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A chromosome-level genome of the kuruma shrimp (Marsupenaeus japonicus) provides insights into its evolution and cold-resistance mechanism

文献类型： 外文期刊

作者： Ren, Xianyun 1 ; Lv, Jianjian 1 ; Liu, Meng 3 ; Shao, Huixin 1 ; Liu, Ping 1 ; Li, Jian 1 ;

作者机构： 1.Chinese Acad Fishery Sci, Yellow Sea Fisheries Res Inst, Key Lab Sustainable Utilizat Marine Fisheries Reso, Minist Agr, Qingdao, Peoples R China

2.Qingdao Natl Lab Marine Sci & Technol, Funct Lab Marine Fisheries Sci & Food Prod Proc, Qingdao, Peoples R China

3.Novogene Bioinformat Inst, Beijing, Peoples R China

4.Shanghai Ocean Univ, Coll Fisheries & Life Sci, Shanghai, Peoples R China

关键词： Cold tolerant genes; Genome sequencing; Hi -C technology; Marsupenaeus japonicas; PacBio; Transcriptome assembly

期刊名称：GENOMICS （ 影响因子：4.31； 五年影响因子：4.38 ）

ISSN： 0888-7543

年卷期： 2022 年 114 卷 3 期

页码：

收录情况： SCI

摘要： Marsupenaeus japonicus is an important marine crustacean species. However, a lack of genomic resources hinders the use of whole genome sequencing to explore their genetic basis and molecular mechanisms for genomeassisted breeding. Consequently, we determined the chromosome-level genome of M. japonicus. Here we determine the chromosome-level genome assembly for M. japonicus with a total of 665.19 Gb genomic sequencing data, yielding an approximately1.54 Gb assembly with a contig N50 size of 229.97 kb and a scaffold N50 size of 38.27 Mb. With the high-throughput chromosome conformation capture (Hi-C) technology, we anchored 18,019 contigs onto 42 pseudo-chromosomes, accounting for 99.40% of the total genome assembly. Analysis of the present M. japonicus genome revealed 24,317 protein-coding genes and a high proportion of repetitive sequences (61.56%). The high-quality genome assembly enabled the identification of genes associated with cold-stress and cold tolerance in kuruma shrimp through the comparison of eyestalk transcriptomes between the low temperature-stressed shrimp (10 degrees C) and normal temperature shrimp (28 degrees C). The genome assembly presented here could be useful in future studies to reveal the molecular mechanisms of M. japonicus in response to low temperature stress and the molecular assisted breeding of M. japonicus in low temperature.

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