The Genome-wide Alternative Splicing And Skin RNA-seq Research On Donkey

Donkey(Equus asinus)as working animal,with strong disease resistance,strong physique and adaptable characteristics.Now,it is the main means of transport in remote mountainous region,and has high nutritional value in its meat,milk and skin.Alternative splicing(AS)plays an important role in the differentiation,growth and signal transduction of eukaryotes.The research on AS in livestock mainly focus on skin color,body size and other phenotypic traits and disease resistance and production of meat,milk and other economic traits,but so far there is still no donkey whole genome-wide alternative splicing report.Donkey skin as the raw material of e-Jiao,it is mainly focused on the identification of the protein level and the identification of trace elements and the ident ification of the quality of e-Jiao,has never been paid attention on donkey skin transcriptome.According to this situation,this paper intends to analyze the transcriptome data of 44 tissues,study alternative splicing in genomic region of donkey skin on the based of genome sequencing;in order to understand the skin molecular mechanism of immune protection and special effects,we compared Dezhou and Xinjiang donkey skin transcriptom.On the platform of Illumina Hiseq 2000,we sequenced total 15 skin tissues from two kinds of donkeys,Dezhou and Xinjiang.Pearson correlation analysis excluded 2 samples.We identified 35429 transcripts from 13 skin RNA-seq data.The high expression gene of top 100 is mainly concentrated in the various pathways of life sustaining activities and the metabolic pathway related to disease resistance and immunity.Through the prediction and assessment of cuffcompare and protein function and other database and compared with the reference annotation file,received a total of 379 new transcripts,including 363 transcripts in the KEGG annotation results show that these new functional enrichment transcripts mainly free of disease resistance related protein,function.The identification of new transcripts can complement the annotation of donkey genome.According to the normal pipeline we detected 1148 lincRNAs,also found that these linc RNAs mainly focuses on the metabolism of amino acid synthesis pathway.A total of 6008 AS genes were identified,which were mainly concentrated in the pathway of disease resistance and metabolism.Compared Dezhou and Xinjiang donkey skin RNA-seq data at the same location,we found 222 differentially expressed genes,which enriched in immune pathway.Finally,we used homologous genes compared different species to find donkey skin specific genes.Functional enrichment revealed that the donkey skin specific genes were mainly concentrated on energy metabolism,immunity and disease resistance pathways.The study on the level of the transcriptome of donkey skin will provide the molecular genetic basis for the effect of donkey skin,the formation of local breeds and environmental adaptability.Astalavista-3.2 was used to predict alternative splicing.We found that 50.73% genes existed alternative splicing and exon skipped was the major AS events.The function of these AS genes mainly enriched in disease resistance,immunity and energy metabolism pathways.Comparison analysis showed that muscle and blood have the less AS events than other tissues.130 AS genes exist in 44 tissues,which functions mainly focus on life activities sustaining,and 42 AS genes have the same AS events in 44 tissues.Comparative analysis on AS and non-AS genes,found that this two kinds of genes were significantly different at gene length,exon length,number and FPKM,which indicated that two types of genes have significant differences in genetic structure.In order to do the survey on tissue-specific AS gene,we compared cow,goat,sheep,horse and donkey by orthologue genes,which we found the conserved tissue-specific AS genes and donkey unique AS genes.In summary,this study,which used high-throughput sequencing,bioinformatics analysis and comparative analysis to do the survey on genome-wide AS gene predication.At the same time to do the survey on the Dezhou and Xinjiang donkey skin RNA-seq from the aspects of the AS,FPKM and prediction of UTs and linc RNAs,which enriched the genome annotation of the donkey.