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Sci Data
2023 Aug 01;101:506. doi: 10.1038/s41597-023-02397-4.
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A chromosome-level genome assembly of a deep-sea starfish (Zoroaster cf. ophiactis).
Liu J
,
Zhou Y
,
Pu Y
,
Zhang H
.
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Understanding of adaptation and evolution of organisms in the deep sea requires more genomic resources. Zoroaster cf. ophiactis is a sea star in the family Zoroasteridae occurring exclusively in the deep sea. In this study, a chromosome-level genome assembly for Z. cf. ophiactis was generated by combining Nanopore long-read, Illumina short-read, and Hi-C sequencing data. The final assembly was 1,002.0 Mb in length, with a contig N50 of 376 Kb and a scaffold N50 of 40.4 Mb, and included 22 pseudo-chromosomes, covering 92.3% of the assembly. Completeness analysis evaluated with BUSCO revealed that 95.91% of the metazoan conserved genes were complete. Additionally, 39,426 protein-coding genes were annotated for this assembly. This chromosome-level genome assembly represents the first high-quality genome for the deep-sea Asteroidea, and will provide a valuable resource for future studies on evolution and adaptation of deep-sea echinoderms.
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37528102
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42106121 National Natural Science Foundation of China (National Science Foundation of China)
Fig. 1. K-mer distribution (K = 19) of Zoroaster cf. ophiacti genome. The x-axis is the k-mer depth, and the y-axis represents the corresponding frequency of the k-mer at a given depth.
Fig. 2. Characteristics of the genome assembly of Zoroaster cf. ophiactis. (a) Genome overview of the 22 chromosomes. Tracks from inner to outer represent repeats coverage (19–96%), genes density (1–85), GC content (35–47%), genome sequence depth (7–100 X), and assembled chromosomes, respectively, with densities calculated within a 500-kb window. (b) Hi-C contact map produced by 3D-DNA. The blue square represents a pseudo-chromosome, and small green squares inside each blue square are contigs that make up the chromosome.
Fig. 3. Chromosomal synteny among genomes of Zoroaster cf. ophiactis and the other two starfish (Asterias rubens, and Plazaster borealis) in the order Forcipulatida. Numbers in the rectangles represent chromosomes of each genome.
Fig. 4. Maximum likelihood phylogenetic tree of Zoroaster cf. ophiactis and other eight echinoderms. Bootstrap support values for all the nodes are equal to 100. Numbers of expanded (red) and contracted (blue) gene families are shown.
Altschul,
Basic local alignment search tool.
1990, Pubmed
Altschul,
Basic local alignment search tool.
1990,
Pubmed
Arshinoff,
Echinobase: leveraging an extant model organism database to build a knowledgebase supporting research on the genomics and biology of echinoderms.
2022,
Pubmed
,
Echinobase
Benson,
Tandem repeats finder: a program to analyze DNA sequences.
1999,
Pubmed
Byrne,
Transcriptomic analysis of sea star development through metamorphosis to the highly derived pentameral body plan with a focus on neural transcription factors.
2020,
Pubmed
,
Echinobase
Chen,
fastp: an ultra-fast all-in-one FASTQ preprocessor.
2018,
Pubmed
Danovaro,
Challenging the paradigms of deep-sea ecology.
2014,
Pubmed
Davidson,
Chromosomal-Level Genome Assembly of the Sea Urchin Lytechinus variegatus Substantially Improves Functional Genomic Analyses.
2020,
Pubmed
,
Echinobase
DeBiasse,
A chromosome-level reference genome for the giant pink sea star, Pisaster brevispinus, a species severely impacted by wasting.
2022,
Pubmed
,
Echinobase
de Oliveira,
Novel Insights on Obligate Symbiont Lifestyle and Adaptation to Chemosynthetic Environment as Revealed by the Giant Tubeworm Genome.
2022,
Pubmed
Dudchenko,
De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds.
2017,
Pubmed
Durand,
Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments.
2016,
Pubmed
Durand,
Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom.
2016,
Pubmed
Edgar,
MUSCLE: multiple sequence alignment with high accuracy and high throughput.
2004,
Pubmed
Emms,
OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy.
2015,
Pubmed
Flynn,
RepeatModeler2 for automated genomic discovery of transposable element families.
