Comparison of 15 dinoflagellate genomes reveals extensive sequence and structural divergence in family Symbiodiniaceae and genus Symbiodinium

[1]  Ø. Moestrup,et al.  Fine-structural characterization and phylogeny of Sphaerodinium (Suessiales, Dinophyceae), with the description of an unusual type of freshwater dinoflagellate cyst. , 2021, European journal of protistology.

[2]  Z. Forsman,et al.  Host-symbiont coevolution, cryptic structure, and bleaching susceptibility, in a coral species complex (Scleractinia; Poritidae) , 2020, Scientific Reports.

[3]  E. Ball,et al.  Dual RNA‐sequencing analyses of a coral and its native symbiont during the establishment of symbiosis , 2020, Molecular ecology.

[4]  C. Grueber,et al.  A demonstration of conservation genomics for threatened species management , 2020, Molecular ecology resources.

[5]  D. Bhattacharya,et al.  Sex in Symbiodiniaceae dinoflagellates: genomic evidence for independent loss of the canonical synaptonemal complex , 2020, Scientific Reports.

[6]  Senjie Lin,et al.  Genome Size, rDNA Copy, and qPCR Assays for Symbiodiniaceae , 2020, Frontiers in Microbiology.

[7]  Timothy G. Stephens,et al.  Genomes of the dinoflagellate Polarella glacialis encode tandemly repeated single-exon genes with adaptive functions , 2020, BMC Biology.

[8]  Benoit Liquet,et al.  Forecasting intensifying disturbance effects on coral reefs , 2020, Global change biology.

[9]  Timothy G. Stephens,et al.  Evidence That Inconsistent Gene Prediction Can Mislead Analysis of Dinoflagellate Genomes , 2019, Journal of phycology.

[10]  David J. Smith,et al.  Coral bleaching patterns are the outcome of complex biological and environmental networking , 2019, Global change biology.

[11]  V. Weis.  Cell biology of coral symbiosis: Foundational study can inform solutions to the coral reef crisis. , 2019, Integrative and comparative biology.

[12]  M. Ragan,et al.  Genome Evolution of Coral Reef Symbionts as Intracellular Residents. , 2019, Trends in ecology & evolution.

[13]  M. Schatz,et al.  GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes , 2019, bioRxiv.

[14]  D. Bourne,et al.  Nutrient Availability and Metabolism Affect the Stability of Coral-Symbiodiniaceae Symbioses. , 2019, Trends in microbiology.

[15]  Erika J. Techera,et al.  Coral reef conservation in the Anthropocene: Confronting spatial mismatches and prioritizing functions , 2019, Biological Conservation.

[16]  P. Wincker,et al.  Transposition favors the generation of large effect mutations that may facilitate rapid adaption , 2019, Nature Communications.

[17]  T. Ravasi,et al.  A genomic view of the reef-building coral Porites lutea and its microbial symbionts , 2019, Nature Microbiology.

[18]  J. Wong,et al.  DNA Damage Response Pathways in Dinoflagellates , 2019, Microorganisms.

[19]  K. Valentin,et al.  An aerobic eukaryotic parasite with functional mitochondria that likely lacks a mitochondrial genome , 2019, Science Advances.

[20]  Shaun P. Wilkinson,et al.  Multi-gene incongruence consistent with hybridisation in Cladocopium (Symbiodiniaceae), an ecologically important genus of coral reef symbionts , 2019, PeerJ.

[21]  Timothy G. Stephens,et al.  Core genes in diverse dinoflagellate lineages include a wealth of conserved dark genes with unknown functions , 2018, Scientific Reports.

[22]  S. Kelly,et al.  OrthoFinder: phylogenetic orthology inference for comparative genomics , 2019, Genome Biology.

[23]  David J. Miller,et al.  Comparative genomics reveals the distinct evolutionary trajectories of the robust and complex coral lineages , 2018, Genome Biology.

[24]  Paul Greenfield,et al.  k-mer Similarity, Networks of Microbial Genomes, and Taxonomic Rank , 2017, mSystems.

[25]  J. Reimer,et al.  Systematic Revision of Symbiodiniaceae Highlights the Antiquity and Diversity of Coral Endosymbionts , 2018, Current Biology.

[26]  Timothy G. Stephens,et al.  Symbiodinium genomes reveal adaptive evolution of functions related to coral-dinoflagellate symbiosis , 2018, Communications Biology.

[27]  M. Kawachi,et al.  Two divergent Symbiodinium genomes reveal conservation of a gene cluster for sunscreen biosynthesis and recently lost genes , 2018, BMC genomics.

[28]  R. Lister,et al.  Recurrent acquisition of cytosine methyltransferases into eukaryotic retrotransposons , 2018, Nature Communications.

[29]  S. Kelly,et al.  STAG: Species Tree Inference from All Genes , 2018, bioRxiv.

