hi-C datasets used in this study}\\
\hline
Hi-C library & Number raw read pairs & Estimated library complexity & Number Hi-C contacts \\
\hline
\endfirsthead
\multicolumn{4}{c}%
{\tablename\ \thetable\ -- \textit{Continued from previous page}} \\
\hline
Hi-C library & Number raw read pairs & Estimated library complexity & Number Hi-C contacts \\
\hline
\endhead
\hline \multicolumn{4}{r}{\textit{Continued on next page}} \\
\endfoot
\hline
\endlastfoot
L142-SSBO1-HIC & 534,609,924 & 920,112,029   & 220,908,462 \\
L533-SSBO1\_27C\_Hi-C          & 556,089,015 & 1,513,268,498 & 151,618,419 \\
L534-SSBO1\_34C\_Hi-C          & 531,461,453 & 2,971,291,849 & 165,231,965 \\
L1240-SSBO1-$\alpha$\_amanitin-0h-Hi-C & 111,333,226 & 233,525,989 & 34,384,671 \\
% L1241+L1242-SSB01-$\alpha$\_amanitin-16h & 128,072,777 & 495,967,910 & 49,755,212 \\
L1241-SSB01-$\alpha$\_amanitin-16h-Hi-C-rep1 & 60,696,609 & 317,650,525 & 24,238,281 \\
L1242-SSB01-$\alpha$\_amanitin-16h-Hi-C-rep2 & 67,376,168 & 227,736,960 & 25,551,603 \\
% L1243+L1244-SSB01-$\alpha$\_amanitin-24h & 187,913,804 & 265,912,578 & 58,445,663 \\
L1243-SSB01-$\alpha$\_amanitin-24h-Hi-C-rep1 & 81,532,584 & 235,898,386 & 29,748,439 \\
L1244-SSB01-$\alpha$\_amanitin-24h-Hi-C-rep2 & 106,381,220 & 110,607,925 & 28,845,306 \\
% L1245+L1246-SSB01-$\alpha$\_amanitin-48h & 169,163,291 & 277,220,794 & 48,946,415 \\
L1245-SSB01-$\alpha$\_amanitin-48h-Hi-C-rep1 & 90,180,763 & 155,046,434 & 27,045,343 \\
L1246-SSB01-$\alpha$\_amanitin-48h-Hi-C-rep2 & 78,982,528 & 152,703,652 & 22,153,117 \\
L1247-SSB01-$\alpha$\_amanitin\_high-48h-Hi-C & 110,015,013 & 157,350,902 & 28,138,017 \\
L1332-SSB01-$\alpha$\_amanitin-0h-Hi-C-technical\_rep & 117,543,007 & 182,213,300 & 34,089,285 \\
L1333-SSB01-$\alpha$\_amanitin-48h-Hi-C-rep1-technical\_rep & 117,821,773 & 82,740,021 & 23,654,760 \\
L1334-SSB01-$\alpha$\_amanitin\_high-48h-Hi-C-technical\_rep & 95,662,202 & 164,149,035 & 23,944,231 \\
% L1335-SSB01-$\alpha$\_amanitin\_high-0h-Hi-C-second\_time\_course & 140,912,027 & 31,287,862 & 11,633,098 \\
L1336-SSB01-$\alpha$\_amanitin\_high-24h-Hi-C-second\_time\_course & 58,747,402 & 103,174,104 & 15,663,160 \\
L1337-SSB01-$\alpha$\_amanitin\_high-48h-Hi-C-second\_time\_course & 83,691,617 & 62,658,394 & 14,523,464 \\
L1344-SSB01-$\alpha$\_amanitin/triptolide\_0h\_NT-Hi-C & 79,383,186 & 208,157,102 & 23,592,335 \\
L1346-SSB01-triptolide\_8h\_normal\_dose-Hi-C & 81,731,190 & 193,514,340 & 22,700,096 \\
L1347-SSB01-triptolide\_8h\_high\_dose-Hi-C & 112,753,865 & 187,235,670 & 28,552,855 \\
L1348-SSB01-Triptolide\_24h NT-Hi-C	& 52,148,987 & 166,057,825 & 15,674,551 \\
L1349-SSB01-triptolide\_24h\_normal\_dose-Hi-C & 132,715,807 & 206,778,720 & 36,745,591 \\
L1350-SSB01-triptolide\_24h\_high\_dose-Hi-C & 98,429,444 & 265,027,975 & 32,121,298 \\
L1351-SSB01-Triptolide\_48h NT-Hi-C	& 96,846,551 & 240,797,245 & 28,296,251 \\
L1352-SSB01-triptolide\_48h\_normal\_dose-Hi-C & 85,347,611 & 255,500,603 & 25,051,605 \\
L1353-SSB01-triptolide\_48h\_high\_dose-Hi-C & 99,978,207 & 215,504,692 & 26,572,806
\label{TableS1}
\end{longtable}
\end{center}
\end{small}

