基于转录组测序分析家蚕中肠、脂肪体和血淋巴组织可变剪接事件  

Alternative Splicing Events in Midgut,Fat Body and Hemolymph of Silkworm Based on Transcriptome Sequencing

作　　者：谢岩 王晖 孙志超 高妍夏 周玲 刘麟菲 李季生 Xie Yan;Wang Hui;Sun Zhichao;Gao Yanxia;Zhou Ling;Liu Linfei;Li Jisheng(Sericultural Research Institute,Chengde Medical University/Applied Technology Research and Development Center of Sericulture and Specialty of Hebei Universities,Chengde 067000,China)

机构地区：[1]承德医学院蚕业研究所/河北省高校特色蚕桑应用技术研发中心,河北承德067000

出　　处：《山东农业科学》2024年第7期135-147,共13页Shandong Agricultural Sciences

基　　金：河北省自然科学基金青年基金项目(C201806033);河北省高等学校科学技术研究项目(BJ2018032);河北省科技厅技术创新引导专项-科技工作会商项目;承德医学院高层次人才科研启动基金项目(201604);河北省重点研发计划项目现代种业科技专项(20326336D)。

摘　　要：可变剪接(alternative splicing, AS)在家蚕基因组中普遍存在,在基因转录后调控和蛋白质多样性方面发挥重要作用。为揭示家蚕物质吸收、循环、合成和代谢相关组织AS事件的特征,分析家蚕品种间抗氧化水平差异的形成机制,本研究采集预蛹期的东肥和彩4这两个家蚕品种的中肠、脂肪体和血淋巴组织样品进行转录组测序(RNA sequencing, RNA-seq),将测序数据比对到参考基因组后,采用rMAT软件进行AS事件分析和发生AS事件的基因(AS基因)鉴定,进一步解析AS基因发生AS事件的数量、类型和组织分布的特征,并对全部AS基因和品种间差异表达AS基因进行GO和KEGG功能富集分析。结果表明,家蚕中肠、脂肪体和血淋巴中分别检测到13 525、7 419、6 965个AS事件,对应发生在4 118、3 109和2 975个AS基因中。3′端可变剪接位点(alternative 3′splice sites, A3SS)、5′端可变剪接位点(alternative 5′splice sites, A5SS)、互斥外显子(mutually exclusive exons, MXE)、内含子保留(retained introns, RI)、外显子跳跃(skipping exon, SE)5种类型AS事件中,SE数量占比最高,在每个组织中的发生比例均不低于64.95%,RI数量占比最低,均不高于1.79%。每个组织中发生1种类型AS事件≤3个的AS基因数量占基因总数的81.14%~100%,单个AS基因发生1种类型AS事件的数量最高为66个。发生A3SS、A5SS、RI事件的AS基因有高达53.19%~61.75%和16.56%~20.57%的3组织和2组织重叠比例,发生SE、MXE事件的AS基因组织特异性高,单一组织独有的比例为43.99%和70.96%。每个组织AS基因总数量里,发生1个单独类型AS事件的基因约占63.40%~69.96%,同时发生3、4、5个类型AS事件的基因合计占比低于7.00%。GO功能注释、KEGG通路富集分析全部AS基因的功能主要为物质的合成、代谢和转运,能量代谢,细胞对刺激的反应和信号转导,基因表达和翻译的调控,蛋白质的加工、修饰和水解,磷酸转移酶和激�Alternative splicing(AS)is ubiquitous in silkworm genome and plays important roles in posttranscriptional regulation of gene and protein diversity.In order to reveal the characteristics of AS events in tissues related to material absorption,circulation,synthesis and metabolism of silkworm,and analyze the forming mechanism of differences in antioxidant levels among silkworm varieties,two silkworm varieties,Dongfei and Cai 4,were chosen as material,and their midgut,fat body and hemolymph tissues were collected for RNA sequencing(RNA-seq).After mapping the sequencing data to reference genome,the AS events and genes with AS events(AS genes)were identified using rMAT software.The characteristics of the number,type and tissue distribution of AS events in AS genes were further analyzed.All AS genes and the differentially expressed AS genes among the two silkworm varieties were analyzed in enrichment of Gene Ontology(GO)terms and KEGG pathways.The results showed that 13525,7419 and 6965 AS events correspondingly in 4118,3109 and 2975 AS genes were detected in midgut,fat body and hemolymph,respectively.Among the 5 types of AS events as alternative 3′splice sites(A3SS),alternative 5′splice sites(A5SS),mutually exclusive exons(MXE),retained introns(RI)and skipping exon(SE),the number of SE event was the highest with a proportion of equal to or over 64.95%in each tissue,while that of RI event was the lowest with a proportion of equal to or under 1.79%.The proportion of AS genes with≤3 of one type AS events was 81.14%~100%,and the maximum number of a single type AS events in one AS gene was 66.The AS genes with A3SS,A5SS and RI events had 53.19%~61.75%and 16.56%~20.57%of overlapping ratios in 3 tissues and 2 tissues respectively,while the AS genes with SE or MXE events had higher tissue specificity with the proportion unique to a single tissue as 43.99%and 70.96%.In the total number of AS genes in each tissue,there were about 63.40%~69.96%genes occurred a single type AS event,and less than 7.00%genes coincide 3,4 or 5 t

关 键 词：家蚕 RNA-SEQ 可变剪接 功能基因 物质合成 

分 类 号：S881.24[农业科学—特种经济动物饲养]