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Chromosome-level reference genome of the jellyfish Rhopilema esculentum

BACKGROUND: Jellyfish belong to the phylum Cnidaria, which occupies an important phylogenetic location in the early-branching Metazoa lineages. The jellyfish Rhopilema esculentum is an important fishery resource in China. However, the genome resource of R. esculentum has not been reported to date. F...

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Autores principales: Li, Yunfeng, Gao, Lei, Pan, Yongjia, Tian, Meilin, Li, Yulong, He, Chongbo, Dong, Ying, Sun, Yamin, Zhou, Zunchun
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7172023/
https://www.ncbi.nlm.nih.gov/pubmed/32315029
http://dx.doi.org/10.1093/gigascience/giaa036
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author Li, Yunfeng
Gao, Lei
Pan, Yongjia
Tian, Meilin
Li, Yulong
He, Chongbo
Dong, Ying
Sun, Yamin
Zhou, Zunchun
author_facet Li, Yunfeng
Gao, Lei
Pan, Yongjia
Tian, Meilin
Li, Yulong
He, Chongbo
Dong, Ying
Sun, Yamin
Zhou, Zunchun
author_sort Li, Yunfeng
collection PubMed
description BACKGROUND: Jellyfish belong to the phylum Cnidaria, which occupies an important phylogenetic location in the early-branching Metazoa lineages. The jellyfish Rhopilema esculentum is an important fishery resource in China. However, the genome resource of R. esculentum has not been reported to date. FINDINGS: In this study, we constructed a chromosome-level genome assembly of R. esculentum using Pacific Biosciences, Illumina, and Hi-C sequencing technologies. The final genome assembly was ∼275.42 Mb, with a contig N50 length of 1.13 Mb. Using Hi-C technology to identify the contacts among contigs, 260.17 Mb (94.46%) of the assembled genome were anchored onto 21 pseudochromosomes with a scaffold N50 of 12.97 Mb. We identified 17,219 protein-coding genes, with an average CDS length of 1,575 bp. The genome-wide phylogenetic analysis indicated that R. esculentum might have evolved more slowly than the other scyphozoan species used in this study. In addition, 127 toxin-like genes were identified, and 1 toxin-related “hub” was found by a genomic survey. CONCLUSIONS: We have generated a chromosome-level genome assembly of R. esculentum that could provide a valuable genomic background for studying the biology and pharmacology of jellyfish, as well as the evolutionary history of Cnidaria.
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spelling pubmed-71720232020-04-27 Chromosome-level reference genome of the jellyfish Rhopilema esculentum Li, Yunfeng Gao, Lei Pan, Yongjia Tian, Meilin Li, Yulong He, Chongbo Dong, Ying Sun, Yamin Zhou, Zunchun Gigascience Data Note BACKGROUND: Jellyfish belong to the phylum Cnidaria, which occupies an important phylogenetic location in the early-branching Metazoa lineages. The jellyfish Rhopilema esculentum is an important fishery resource in China. However, the genome resource of R. esculentum has not been reported to date. FINDINGS: In this study, we constructed a chromosome-level genome assembly of R. esculentum using Pacific Biosciences, Illumina, and Hi-C sequencing technologies. The final genome assembly was ∼275.42 Mb, with a contig N50 length of 1.13 Mb. Using Hi-C technology to identify the contacts among contigs, 260.17 Mb (94.46%) of the assembled genome were anchored onto 21 pseudochromosomes with a scaffold N50 of 12.97 Mb. We identified 17,219 protein-coding genes, with an average CDS length of 1,575 bp. The genome-wide phylogenetic analysis indicated that R. esculentum might have evolved more slowly than the other scyphozoan species used in this study. In addition, 127 toxin-like genes were identified, and 1 toxin-related “hub” was found by a genomic survey. CONCLUSIONS: We have generated a chromosome-level genome assembly of R. esculentum that could provide a valuable genomic background for studying the biology and pharmacology of jellyfish, as well as the evolutionary history of Cnidaria. Oxford University Press 2020-04-21 /pmc/articles/PMC7172023/ /pubmed/32315029 http://dx.doi.org/10.1093/gigascience/giaa036 Text en © The Author(s) 2020. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Data Note
Li, Yunfeng
Gao, Lei
Pan, Yongjia
Tian, Meilin
Li, Yulong
He, Chongbo
Dong, Ying
Sun, Yamin
Zhou, Zunchun
Chromosome-level reference genome of the jellyfish Rhopilema esculentum
title Chromosome-level reference genome of the jellyfish Rhopilema esculentum
title_full Chromosome-level reference genome of the jellyfish Rhopilema esculentum
title_fullStr Chromosome-level reference genome of the jellyfish Rhopilema esculentum
title_full_unstemmed Chromosome-level reference genome of the jellyfish Rhopilema esculentum
title_short Chromosome-level reference genome of the jellyfish Rhopilema esculentum
title_sort chromosome-level reference genome of the jellyfish rhopilema esculentum
topic Data Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7172023/
https://www.ncbi.nlm.nih.gov/pubmed/32315029
http://dx.doi.org/10.1093/gigascience/giaa036
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