\clearpage

\begin{small}
\begin{center}
\begin{longtable}{m{2.5cm}m{7cm}m{0.5cm}m{0.5cm}m{0.5cm}m{0.5cm}m{0.7cm}m{0.5cm}m{0.5cm}m{0.5cm}m{0.5cm}}
\caption[]{Inventory of topoisomerases and some other proteins involved in DNA replication in dinoflagellates and other eukaryotes as annotated by transcriptome assemblies in the MMETSP databses}\\
\hline
clade & species & TOP1 & TOP2 & TOP3 & MCM & PCNA & RPA1 & RPA2 & RPA3 & RFC1 \\
\hline
\endfirsthead
\multicolumn{11}{c}%
{\tablename\ \thetable\ -- \textit{Continued from previous page}} \\
\hline
clade & species & TOP1 & TOP2 & TOP3 & MCM & PCNA & RPA1 & RPA2 & RPA3 & RFC1 \\
\hline
\endhead
\hline \multicolumn{11}{r}{\textit{Continued on next page}} \\
\endfoot
\hline
\endlastfoot
Amoebozoa & \textit{Stereomyxa ramosa} Chinc5 & 1 & 2 & 2 & 6 & 2 & 3 & 0 & 2 & 1 \\
Amoebozoa & \textit{Vexillifera} sp. DIVA3 564 2 & 1 & 2 & 2 & 7 & 1 & 2 & 0 & 0 & 1 \\
Apicomplexa & \textit{Lankesteria abbottii} Grappler Inlet BC & 1 & 1 & 0 & 12 & 5 & 1 & 0 & 0 & 1 \\
Bicosoecid & Bicosoecid sp ms1 & 1 & 0 & 0 & 3 & 1 & 1 & 1 & 1 & 0 \\
Bicosoecid & \textit{Cafeteria roenbergensis} E4 10 & 1 & 0 & 2 & 6 & 1 & 0 & 0 & 1 & 0 \\
Bicosoecid & \textit{Cafeteria} sp. Caron Lab Isolate & 1 & 1 & 4 & 15 & 1 & 1 & 0 & 1 & 1 \\
Bolidophyte & \textit{Bolidomonas pacifica} CCMP 1866 & 2 & 5 & 7 & 8 & 1 & 1 & 0 & 0 & 1 \\
Chlorarachniophyte & \textit{Bigelowiella natans} CCMP1258.1 & 1 & 1 & 9 & 3 & 1 & 4 & 1 & 0 & 0 \\
Chlorarachniophyte & \textit{Bigelowiella natans} CCMP1259 & 1 & 1 & 6 & 7 & 1 & 4 & 1 & 0 & 1 \\
Chlorarachniophyte & \textit{Bigelowiella natans} CCMP 2755 & 0 & 0 & 4 & 5 & 1 & 4 & 1 & 0 & 1 \\
Chlorarachniophyte & \textit{Bigelowiella natans} CCMP623 & 1 & 3 & 7 & 9 & 1 & 2 & 1 & 0 & 1 \\
Chlorarachniophyte & \textit{Chlorarachnion reptans} CCCM449 & 2 & 4 & 8 & 11 & 2 & 3 & 1 & 0 & 1 \\
Chlorarachniophyte & \textit{Lotharella amoebiformis} CCMP2058 & 2 & 6 & 5 & 10 & 1 & 4 & 1 & 0 & 1 \\
Chlorarachniophyte & \textit{Lotharella globosa} CCCM811 & 1 & 2 & 1 & 0 & 1 & 1 & 1 & 1 & 1 \\
Chlorarachniophyte & \textit{Lotharella oceanica} CCMP622 & 1 & 0 & 0 & 1 & 1 & 2 & 1 & 1 & 1 \\
Chlorarachniophyte & \textit{Norrisiella sphaerica} BC52 & 1 & 0 & 3 & 0 & 1 & 2 & 1 & 1 & 0 \\
Chlorarachniophyte & \textit{Partenskyella glossopodia} RCC365 & 1 & 2 & 1 & 7 & 1 & 3 & 1 & 2 & 1 \\
Chlorophyte & \textit{Bathycoccus prasinos} CCMP1898 & 1 & 2 & 3 & 9 & 1 & 2 & 0 & 0 & 0 \\
Chlorophyte & \textit{Bathycoccus prasinos} RCC716 & 1 & 2 & 3 & 7 & 1 & 3 & 0 & 0 & 1 \\
Chlorophyte & \textit{Chlamydomonas} cf sp CCMP681 & 1 & 0 & 0 & 5 & 2 & 1 & 0 & 0 & 1 \\
Chlorophyte & \textit{Crustomastix stigmata} CCMP3273 & 1 & 2 & 4 & 10 & 1 & 1 & 1 & 0 & 1 \\
Chlorophyte & \textit{Cyanoptyche gloeocystis} SAG4.97 & 1 & 0 & 0 & 4 & 1 & 1 & 1 & 0 & 0 \\
Chlorophyte & \textit{Dolichomastix tenuilepis} CCMP3274 & 1 & 1 & 3 & 1 & 2 & 1 & 0 & 1 & 1 \\
Chlorophyte & \textit{Dunaliella tertiolecta} CCMP1320 & 1 & 2 & 3 & 10 & 1 & 2 & 0 & 1 & 1 \\
Chlorophyte & \textit{Mantoniella antarctica} SL 175 & 1 & 8 & 4 & 13 & 1 & 2 & 2 & 1 & 1 \\
Chlorophyte & \textit{Mantoniella} sp CCMP1436 & 1 & 2 & 1 & 2 & 1 & 1 & 1 & 1 & 1 \\
Chlorophyte & \textit{Micromonas} sp CCMP2099 & 1 & 2 & 2 & 9 & 1 & 2 & 0 & 1 & 1 \\
Chlorophyte & \textit{Micromonas} sp NEPCC29 & 1 & 2 & 3 & 7 & 1 & 2 & 0 & 1 & 1 \\
Chlorophyte & \textit{Micromonas} sp RCC472 & 1 & 2 & 2 & 7 & 1 & 2 & 1 & 0 & 1 \\
Chlorophyte & \textit{Nephroselmis pyriformis} CCMP717 & 1 & 4 & 8 & 10 & 1 & 2 & 0 & 1 & 1 \\
Chlorophyte & \textit{Picochlorum oklahomensis} CCMP2329 & 1 & 2 & 2 & 6 & 2 & 2 & 1 & 0 & 1 \\
Chlorophyte & \textit{Picochlorum} sp. RCC944 & 1 & 1 & 2 & 6 & 1 & 2 & 0 & 2 & 1 \\
Chlorophyte & \textit{Picocystis salinarum} CCMP1897 & 1 & 2 & 1 & 8 & 2 & 2 & 1 & 2 & 1 \\
Chlorophyte & \textit{Polytomella parva} SAG 63 3 & 1 & 5 & 3 & 18 & 2 & 3 & 0 & 0 & 1 \\
Chlorophyte & \textit{Prasinoderma coloniale} CCMP1413 & 1 & 2 & 0 & 2 & 1 & 1 & 0 & 0 & 0 \\
Chlorophyte & \textit{Prasinoderma singularis} RCC927 & 1 & 1 & 1 & 7 & 1 & 1 & 0 & 1 & 1 \\
Chlorophyte & \textit{Pterosperma} sp. CCMP1384 & 1 & 0 & 0 & 3 & 1 & 1 & 1 & 1 & 1 \\
Chlorophyte & \textit{Pycnococcus provasolii} RCC2336 & 1 & 1 & 0 & 9 & 1 & 1 & 0 & 0 & 1 \\
Chlorophyte & \textit{Pycnococcus provasolii} RCC931 & 1 & 0 & 0 & 7 & 1 & 1 & 0 & 0 & 1 \\
Chlorophyte & \textit{Pyramimonas parkeae} CCMP726 & 1 & 0 & 4 & 7 & 1 & 2 & 1 & 1 & 1 \\
Chlorophyte & \textit{Stichococcus} sp RCC1054 & 1 & 1 & 1 & 8 & 1 & 1 & 0 & 0 & 1 \\
Chlorophyte & \textit{Tetraselmis chuii} PLY429 & 2 & 0 & 0 & 0 & 0 & 2 & 0 & 1 & 2 \\
Chlorophyte & \textit{Tetraselmis striata} LANL1001 & 1 & 4 & 4 & 11 & 1 & 2 & 0 & 1 & 1 \\
Choanoflagellata & \textit{Acanthoeca} like sp 10tr & 1 & 3 & 4 & 10 & 1 & 1 & 0 & 1 & 1 \\
Chromerida & \textit{Chromera velia} CCMP2878 & 1 & 1 & 3 & 10 & 2 & 2 & 0 & 0 & 1 \\
Chromerida & \textit{Vitrella brassicaformis} CCMP3346 & 1 & 1 & 2 & 9 & 2 & 1 & 0 & 0 & 1 \\
Chrysophyte & \textit{Chromulina nebulosa} UTEXLB2642 & 1 & 1 & 1 & 2 & 1 & 1 & 0 & 0 & 1 \\
