Mollah Md Bazlur Rahman, Khan Mohd Golam Quader, Islam Md Shahidul, Alam Md Samsul
Poultry Biotechnology and Genomics Laboratory, Department of Poultry Science, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh.
Department of Fisheries Biology and Genetics, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh.
F1000Res. 2019 Mar 22;8:320. doi: 10.12688/f1000research.18325.1. eCollection 2019.
: Hilsa shad ( ), a widely distributed migratory fish, contributes substantially to the economy of Bangladesh. The harvest of hilsa from inland waters has been fluctuating due to anthropological and climate change-induced degradation of the riverine habitats. The whole genome sequence of this valuable fish could provide genomic tools for sustainable harvest, conservation and productivity cycle maintenance. Here, we report the first draft genome of from the Bay of Bengal, the largest reservoir of the migratory fish. : A live specimen of was collected from the Bay of Bengal. The whole genome sequencing was performed by the Illumina HiSeqX platform (2 × 150 paired end configuration). We assembled the short reads using SOAPdenovo2 genome assembler and predicted protein coding genes by AUGUSTUS. The completeness of the genome assembly was evaluated by BUSCO (Benchmarking Universal Single Copy Orthologs). We identified single nucleotide polymorphisms (SNPs) by calling them directly from unassembled sequence reads using discoSnp++. : We assembled the draft genome of 710.28 Mb having an N50 scaffold length of 64157 bp and GC content of 42.95%. A total of 37,450 protein coding genes were predicted of which 29,339 (78.34%) were annotated with other vertebrate genomes. We also identified 792,939 isolated SNPs with transversion:transition ratio of 1:1.8. The BUSCO evaluation showed 78.1% completeness of this genome. s: The genomic data generated in this study could be used as a reference to identify genes associated with physiological and ecological adaptations, population connectivity, and migration behaviour of this biologically and economically important anadromous fish species of the Clupeidae family.
印度鲥（ ）是一种广泛分布的洄游鱼类，对孟加拉国的经济贡献巨大。由于人类活动和气候变化导致河流栖息地退化，内陆水域印度鲥的捕捞量一直波动不定。这种珍贵鱼类的全基因组序列可为可持续捕捞、保护和维持生产力周期提供基因组工具。在此，我们报告了来自孟加拉湾（洄游鱼类的最大储存库）的印度鲥的首个基因组草图。：从孟加拉湾采集了一条印度鲥的活体样本。全基因组测序由Illumina HiSeqX平台（2×150双端配置）进行。我们使用SOAPdenovo2基因组组装器组装短读长，并通过AUGUSTUS预测蛋白质编码基因。通过BUSCO（基准通用单拷贝直系同源物）评估印度鲥基因组组装的完整性。我们使用discoSnp++直接从未组装的序列读段中识别单核苷酸多态性（SNP）。：我们组装了710.28 Mb的基因组草图，N50支架长度为64157 bp，GC含量为42.95%。共预测了37450个蛋白质编码基因，其中29339个（78.34%）与其他脊椎动物基因组进行了注释。我们还识别出792939个孤立的SNP，颠换与转换的比例为1:1.8。BUSCO评估显示该基因组的完整性为78.1%。：本研究中生成的基因组数据可作为参考，用于识别与这种生物学和经济上重要的鲱科溯河鱼类的生理和生态适应、种群连通性及洄游行为相关的基因。