2020,
Pubmed
Goldstein,
Preface.
2022,
Pubmed
Haas,
Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies.
2003,
Pubmed
Haas,
Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments.
2008,
Pubmed
Hall,
The crown-of-thorns starfish genome as a guide for biocontrol of this coral reef pest.
2017,
Pubmed
,
Echinobase
He,
NGenomeSyn: an easy-to-use and flexible tool for publication-ready visualization of syntenic relationships across multiple genomes.
2023,
Pubmed
Hu,
NextPolish: a fast and efficient genome polishing tool for long-read assembly.
2020,
Pubmed
Kent,
BLAT--the BLAST-like alignment tool.
2002,
Pubmed
Kim,
Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype.
2019,
Pubmed
Lawniczak,
The genome sequence of the spiny starfish, Marthasterias glacialis (Linnaeus, 1758).
2021,
Pubmed
,
Echinobase
Lee,
Chromosome-level genome assembly of Plazaster borealis sheds light on the morphogenesis of multiarmed starfish and its regenerative capacity.
2022,
Pubmed
,
Echinobase
Li,
Genomic insights of body plan transitions from bilateral to pentameral symmetry in Echinoderms.
2020,
Pubmed
,
Echinobase
Li,
Genomic adaptations to chemosymbiosis in the deep-sea seep-dwelling tubeworm Lamellibrachia luymesi.
2019,
Pubmed
Li,
Fast and accurate short read alignment with Burrows-Wheeler transform.
2009,
Pubmed
Liu,
A chromosome-level genome assembly of a deep-sea starfish (Zoroaster cf. ophiactis).
2023,
Pubmed
,
Echinobase
Liu,
De Novo Genome Assembly of Limpet Bathyacmaea lactea (Gastropoda: Pectinodontidae): The First Reference Genome of a Deep-Sea Gastropod Endemic to Cold Seeps.
2020,
Pubmed
Mah,
Global diversity and phylogeny of the Asteroidea (Echinodermata).
2012,
Pubmed
,
Echinobase
Majoros,
TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders.
2004,
Pubmed
Manni,
BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes.
2021,
Pubmed
Marçais,
A fast, lock-free approach for efficient parallel counting of occurrences of k-mers.
2011,
Pubmed
Mendes,
CAFE 5 models variation in evolutionary rates among gene families.
2021,
Pubmed
Mu,
Whole genome sequencing of a snailfish from the Yap Trench (~7,000 m) clarifies the molecular mechanisms underlying adaptation to the deep sea.
2021,
Pubmed
Ruan,
Fast and accurate long-read assembly with wtdbg2.
2020,
Pubmed
Ruiz-Ramos,
An initial comparative genomic autopsy of wasting disease in sea stars.
2020,
Pubmed
,
Echinobase
Saotome,
Chromosomes of Japanese starfishes.
2002,
Pubmed
,
Echinobase
Sodergren,
The genome of the sea urchin Strongylocentrotus purpuratus.
2006,
Pubmed
,
Echinobase
Stamatakis,
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies.
2014,
Pubmed
Stanke,
Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources.
2006,
Pubmed
Sun,
Genomic Signatures Supporting the Symbiosis and Formation of Chitinous Tube in the Deep-Sea Tubeworm Paraescarpia echinospica.
2021,
Pubmed
Sun,
Adaptation to deep-sea chemosynthetic environments as revealed by mussel genomes.
2017,
Pubmed
Tarailo-Graovac,
Using RepeatMasker to identify repetitive elements in genomic sequences.
2009,
Pubmed
Wang,
Morphology and genome of a snailfish from the Mariana Trench provide insights into deep-sea adaptation.
2019,
Pubmed
Yuasa,
Elucidation of the speciation history of three sister species of crown-of-thorns starfish (Acanthaster spp.) based on genomic analysis.
2021,
Pubmed
,
Echinobase
Zhang,
The sea cucumber genome provides insights into morphological evolution and visceral regeneration.
2017,
Pubmed
,
Echinobase
Zhou,
The First Draft Genome of a Cold-Water Coral Trachythela sp. (Alcyonacea: Stolonifera: Clavulariidae).
2021,
Pubmed