Chrysophyte & \textit{Dinobryon} sp UTEXLB2267 & 1 & 3 & 0 & 8 & 1 & 1 & 0 & 0 & 1 \\
Chrysophyte & \textit{Mallomonas} Sp CCMP3275 & 1 & 2 & 1 & 9 & 1 & 1 & 0 & 1 & 1 \\
Chrysophyte & \textit{Ochromonas} sp CCMP1393 & 1 & 2 & 2 & 7 & 1 & 1 & 0 & 0 & 1 \\
Chrysophyte & \textit{Paraphysomonas bandaiensis} Caron Lab Isolate & 1 & 2 & 3 & 9 & 2 & 1 & 1 & 1 & 1 \\
Chrysophyte & \textit{Paraphysomonas imperforata} PA2 & 0 & 1 & 3 & 6 & 1 & 1 & 1 & 1 & 1 \\
Chrysophyte & \textit{Pelagococcus subviridis} CCMP1429 & 1 & 1 & 2 & 11 & 1 & 0 & 0 & 0 & 1 \\
Chrysophyte & \textit{Spumella elongata} CCAP 955 1 & 1 & 1 & 3 & 10 & 4 & 3 & 0 & 1 & 1 \\
Ciliate & \textit{Aristerostoma} sp. ATCC 50986 & 2 & 1 & 1 & 0 & 2 & 1 & 0 & 0 & 2 \\
Ciliate & \textit{Blepharisma japonicum} Stock R1072 & 0 & 0 & 0 & 7 & 4 & 1 & 0 & 0 & 0 \\
Ciliate & \textit{Climacostomum virens} Stock W 24 & 1 & 2 & 2 & 9 & 3 & 1 & 0 & 0 & 3 \\
Ciliate & \textit{Condylostoma magnum} COL2 & 0 & 0 & 0 & 2 & 0 & 0 & 0 & 0 & 0 \\
Ciliate & \textit{Euplotes focardii} TN1 & 1 & 0 & 0 & 5 & 2 & 1 & 0 & 2 & 0 \\
Ciliate & \textit{Euplotes harpa} FSP1.4 & 2 & 0 & 5 & 3 & 1 & 0 & 0 & 1 & 0 \\
Ciliate & \textit{Fabrea salina} Unknown & 1 & 1 & 3 & 7 & 2 & 3 & 0 & 0 & 2 \\
Ciliate & \textit{Favella taraikaensis} FeNarragansettBay & 0 & 1 & 2 & 7 & 3 & 0 & 0 & 0 & 0 \\
Ciliate & \textit{Litonotus pictus} P1 & 1 & 1 & 2 & 0 & 0 & 0 & 0 & 0 & 0 \\
Ciliate & \textit{Mesodinium pulex} SPMC105 & 2 & 13 & 2 & 16 & 9 & 4 & 0 & 0 & 6 \\
Ciliate & \textit{Myrionecta rubra} CCMP2563 & 0 & 1 & 4 & 11 & 1 & 1 & 0 & 1 & 0 \\
Ciliate & \textit{Platyophrya macrostoma} WH & 4 & 4 & 4 & 23 & 4 & 6 & 0 & 0 & 3 \\
Ciliate & \textit{Protocruzia adherens} Boccale & 3 & 1 & 0 & 9 & 3 & 3 & 0 & 0 & 1 \\
Ciliate & \textit{Pseudokeronopsis} sp. OXSARD2 & 1 & 1 & 1 & 6 & 1 & 0 & 0 & 1 & 1 \\
Ciliate & \textit{Strombidinopsis acuminatum} SPMC142 & 2 & 6 & 0 & 32 & 10 & 5 & 0 & 0 & 0 \\
Ciliate & \textit{Strombidinopsis} sp. SopsisLIS2011 & 1 & 0 & 0 & 8 & 3 & 2 & 0 & 0 & 0 \\
Ciliate & \textit{Strombidium} inclinatum S3 & 1 & 1 & 2 & 8 & 1 & 1 & 0 & 0 & 1 \\
Ciliate & \textit{Strombidium rassoulzadegani} ras09 & 1 & 0 & 1 & 6 & 1 & 1 & 0 & 1 & 0 \\
Ciliate & \textit{Tiarina fusus} LIS & 1 & 7 & 3 & 16 & 3 & 4 & 2 & 1 & 1 \\
Cryptophyte & \textit{Chroomonas mesostigmatica} cf CCMP1168 & 1 & 5 & 4 & 8 & 1 & 2 & 2 & 0 & 1 \\
Cryptophyte & \textit{Cryptomonas curvata} CCAP979 52 & 2 & 0 & 2 & 0 & 1 & 1 & 0 & 1 & 0 \\
Cryptophyte & \textit{Cryptomonas paramecium} CCAP977 2a & 3 & 2 & 2 & 5 & 1 & 1 & 0 & 0 & 1 \\
Cryptophyte & \textit{Geminigera cryophila} CCMP2564 & 2 & 1 & 5 & 11 & 1 & 2 & 0 & 1 & 2 \\
Cryptophyte & \textit{Geminigera} sp. Caron Lab Isolate & 1 & 3 & 5 & 18 & 1 & 5 & 0 & 1 & 1 \\
Cryptophyte & \textit{Goniomonas pacifica} CCMP1869 & 8 & 4 & 4 & 12 & 1 & 5 & 1 & 3 & 7 \\
Cryptophyte & \textit{Guillardia theta} CCMP 2712 & 1 & 0 & 2 & 3 & 1 & 1 & 0 & 1 & 0 \\
Cryptophyte & \textit{Hemiselmis andersenii} CCMP644 & 1 & 2 & 5 & 12 & 1 & 2 & 0 & 1 & 1 \\
Cryptophyte & \textit{Hemiselmis rufescens} PCC563 & 1 & 0 & 3 & 7 & 1 & 1 & 1 & 1 & 1 \\
Cryptophyte & \textit{Hemiselmis tepida} CCMP443 & 3 & 2 & 0 & 3 & 1 & 1 & 1 & 1 & 1 \\
Cryptophyte & \textit{Hemiselmis viresens} PCC157 & 1 & 0 & 0 & 7 & 1 & 1 & 0 & 1 & 0 \\
Cryptophyte & \textit{Palpitomonas bilix} NIES 2562 & 0 & 1 & 2 & 13 & 4 & 3 & 0 & 1 & 3 \\
Cryptophyte & \textit{Proteomonas sulcata} CCMP704 & 0 & 1 & 0 & 3 & 1 & 1 & 0 & 0 & 1 \\
Cryptophyte & \textit{Rhodomonas lens} RHODO & 2 & 3 & 2 & 2 & 2 & 2 & 0 & 1 & 0 \\
Cryptophyte & \textit{Rhodomonas} sp. CCMP768 & 1 & 0 & 1 & 0 & 1 & 1 & 0 & 0 & 0 \\
Diatome & \textit{Amphiprora} sp. & 1 & 4 & 3 & 9 & 1 & 1 & 0 & 0 & 1 \\
Diatome & \textit{Amphora coffeaeformis} CCMP127 & 1 & 1 & 0 & 4 & 1 & 1 & 0 & 0 & 0 \\
Diatome & \textit{Asterionellopsis glacialis} CCMP134 & 1 & 7 & 1 & 10 & 1 & 1 & 0 & 0 & 1 \\
Diatome & \textit{Astrosyne radiata} 13vi08 1A & 1 & 8 & 3 & 6 & 3 & 2 & 0 & 0 & 1 \\
Diatome & \textit{Attheya septentrionalis} CCMP2084 & 1 & 2 & 0 & 9 & 1 & 1 & 0 & 0 & 1 \\
Diatome & \textit{Aulacoseira subarctica} CCAP 1002 5 & 1 & 2 & 3 & 8 & 2 & 1 & 0 & 0 & 1 \\
Diatome & \textit{Chaetoceros affinis} CCMP159 & 1 & 3 & 1 & 8 & 1 & 1 & 0 & 0 & 1 \\
Diatome & \textit{Chaetoceros curvisetus} & 1 & 4 & 4 & 6 & 1 & 3 & 0 & 0 & 1 \\
Diatome & \textit{Chaetoceros debilis} MM31A\_1 & 1 & 3 & 1 & 12 & 1 & 1 & 0 & 0 & 1 \\
Diatome & \textit{Chaetoceros neogracile} CCMP1317 & 1 & 9 & 3 & 10 & 1 & 1 & 0 & 1 & 1 \\
Diatome & \textit{Coscinodiscus wailesii} CCMP2513 & 1 & 3 & 6 & 10 & 1 & 1 & 0 & 1 & 1 \\
Diatome & \textit{Craspedostauros australis} CCMP3328 & 1 & 0 & 0 & 4 & 0 & 1 & 0 & 0 & 0 \\
Diatome & \textit{Cyclophora tenuis} ECT3854 & 1 & 1 & 0 & 3 & 1 & 1 & 0 & 0 & 0 \\
Diatome & \textit{Cyclotella meneghiniana} CCMP 338 & 1 & 4 & 3 & 8 & 1 & 1 & 0 & 0 & 1 \\
Diatome & \textit{Cylindrotheca closterium} KMMCC:B 181 & 3 & 7 & 3 & 14 & 1 & 2 & 0 & 0 & 1 \\
Diatome & \textit{Dactyliosolen fragilissimus} Unknown & 1 & 3 & 3 & 8 & 1 & 1 & 0 & 1 & 1 \\
