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利用 SMRT 测序和 Hi-C 分析获得桡足类海虱 Caligus rogercresseyi 的染色体级基因组组装。

Chromosome-scale genome assembly of the sea louse Caligus rogercresseyi by SMRT sequencing and Hi-C analysis.

机构信息

Interdisciplinary Center for Aquaculture Research, University of Concepción, Concepción, Chile.

Laboratory of Biotechnology and Aquatic Genomics, Center of Biotechnology, University of Concepción, Concepción, Chile.

出版信息

Sci Data. 2021 Feb 11;8(1):60. doi: 10.1038/s41597-021-00842-w.

DOI:10.1038/s41597-021-00842-w
PMID:33574331
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC7878743/
Abstract

Caligus rogercresseyi, commonly known as sea louse, is an ectoparasite copepod that impacts the salmon aquaculture in Chile, causing losses of hundreds of million dollars per year. In this study, we report a chromosome-scale assembly of the sea louse (C. rogercresseyi) genome based on single-molecule real-time sequencing (SMRT) and proximity ligation (Hi-C) analysis. Coding RNAs and non-coding RNAs, and specifically long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) were identified through whole transcriptome sequencing from different life stages. A total of 23,686 protein-coding genes and 12,558 non-coding RNAs were annotated. In addition, 6,308 lncRNAs and 5,774 miRNAs were found to be transcriptionally active from larvae to adult stages. Taken together, this genomic resource for C. rogercresseyi represents a valuable tool to develop sustainable control strategies in the salmon aquaculture industry.

摘要

罗杰氏海虱，俗称海虱，是一种寄生在鲑鱼养殖中的桡足类寄生虫，每年给智利造成数亿美元的损失。在这项研究中，我们基于单分子实时测序 (SMRT) 和邻近连接 (Hi-C) 分析，报告了一种虱（C. rogercresseyi）染色体水平的基因组组装。通过来自不同生命阶段的全转录组测序，鉴定了编码 RNA 和非编码 RNA，特别是长非编码 RNA (lncRNA) 和 microRNA (miRNA)。总共注释了 23686 个蛋白质编码基因和 12558 个非编码 RNA。此外，从幼虫到成虫阶段共发现 6308 个 lncRNA 和 5774 个 miRNA 转录活跃。总的来说，这种罗杰氏海虱的基因组资源为鲑鱼养殖业开发可持续的控制策略提供了有价值的工具。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9298/7878743/39986afe44cb/41597_2021_842_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9298/7878743/76a1c109f696/41597_2021_842_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9298/7878743/81b9c52a62e9/41597_2021_842_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9298/7878743/0b193d5bef21/41597_2021_842_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9298/7878743/39986afe44cb/41597_2021_842_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9298/7878743/76a1c109f696/41597_2021_842_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9298/7878743/81b9c52a62e9/41597_2021_842_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9298/7878743/0b193d5bef21/41597_2021_842_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9298/7878743/39986afe44cb/41597_2021_842_Fig4_HTML.jpg

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