A high-quality de novo genome assembly of one swamp eel (Monopterus albus) strain with PacBio and Hi-C sequencing data

文献类型： 外文期刊

第一作者： Tian, Hai-Feng

作者： Tian, Hai-Feng;Hu, Qiao-Mu;Li, Zhong

作者机构：

关键词： Monopterus albus; swamp eel; genome assembly; PacBio; Hi-C

期刊名称：G3-GENES GENOMES GENETICS （ 影响因子：2.781； 五年影响因子：3.026 ）

ISSN： 2160-1836

年卷期： 2021 年 11 卷 1 期

页码：

收录情况： SCI

摘要： Y The swamp eel (Monopterus albus) is one economically important fish in China and South-Eastern Asia and a good model species to study sex inversion. There are different genetic lineages and multiple local strains of swamp eel in China, and one local strain of M. albus with deep yellow and big spots has been selected for consecutive selective breeding due to superiority in growth rate and fecundity. A high-quality reference genome of the swamp eel would be a very useful resource for future selective breeding program. In the present study, we applied PacBio single-molecule sequencing technique (SMRT) and the high-throughput chromosome conformation capture (Hi-C) technologies to assemble the M. albus genome. A 799Mb genome was obtained with the contig N50 length of 2.4 Mb and scaffold N50 length of 67.24 Mb, indicating 110-fold and similar to 31.87-fold improvement compared to the earlier released assembly (similar to 22.24 Kb and 2.11 Mb, respectively). Aided with Hi-C data, a total of 750 contigs were reliably assembled into 12 chromosomes. Using 22,373 protein-coding genes annotated here, the phylogenetic relationships of the swamp eel with other teleosts showed that swamp eel separated from the common ancestor of Zig-zag eel similar to 49.9 million years ago, and 769 gene families were found expanded, which are mainly enriched in the immune system, sensory system, and transport and catabolism. This highly accurate, chromosome-level reference genome of M. albus obtained in this work will be used for the development of genome-scale selective breeding.

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