[30]  Adam M. Phillippy,et al.  MUMmer4: A fast and versatile genome alignment system , 2018, PLoS Comput. Biol..

[31]  B. Willis,et al.  Temperature and Water Quality-Related Patterns in Sediment-Associated Symbiodinium Communities Impact Symbiont Uptake and Fitness of Juveniles in the Genus Acropora , 2017, Front. Mar. Sci..

[32]  M. Ragan,et al.  Signatures of adaptation and symbiosis in genomes and transcriptomes of Symbiodinium , 2017, Scientific Reports.

[33]  Wenbin Chen,et al.  Comparative Genomics Reveals Two Major Bouts of Gene Retroposition Coinciding with Crucial Periods of Symbiodinium Evolution , 2017, Genome biology and evolution.

[34]  James M. Hogan,et al.  Alignment-free inference of hierarchical and reticulate phylogenomic relationships , 2017, Briefings Bioinform..

[35]  M. Scheffer,et al.  Coral reefs in the Anthropocene , 2017, Nature.

[36]  S. Kelly,et al.  STRIDE: Species Tree Root Inference from Gene Duplication Events , 2017, bioRxiv.

[37]  E. Howells,et al.  Population genetics of reef coral endosymbionts (Symbiodinium, Dinophyceae) , 2017, Molecular ecology.

[38]  Will F. Figueira,et al.  Global warming and recurrent mass bleaching of corals , 2017, Nature.

[39]  Manuel Aranda,et al.  Condition-specific RNA editing in the coral symbiont Symbiodinium microadriaticum , 2017, PLoS genetics.

[40]  Vincent Moulton,et al.  Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus , 2017, Nature.

[41]  Cheong Xin Chan,et al.  Recapitulating phylogenies using k-mers: from trees to networks , 2016, F1000Research.

[42]  S. Baumgarten,et al.  Genomes of coral dinoflagellate symbionts highlight evolutionary adaptations conducive to a symbiotic lifestyle , 2016, Scientific Reports.

[43]  Sergey Koren,et al.  Hybrid assembly of the large and highly repetitive genome of Aegilops tauschii , a progenitor of bread wheat , with the mega-reads algorithm , 2016 .

[44]  Y. Loya,et al.  Ancestral genetic diversity associated with the rapid spread of stress-tolerant coral symbionts in response to Holocene climate change , 2016, Proceedings of the National Academy of Sciences.

[45]  Stephen J. Callister,et al.  Evidence-based green algal genomics reveals marine diversity and ancestral characteristics of land plants , 2016, BMC Genomics.

[46]  Robert D. Finn,et al.  The Pfam protein families database: towards a more sustainable future , 2015, Nucleic Acids Res..

[47]  I. Bravo,et al.  The Hidden Sexuality of Alexandrium Minutum: An Example of Overlooked Sex in Dinoflagellates , 2015, PloS one.

[48]  Huanming Yang,et al.  The Symbiodinium kawagutii genome illuminates dinoflagellate gene expression and coral symbiosis , 2015, Science.

[49]  N. Satoh,et al.  The Large Mitochondrial Genome of Symbiodinium minutum Reveals Conserved Noncoding Sequences between Dinoflagellates and Apicomplexans , 2015, Genome biology and evolution.

[50]  Rodrigo Lopez,et al.  The EMBL-EBI bioinformatics web and programmatic tools framework , 2015, Nucleic Acids Res..

[51]  Tae Young Jang,et al.  Symbiodinium tridacnidorum sp. nov., a dinoflagellate common to Indo-Pacific giant clams, and a revised morphological description of Symbiodinium microadriaticum Freudenthal, emended Trench & Blank , 2015 .

[52]  S. Davy,et al.  The effect of elevated temperature and substrate on free-living Symbiodinium cultures , 2015, Coral Reefs.

[53]  Ole Schulz-Trieglaff,et al.  NxTrim: optimized trimming of Illumina mate pair reads , 2014, bioRxiv.

[54]  N. Satoh,et al.  Massive Gene Transfer and Extensive RNA Editing of a Symbiotic Dinoflagellate Plastid Genome , 2014, Genome biology and evolution.

[55]  M. Dunthorn,et al.  Cryptic Sex in Symbiodinium (Alveolata, Dinoflagellata) is Supported by an Inventory of Meiotic Genes , 2014, The Journal of eukaryotic microbiology.

[56]  Björn Usadel,et al.  Trimmomatic: a flexible trimmer for Illumina sequence data , 2014, Bioinform..

[57]  D. Thornhill,et al.  HOST‐SPECIALIST LINEAGES DOMINATE THE ADAPTIVE RADIATION OF REEF CORAL ENDOSYMBIONTS , 2014, Evolution; international journal of organic evolution.

