Identification And Validation Of New Transcripts And New LncRNAs In Sheep Biceps Brachii Transcriptome

In recent years, the high-throughput whole transcriptome sequencing technology(RNA-seq) have been widely applied in the functional genomic studies of sheep. The high-throughput mRNA sequencing method allows to reveal the expression profile in a single-base resolution underlying phenotype, metabolic and physiological changes, as well as different stages of development and environmental impacts, the characteristics of this technology made it possible to decipher unannotated transcriptional activity by revealing tissue-specific alternative splicing, novel genes and transcripts, and genomic structural variations.In this study, using bioinformatics methods and semi-qRT PCR, a group of novel transcripts and lncRNAs were identified and classified from the cDNA library of small-tail Han sheep and dorper sheep brachial biceps transcriptome. The main results are as follows:(1) With the comparison and annotation of transcriptome data, a total of 40129 co-expressed trancripts found during two transcriptome libraries, from which 5553 novel transcripts were detected.(2) Applied with coding potential prediction and sequence homology analysis with known RNA of human, cattle and sheep, a group of novel transcript received acceptable identification results. 634 novel transcripts have been annotated into 473 annotated gene locis, 49 novel transcripts were annotated into 27 novel protein coding gene locis, 100 novel transcripts were identified into 88 lncRNA locis, 4 novel transcripts were detected as 4 pseudogenes, and 30 novel transcripts were annotated into 27 unnamed protein locis.(3) The novel transcripts that predicted as noncoding potential without acceptable comparison results were furtherly analysed. 2312 high reliability lncRNA transcripts were forecasted belonging to 2282 lncRNA locs, during which 2132 of these transcripts showed a single exon structure. The function of lncRNA were furtherly predicted by the annotation of reciprocal genes.(4) 15 novel transcripts were selected for exon structure testing.With partial sequence cloning and sequencing, 13 of them were successfully cloned, the sequencing result were compared with sheep reference genome and transcriptome data registration results, as a sesult of our analyse, the sequence information and exon structure prediction data of novel transcripts were validated. With the semi quantitative RT-PCR analysis, the expression during different tissue of 12 selected transcripts were accessed.In general, with the using of bioinformatic technologies, a group of novel transcripts were successfully identified from two sheep biceps brachii transcriptome sequencing data. Annotation and prediction were given to these novel transcripts and a number of lncRNAs.With experimental testing of molecular biology, the reliability of identification and prediction results were confirmed. This study provided complementary annotation information for the sheep genome, which also brings foundation for further regulation mechanism analyse.