鼩鼱科三物种转录组初步分析

Transcriptome analyses for three Soricid shrews

中国是鼩鼱科物种十分丰富的国家,已知有12属61个物种在中国分布,并演化出多种生态适应型。本研究采用高通量测序技术对小纹背鼩鼱、云南长尾鼩鼱和蹼足鼩3个物种的心和肺组织样本进行转录组测序。其中小纹背鼩鼱和云南长尾鼩营地表生活,蹼足鼩适应半水生生活。3个物种的转录组测序一共获得20.5 Gb的Clean Data,拼接后分别获得131045条、153621条和135838条Unigenes,BUSCO分析显示其中完整的保守基因最高为82.2%,共有同源基因家族超过8000个。此外,我们发现通过优化分析方案,可以将单拷贝基因的比例提高18%~25%,同时将多拷贝基因比例从28.4%~31.8%降为0.7%~1.1%。同物种不同组织间的基因差异表达分析找到各组织的标志性基因。转录组差异表达分析发现,蹼足鼩心脏和肺均高表达HIF1A基因,该基因是缺氧诱导因子信号通路中的关键基因,调节下游与缺氧应激相关基因的表达,可能与水生适应有关。

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 131045,153621,and 135838 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 8000 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 HIF1A highly expressed in both heart and lung of N.elegans.HIF1A 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.