title: RNA-seq transcriptome analysis of extensor digitorum longus and soleus muscles in large white pigs.
abstract: Skeletal muscle fibers are mainly categorized into red and white fiber types, and the ratio of red/white fibers within muscle mass plays a crucial role in meat quality such as tenderness and flavor. To better understand the molecular difference between the two muscle fibers, this study takes advantage of RNA-seq to compare differences in the transcriptome between extensor digitorum longus (EDL; white fiber) and soleus (Sol; red fiber) muscles of large white pigs. In total, 89,658,562 and 46,723,568 raw reads from EDL and Sol were generated, respectively. Comparison between the two transcriptomes revealed 561 differentially expressed genes, with 408 displaying higher and 153 lower levels of expression in Sol. Quantitative real-time polymerase chain reaction validated the differential expression of nine genes. Gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis discovered several differentially enriched biological functions and processes of the two muscles. Moreover, transcriptome comparison between EDL and Sol identified many muscle-related genes (CSRP3, ACTN2, MYL1, and MYH6) and pathways related to myofiber formation, such as focal adhesion, tight junction formation, extracellular matrix (ECM)-receptor pathway, calcium signaling, and Wnt signaling. In addition, 58,362 and 58,359 single nucleotide polymorphisms were identified in EDL and Sol, respectively, and the sequence of 9069 genes was refined at the 5', 3' or both ends. Numerous novel transcripts and alternatively spliced RNAs were also identified. Our transcriptome analysis constitutes valuable sequence resource for uncovering important genes and pathways involved in muscle fiber type determination, and might help further our understanding of the molecular mechanisms in different types of muscle.
authors.affiliation: Laboratory of Animal Fat Deposition and Muscle Development, College of Animal Science and Technology, Northwestern A&F University, 22 Xinong Road, Yangling, 712100, Shaanxi Province, People's Republic of China.
authors.forename: Jiayu
authors.initials: J
authors.lastname: Zhu
authors.affiliation: Laboratory of Animal Fat Deposition and Muscle Development, College of Animal Science and Technology, Northwestern A&F University, 22 Xinong Road, Yangling, 712100, Shaanxi Province, People's Republic of China.
authors.forename: Xin'e
authors.initials: X
authors.lastname: Shi
authors.affiliation: Laboratory of Animal Fat Deposition and Muscle Development, College of Animal Science and Technology, Northwestern A&F University, 22 Xinong Road, Yangling, 712100, Shaanxi Province, People's Republic of China.|School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, 723000, Shaanxi Province, People's Republic of China.
authors.forename: Hongzhao
authors.initials: H
authors.lastname: Lu
authors.affiliation: Laboratory of Animal Fat Deposition and Muscle Development, College of Animal Science and Technology, Northwestern A&F University, 22 Xinong Road, Yangling, 712100, Shaanxi Province, People's Republic of China.
authors.forename: Bo
authors.initials: B
authors.lastname: Xia
authors.affiliation: Laboratory of Animal Fat Deposition and Muscle Development, College of Animal Science and Technology, Northwestern A&F University, 22 Xinong Road, Yangling, 712100, Shaanxi Province, People's Republic of China.
authors.forename: Yuefeng
authors.initials: Y
authors.lastname: Li
authors.affiliation: Laboratory of Animal Fat Deposition and Muscle Development, College of Animal Science and Technology, Northwestern A&F University, 22 Xinong Road, Yangling, 712100, Shaanxi Province, People's Republic of China.
authors.forename: Xiao
authors.initials: X
authors.lastname: Li
authors.affiliation: Laboratory of Animal Fat Deposition and Muscle Development, College of Animal Science and Technology, Northwestern A&F University, 22 Xinong Road, Yangling, 712100, Shaanxi Province, People's Republic of China.
authors.forename: Qiangling
authors.initials: Q
authors.lastname: Zhang
authors.affiliation: Laboratory of Animal Fat Deposition and Muscle Development, College of Animal Science and Technology, Northwestern A&F University, 22 Xinong Road, Yangling, 712100, Shaanxi Province, People's Republic of China. gsyang999@hotmail.com.
authors.forename: Gongshe
authors.initials: G
authors.lastname: Yang
mesh_terms: D000818:Animals; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D059014:High-Throughput Nucleotide Sequencing; D008460:Meat; D018482:Muscle, Skeletal / Q000254:growth & development / Q000378:metabolism*; D012313:RNA / Q000096:biosynthesis* / Q000378:metabolism; D013552:Swine; D059467:Transcriptome / Q000235:genetics*
chemical_list: D012313:RNA
keywords: Extensor digitorum longus; Muscle-related genes; RNA-seq; Soleus