[58]  I. Bravo,et al.  Towards an Ecological Understanding of Dinoflagellate Cyst Functions , 2014, Microorganisms.

[59]  T. Lajeunesse,et al.  Long-Range Dispersal and High-Latitude Environments Influence the Population Structure of a “Stress-Tolerant” Dinoflagellate Endosymbiont , 2013, PloS one.

[60]  Jiongtang Li,et al.  L_RNA_scaffolder: scaffolding genomes with transcripts , 2013, BMC Genomics.

[61]  S. Sugano,et al.  Draft Assembly of the Symbiodinium minutum Nuclear Genome Reveals Dinoflagellate Gene Structure , 2013, Current Biology.

[62]  Colin N. Dewey,et al.  De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis , 2013, Nature Protocols.

[63]  A. Salamov,et al.  Pan genome of the phytoplankton Emiliania underpins its global distribution , 2013, Nature.

[64]  Paul Greenfield,et al.  Answering biological questions by querying k‐mer databases , 2013, Concurr. Comput. Pract. Exp..

[65]  Zhengwei Zhu,et al.  CD-HIT: accelerated for clustering the next-generation sequencing data , 2012, Bioinform..

[66]  S. Sunagawa,et al.  Symbiodinium Transcriptomes: Genome Insights into the Dinoflagellate Symbionts of Reef-Building Corals , 2012, PloS one.

[67]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[68]  Jeremy D. DeBarry,et al.  MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity , 2012, Nucleic acids research.

[69]  Mark Yandell,et al.  MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects , 2011, BMC Bioinformatics.

[70]  A. Cembella,et al.  Comparative Genomic and Transcriptomic Characterization of the Toxigenic Marine Dinoflagellate Alexandrium ostenfeldii , 2011, PloS one.

[71]  N. Moran,et al.  Extreme genome reduction in symbiotic bacteria , 2011, Nature Reviews Microbiology.

[72]  W. Kiessling,et al.  EVOLUTIONARY DIVERSIFICATION OF REEF CORALS: A COMPARISON OF THE MOLECULAR AND FOSSIL RECORDS , 2011, Evolution; international journal of organic evolution.

[73]  S. Salzberg,et al.  FLASH: fast length adjustment of short reads to improve genome assemblies , 2011, Bioinform..

[74]  Jennifer H. Wisecaver,et al.  Dinoflagellate genome evolution. , 2011, Annual review of microbiology.

[75]  Senjie Lin.  Genomic understanding of dinoflagellates. , 2011, Research in microbiology.

[76]  Carl Kingsford,et al.  A fast, lock-free approach for efficient parallel counting of occurrences of k-mers , 2011, Bioinform..

[77]  Carsten O. Daub,et al.  SAMStat: monitoring biases in next generation sequencing data , 2010, Bioinform..

[78]  Todd C. LaJeunesse,et al.  Long‐standing environmental conditions, geographic isolation and host–symbiont specificity influence the relative ecological dominance and genetic diversification of coral endosymbionts in the genus Symbiodinium , 2010 .

[79]  Richard Durbin,et al.  Fast and accurate long-read alignment with Burrows–Wheeler transform , 2010, Bioinform..

[80]  M. Batzer,et al.  The impact of retrotransposons on human genome evolution , 2009, Nature Reviews Genetics.

[81]  Senjie Lin,et al.  Dinoflagellate spliced leader RNA genes display a variety of sequences and genomic arrangements. , 2009, Molecular biology and evolution.

[82]  Y. Sako,et al.  Analysis of the mitochondrial genome, transcripts, and electron transport activity in the dinoflagellate Alexandrium catenella (Gonyaulacales, Dinophyceae) , 2009 .

[83]  A. Correa,et al.  Understanding diversity in coral-algal symbiosis: a cluster-based approach to interpreting fine-scale genetic variation in the genus Symbiodinium , 2009, Coral Reefs.

[84]  G. Hansen,et al.  SYMBIODINIUM NATANS SP. NOV.: A “FREE‐LIVING” DINOFLAGELLATE FROM TENERIFE (NORTHEAST‐ATLANTIC OCEAN) 1 , 2009, Journal of phycology.

[85]  A. Place,et al.  From Stop to Start: Tandem Gene Arrangement, Copy Number and Trans-Splicing Sites in the Dinoflagellate Amphidinium carterae , 2008, PloS one.

[86]  Jonathan E. Allen,et al.  Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments , 2007, Genome Biology.

[87]  R. Waller,et al.  Broad genomic and transcriptional analysis reveals a highly derived genome in dinoflagellate mitochondria , 2007, BMC Biology.

[88]  Keith Bradnam,et al.  CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes , 2007, Bioinform..

[89]  T. Gaasterland,et al.  Spliced leader RNA trans-splicing in dinoflagellates , 2007, Proceedings of the National Academy of Sciences.

