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Structural rearrangements drive extensive genome divergence between symbiotic and free-living Symbiodinium

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1007/978-3-319-28068-4_10openalex-snapshot

Animal–Symbiodinium Symbioses: Foundations of Coral Reef Ecosystems

inferredcites →https://doi.org/10.1007/bf00023563openalex-snapshot

Nucleotide sequence of a cDNA clone encoding the precursor of the peridinin-chlorophyll a-binding protein from the dinoflagellate Symbiodinium sp.

inferredcites →https://doi.org/10.1007/bf01731581openalex-snapshot

A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences

inferredcites →https://doi.org/10.1007/s00227-002-0829-2openalex-snapshot

Diversity and community structure of symbiotic dinoflagellates from Caribbean coral reefs

inferredcites →https://doi.org/10.1007/s002270000290openalex-snapshot

Genetic variation in Symbiodinium isolates from giant clams based on random-amplified-polymorphic DNA (RAPD) patterns

inferredcites →https://doi.org/10.1007/s00338-014-1220-8openalex-snapshot

The effect of elevated temperature and substrate on free-living Symbiodinium cultures

inferredcites →https://doi.org/10.1007/s004380050533openalex-snapshot

Structure and organization of the peridinin-chlorophyll a-binding protein gene in Gonyaulax polyedra

inferredcites →https://doi.org/10.1016/j.cub.2008.04.054openalex-snapshot

Widespread recycling of processed cDNAs in dinoflagellates

inferredcites →https://doi.org/10.1016/j.cub.2018.07.008openalex-snapshot

Systematic Revision of Symbiodiniaceae Highlights the Antiquity and Diversity of Coral Endosymbionts

inferredcites →https://doi.org/10.1016/j.gde.2004.09.003openalex-snapshot

Genomic changes following host restriction in bacteria

inferredcites →https://doi.org/10.1016/j.protis.2019.06.003openalex-snapshot

A Transcriptome-based Perspective of Meiosis in Dinoflagellates

inferredcites →https://doi.org/10.1016/j.tree.2019.04.010openalex-snapshot

Genome Evolution of Coral Reef Symbionts as Intracellular Residents

inferredcites →https://doi.org/10.1016/j.ympev.2005.04.028openalex-snapshot

Molecular phylogeny, evolutionary rates, and divergence timing of the symbiotic dinoflagellate genus Symbiodinium

inferredcites →https://doi.org/10.1038/nature05149openalex-snapshot

Sodium-dependent uptake of inorganic phosphate by the intracellular malaria parasite

inferredcites →https://doi.org/10.1038/nbt.1883openalex-snapshot

Full-length transcriptome assembly from RNA-Seq data without a reference genome

inferredcites →https://doi.org/10.1038/nmeth.1923openalex-snapshot

Fast gapped-read alignment with Bowtie 2

inferredcites →https://doi.org/10.1038/nrg2640openalex-snapshot

The impact of retrotransposons on human genome evolution

inferredcites →https://doi.org/10.1038/nrg928openalex-snapshot

Splitting pairs: the diverging fates of duplicated genes

inferredcites →https://doi.org/10.1038/nrmicro2670openalex-snapshot

Extreme genome reduction in symbiotic bacteria

inferredcites →https://doi.org/10.1038/s41467-018-03724-9openalex-snapshot

Recurrent acquisition of cytosine methyltransferases into eukaryotic retrotransposons

inferredcites →https://doi.org/10.1038/s41467-019-11385-5openalex-snapshot

Transposition favors the generation of large effect mutations that may facilitate rapid adaption

inferredcites →https://doi.org/10.1038/s41598-018-35620-zopenalex-snapshot

Core genes in diverse dinoflagellate lineages include a wealth of conserved dark genes with unknown functions

inferredcites →https://doi.org/10.1038/s42003-018-0098-3openalex-snapshot

Symbiodinium genomes reveal adaptive evolution of functions related to coral-dinoflagellate symbiosis

inferredcites →https://doi.org/10.1046/j.1529-8817.2001.01031.xopenalex-snapshot

INVESTIGATING THE BIODIVERSITY, ECOLOGY, AND PHYLOGENY OF ENDOSYMBIOTIC DINOFLAGELLATES IN THE GENUS SYMBIODINIUM USING THE ITS REGION: IN SEARCH OF A “SPECIES” LEVEL MARKER

inferredcites →https://doi.org/10.1073/pnas.0700258104openalex-snapshot

Spliced leader RNA trans-splicing in dinoflagellates

inferredcites →https://doi.org/10.1073/pnas.89.8.3639openalex-snapshot

Ribosomal RNA sequences and the diversity of symbiotic dinoflagellates (zooxanthellae).

