Identification of Candidate Genes for the Plateau Adaptation of a Tibetan Amphipod, Gammarus lacustris , Through Integration of Genome and Transcriptome Sequencing

Frontiers in Genetics
Shubo JinHongtuo Fu

Abstract

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 p...Continue Reading

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Datasets Mentioned

BETA
SRP133982
SRP132243

Methods Mentioned

BETA
chips
PCR
electrophoresis
EB-seq
ubiquitination

Software Mentioned

BLAST2GO
Blast
Quiver
CD
RS IsoSeq
Trinity
ESTScan
SOAPdenovo2
RSEM
EST

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