Alternative Splicing Events in Midgut,Fat Body and Hemolymph of Silkworm Based on Transcriptome Sequencing
Alternative splicing(AS)is ubiquitous in silkworm genome and plays important roles in post-transcriptional regulation of gene and protein diversity.In order to reveal the characteristics of AS events in tis-sues 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 se-quencing(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 13 525,7 419 and 6 965 AS events correspondingly in 4 118,3 109 and 2 975 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 types of AS events.According to GO functional annotation and KEGG pathway enrichment analysis,the functions of all the AS genes mainly involved material synthesis,metabolism and transport,energy metabolism,cell response to stimulation and signal transduction,regulation of gene expression and translation,protein processing,modification and hydrolysis,phosphotrans-ferase and kinase activities,etc.Between the two silkworm varieties,the number of differentially expressed AS events in midgut,fat body and hemolymph were 302,176 and 244,and the corresponding AS genes were 266,137 and 186,respectively.The differentially expressed AS genes could be enriched in the oxidation-re-duction process and the biosynthesis processes of compounds including nuclear bases,aromatic compounds,heterocycles,organic cyclic compounds and macromolecules.So,there were the considerable number of AS e-vents and AS genes in the 3 tested tissues of silkworm,and the number and type of AS events were tissue-spe-cific.The 2 silkworm varieties with high and low antioxidant levels had differentially expressed AS genes in-volved in the synthesis of antioxidant substances.These discoveries could provide important functional candi-date genes for the study of material utilization and transformation in silkworm body.
万方数据
维普
