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A chromosome-level assembly of the black tiger shrimp (Penaeus monodon) genome facilitates the identification of growth-associated genes
Molecular Ecology Resources ( IF 7.7 ) Pub Date : 2021-02-15 , DOI: 10.1111/1755-0998.13357
Tanaporn Uengwetwanit 1 , Wirulda Pootakham 2 , Intawat Nookaew 3 , Chutima Sonthirod 2 , Pacharaporn Angthong 1 , Kanchana Sittikankaew 1 , Wanilada Rungrassamee 1 , Sopacha Arayamethakorn 1 , Thidathip Wongsurawat 3, 4 , Piroon Jenjaroenpun 3, 4 , Duangjai Sangsrakru 2 , Rungnapa Leelatanawit 1 , Jutatip Khudet 5 , Jasper J Koehorst 6 , Peter J Schaap 6 , Vitor Martins Dos Santos 6 , Frédéric Tangy 7 , Nitsara Karoonuthaisiri 1
Affiliation  

To salvage marine ecosystems from fishery overexploitation, sustainable and efficient aquaculture must be emphasized. The knowledge obtained from available genome sequence of marine organisms has accelerated marine aquaculture in many cases. The black tiger shrimp (Penaeus monodon) is one of the most prominent cultured penaeid shrimps (Crustacean) with an average annual global production of half a million tons in the last decade. However, its currently available genome assemblies lack the contiguity and completeness required for accurate genome annotation due to the highly repetitive nature of the genome and technical difficulty in extracting high-quality, high-molecular weight DNA. Here, we report the first chromosome-level whole-genome assembly of P. monodon. The combination of long-read Pacific Biosciences (PacBio) and long-range Chicago and Hi-C technologies enabled a successful assembly of this first high-quality genome sequence. The final assembly covered 2.39 Gb (92.3% of the estimated genome size) and contained 44 pseudomolecules, corresponding to the haploid chromosome number. Repetitive elements occupied a substantial portion of the assembly (62.5%), the highest of the figures reported among crustacean species. The availability of this high-quality genome assembly enabled the identification of genes associated with rapid growth in the black tiger shrimp through the comparison of hepatopancreas transcriptome of slow-growing and fast-growing shrimps. The results highlighted several growth-associated genes. Our high-quality genome assembly provides an invaluable resource for genetic improvement and breeding penaeid shrimp in aquaculture. The availability of P. monodon genome enables analyses of ecological impact, environment adaptation and evolution, as well as the role of the genome to protect the ecological resources by promoting sustainable shrimp farming.

中文翻译:

黑虎虾(斑节对虾)基因组的染色体水平组装有助于识别生长相关基因

为了挽救海洋生态系统免受渔业过度开发的影响,必须强调可持续和高效的水产养殖。从现有的海洋生物基因组序列中获得的知识在许多情况下加速了海水养殖。黑虎虾(斑节对虾)是最著名的养殖对虾(甲壳类)之一,过去十年全球平均产量达 50 万吨。然而,由于基因组的高度重复性以及提取高质量、高分子量 DNA 的技术难度,目前可用的基因组组装缺乏准确基因组注释所需的连续性和完整性。在这里,我们报告了斑节对虾的首次染色体水平全基因组组装。长读 Pacific Biosciences (PacBio) 与长程 Chicago 和 Hi-C 技术的结合,成功组装了第一个高质量基因组序列。最终组装覆盖 2.39 Gb(估计基因组大小的 92.3%)并包含 44 个假分子,对应于单倍体染色体数。重复元素占据了组合的很大一部分(62.5%),是甲壳类物种中报道的最高数字。这种高质量基因组组装的可用性使得能够通过比较生长缓慢和快速生长的虾的肝胰腺转录组来鉴定与黑虎虾快速生长相关的基因。结果突出了几个与生长相关的基因。我们的高质量基因组组装为水产养殖中的遗传改良和对虾育种提供了宝贵的资源。斑节对虾基因组的可用性可以分析生态影响、环境适应和进化,以及基因组通过促进可持续养虾业保护生态资源的作用。
更新日期:2021-02-15
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