Diatome & \textit{Ditylum brightwellii} GSO103 & 1 & 4 & 3 & 11 & 1 & 1 & 0 & 1 & 1 \\
Diatome & \textit{Ditylum brightwellii} GSO104 & 1 & 4 & 5 & 10 & 1 & 1 & 0 & 1 & 1 \\
Diatome & \textit{Ditylum brightwellii} GSO105 & 1 & 2 & 3 & 11 & 2 & 1 & 0 & 1 & 1 \\
Diatome & \textit{Entomoneis} sp. CCMP2396 & 0 & 1 & 0 & 0 & 1 & 1 & 0 & 0 & 0 \\
Diatome & \textit{Eucampia antarctica} CCMP1452 & 1 & 3 & 0 & 5 & 1 & 1 & 1 & 1 & 1 \\
Diatome & \textit{Extubocellulus spinifer} CCMP396 & 1 & 4 & 10 & 13 & 2 & 5 & 3 & 1 & 2 \\
Diatome & \textit{Fragilariopsis kerguelensis} L2\_C3 & 1 & 3 & 3 & 11 & 1 & 1 & 2 & 0 & 1 \\
Diatome & \textit{Fragilariopsis kerguelensis} L26\_C5 & 1 & 3 & 5 & 22 & 1 & 1 & 3 & 0 & 1 \\
Diatome & \textit{Grammatophora oceanica} CCMP 410 & 1 & 1 & 3 & 5 & 1 & 1 & 0 & 0 & 1 \\
Diatome & \textit{Helicotheca tamensis} CCMP826 & 0 & 1 & 0 & 1 & 1 & 1 & 0 & 1 & 0 \\
Diatome & \textit{Leptocylindrus danicus} var. apora B651 & 3 & 5 & 3 & 0 & 3 & 2 & 0 & 1 & 1 \\
Diatome & \textit{Leptocylindrus danicus} var. danicus B650 & 3 & 11 & 3 & 19 & 1 & 1 & 0 & 1 & 2 \\
Diatome & \textit{Licmophora paradoxa} CCMP2313 & 1 & 1 & 3 & 7 & 1 & 2 & 0 & 0 & 1 \\
Diatome & \textit{Minutocellus polymorphus} CCMP3303 & 0 & 0 & 0 & 3 & 1 & 1 & 1 & 1 & 0 \\
Diatome & \textit{Minutocellus polymorphus} NH13 & 2 & 8 & 7 & 21 & 1 & 0 & 1 & 0 & 3 \\
Diatome & \textit{Minutocellus polymorphus} RCC2270 & 1 & 2 & 1 & 7 & 1 & 1 & 1 & 1 & 1 \\
Diatome & \textit{Nitzschia punctata} CCMP561 & 1 & 2 & 2 & 9 & 1 & 1 & 1 & 1 & 1 \\
Diatome & \textit{Odontella aurita} isolate 1302 5 & 1 & 3 & 7 & 11 & 2 & 2 & 1 & 1 & 1 \\
Diatome & \textit{Odontella sinensis} Grunow 1884 & 1 & 3 & 0 & 2 & 1 & 1 & 1 & 1 & 1 \\
Diatome & \textit{Proboscia alata} PI\_D3 & 1 & 7 & 2 & 21 & 1 & 1 & 2 & 0 & 1 \\
Diatome & \textit{Pseudo-nitzschia australis} 10249\_10\_AB & 1 & 3 & 4 & 8 & 1 & 1 & 1 & 0 & 1 \\
Diatome & \textit{Pseudo-nitzschia fradulenta} WWA7 & 2 & 11 & 6 & 24 & 4 & 5 & 0 & 0 & 3 \\
Diatome & \textit{Rhizosolenia setigera} CCMP 1694 & 1 & 7 & 4 & 18 & 1 & 2 & 0 & 0 & 2 \\
Diatome & \textit{Skeletonema dohrnii} SkelB & 1 & 2 & 0 & 14 & 1 & 1 & 2 & 1 & 1 \\
Diatome & \textit{Skeletonema marinoi} SkelA & 1 & 1 & 2 & 7 & 1 & 1 & 2 & 0 & 1 \\
Diatome & \textit{Skeletonema menzelii} CCMP793 & 1 & 4 & 4 & 8 & 1 & 1 & 2 & 0 & 1 \\
Diatome & \textit{Stauroneis constricta} CCMP1120 & 1 & 0 & 1 & 1 & 1 & 1 & 1 & 0 & 0 \\
Diatome & \textit{Staurosira complex} sp. CCMP2646 & 1 & 3 & 4 & 8 & 1 & 1 & 0 & 1 & 1 \\
Diatome & \textit{Stephanopyxis turris} CCMP 815 & 2 & 0 & 1 & 7 & 3 & 2 & 0 & 1 & 1 \\
Diatome & \textit{Striatella unipunctata} CCMP2910 & 4 & 2 & 1 & 6 & 3 & 0 & 1 & 0 & 2 \\
Diatome & \textit{Synedropsis recta} cf CCMP1620 & 1 & 2 & 0 & 1 & 1 & 1 & 1 & 1 & 0 \\
Diatome & \textit{Thalassionema frauenfeldii} CCMP 1798 & 1 & 5 & 7 & 15 & 1 & 3 & 1 & 1 & 2 \\
Diatome & \textit{Thalassionema nitzschioides} L26\_B & 1 & 3 & 4 & 8 & 1 & 1 & 1 & 1 & 1 \\
Diatome & \textit{Thalassiosira antarctica} CCMP982 & 1 & 4 & 2 & 12 & 1 & 1 & 3 & 1 & 1 \\
Diatome & \textit{Thalassiosira gravida} GMp14c1 & 1 & 1 & 3 & 13 & 1 & 1 & 2 & 1 & 1 \\
Diatome & \textit{Thalassiosira miniscula} CCMP1093 & 1 & 13 & 6 & 10 & 1 & 1 & 2 & 1 & 1 \\
Diatome & \textit{Thalassiosira oceanica} CCMP1005 & 1 & 10 & 1 & 10 & 1 & 1 & 0 & 0 & 1 \\
Diatome & \textit{Thalassiosira rotula} CCMP3096 & 1 & 5 & 3 & 11 & 1 & 1 & 2 & 1 & 1 \\
Diatome & \textit{Thalassiosira rotula} GSO102 & 1 & 3 & 2 & 11 & 1 & 1 & 1 & 1 & 1 \\
Diatome & \textit{Thalassiosira weissflogii} CCMP1010 & 1 & 4 & 1 & 9 & 1 & 0 & 1 & 0 & 1 \\
Diatome & \textit{Thalassiosira weissflogii} CCMP1336 & 1 & 4 & 1 & 8 & 1 & 0 & 1 & 0 & 1 \\
Diatome & \textit{Thalassiothrix antarctica} L6\_D1 & 1 & 2 & 4 & 6 & 1 & 1 & 0 & 1 & 1 \\
Diatome & \textit{Triceratium dubium} CCMP147 & 0 & 1 & 1 & 1 & 1 & 0 & 1 & 1 & 0 \\
Dinoflagellata & \textit{Alexandrium temarense} CCMP1771 & 3 & 18 & 12 & 45 & 18 & 10 & 3 & 4 & 2 \\
Dinoflagellata & \textit{Amphidinium carterae} CCMP1314 & 2 & 5 & 5 & 8 & 2 & 4 & 0 & 0 & 3 \\
Dinoflagellata & \textit{Azadinium spinosum} 3D9 & 1 & 12 & 13 & 35 & 11 & 6 & 0 & 0 & 3 \\
Dinoflagellata & \textit{Brandtodinium nutriculum} RCC3387 & 1 & 13 & 9 & 30 & 21 & 4 & 0 & 0 & 3 \\
Dinoflagellata & \textit{Ceratium fusus} PA161109 & 1 & 15 & 10 & 18 & 12 & 9 & 1 & 1 & 3 \\
Dinoflagellata & \textit{Crypthecodinium cohnii} Seligo & 1 & 6 & 5 & 15 & 2 & 4 & 0 & 0 & 3 \\
Dinoflagellata & \textit{Dinophysis acuminata} DAEP01 & 4 & 15 & 9 & 29 & 13 & 8 & 0 & 0 & 2 \\
Dinoflagellata & \textit{Durinskia baltica} CSIRO\_CS 38 & 2 & 12 & 9 & 18 & 9 & 8 & 0 & 0 & 4 \\
Dinoflagellata & \textit{Gambierdiscus australes} CAWD 149 & 1 & 5 & 0 & 9 & 14 & 6 & 0 & 0 & 2 \\
Dinoflagellata & \textit{Glenodinium foliaceum} CCAP1116\_3 & 2 & 9 & 3 & 23 & 7 & 6 & 0 & 1 & 4 \\
Dinoflagellata & \textit{Gonyaulax spinifera} CCMP409 & 1 & 2 & 0 & 10 & 10 & 8 & 1 & 1 & 1 \\
Dinoflagellata & \textit{Heterocapsa rotundata} SCCAP K 0483 & 2 & 19 & 4 & 12 & 6 & 4 & 0 & 0 & 6 \\
Dinoflagellata & \textit{Heterocapsa triquestra} CCMP 448 & 1 & 8 & 5 & 13 & 5 & 4 & 0 & 0 & 3 \\
