The Differential Expression Of Long Noncoding RNA And Analysis Of Alternative Splicing Of The Large Yellow Croaker (Larimichthyscrocea) Infected By Cryptocaryon Irritans

Large yellow croaker(Larimichthys crocea)is also known as cucumber fish and yellow fish.For a long time,L.crocea has been popular in consumers at home and abroad because of the delicious meat and rich nutrients.It is also one of the most important maricultural species in China.At the same time,with high density aquaculture and disease infestation,the L.crocea industry is encountering serious obstacles for sustainable development.A common parasitic disease caused by Cryptocaryon irritans has resulted in high mortalities and great economic losses.Therefore,it is imminent to analyze the molecular mechanism of large yellow croaker and find effective ways to control disease.However,the previous studies of L.crocea were mainly focused on proteincoding transcripts or peptides,the roles of lncRNAs(long non-coding RNAs)and alternative splicing events in transcriptional regulation were needed to analyze.First,to generate a comprehensive transcriptome of L.crocea,101 RNAseq datasets were used,and lncRNAs were identified through a strict pipeline.Second,in order to understand the molecular regulation mechanism of L.crocea infected by C.irritans,the differential expression pattern of lncRNA and alternative splicing events were analyzed.The main results are as following:1.101 RNA-seq datasets varied in ages,sexes,and tissues were retrieved to generate a comprehensive catalog of large yellow croaker transcriptome database.A set of 14,599 highconfidence lncRNAs from 13.673 loci were identified and characterized.Compared to mRNAs,lncRNAs have shorter transcript length,fewer exons and lower level of conservation,which is in accordance with the previous study.2.DE analysis identified 77 DElncRNAs in response to the infection of C.irritans,and 567 differentially expressed protein-coding genes were regarded as target genes.A set of immunerelated GO terms and KEGG pathways were enriched,in which immune genes including Tlr5,MMP9,CD2AP,and IL1R2 were up-regulated significantly.3.Alternative splicing analysis identified 1,155 differential alternative splicing events from 866 genes in L.crocea infected by C.irritans and the number were increasing during the infection experiment.GO and KEGG enrichment analysis identified a large number of differentially alternatively spliced genes participated in the processes of post-transcriptional regulation,protein transport and immune regulation,including u2af2a、cltcll、polr3a.4.Genomics study(GWAS)and transcriptomics study(mRNA,lncRNA,alternative splicing)were compared to identify the core genes in L.crocea infected by C.irritans.Several immunerelated genes were identified in different omics including AP-1,Tpl2,CCL19 and mapk8ipl.The low overlap rate of genes in different omics reveals the diversity of gene expression and regulation forms;while genes in different omics were enriched in the same immune pathway,including Tolllike receptor signaling and cytokine-cytokine receptor interaction pathway,indicates that genes can play a synergistic role in immune regulation through different forms.This study provides a new insight for lncRNAs annotation in L.crocea genome and helps to deepen the understanding of the roles of lncRNAs and alternative splicing in immune response to C.irritans.