Abstract
Muscle growth and development from fetal to neonatal stages consist of a series of delicately regulated and orchestrated changes in expression of genes. In this study, we performed whole transcriptome profiling based on RNA-Seq of caprine longissimus dorsi muscle tissue obtained from prenatal stages (days 45, 60, and 105 of gestation) and neonatal stage (the 3-day-old newborn) to identify genes that are differentially expressed and investigate their temporal expression profiles. A total of 3276 differentially expressed genes (DEGs) were identified (Q value < 0.01). Time-series expression profile clustering analysis indicated that DEGs were significantly clustered into eight clusters which can be divided into two classes (Q value < 0.05), class I profiles with downregulated patterns and class II profiles with upregulated patterns. Based on cluster analysis, GO enrichment analysis found that 75, 25, and 8 terms to be significantly enriched in biological process (BP), cellular component (CC), and molecular function (MF) categories in class I profiles, while 35, 21, and 8 terms to be significantly enriched in BP, CC, and MF in class II profiles. KEGG pathway analysis revealed that DEGs from class I profiles were significantly enriched in 22 pathways and the most enriched pathway was Rap1 signaling pathway. DEGs from class II profiles were significantly enriched in 17 pathways and the mainly enriched pathway was AMPK signaling pathway. Finally, six selected DEGs from our sequencing results were confirmed by qPCR. Our study provides a comprehensive understanding of the molecular mechanisms during goat skeletal muscle development from fetal to neonatal stages and valuable information for future studies of muscle development in goats.
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Acknowledgements
We thank all contributors of the present study. We also thank Mr. Cheng Zufu and his colleagues at Gene Denovo Ltd., Co (Guangzhou, China) for assistance in data processing.
Funding
This work was supported by the National Natural Science Foundation of China (31672402), Sichuan Province Science and Technology Support Program (2016NYZ0045), and the Tibet Autonomous Region Science and Technology Major Project (Z2016B01N04-06).
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The raw data we obtained from RNA-Seq are available in the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) (accession number: SRR3567144).
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Table S1
Summary of RNA-seq data and reads mapped to the Capra hircus reference genome. (XLSX 13 kb)
Table S2
List of identified DEGs from pairwise comparisons. (XLSX 553 kb)
Table S3
Significantly enriched GO terms for ClassIprofiles (profiles 9, 3, 0, and 12) with down-regulated patterns. (XLSX 54 kb)
Table S4
Significantly enriched GO terms for ClassIIprofiles (profiles 16, 25, 13, and 24) with up-regulated patterns. (XLSX 22 kb)
Table S5
Significantly enriched KEGG pathways for ClassIprofiles (profiles 9, 3, 0, and 12) with down-regulated patterns. (XLSX 13 kb)
Table S6
Significantly enriched KEGG pathways for ClassIIprofiles (profiles 16, 25, 13, and 24) with up-regulated patterns. (XLSX 11 kb)
Table S7
Primers used in the qPCR analysis. (XLSX 9 kb)
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Zhan, S., Zhao, W., Song, T. et al. Dynamic transcriptomic analysis in hircine longissimus dorsi muscle from fetal to neonatal development stages. Funct Integr Genomics 18, 43–54 (2018). https://doi.org/10.1007/s10142-017-0573-9
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DOI: https://doi.org/10.1007/s10142-017-0573-9