Dinoflagellata & \textit{Karenia brevis} CCMP2229 & 1 & 14 & 8 & 10 & 8 & 7 & 0 & 1 & 4 \\
Dinoflagellata & \textit{Karenia brevis} SP1 & 1 & 14 & 13 & 16 & 6 & 8 & 0 & 1 & 4 \\
Dinoflagellata & \textit{Karenia brevis} SP3 & 1 & 12 & 9 & 13 & 8 & 10 & 0 & 1 & 4 \\
Dinoflagellata & \textit{Karenia brevis} Wilson & 1 & 14 & 7 & 14 & 9 & 8 & 0 & 2 & 5 \\
Dinoflagellata & \textit{Karlodinium micrum} CCMP2283 & 2 & 9 & 7 & 46 & 13 & 31 & 2 & 0 & 5 \\
Dinoflagellata & \textit{Kryptoperidinium foliaceum} CCMP1326 & 4 & 14 & 11 & 64 & 16 & 10 & 1 & 0 & 7 \\
Dinoflagellata & \textit{Lingulodinium polyedra} CCMP1738 & 1 & 17 & 8 & 19 & 11 & 11 & 1 & 0 & 3 \\
Dinoflagellata & \textit{Noctiluca scintillans} Unknown & 1 & 7 & 3 & 9 & 1 & 6 & 0 & 1 & 1 \\
Dinoflagellata & \textit{Oxyrrhis marina} & 1 & 2 & 5 & 9 & 7 & 3 & 0 & 1 & 2 \\
Dinoflagellata & \textit{Oxyrrhis marina} CCMP1795 & 0 & 0 & 0 & 0 & 3 & 0 & 0 & 0 & 0 \\
Dinoflagellata & \textit{Oxyrrhis marina} LB1974 & 1 & 2 & 4 & 10 & 4 & 2 & 0 & 0 & 2 \\
Dinoflagellata & \textit{Pelagodinium beii} RCC1491 & 1 & 8 & 2 & 12 & 11 & 4 & 0 & 0 & 4 \\
Dinoflagellata & \textit{Peridinium aciculiferum} PAER\_2 & 1 & 7 & 5 & 11 & 6 & 5 & 0 & 0 & 3 \\
Dinoflagellata & \textit{Polarella glacialis} CCMP 1383 & 1 & 28 & 5 & 23 & 5 & 5 & 0 & 0 & 8 \\
Dinoflagellata & \textit{Prorocentrum minimum} CCMP1329 & 1 & 15 & 6 & 29 & 13 & 6 & 0 & 0 & 3 \\
Dinoflagellata & \textit{Prorocentrum minimum} CCMP2233 & 1 & 14 & 4 & 29 & 12 & 5 & 0 & 0 & 3 \\
Dinoflagellata & \textit{Protoceratium reticulatum} CCCM 535 CCMP 1889 & 2 & 20 & 9 & 18 & 11 & 10 & 0 & 0 & 2 \\
Dinoflagellata & \textit{Pyrodinium bahamense} pbaha01 & 1 & 21 & 8 & 29 & 19 & 11 & 0 & 0 & 3 \\
Dinoflagellata & \textit{Scrippsiella hangoei} like SHHI\_4 & 1 & 8 & 6 & 22 & 6 & 16 & 0 & 2 & 2 \\
Dinoflagellata & \textit{Scrippsiella hangoei} SHTV5 & 1 & 8 & 11 & 14 & 3 & 5 & 0 & 0 & 2 \\
Dinoflagellata & \textit{Scrippsiella trochoidea} CCMP3099 & 1 & 27 & 10 & 38 & 12 & 8 & 1 & 1 & 3 \\
Dinoflagellata & \textit{Symbiodinium kawagutii} CCMP2468 & 0 & 0 & 0 & 0 & 2 & 0 & 0 & 0 & 0 \\
Dinoflagellata & \textit{Symbiodinium} sp. C1 & 1 & 9 & 4 & 9 & 6 & 4 & 0 & 0 & 3 \\
Dinoflagellata & \textit{Symbiodinium} sp. C15 & 1 & 7 & 2 & 12 & 3 & 4 & 1 & 0 & 3 \\
Dinoflagellata & \textit{Symbiodinium} sp. CCMP2430 & 1 & 7 & 2 & 10 & 7 & 4 & 0 & 0 & 3 \\
Dinoflagellata & \textit{Symbiodinium} sp. Mp & 1 & 7 & 3 & 13 & 6 & 3 & 0 & 0 & 3 \\
Dinoflagellata & \textit{Togula jolla} CCCM 725 & 1 & 17 & 3 & 21 & 3 & 6 & 0 & 0 & 4 \\
Discosea & \textit{Mayorella} sp. BSH 02190019 & 1 & 3 & 2 & 5 & 1 & 1 & 0 & 1 & 1 \\
Discosea & \textit{Neoparamoeba aestuarina} SoJaBio B1 5 56 2 & 3 & 3 & 3 & 12 & 3 & 3 & 0 & 1 & 1 \\
Discosea & \textit{Paramoeba atlantica} 621 1   CCAP 1560 9 & 1 & 3 & 2 & 8 & 3 & 2 & 0 & 1 & 1 \\
Discosea & \textit{Pessonella} sp. PRA 29 & 1 & 1 & 3 & 0 & 1 & 5 & 0 & 2 & 3 \\
Discosea & \textit{Stygamoeba regulata} BSH 02190019 & 3 & 8 & 2 & 7 & 2 & 4 & 0 & 0 & 2 \\
Discosea & \textit{Trichosphaerium} sp. Am I 7 wt & 2 & 0 & 0 & 1 & 2 & 3 & 0 & 0 & 2 \\
Eugelnophyta & \textit{Eutreptiella gymnastica} like CCMP1594 & 1 & 1 & 1 & 5 & 2 & 1 & 0 & 1 & 1 \\
Foraminifera & \textit{Ammonia} sp. Unknown & 1 & 1 & 3 & 9 & 5 & 2 & 0 & 1 & 1 \\
Foraminifera & \textit{Elphidium margaritaceum} Unknown & 1 & 1 & 2 & 8 & 3 & 1 & 1 & 0 & 1 \\
Foraminifera & \textit{Rosalina} sp. Unknown & 1 & 0 & 0 & 9 & 5 & 0 & 2 & 0 & 1 \\
Foraminifera & \textit{Sorites} sp. Unknown & 3 & 3 & 0 & 27 & 12 & 3 & 0 & 0 & 2 \\
Fungi & \textit{Debaryomyces hansenii} J26 & 1 & 0 & 0 & 4 & 0 & 0 & 0 & 0 & 1 \\
Glaucophyte & \textit{Gloeochaete witrockiana} SAG46\_84 & 2 & 2 & 3 & 9 & 2 & 2 & 1 & 1 & 1 \\
Haptophyte & \textit{Calcidiscus leptoporus} RCC1130 & 1 & 3 & 0 & 7 & 1 & 1 & 1 & 0 & 1 \\
Haptophyte & \textit{Chrysochromulina brevifilum} UTEX LB 985 & 1 & 2 & 1 & 4 & 1 & 3 & 0 & 1 & 0 \\
Haptophyte & \textit{Chrysochromulina ericina} CCMP281 & 2 & 1 & 0 & 10 & 1 & 3 & 1 & 1 & 2 \\
Haptophyte & \textit{Chrysochromulina polylepis} CCMP1757 & 1 & 3 & 5 & 9 & 1 & 2 & 1 & 1 & 1 \\
Haptophyte & \textit{Chrysoculter rhomboideus} RCC1486 & 1 & 0 & 0 & 9 & 1 & 0 & 0 & 1 & 0 \\
Haptophyte & \textit{Coccolithus pelagicus} ssp \textit{braarudi} PLY182g & 1 & 3 & 0 & 7 & 1 & 2 & 1 & 1 & 0 \\
Haptophyte & \textit{Emiliania huxleyi} 374 & 1 & 2 & 1 & 9 & 1 & 1 & 0 & 0 & 0 \\
Haptophyte & \textit{Emiliania huxleyi} 379 & 1 & 1 & 1 & 0 & 0 & 2 & 0 & 0 & 0 \\
Haptophyte & \textit{Emiliania huxleyi} CCMP370 & 1 & 3 & 5 & 9 & 0 & 2 & 1 & 1 & 1 \\
Haptophyte & \textit{Emiliania huxleyi} PLYM219 & 1 & 3 & 4 & 10 & 0 & 2 & 1 & 1 & 1 \\
Haptophyte & \textit{Exanthemachrysis gayraliae} RCC1523 & 1 & 2 & 0 & 1 & 1 & 1 & 0 & 1 & 1 \\
Haptophyte & \textit{Gephyrocapsa oceanica} RCC1303 & 1 & 3 & 5 & 11 & 1 & 1 & 0 & 0 & 1 \\
Haptophyte & \textit{Imantonia} sp. RCC918 & 3 & 1 & 1 & 4 & 2 & 1 & 1 & 1 & 0 \\
Haptophyte & \textit{Isochrysis galbana} CCMP1323 & 2 & 5 & 6 & 13 & 2 & 3 & 1 & 0 & 2 \\
