RNA-seq transcriptome analysis of extensor digitorum longus and soleus muscles in large white pigs

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• 作者：Jiayu Zhu ; Xin'e Shi ; Hongzhao Lu ; Bo Xia ; Yuefeng Li…
• 关键词：RNA ; seq ; Extensor digitorum longus ; Soleus ; Muscle ; related genes
• 刊名：Molecular Genetics and Genomics
• 出版年：2016
• 出版时间：April 2016
• 年：2016
• 卷：291
• 期：2
• 页码：687-701
• 全文大小：2,494 KB
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• 作者单位：Jiayu Zhu (1)
  Xin’e Shi (1)
  Hongzhao Lu (1) (2)
  Bo Xia (1)
  Yuefeng Li (1)
  Xiao Li (1)
  Qiangling Zhang (1)
  Gongshe Yang (1)
  
  1. 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
  2. School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, 723000, Shaanxi Province, People’s Republic of China
  
• 刊物类别：Biomedical and Life Sciences
• 刊物主题：Life Sciences
  Cell Biology
  Biochemistry
  Microbial Genetics and Genomics
  
• 出版者：Springer Berlin / Heidelberg
• ISSN：1617-4623

文摘

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.