| Background:The current order of Lipotyphla includes 4 families:Solenodontidae,Talpidae,Soricidae and Erinaceidae.Another family of the order,Nesophontidae,was extincted in the late Pleistocene.To date,however,there have been no reports of transcriptomes of any species of this order.Objective:To best of our knowledge,the transcriptome study of the Talpidae,Soricidae and Erinaceidae was the first report in this field.These sequencing data not only provide an important reference for evolution of species and adaptive evolution researchn,but also crucial for the gene function identification in specific tissues and the molecular mechanism study in bioscience and medical research.In addition,it is also valuable for the prevention and control of human epidemics and biodiversity protection.Methods:In this study,we chose Uropsilus gracilis,Euroscaptor kuznetsovi,Episoriculus mbrinus,Nectogale elegans,Sorex bedfordiae and Neotetracus sinensis from Talpidae,Soricidae,and Erinaceidae,respectively,as the research objects and extracted RNAs from their heart,spleen and lung(two tissues from each animal),then constructed the cDNA libraries and sequenced by Illumina Hiseq X10 platform with PE 150.We performed the quality control,de novo assembly and redundant sequences removement with raw data.We analyzed the sequence integrity,identified and annotated homologous genes,the enrichment analysis,and homologous protein analysis.Also we performed differential expressed gene analysis between samples.Contents and results:(1)For the first time,we obtained the data of transcriptome for each of the two organs from six species,separately belongs to three families of the order Lipotyphla.(2)By de novo assembling,we captured transcripts with numbers different from 147,194 to 223,124.(3)We analyzed the completeness of the transcriptome assembly using BUSCO,and found that the complete genes obtained by the Trinity Assembly through the scheme two were 43-56.6%,66.5%-71.1%and 79.4%respectively in the families Talpidae,Soricidae and Erinaceidae.(4)We compared the transcripts of Neotetracus sinensisthe that we obtained here,to the transcripts we annotated from the genomic sequences of GenBank for two species Cerex araneus and Condylura cristata,and found that there are 11,182 direct homologous genes among the three species.(5)We identified the high expressed marker genes for each of the organs within each of the three families by analysis of gene expression difference.Examples follow here.For family Talpidae,they are LY86 and CD180 for spleen,SFTPB and SFTPA1 for lung,and HRC and MB for heart.For family Soricidae,they are MB and MYH6 for heart,and SFTPB and SFTPC for lung.For family Erinaceidae,they are MYL2 and MYL3 for heart,and SFTPC and SFTP1 for lung.The comparison of transcriptome among different species,and their evolutionary or functional analysis are still in progress.The comparison of transcriptome among different species,and their evolutionary or functional analysis are still in progress.(6)We revealed that 335 genes were highly expressed in the lung of E.kuznetsovi,including HMGB1,HSPD1,SF3B1,COL3A1,SUMO1 and JUNB by comparing the expression differences of lung genes between the two species,These genes were reported to be related with hypoxia or high-altitude adaptation.Conclusions:(1)we reported transcriptome data of six species from Talpidae,Soricidae and Erinaceidae for the first time in this field.(2)We annotated the transcripts of those animals and obtained their marker genes through bioinformatic analysis.(3)We compared the two analysis schemes for redundant sequences removal by BUSCO,and found that the optimized Trinity scheme significantly increased the alignment ratio and the data quality.(4)We obtained the marker genes of heart,lung and spleen within each species by differential expressed analysis between different organs.These organ-specific genes may have important significance for the function of the organs.(5)We revealed highly expressed genes in the lung tissue of U.gracilis and E.kuznetsovi. |
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