Haptophyte & \textit{Isochrysis} sp. CCMP1244 & 1 & 2 & 5 & 11 & 1 & 1 & 0 & 1 & 1 \\
Haptophyte & \textit{Isochrysis} sp. CCMP1324 & 1 & 2 & 0 & 12 & 1 & 2 & 1 & 0 & 1 \\
Haptophyte & \textit{Pavlova} sp. CCMP459 & 1 & 2 & 1 & 6 & 2 & 1 & 2 & 1 & 1 \\
Haptophyte & \textit{Phaeocystis antarctica} Caron Lab Isolate & 3 & 7 & 2 & 12 & 1 & 3 & 2 & 0 & 2 \\
Haptophyte & \textit{Phaeocystis} sp. CCMP2710 & 1 & 0 & 1 & 2 & 1 & 1 & 1 & 1 & 1 \\
Haptophyte & \textit{Pleurochrysis carterae} CCMP645 & 3 & 2 & 1 & 7 & 1 & 2 & 1 & 1 & 1 \\
Haptophyte & \textit{Prymnesium parvum} Texoma1 & 1 & 6 & 4 & 1 & 1 & 2 & 1 & 1 & 1 \\
Haptophyte & \textit{Scyphosphaera apsteinii} RCC1455 & 1 & 3 & 1 & 7 & 1 & 2 & 1 & 0 & 1 \\
Heterolobosea & \textit{Percolomonas cosmopolitus} AE 1 ATCC 50343 & 1 & 4 & 2 & 9 & 2 & 2 & 0 & 0 & 1 \\
Heterolobosea & \textit{Percolomonas cosmopolitus} WS & 1 & 3 & 1 & 12 & 1 & 2 & 0 & 0 & 3 \\
Khakista & \textit{Corethron pennatum} L29A3 & 2 & 5 & 5 & 16 & 1 & 1 & 1 & 0 & 1 \\
Khakista & \textit{Detonula confervacea} CCMP 353 & 1 & 3 & 2 & 9 & 1 & 1 & 2 & 1 & 1 \\
Kinetoplastida & \textit{Neobodo designis} CCAP 1951 1 & 1 & 1 & 4 & 8 & 1 & 1 & 0 & 0 & 1 \\
Labyrinthulida & \textit{Aplanochytrium} sp. PBS07 & 1 & 2 & 1 & 3 & 1 & 1 & 1 & 2 & 1 \\
Labyrinthulida & \textit{Aplanochytrium stocchinoi} GSBS06 & 1 & 2 & 0 & 7 & 1 & 1 & 1 & 1 & 1 \\
Pelagophyte & \textit{Aureococcus anophagefferens} CCMP1850 & 6 & 2 & 3 & 45 & 1 & 2 & 0 & 0 & 1 \\
Pelagophyte & \textit{Aureoumbra lagunensis} CCMP1510 & 1 & 2 & 2 & 9 & 1 & 2 & 1 & 0 & 1 \\
Pelagophyte & \textit{Chrysocystis fragilis} CCMP3189 & 2 & 0 & 2 & 6 & 1 & 1 & 1 & 0 & 1 \\
Pelagophyte & \textit{Chrysoreinhardia} sp. CCMP2950 & 1 & 2 & 1 & 5 & 0 & 1 & 0 & 0 & 1 \\
Pelagophyte & \textit{Chrysoreinhardia} sp. CCMP3193 & 1 & 3 & 2 & 10 & 1 & 2 & 1 & 0 & 1 \\
Pelagophyte & \textit{Pelagomonas calceolata} CCMP1756 & 1 & 2 & 1 & 9 & 1 & 1 & 2 & 0 & 1 \\
Pelagophyte & \textit{Sarcinochrysis} sp. CCMP770 & 0 & 0 & 0 & 2 & 1 & 1 & 1 & 1 & 0 \\
Perkinsid & \textit{Perkinsus chesapeaki} ATCC\_PRA\_65 & 2 & 0 & 0 & 0 & 0 & 0 & 0 & 0 & 0 \\
Perkinsid & \textit{Perkinsus marinus} ATCC50439 & 1 & 0 & 0 & 1 & 2 & 0 & 0 & 0 & 0 \\
Pinguiophyte & \textit{Phaeomonas parva} CCMP2877 & 1 & 3 & 1 & 5 & 3 & 1 & 0 & 1 & 0 \\
Pinguiophyte & \textit{Pinguiococcus pyrenoidosus} CCMP2078 & 1 & 2 & 3 & 0 & 1 & 1 & 0 & 1 & 0 \\
Raphidophyte & \textit{Chattonella subsalsa} CCMP2191 & 1 & 3 & 0 & 5 & 1 & 1 & 1 & 0 & 1 \\
Raphidophyte & \textit{Fibrocapsa japonica} CCMP1661 & 0 & 1 & 1 & 5 & 1 & 1 & 0 & 1 & 0 \\
Raphidophyte & \textit{Heterosigma akashiwo} CCMP2393 & 1 & 4 & 2 & 11 & 2 & 1 & 0 & 1 & 1 \\
Raphidophyte & \textit{Heterosigma akashiwo} CCMP3107 & 1 & 7 & 2 & 0 & 1 & 1 & 0 & 0 & 0 \\
Raphidophyte & \textit{Heterosigma akashiwo} CCMP452 & 0 & 1 & 0 & 4 & 1 & 1 & 0 & 0 & 0 \\
Raphidophyte & \textit{Heterosigma akashiwo} NB & 1 & 6 & 1 & 8 & 1 & 1 & 0 & 1 & 1 \\
Rhodophyte  & \textit{Compsopogon coeruleus} SAG 36.94 & 1 & 3 & 2 & 11 & 1 & 1 & 0 & 0 & 1 \\
Rhodophyte  & \textit{Erythrolobus australicus} CCMP3124 & 1 & 2 & 3 & 0 & 1 & 1 & 0 & 1 & 1 \\
Rhodophyte  & \textit{Erythrolobus madagascarensis} CCMP3276 & 1 & 1 & 1 & 3 & 1 & 2 & 0 & 1 & 0 \\
Rhodophyte  & \textit{Madagascaria erythrocladiodes} CCMP3234 & 3 & 4 & 5 & 12 & 1 & 2 & 0 & 1 & 2 \\
Rhodophyte  & \textit{Porphyridium aerugineum} SAG 1380 2 & 2 & 1 & 2 & 5 & 1 & 2 & 1 & 0 & 1 \\
Rhodophyte  & \textit{Rhodella maculata} CCMP736 & 1 & 3 & 3 & 12 & 1 & 1 & 0 & 0 & 1 \\
Rhodophyte  & \textit{Rhodosorus marinus} CCMP 769 & 1 & 8 & 6 & 17 & 0 & 3 & 0 & 0 & 2 \\
Rhodophyte  & \textit{Timspurckia oligopyrenoides} CCMP3278 & 1 & 2 & 4 & 6 & 1 & 2 & 1 & 1 & 1 \\
Silicoflagellates & \textit{Dictyocha speculum} CCMP1381 & 1 & 4 & 2 & 9 & 1 & 2 & 1 & 1 & 1 \\
Silicoflagellates & \textit{Pseudopedinella elastica} CCMP716 & 1 & 5 & 6 & 9 & 1 & 1 & 1 & 1 & 1 \\
Silicoflagellates & \textit{Pteridomonas danica} PT & 1 & 1 & 1 & 2 & 1 & 1 & 1 & 1 & 0 \\
Silicoflagellates & \textit{Rhizochromulina marina} cf CCMP1243 & 1 & 5 & 2 & 8 & 2 & 2 & 1 & 1 & 1 \\
Synchromophyceae & \textit{Synchroma pusillum} CCMP3072 & 1 & 0 & 1 & 3 & 3 & 1 & 0 & 1 & 1 \\
Syndinian & \textit{Amoebophrya} sp. Ameob2 & 2 & 8 & 1 & 13 & 0 & 1 & 0 & 0 & 0 \\
Thraustochytrid & \textit{Aurantiochytrium limacinum} ATCCMYA1381 & 1 & 3 & 2 & 9 & 1 & 1 & 0 & 1 & 1 \\
Thraustochytrid & \textit{Schizochytrium aggregatum} ATCC28209 & 1 & 1 & 1 & 4 & 1 & 1 & 0 & 0 & 1 \\
Thraustochytrid & \textit{Thraustochytrium} sp. LLF1b & 1 & 2 & 1 & 9 & 1 & 1 & 0 & 1 & 1 \\
Tubulinid & \textit{Filamoeba nolandi} NC AS 23 1 & 2 & 4 & 1 & 13 & 0 & 3 & 1 & 0 & 1 \\
Tubulinid & \textit{Sexangularia} sp. ATCC50979 & 0 & 6 & 7 & 14 & 2 & 2 & 1 & 0 & 3 \\
Vanellinid & \textit{Vannella robusta} DIVA3 518 3 11 1 6 & 1 & 2 & 3 & 6 & 1 & 2 & 1 & 1 & 1 \\
Vanellinid & \textit{Vannella} sp. DIVA3 517 6 12 & 6 & 6 & 9 & 13 & 1 & 1 & 0 & 1 & 1 \\
Xantophyte & \textit{Vaucheria litorea} CCMP2940 & 1 & 2 & 0 & 6 & 1 & 1 & 0 & 1 & 1 \\
\label{TableS2}
\end{longtable}
\end{center}
\end{small}