inferredcites →https://doi.org/10.1080/09670262.2015.1018336openalex-snapshot

Symbiodinium tridacnidorumsp. nov., a dinoflagellate common to Indo-Pacific giant clams, and a revised morphological description ofSymbiodinium microadriaticumFreudenthal, emended Trench & Blank

inferredcites →https://doi.org/10.1093/bioinformatics/btl158openalex-snapshot

Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences

inferredcites →https://doi.org/10.1093/bioinformatics/btm071openalex-snapshot

CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes

inferredcites →https://doi.org/10.1093/bioinformatics/btp698openalex-snapshot

Fast and accurate long-read alignment with Burrows–Wheeler transform

inferredcites →https://doi.org/10.1093/bioinformatics/btq614openalex-snapshot

SAMStat: monitoring biases in next generation sequencing data

inferredcites →https://doi.org/10.1093/bioinformatics/btq683openalex-snapshot

Scaffolding pre-assembled contigs using SSPACE

inferredcites →https://doi.org/10.1093/bioinformatics/btr507openalex-snapshot

FLASH: fast length adjustment of short reads to improve genome assemblies

inferredcites →https://doi.org/10.1093/bioinformatics/bts565openalex-snapshot

CD-HIT: accelerated for clustering the next-generation sequencing data

inferredcites →https://doi.org/10.1093/bioinformatics/btt476openalex-snapshot

The MaSuRCA genome assembler

inferredcites →https://doi.org/10.1093/bioinformatics/btu170openalex-snapshot

Trimmomatic: a flexible trimmer for Illumina sequence data

inferredcites →https://doi.org/10.1093/bioinformatics/btv057openalex-snapshot

NxTrim: optimized trimming of Illumina mate pair reads

inferredcites →https://doi.org/10.1093/gbe/evx144openalex-snapshot

Comparative Genomics Reveals Two Major Bouts of Gene Retroposition Coinciding with Crucial Periods of Symbiodinium Evolution

inferredcites →https://doi.org/10.1093/icb/icz067openalex-snapshot

Cell Biology of Coral Symbiosis: Foundational Study Can Inform Solutions to the Coral Reef Crisis

inferredcites →https://doi.org/10.1093/molbev/msg233openalex-snapshot

PCP Gene Family in Symbiodinium from Hippopus hippopus: Low Levels of Concerted Evolution, Isoform Diversity, and Spectral Tuning of Chromophores

inferredcites →https://doi.org/10.1093/nar/gkg770openalex-snapshot

Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies

inferredcites →https://doi.org/10.1093/nar/gkh121openalex-snapshot

The Pfam protein families database

inferredcites →https://doi.org/10.1093/nar/gki937openalex-snapshot

Gene identification in novel eukaryotic genomes by self-training algorithm

inferredcites →https://doi.org/10.1093/nar/gkl200openalex-snapshot

AUGUSTUS: ab initio prediction of alternative transcripts

inferredcites →https://doi.org/10.1093/nar/gkr1293openalex-snapshot

MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity

inferredcites →https://doi.org/10.1093/nar/gkv279openalex-snapshot

The EMBL-EBI bioinformatics web and programmatic tools framework

inferredcites →https://doi.org/10.1098/rspb.1998.0525openalex-snapshot

Allozyme electrophoresis as a tool for distinguishing different zooxanthellae symbiotic with giant clams

inferredcites →https://doi.org/10.1101/652131openalex-snapshot

Transcriptomic insights into the establishment of coral-algal symbioses from the symbiont perspective

inferredcites →https://doi.org/10.1111/evo.12270openalex-snapshot

HOST-SPECIALIST LINEAGES DOMINATE THE ADAPTIVE RADIATION OF REEF CORAL ENDOSYMBIONTS

inferredcites →https://doi.org/10.1111/j.1529-8817.2008.00621.xopenalex-snapshot

SYMBIODINIUM NATANS SP. NOV.: A “FREE‐LIVING” DINOFLAGELLATE FROM TENERIFE (NORTHEAST‐ATLANTIC OCEAN) 1

inferredcites →https://doi.org/10.1111/j.2517-6161.1995.tb02031.xopenalex-snapshot

Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing

inferredcites →https://doi.org/10.1111/jeu.12110openalex-snapshot

Cryptic Sex in Symbiodinium (Alveolata, Dinoflagellata) is Supported by an Inventory of Meiotic Genes

inferredcites →https://doi.org/10.1111/jpy.12947openalex-snapshot

Evidence That Inconsistent Gene Prediction Can Mislead Analysis of Dinoflagellate Genomes

inferredcites →https://doi.org/10.1126/science.290.5494.1151openalex-snapshot

The Evolutionary Fate and Consequences of Duplicate Genes

inferredcites →https://doi.org/10.1126/science.aad0408openalex-snapshot

The Symbiodinium kawagutii genome illuminates dinoflagellate gene expression and coral symbiosis

inferredcites →https://doi.org/10.1128/mmbr.05014-11openalex-snapshot

Cell Biology of Cnidarian-Dinoflagellate Symbiosis

inferredcites →https://doi.org/10.1146/annurev.ecolsys.34.011802.132417openalex-snapshot

Flexibility and Specificity in Coral-Algal Symbiosis: Diversity, Ecology, and Biogeography of Symbiodinium

inferredcites →https://doi.org/10.1186/1471-2105-12-491openalex-snapshot

MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects

inferredcites →https://doi.org/10.1186/1471-2105-5-1openalex-snapshot

PyEvolve: a toolkit for statistical modelling of molecular evolution

inferredcites →https://doi.org/10.1186/1471-2105-5-59openalex-snapshot

Gene finding in novel genomes

inferredcites →https://doi.org/10.1186/1471-2164-14-604openalex-snapshot

L_RNA_scaffolder: scaffolding genomes with transcripts

inferredcites →https://doi.org/10.1186/gb-2008-9-1-r7openalex-snapshot

Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

inferredcites →https://doi.org/10.1186/s12915-020-00782-8openalex-snapshot

Genomes of the dinoflagellate Polarella glacialis encode tandemly repeated single-exon genes with adaptive functions

inferredcites →https://doi.org/10.1186/s13059-018-1552-8openalex-snapshot

Comparative genomics reveals the distinct evolutionary trajectories of the robust and complex coral lineages

inferredcites →https://doi.org/10.1186/s13059-019-1832-yopenalex-snapshot

OrthoFinder: phylogenetic orthology inference for comparative genomics

inferredcites →https://doi.org/10.1371/journal.pcbi.1005944openalex-snapshot

MUMmer4: A fast and versatile genome alignment system

inferredcites →https://doi.org/10.1371/journal.pone.0002929openalex-snapshot

From Stop to Start: Tandem Gene Arrangement, Copy Number and Trans-Splicing Sites in the Dinoflagellate Amphidinium carterae

inferredcites →https://doi.org/10.1371/journal.pone.0079208openalex-snapshot

Long-Range Dispersal and High-Latitude Environments Influence the Population Structure of a “Stress-Tolerant” Dinoflagellate Endosymbiont

inferredcites →https://doi.org/10.3389/fmars.2017.00401openalex-snapshot

Temperature and Water Quality-Related Patterns in Sediment-Associated Symbiodinium Communities Impact Symbiont Uptake and Fitness of Juveniles in the Genus Acropora

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1038/s41598-020-66429-4openalex-snapshot

Sex in Symbiodiniaceae dinoflagellates: genomic evidence for independent loss of the canonical synaptonemal complex

inferred← citeshttps://doi.org/10.1101/2020.09.26.314773openalex-snapshot

Genotypic similarity among algal symbionts corresponds to associations with closely related coral hosts

inferred← citeshttps://doi.org/10.1111/jpy.12999openalex-snapshot

Description of Freudenthalidium gen. nov. and Halluxium gen. nov. to Formally Recognize Clades Fr3 and H as Genera in the Family Symbiodiniaceae (Dinophyceae)

inferred← citeshttps://doi.org/10.1186/s12915-021-00994-6openalex-snapshot

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

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