Identification of Candidate Genes for the Plateau Adaptation of a Tibetan Amphipod, Gammarus lacustris, Through Integration of Genome and Transcriptome Sequencing
文献类型： 外文期刊
作者： Jin, Shubo 1 ; Bian, Chao 2 ; Jiang, Sufei 1 ; Sun, Shengming 1 ; Xu, Lei 5 ; Xiong, Yiwei 1 ; Qiao, Hui 1 ; Zhang, Wenyi 1 ;
作者机构： 1.Chinese Acad Fishery Sci, Freshwater Fisheries Res Ctr, Key Lab Freshwater Fisheries & Germplasm Resource, Minist Agr, Wuxi, Peoples R China
2.Chinese Acad Fishery Sci, BGI Res Ctr Aquat Genom, Shenzhen, Peoples R China
3.BGI, Shenzhen Key Lab Marine Genom, Guangdong Prov Key Lab Mol Breeding Marine Econ A, Shenzhen, Peoples R China
4.Univ Macau, Ctr Reprod Dev & Aging, Fac Hlth Sci, Taipa, Macao, Peoples R China
5.Nanjing Agr Univ, Wuxi Fisheries Coll, Wuxi, Peoples R China
6.Chinese Acad Fishery Sci, Heilongjiang River Fisheries Res Inst, Haebin, Peoples R China
关键词： Gammarus lacustris; Gammarus pisinnus; whole-genome sequencing; full-length transcriptome; comparative transcriptome; plateau adaptation
期刊名称：FRONTIERS IN GENETICS （ 影响因子：4.599； 五年影响因子：4.888 ）
ISSN： 1664-8021
年卷期： 2019 年 10 卷
页码：
收录情况： SCI
摘要： The amphipod Gammarus lacustris has been distributing in the Tibetan region with well-known uplifts of the Tibetan plateau. It is hence considered as a good model for investigating stress adaptations of the plateau. Here, we sequenced the whole-genome and full-length transcriptome of G. lacustris, and compared the transcriptome results with its counterpart Gammarus pisinnus from a nearby plain. Our main goal was to provide a genomic resource for investigation of genetic mechanisms, by which G. lacustris adapted to living on the plateau. The final draft genome assembly of G. lacustris was 5.07 gigabases (Gb), and it contained 443,304 scaffolds (>2 kb) with an N50 of 2,578 bp. A total of 8,858 unigenes were predicted in the full-length transcriptome of G. lacustris, with an average gene length of 1,811 bp. Compared with the G. pisinnus transcriptome, 2,672 differentially expressed genes (DEGs) were up-regulated and 2,881 DEGs were down-regulated in the G. lacustris transcriptome. Along with these critical DEGs, several enriched metabolic pathways, such as oxidative phosphorylation, ribosome, cell energy homeostasis, glycolysis and gluconeogenesis, were predicted to play essential roles in the plateau adaptation. In summary, the present study provides a genomic basis for understanding the plateau adaption of G. lacustris, which lays a fundamental basis for further biological and ecological studies on other resident aquatic species in the Tibetan plateau.
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