\clearpage

\section*{Supplementary Figures}

\begin{figure*}[!ht]
\begin{center}
\includegraphics[width=10cm]{FigS1-V2.png}
\end{center}
\captionsetup{singlelinecheck=off,justification=justified}
\caption{
{\bf Cumulative distribution of scaffolds and pseudochromosome sizes before and after Hi-C scaffolding of the draft \textit{Breviolum}/\textit{Symbiodinium minutum} assembly\cite{Shoguchi2013}}. 3D DNA\cite{Dudchenko2017} scaffolding of the assembly results in 91 major pseudochromosomes $\geq$500kb encompassing $\sim$94\% of the assembled sequence.
}
\label{FigS1}
\end{figure*}

\clearpage

\begin{figure*}[!ht]
\begin{center}
\includegraphics[width=16cm]{FigS2-500KB-resolution.png}
\end{center}
\captionsetup{singlelinecheck=off,justification=justified}
\caption{
{\bf Broad-level bipartite to tripartite topological structure of dinoflagellate chromosomes}. Shown are 1Mbp-resolution KR-normalized\cite{KR} Hi-C matrices for four of the \textit{B. minutum} pseudochromosomes.
}
\label{FigS2}
\end{figure*}

\clearpage

\begin{figure*}[!ht]
\begin{center}
\includegraphics[width=18.5cm]{FigS3-scaffold17.png}
\end{center}
\captionsetup{singlelinecheck=off,justification=justified}
\caption{
{\bf The topological domain organization of dinoflagellate chromosomes is related to polycistronic gene array orientation}. Shown is the 5kb-resolution KR-normalized Hi-C map together with strand-specific RNA expression levels for pseudochromosome 17.
}
\label{FigS3}
\end{figure*}

\clearpage

\begin{figure*}[!ht]
\begin{center}
\includegraphics[width=18.5cm]{FigS4-scaffold18.png}
\end{center}
\captionsetup{singlelinecheck=off,justification=justified}
\caption{
{\bf The topological domain organization of dinoflagellate chromosomes is related to polycistronic gene array orientation}. Shown is the 5kb-resolution KR-normalized Hi-C map together with strand-specific RNA expression levels for pseudochromosome 18.
}
\label{FigS4}
\end{figure*}

\clearpage

\begin{figure*}[!ht]
\begin{center}
\includegraphics[width=18.5cm]{FigS5-scaffold21.png}
\end{center}
\captionsetup{singlelinecheck=off,justification=justified}
\caption{
{\bf The topological domain organization of dinoflagellate chromosomes is related to polycistronic gene array orientation}. Shown is the 5kb-resolution KR-normalized Hi-C map together with strand-specific RNA expression levels for pseudochromosome 21.
}
\label{FigS5}
\end{figure*}

\clearpage

\begin{figure*}[!ht]
\begin{center}
\includegraphics[width=18.5cm]{FigS6-scaffold26.png}
\end{center}
\captionsetup{singlelinecheck=off,justification=justified}
\caption{
{\bf The topological domain organization of dinoflagellate chromosomes is related to polycistronic gene array orientation}. Shown is the 5kb-resolution KR-normalized Hi-C map together with strand-specific RNA expression levels for pseudochromosome 26.
}
\label{FigS6}
\end{figure*}

\clearpage

\begin{figure*}[!ht]
\begin{center}
\includegraphics[width=18.5cm]{FigS8-scaffold32.png}
\end{center}
\captionsetup{singlelinecheck=off,justification=justified}
\caption{
{\bf The topological domain organization of dinoflagellate chromosomes is related to polycistronic gene array orientation}. Shown is the 5kb-resolution KR-normalized Hi-C map together with strand-specific RNA expression levels for pseudochromosome 32.
}
\label{FigS8}
\end{figure*}

\clearpage

\begin{figure*}[!ht]
\begin{center}
\includegraphics[width=18.5cm]{FigS9-scaffold36.png}
\end{center}
\captionsetup{singlelinecheck=off,justification=justified}
\caption{
{\bf The topological domain organization of dinoflagellate chromosomes is related to polycistronic gene array orientation}. Shown is the 5kb-resolution KR-normalized Hi-C map together with strand-specific RNA expression levels for pseudochromosome 36.
}
\label{FigS9}
\end{figure*}

\clearpage

\begin{figure*}[!ht]
\begin{center}
\includegraphics[width=18.5cm]{FigS10-scaffold71.png}
\end{center}
\captionsetup{singlelinecheck=off,justification=justified}
\caption{
{\bf The topological domain organization of dinoflagellate chromosomes is related to polycistronic gene array orientation}. Shown is the 5kb-resolution KR-normalized Hi-C map together with strand-specific RNA expression levels for pseudochromosome 71.
}
\label{FigS10}
\end{figure*}

\clearpage

\begin{figure*}[!ht]
\begin{center}
\includegraphics[width=18.5cm]{FigS11-scaffold77.png}
\end{center}
\captionsetup{singlelinecheck=off,justification=justified}
\caption{
{\bf The topological domain organization of dinoflagellate chromosomes is related to polycistronic gene array orientation}. Shown is the 5kb-resolution KR-normalized Hi-C map together with strand-specific RNA expression levels for pseudochromosome 77.
}
\label{FigS11}
\end{figure*}

\clearpage

\begin{figure*}[!ht]
\begin{center}
\includegraphics[width=18.5cm]{FigS12-scaffold78.png}
\end{center}
\captionsetup{singlelinecheck=off,justification=justified}
\caption{
{\bf The topological domain organization of dinoflagellate chromosomes is related to polycistronic gene array orientation}. Shown is the 5kb-resolution KR-normalized Hi-C map together with strand-specific RNA expression levels for pseudochromosome 78.
}
\label{FigS12}
\end{figure*}

\clearpage

\begin{figure*}[!ht]
\begin{center}
\includegraphics[width=18.5cm]{FigS13-scaffold88.png}
\end{center}
\captionsetup{singlelinecheck=off,justification=justified}
\caption{
{\bf The topological domain organization of dinoflagellate chromosomes is related to polycistronic gene array orientation}. Shown is the 5kb-resolution KR-normalized Hi-C map together with strand-specific RNA expression levels for pseudochromosome 88.
}
\label{FigS13}
\end{figure*}

\clearpage

\begin{figure*}[!ht]
\begin{center}
\includegraphics[width=18.5cm]{FigS14-scaffold89.png}
\end{center}
\captionsetup{singlelinecheck=off,justification=justified}
\caption{
{\bf The topological domain organization of dinoflagellate chromosomes is related to polycistronic gene array orientation}. Shown is the 5kb-resolution KR-normalized Hi-C map together with strand-specific RNA expression levels for pseudochromosome 89.
}
\label{FigS14}
\end{figure*}

\clearpage

\begin{figure*}[!ht]
\begin{center}
\includegraphics[width=18.5cm]{FigS31-Caulobacter-GSM1120448.png}
\end{center}
\captionsetup{singlelinecheck=off,justification=justified}
\caption{
{\bf Topological structure of the \textit{Caulobacter crescentus} CB15 genome}. Shown is the KR-normalized 5-kb resolution maps for the whole \textit{Caulobacter} chromosome (GEO accession GSM1120448).
\label{FigS31}
}
\end{figure*}