[90]  G. McFadden,et al.  Sodium-dependent uptake of inorganic phosphate by the intracellular malaria parasite , 2006, Nature.

[91]  O. Hoegh‐Guldberg,et al.  The evolutionary history of Symbiodinium and scleractinian hosts-Symbiosis, diversity, and the effect of climate change , 2006 .

[92]  Burkhard Morgenstern,et al.  AUGUSTUS: ab initio prediction of alternative transcripts , 2006, Nucleic Acids Res..

[93]  Adam Godzik,et al.  Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences , 2006, Bioinform..

[94]  M. Borodovsky,et al.  Gene identification in novel eukaryotic genomes by self-training algorithm , 2005, Nucleic acids research.

[95]  S. Ho,et al.  Improving the analysis of dinoflagellate phylogeny based on rDNA. , 2005, Protist.

[96]  Todd C. LaJeunesse,et al.  SYMBIODINIUM (PYRRHOPHYTA) GENOME SIZES (DNA CONTENT) ARE SMALLEST AMONG DINOFLAGELLATES 1 , 2005 .

[97]  T. Lajeunesse.  "Species" radiations of symbiotic dinoflagellates in the Atlantic and Indo-Pacific since the Miocene-Pliocene transition. , 2005, Molecular biology and evolution.

[98]  N. Moran,et al.  Genomic changes following host restriction in bacteria. , 2004, Current opinion in genetics & development.

[99]  Ian Korf,et al.  Gene finding in novel genomes , 2004, BMC Bioinformatics.

[100]  A. Baker.  Flexibility and Specificity in Coral-Algal Symbiosis: Diversity, Ecology, and Biogeography of Symbiodinium , 2003 .

[101]  Stephen M. Mount,et al.  Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. , 2003, Nucleic acids research.

[102]  L. Medlin,et al.  The application of a molecular clock based on molecular sequences and the fossil record to explain biogeographic distributions within the Alexandrium tamarense "species complex" (Dinophyceae). , 2003, Molecular biology and evolution.

[103]  F. B. Pickett,et al.  Splitting pairs: the diverging fates of duplicated genes , 2002, Nature Reviews Genetics.

[104]  Todd C. LaJeunesse,et al.  Diversity and community structure of symbiotic dinoflagellates from Caribbean coral reefs , 2002 .

[105]  W. J. Kent,et al.  BLAT--the BLAST-like alignment tool. , 2002, Genome research.

[106]  E. Gomez,et al.  Genetic variation in Symbiodinium isolates from giant clams based on random-amplified-polymorphic DNA (RAPD) patterns , 2000 .

[107]  M. Kawachi,et al.  PHYLOGENETIC POSITION OF SYMBIODINIUM (DINOPHYCEAE) ISOLATES FROM TRIDACNIDS (BIVALVIA), CARDIIDS (BIVALVIA), A SPONGE (PORIFERA), A SOFT CORAL (ANTHOZOA), AND A FREE‐LIVING STRAIN , 1999 .

[108]  T. Cavalier-smith,et al.  Single gene circles in dinoflagellate chloroplast genomes , 1999, Nature.

[109]  G. Procaccini,et al.  POLARELLA GLACIALIS, GEN. NOV., SP. NOV. (DINOPHYCEAE): SUESSIACEAE ARE STILL ALIVE! , 1999 .

[110]  B. Baillie,et al.  Allozyme electrophoresis as a tool for distinguishing different zooxanthellae symbiotic with giant clams , 1998, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[111]  D. Morse,et al.  Structure and organization of the peridinin-chlorophyll a-binding protein gene in Gonyaulax polyedra , 1997, Molecular and General Genetics MGG.

[112]  Paul G. Falkowski,et al.  Fate of photosynthetic fixed carbon in light- and shade-adapted colonies of the symbiotic coral Stylophora pistillata , 1984, Proceedings of the Royal Society of London. Series B. Biological Sciences.

[113]  M. Kimura.  A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences , 1980, Journal of Molecular Evolution.

[114]  M. Kimura.  Evolutionary Rate at the Molecular Level , 1968, Nature.

[115]  M. Ragan,et al.  Genome assemblies and the associated annotations for seven Symbiodinium isolates , 2021 .

[116]  A. Barbrook,et al.  The chloroplast genome of a Symbiodinium sp. clade C3 isolate. , 2014, Protist.

[117]  P. Ralph,et al.  Coral bleaching: the role of the host. , 2009, Trends in ecology & evolution.

[118]  X. Pochon,et al.  Molecular phylogeny, evolutionary rates, and divergence timing of the symbiotic dinoflagellate genus Symbiodinium. , 2006, Molecular phylogenetics and evolution.

[119]  Agaricia tenuifolia,et al.  Diversity and community structure of symbiotic dinoflagellates from Caribbean coral reefs , 2002 .

[120]  Y. Benjamini,et al.  Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .