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Improved genomic resources for the black tiger prawn (Penaeus monodon)

机译：改善黑虎虾的基因组资源（Penaeus Monodon）

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摘要

World production of farmed crustaceans was 7.8 million tons in 2016. While only making up approximately 10% of world aquaculture production, crustaceans are generally high-value species and can earn significant export income for producing countries. Viet Nam is a major seafood producing country earning USD 7.3 billion in 2016 in export income with shrimp as a major commodity. However, there is a general lack of genomic resources available for shrimp species, which is challenging to obtain due to the need to deal with large repetitive genomes, which characterize many decapod crustaceans. The first tiger prawn (P. monodon) genome assembly was assembled in 2016 using the standard Illumina PCR-based pair-end reads and a computationally-efficient but relatively suboptimal assembler, SOAPdenovo v2. As a result, the current P. monodon draft genome is highly fragmented (> 2 million scaffolds with N-50 length of <1000 bp), exhibiting only moderate genome completeness (< 35% BUSCO complete single-copy genes). We sought to improve upon the recently published P. monodon genome assembly and completeness by generating Illumina PCR-free pair-end sequencing reads to eliminate genomic gaps associated with PCR-bias and performing de novo assembly using the updated MaSurCA de novo assembler. Furthermore, we scaffolded the assembly with low coverage Nanopore long reads and several recently published deep Illumina transcriptome paired-end sequencing data, producing a final genome assembly of 1.6 Gbp (1,211,364 scaffolds; N-50 length of 1982 bp) with an Arthropod BUSCO completeness of 96.8%. Compared to the previously published P. monodon genome assembly from China (NCBI Accession Code: NIUS01), this represents an almost 20% increase in the overall BUSCO genome completeness that now consists of more than 90% of Arthropod BUSCO single-copy genes. The revised P. monodon genome assembly (NCBI Accession Code: VIGR01) will be a valuable resource to support ongoing functional genomics and molecular-based breeding studies in Vietnam.
机译：2016年世界养殖甲壳类动物的生产量为780万吨。同时只占世界水产养殖产量的约10％，甲壳类动物通常是高价值物种，可以获得生产国家的大量出口收入。越南是一家主要的海鲜生产州，2016年在2016年赚取73亿美元，以虾作为主要商品。然而，由于需要处理许多甲板甲壳类动物的表征，虾类普遍缺乏可用于获得的基因组资源，这是挑战。第一虎虾（P.Monodon）基因组组件在2016年使用标准的Illumina PCR基对末端读取和计算有效但相对次优汇编器Soapdenovo V2。结果，目前的P.Monodon草案基因组是高度碎片化的（> 200万支架，N-50长度为<1000bp），其仅具有中度基因组完整性（<35％的Busco Complete单拷贝基因）。我们试图通过产生illumina PCR的对对端测序来改善最近公开的P. Monodon基因组组装和完整性，以消除与PCR-BIAS相关的基因组间隙，并使用更新的Masurca de Novo汇编程序进行DE Novo组件。此外，我们用低覆盖纳米孔长度读取的组装和最近发表的深illumina转录组合末端测序数据，产生1.6英镑的最终基因组组装（1,211,364个支架; N-50长度为1982年的BP），具有节肢动物Busco完整性96.8％。与来自中国的先前公布的P. Monodon Genome集会（NCBI加入码：Nius01）相比，这代表了整体Busco基因组完整性增加了几乎20％，现在包含超过90％的节肢动物Busco单拷贝基因。修订后的P. Monodon Genome组件（NCBI加入码：VIGR01）将是一种有价值的资源，以支持越南的持续功能基因组学和基于分子的育种研究。

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  • 来源
    《Marine genomics》 |2020年第2020期|共10页
  • 作者

    Dong Van Quyen; Gan Han Ming; Lee Yin Peng; Dinh Duy Nguyen; Thi Hoa Nguyen; Xuan Thach Tran; Van Sang Nguyen; Dinh Duy Khang; Austin Christopher M.;

  • 作者单位

    Vietnam Acad Sci &

    Technol Inst Biotechnol Lab Mol Microbiol 18 Hoang Quoc Vier Hanoi Vietnam;

    Deakin Univ Ctr Integrat Ecol Sch Life &

    Environm Sci Geelong Vic Australia;

    Deakin Univ Ctr Integrat Ecol Sch Life &

    Environm Sci Geelong Vic Australia;

    Vietnam Acad Sci &

    Technol Inst Biotechnol Lab Mol Microbiol 18 Hoang Quoc Vier Hanoi Vietnam;

    Vietnam Acad Sci &

    Technol Inst Biotechnol Lab Mol Microbiol 18 Hoang Quoc Vier Hanoi Vietnam;

    Vietnam Acad Sci &

    Technol Inst Biotechnol Lab Mol Microbiol 18 Hoang Quoc Vier Hanoi Vietnam;

    Inst Aquaculture 2 RIA2 116 Nguyen Dinh Chieu St Dist 1 Ho Chi Minh City Vietnam;

    Vietnam Acad Sci &

    Technol Inst Biotechnol Lab Mol Microbiol 18 Hoang Quoc Vier Hanoi Vietnam;

    Deakin Univ Ctr Integrat Ecol Sch Life &

    Environm Sci Geelong Vic Australia;

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  • 原文格式 PDF
  • 正文语种 eng
  • 中图分类 遗传学;
  • 关键词

    Tiger prawn; Aquaculture; Nanopore; Illumina; Genome;

    机译：虎虾;水产养殖;纳米孔;illumina;基因组;

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