2022
DOI: 10.1038/s42003-022-03176-4
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The genome of an apodid holothuroid (Chiridota heheva) provides insights into its adaptation to a deep-sea reducing environment

Abstract: Cold seeps and hydrothermal vents are deep-sea reducing environments that are characterized by lacking oxygen and photosynthesis-derived nutrients. Most animals acquire nutrition in cold seeps or hydrothermal vents by maintaining epi- or endosymbiotic relationship with chemoautotrophic microorganisms. Although several seep- and vent-dwelling animals hosting symbiotic microbes have been well-studied, the genomic basis of adaptation to deep-sea reducing environment in nonsymbiotic animals is still lacking. Here,… Show more

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Cited by 18 publications
(21 citation statements)
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“…Additionally, many echinoderms also undergo dramatic metamorphosis, transitioning from a free swimming planktonic larvae, to a benthic juvenile following extensive, often with very rapid morphogenesis. Some species of echinoderms are extremophiles living in antarctic seas and in deep ocean vents (Chen et al, 2022; Zhang et al, 2022). While fascinating, very little is known about genetic control of these processes because there are not yet tools to genetically edit post embryonic stages whilst preserving early developmental processes.…”
Section: Introductionmentioning
confidence: 99%
“…Additionally, many echinoderms also undergo dramatic metamorphosis, transitioning from a free swimming planktonic larvae, to a benthic juvenile following extensive, often with very rapid morphogenesis. Some species of echinoderms are extremophiles living in antarctic seas and in deep ocean vents (Chen et al, 2022; Zhang et al, 2022). While fascinating, very little is known about genetic control of these processes because there are not yet tools to genetically edit post embryonic stages whilst preserving early developmental processes.…”
Section: Introductionmentioning
confidence: 99%
“…Low-quality Nanopore reads were filtered using a previously published Python script ( Zhang et al, 2022 ). The filtered reads were then corrected using NextDenovo (v1.0) (https://github.com/Nextomics/NextDenovo).…”
Section: Methodsmentioning
confidence: 99%
“…The following methods were combined to identify the repeat contents in the P. vachelli genome: homology-based and de novo prediction. Homology-based analysis: we identified the known TEs within the P. vachelli genome using RepeatMasker (v4.1.0) ( Zhang et al, 2022 ) with the Repbase TE library ( Jurka et al, 2005 ). RepeatProteinMask searches were also conducted using the TE protein database as a query library.…”
Section: Methodsmentioning
confidence: 99%
“…We predicted protein-coding genes of the P. vachelli genome using three methods, including ab initio gene prediction, homology-based gene prediction and RNA-Seq-aided gene prediction. Prior to gene prediction, the assembled genome was hard and soft masked using RepeatMasker (v 4.1.0) ( Zhang et al, 2022 ). We adopted Augustus (v3.2) ( Ng et al, 2021 ) and Genescan (v3.1) ( Vidal et al, 2021 ) to perform ab initio gene prediction.…”
Section: Methodsmentioning
confidence: 99%