\clearpage

\begin{figure*}[!ht]
\begin{center}
\includegraphics[width=18.5cm]{FigS32-pombe.png}
\end{center}
\captionsetup{singlelinecheck=off,justification=justified}
\caption{
{\bf Topological structure of the \textit{Schizosaccharomyces pombe} genome}. Shown are the KR-normalized 5-kb resolution maps for all three \textit{S. pombe} chromosome (GEO accession GSM1379427).
\label{FigS32}
}
\end{figure*}

\clearpage

\begin{figure*}[!ht]
\begin{center}
\includegraphics[width=18.5cm]{FigS30-Trypanosoma.png}
\end{center}
\captionsetup{singlelinecheck=off,justification=justified}
\caption{
{\bf No topological domains associated with gene arrays are observed in the kinetoplastid \textit{Trypanosoma brucei}}. Shown are KR-normalized 10-kb resolution maps for chr11 (A) and chr10 (B) for GEO accession GSM3346690.
\label{FigS30}
}
\end{figure*}

\clearpage

\begin{figure*}[!ht]
\begin{center}
\includegraphics[width=18.5cm]{FigS15-Topo-PCNA-MCM-RPA-RFC1-V2.png}
\end{center}
\captionsetup{singlelinecheck=off,justification=justified}
\caption{
{\bf Expansion of the Type II and II topoisomerase gene repertoire as well as of certain other replication-related proteins in dinoflagellates}. Shown are the number of genes annotated in MMETSP transcriptome assemblies of dinoflagellates and other eukaryotes. 
(A) Number of Type I topoisomerase genes;
(B) Number of Type II topoisomerase genes;
(C) Number of Type III topoisomerase genes;
(D) Number of PCNA genes;
(E) Number of MCM genes;
(F) Number of RPA1 genes;
(G) Number of RPA2 genes;
(H) Number of RPA3 genes;
(I) Number of RFC1 genes.
}
\label{FigS15}
\end{figure*}

\clearpage

\begin{figure*}[!ht]
\begin{center}
\includegraphics[width=18.5cm]{FigS16-34C-scaffold10-V2.png}
\end{center}
\captionsetup{singlelinecheck=off,justification=justified}
\caption{
{\bf Moderate decompaction of dinoTADs upon exposure to elevated temperatures}. Shown is pseudochromosome 10 (KR-normalized) and the difference between the KR-normalized Hi-C maps generated from \textit{B. minutum} grown at 34$\,^{\circ}\mathrm{C}$ and at 27$\,^{\circ}\mathrm{C}$ at 100-kb resolution (lower right) and 5-kb resolution (upper right).
\label{FigS16}
}
\end{figure*}

\clearpage

\begin{figure*}[!ht]
\begin{center}
\includegraphics[width=18.5cm]{FigS17-34C-scaffold17-V2.png}
\end{center}
\captionsetup{singlelinecheck=off,justification=justified}
\caption{
{\bf Moderate decompaction of dinoTADs upon exposure to elevated temperatures}. Shown is pseudochromosome 17 (KR-normalized) and the difference between the KR-normalized Hi-C maps generated from \textit{B. minutum} grown at 34$\,^{\circ}\mathrm{C}$ and at 27$\,^{\circ}\mathrm{C}$ at 100-kb resolution (lower right) and 5-kb resolution (upper right).
\label{FigS17}
}
\end{figure*}

\clearpage

\begin{figure*}[!ht]
\begin{center}
\includegraphics[width=18.5cm]{FigS18-34C-scaffold18-V2.png}
\end{center}
\captionsetup{singlelinecheck=off,justification=justified}
\caption{
{\bf Moderate decompaction of dinoTADs upon exposure to elevated temperatures}. Shown is pseudochromosome 18 (KR-normalized) and the difference between the KR-normalized Hi-C maps generated from \textit{B. minutum} grown at 34$\,^{\circ}\mathrm{C}$ and at 27$\,^{\circ}\mathrm{C}$ at 100-kb resolution (lower right) and 5-kb resolution (upper right).
\label{FigS18}
}
\end{figure*}

\clearpage

\begin{figure*}[!ht]
\begin{center}
\includegraphics[width=18.5cm]{FigS33-amanitin-scaffold10.png}
\end{center}
\captionsetup{singlelinecheck=off,justification=justified}
\caption{
{\bf Decompaction of dinoTADs upon transcriptional inhibition using $\alpha$-amanitin}. Shown is pseudochromosome 10. Two time courses were carried out following the outline presented in Figure \ref{Fig2}B.
\label{FigS33}
}
\end{figure*}

\clearpage

\begin{figure*}[!ht]
\begin{center}
\includegraphics[width=18.5cm]{FigS34-amanitin-scaffold17.png}
\end{center}
\captionsetup{singlelinecheck=off,justification=justified}
\caption{
{\bf Decompaction of dinoTADs upon transcriptional inhibition using $\alpha$-amanitin}. Shown is pseudochromosome 17. Two time courses were carried out following the outline presented in Figure \ref{Fig2}B.
\label{FigS34}
}
\end{figure*}

\clearpage

\begin{figure*}[!ht]
\begin{center}
\includegraphics[width=18.5cm]{FigS35-amanitin-scaffold18.png}
\end{center}
\captionsetup{singlelinecheck=off,justification=justified}
\caption{
{\bf Decompaction of dinoTADs upon transcriptional inhibition using $\alpha$-amanitin}. Shown is pseudochromosome 18. Two time courses were carried out following the outline presented in Figure \ref{Fig2}B.
\label{FigS35}
}
\end{figure*}

\clearpage

\begin{figure*}[!ht]
\begin{center}
\includegraphics[width=18.5cm]{FigS40-metaplots-amanitin.png}
\end{center}
\captionsetup{singlelinecheck=off,justification=justified}
\caption{
{\bf Decompaction of dinoTADs upon transcriptional inhibition using $\alpha$-amanitin}. Shown are 50-kb resolution metaplots centered on dinoTAD domain boundaries. Two time courses were carried out following the outline presented in Figure \ref{Fig2}B.
\label{FigS40}
}
\end{figure*}

\clearpage

\begin{figure*}[!ht]
\begin{center}
\includegraphics[width=18.5cm]{FigS36-triptolide-scaffold10.png}
\end{center}
\captionsetup{singlelinecheck=off,justification=justified}
\caption{
{\bf Blurring of dinoTAD boundaries upon transcriptional inhibition using triptolide}. Shown is pseudochromosome 10. The triptolide time course was carried out following the outline presented in Figure \ref{Fig2}B.
\label{FigS36}
}
\end{figure*}

\clearpage

\begin{figure*}[!ht]
\begin{center}
\includegraphics[width=18.5cm]{FigS37-triptolide-scaffold17.png}
\end{center}
\captionsetup{singlelinecheck=off,justification=justified}
\caption{
{\bf Blurring of dinoTAD boundaries upon transcriptional inhibition using triptolide}. Shown is pseudochromosome 17. The triptolide time course was carried out following the outline presented in Figure \ref{Fig2}B.
\label{FigS37}
}
\end{figure*}

\clearpage

\begin{figure*}[!ht]
\begin{center}
\includegraphics[width=18.5cm]{FigS38-triptolide-scaffold18.png}
\end{center}
\captionsetup{singlelinecheck=off,justification=justified}
\caption{
{\bf Blurring of dinoTAD boundaries upon transcriptional inhibition using triptolide}. Shown is pseudochromosome 18. The triptolide time course was carried out following the outline presented in Figure \ref{Fig2}B.
\label{FigS38}
}
\end{figure*}

\clearpage

\begin{figure*}[!ht]
\begin{center}
\includegraphics[width=18.5cm]{FigS39-metaplots-triptolide.png}
\end{center}
\captionsetup{singlelinecheck=off,justification=justified}
\caption{
{\bf Blurring of dinoTAD boundaries upon transcriptional inhibition using triptolide}. Shown are 50-kb resolution metaplots centered on dinoTAD domain boundaries. The triptolide time course was carried out following the outline presented in Figure \ref{Fig2}B.
\label{FigS39}
}
\end{figure*}

\clearpage

% \begin{figure*}[!ht]
% \begin{center}
% \includegraphics[width=10cm]{FigS28-FvFm-V2.png}
% \end{center}
% \captionsetup{singlelinecheck=off,justification=justified}
% \caption{
% {\bf \hl{XXX LEGEND Fv/FM}}. \hl{LEGEND GOES HERE}.
% \label{FigS28}
% }
% \end{figure*}

% \clearpage

\end{document}