Transcriptome analyses for three Soricid shrews

ZHOU Jingjing; QIU Yinbin; WAN Tao; HE Shuiwang; JIANG Xuelong; PAN Xinghua; HE Kai

doi:10.16829/j.slxb.150403

ACTA THERIOLOGICA SINICA >

2021 , Vol. 41 >Issue 2: 173 - 181

DOI: https://doi.org/10.16829/j.slxb.150403

ORIGINAL PAPERS

Transcriptome analyses for three Soricid shrews

ZHOU Jingjing ,
QIU Yinbin ,
WAN Tao ,
HE Shuiwang ,
JIANG Xuelong ,
PAN Xinghua ,
HE Kai

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1 Southern Medical University, School of Basic Medical Science, Guangdong Provincial Key Laboratory of Single Cell Technology and Application, Guangzhou 510515, China;
2 College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China;
3 Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China

Received date: 2019-12-30

Online published: 2021-04-02

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Abstract

China harbors high species diversity of Soricid shrews.Sixty-one species representing 12 genera are distributed in China,inhabiting various habitats.In this study,we sequenced the transcriptome of heart and lung tissue from three species,namely, Episoriculus umbrinus,Nectogale elegans,and Sorex bedfordiae,and obtained 20.5 Gb clean data.After de novo assembly,we obtained 131 045,153 621,and 135 838 unigenes for E.umbrinus,N.elegans,and S.bedfordiae,respectively.BUSCO analyses suggested we recovered as many as 82.2% full-length transcripts of genes.Ortho Finder recognized more than 8 000 homologous gene families as shared by soricid and talpid species.We compared two post-Trinity pipelines to optimize the quality of unigenes.When combining Trinity scripts,CD-Hit and TransRate,the proportions of single-copy genes increased 18%-25% compared with using CD-Hit alone,and the proportions of multi-copy genes decreased from 28.4%-31.8% to 0.7%-1.1%.Analysis of differentially expressed genes (DEGs) identified tissue enriched genes,validating our analysis pipeline.Our analyses HIF 1 A highly expressed in both heart and lung of N.elegans.HIF 1 A is a key gene in the hypoxia-inducible factor signaling pathway and regulates the expression of downstream genes related to hypoxia,probably associated with aquatic adaptation.This is the first report of shrew transcriptome,providing important data for understanding the evolution and physiology in Soricidae.Our analysis pipeline could also inspire transcriptomic study in other non-model organisms.

Key words： Eulipotyphla; Soricidae; Transcriptome de novo assembly; Adaptation to hypoxia

Cite this article

ZHOU Jingjing , QIU Yinbin , WAN Tao , HE Shuiwang , JIANG Xuelong , PAN Xinghua , HE Kai . Transcriptome analyses for three Soricid shrews[J]. ACTA THERIOLOGICA SINICA, 2021 , 41(2) : 173 -181 . DOI: 10.16829/j.slxb.150403

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