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豹猫转录组从头组装及组织特异性表达分析
De novo Transcriptome and Tissues-Specific Expression Analysis of Prionailurus bengalensis
蒋兰1#, 张雪艳1#, 王俊茵2, 李静1*
点击:96次 下载:12次
DOI:10.11984/j.issn.1000-7083.20210126
作者单位:1. 四川大学生命科学学院, 生物资源与生态环境教育部重点实验室, 成都 610065;
2. 峨眉山景区管委会, 峨眉山生物多样性保护研究所, 四川峨眉山 614200
中文关键字:豹猫;转录组;从头组装;组织特异性表达
英文关键字:Prionailurus bengalensis; transcriptome; de novo assembly; tissue-specific expression
中文摘要:豹猫Prionailurus bengalensis是亚洲分布最广的食肉动物之一,国家二级重点保护野生动物。本研究对豹猫6个组织(大脑、心脏、肾脏、肝脏、肺和骨骼肌)进行了转录组测序,共获得51.4 Gb的原始数据。使用Trinity进行从头组装,最终获得了369 246条转录本,其平均长度为1 465 bp,转录本N50长度为2 660 bp,组装质量较高。注释结果显示,约42.44%(114 517条)的转录本在4个公共数据库中成功获得注释,65 895条转录本被分配到了386条KEGG通路中。根据转录本表达量构建各组织的表达图谱、计算组织特异性指数(TSI),39.65%的转录本为0.15≤TSI≤0.85,具有中等组织特异性,60.34%的转录本TSI>0.85,具有较高的组织特异性。统计豹猫每个组织中表达量最高的10条转录本,共39条转录本,其中26条的表达具有高组织特异性(TSI>0.85),显示大部分高表达基因都表现出高组织特异性。
英文摘要:The leopard cat (Prionailurus bengalensis) is one of the most widespread Asian carnivores, and it is listed as class Ⅱ nationally key protected wild animals in China databas. In this study, RNA-Seq was performed on 6 tissues (cerebrum, heart, kidney, liver, lung and skeletal muscle) of leopard cat and 51.4 Gb raw data was obtained.De novo assembly by Trinity software obtained a high-quality assembly including 369 246 transcripts with an average length of 1 465 bp, and Contig N50 has a length of 2 660 bp. Annotation results showed that approximately 42.44% (114 517) of the transcripts were aligned in 4 publices. KEGG pathway prediction revealed that 65 895 transcripts were assigned to 386 KEGG pathways. According to the expression quantity of transcripts, the expression profiles of 6 tissues were constructed, and the tissue-specific index (TSI) was calculated. The results showed that 39.65% of the transcripts (0.15 ≤ TSI ≤ 0.85) had medium tissue specificity, and 60.34% of the transcripts (TSI>0.85) had high tissue specificity. A total of 39 transcripts were obtained from the top 10 transcripts with the highest FPKM value in each tissue, and 26 of them were highly tissue-specific (TSI>0.85).
2021,40(5): 497-508 收稿日期:2021-04-06
分类号:Q78;Q959.838
基金项目:国家自然科学基金项目(31770415)
作者简介:蒋兰(1995-),女,硕士,主要研究动物转录组,E-mail:2017222040127@stu.scu.edu.cn;张雪艳(1990-),女,硕士,主要研究动物转录组,E-mail:516004671@qq.com
*通信作者:李静,E-mail:ljtjf@126.com
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