Applications of Environmental DNA (eDNA) in Monitoring the Endangered Status and Evaluating the Stock Enhancement Effect of Tropical Sea Cucumber Holothuria Scabra

E, Zixuan; Luo, Peng; Ren, Chunhua; Cheng, Chuhang; Pan, Wenjie; Jiang, Xiao; Jiang, Fajun; Ma, Bo; Yu, Suzhong; Zhang, Xin; Chen, Ting; Hu, Chaoqun

doi:10.1007/s10126-023-10239-y

Mar Biotechnol

2023

DOI: 10.1007/s10126-023-10239-y

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Applications of Environmental DNA (eDNA) in Monitoring the Endangered Status and Evaluating the Stock Enhancement Effect of Tropical Sea Cucumber Holothuria Scabra

Zixuan E,

Peng Luo,

Chunhua Ren

et al.

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2024

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Cited by 3 publications

References 43 publications

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Sea cucumbers and their symbiotic microbiome have evolved to feed on seabed sediments

Pan,

Wang,

Ren

et al. 2024

Nat Commun

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Sea cucumbers, classified as Holothuroidea within the phylum Echinodermata, are large and abundant members in marine benthic communities 1 . Sea cucumbers greatly impact the health and integrity of the marine ecosystem through bioturbation, organic matter processing, nutrient recycling, seawater chemistry balancing, biodiversity supporting, energy transfer in food chains 1,2 , and provide significant protective benefits to coral reefs by reducing their diseases 3 . Most sea cucumbers are deposit feeders, acquiring nutrients through the consumption of bacteria, microalgae, decayed plants, and meiofauna, along with other organic detritus [4][5][6] . By ingesting and defecating a large amount of seabed sediment, sea cucumbers facilitate bacterial decomposition and reduce the organic load 4,7 . To date, the specific

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Sea cucumbers and their symbiotic microbiome have evolved to feed on seabed sediments

Pan,

Wang,

Ren

et al. 2024

Nat Commun

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Chromosomal-level genome assembly and annotation of the tropical sea cucumber Holothuria scabra

Zhong,

Liu,

et al. 2024

Sci Data

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Holothuria scabra, a commercially valuable yet ecologically vulnerable tropical holothuroid, has experienced a severe decline in its wild populations, especially in China. Genomic resources are crucial for the development of effective genomic breeding projects and stock conservation strategies to restore these natural populations. Until now, a high-quality, chromosome-level reference genome for H. scabra has not been available. Here, we employed Oxford Nanopore and Hi-C sequencing technologies to assemble and annotate a high-quality, chromosome-level reference genome of H. scabra. The final genome comprised 31 scaffolds with a total length of 1.19 Gb and a scaffold N50 length of 53.52 Mb. Remarkably, 1,191.67 Mb (99.95%) of the sequences were anchored to 23 pseudo-chromosomes, with the longest one spanning 79.75 Mb. A total of 34,418 protein-coding genes were annotated in the final genome, with BUSCO analysis revealing 98.01% coverage of metazoa_odb10 genes, marking a significant improvement compared to the previous report. These chromosome-level sequences and annotations will provide an essential genomic basis for further investigation into molecular breeding and conservation management of H. scabra.

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Chromosome-level genome assembly and annotation of the tropical sea cucumber Stichopus monotuberculatus

Chen,

Yang,

Wang

et al. 2024

Sci Data

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In this study, a chromosome-level genome of the tropical sea cucumber Stichopus monotuberculatus was generated by a combination of Nanopore long-read, Illumina short-read, and Hi-C sequencing technologies. The final assembly was 810.54 Mb in length, with contig N50 and scaffold N50 values of 10.15 Mb and 35.36 Mb, respectively. This assembly comprised 23 pseudo-chromosomes, covering 99.82% of the genome. Completeness analysis using BUSCO indicated that 97.8% of the metazoan conserved genes were presented in their entirety. A total of 29,596 protein-coding genes were predicted, with functional annotations available for 94.43% of these genes. The high-quality genome assembly produced in this study may provide an essential foundation for future researches on resource conservation and genetic breeding of S. monotuberculatus .

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Applications of Environmental DNA (eDNA) in Monitoring the Endangered Status and Evaluating the Stock Enhancement Effect of Tropical Sea Cucumber Holothuria Scabra

Cited by 3 publications

References 43 publications

Sea cucumbers and their symbiotic microbiome have evolved to feed on seabed sediments

Sea cucumbers and their symbiotic microbiome have evolved to feed on seabed sediments

Chromosomal-level genome assembly and annotation of the tropical sea cucumber Holothuria scabra

Chromosome-level genome assembly and annotation of the tropical sea cucumber Stichopus monotuberculatus

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