title: Identification and Classification of New Transcripts in Dorper and Small-Tailed Han Sheep Skeletal Muscle Transcriptomes.
abstract: High-throughput mRNA sequencing enables the discovery of new transcripts and additional parts of incompletely annotated transcripts. Compared with the human and cow genomes, the reference annotation level of the sheep genome is still low. An investigation of new transcripts in sheep skeletal muscle will improve our understanding of muscle development. Therefore, applying high-throughput sequencing, two cDNA libraries from the biceps brachii of small-tailed Han sheep and Dorper sheep were constructed, and whole-transcriptome analysis was performed to determine the unknown transcript catalogue of this tissue. In this study, 40,129 transcripts were finally mapped to the sheep genome. Among them, 3,467 transcripts were determined to be unannotated in the current reference sheep genome and were defined as new transcripts. Based on protein-coding capacity prediction and comparative analysis of sequence similarity, 246 transcripts were classified as portions of unannotated genes or incompletely annotated genes. Another 1,520 transcripts were predicted with high confidence to be long non-coding RNAs. Our analysis also revealed 334 new transcripts that displayed specific expression in ruminants and uncovered a number of new transcripts without intergenus homology but with specific expression in sheep skeletal muscle. The results confirmed a complex transcript pattern of coding and non-coding RNA in sheep skeletal muscle. This study provided important information concerning the sheep genome and transcriptome annotation, which could provide a basis for further study.
authors.affiliation: Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Taian 271018, China.
authors.forename: Tianle
authors.initials: T
authors.lastname: Chao
authors.affiliation: Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Taian 271018, China.
authors.forename: Guizhi
authors.initials: G
authors.lastname: Wang
authors.affiliation: Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Taian 271018, China.
authors.forename: Jianmin
authors.initials: J
authors.lastname: Wang
authors.affiliation: Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Taian 271018, China.
authors.forename: Zhaohua
authors.initials: Z
authors.lastname: Liu
authors.affiliation: Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Taian 271018, China.
authors.forename: Zhibin
authors.initials: Z
authors.lastname: Ji
authors.affiliation: Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Taian 271018, China.
authors.forename: Lei
authors.initials: L
authors.lastname: Hou
authors.affiliation: College of Biological and Agricultural Engineering, Weifang University, Key Laboratory of Biochemistry and Molecular Biology in Universities of Shandong, Weifang 261061, China.
authors.forename: Chunlan
authors.initials: C
authors.lastname: Zhang
mesh_terms: D017398:Alternative Splicing; D000818:Animals; D002874:Chromosome Mapping; D015723:Gene Library; D063990:Gene Ontology; D016678:Genome; D058977:Molecular Sequence Annotation; D018482:Muscle, Skeletal / Q000254:growth & development / Q000378:metabolism*; D062085:RNA, Long Noncoding / Q000235:genetics*; D012333:RNA, Messenger / Q000235:genetics*; D034561:Sheep, Domestic / Q000235:genetics* / Q000254:growth & development; D013045:Species Specificity; D059467:Transcriptome
chemical_list: D062085:RNA, Long Noncoding; D012333:RNA, Messenger