Abstract
Myogenesis is accompanied by a number of changes in gene expression in mammals, and the transcriptional events that underlie these processes have not been yet fully elucidated. In this study, RNA-seq was used to comprehensively compare the transcription profiles of skeletal muscle between Tongcheng (TC) and Yorkshire (YK) pigs at 40, 55, 63, 70, and 90 days of gestation. One thousand three hundred seventeen and 691 differentially expressed genes (DEGs) were detected in TC and YK, respectively, among which 321 DEGs were shown to be common in TC and YK. STEM (Time-series Expression Miner) analysis revealed different gene expression profiles between the two breeds. One thousand six hundred seventy-seven genes showed significant differential expression between TC and YK at the identical stages, while three genes were found to be common in all comparisons. A total of 3185 new putative transcripts were also predicted. Several gene expression profiles were further validated by qRT-PCR. Fifty-five dpc (days post coitum) was suggested to be the key stage to contribute developmental differences between TC and YK. PTEN, EP300, ENSSSCG00000004979 (Myosin 9A), CDK14, IRS1, PPP1CC, and some ribosomal proteins were suggested to be the key candidate genes for elucidating the developmental differences between the two breeds. In conclusion, we constructed comprehensive high-resolution gene expression maps of these two pig breeds, which not only provides an in-depth understanding of the dynamics of transcriptional regulation during myogenesis in this study, but also would facilitate the elucidation of molecular mechanisms underlying myogenesis in the future studies.
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Acknowledgments
We appreciate the Beijing Genomics Institute (BGI) and Gene Denovo for providing us with technical assistance in RNA sequencing and bioinformatics analysis; we also thank the help of Animal Husbandry Bureau of Tongcheng County.
Funding
This search project was supported financially by the National Porcine Industry Technology System (CARS-36).
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ML conceived this study and supervised the experiment. YZ and JL designed the breeding and sampling plan. HL, YX, GL, YZ, and JL participated in sampling. HL carried out the experiment and drafted the manuscript. HL analyzed the data. All authors read and approved the final version of the manuscript.
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The transcriptome raw data of Tongcheng and Yorkshire pigs were submitted to the Sequence Read Archive (SRA) of the NCBI (accession number: SRP 066398).
ESM Figure 1
Distribution of genes’ coverage (GIF 92 kb)
High Resolution Image
(TIFF 771 kb)
ESM Table 1
GO enrichment analysis of profile 39 in TC and that in YK (XLSX 309 kb)
ESM Table 2
GO enrichment analysis of profile 0 in TC and that in YK (XLSX 308 kb)
ESM Table 3
KEGG pathway analysis of the differentially expressed genes in specific profiles in TC and YK (XLSX 41 kb)
ESM Table 4
KEGG pathway analysis of the differentially expressed genes between TC and YK, and the genes involved in oxidative phosphorylation (XLSX 42 kb)
Table 5
The topological property of the networks with the DEGs between TC and YK (XLSX 120 kb)
ESM Table 6
The topological property of the networks with the stage-specific DEGs in 55 dpc between TC and YK (XLSX 48 kb)
ESM Table 7
The topological property of the networks with the up-regulated DEGs in TC at 55 dpc between TC and YK (XLSX 9 kb)
ESM Table 8
Novel transcripts predicted by RNA-seq (XLSX 914 kb)
ESM Table 9
KEGG pathway analysis of the genes which occurred alternative splicing events (XLSX 955 kb)
ESM Table 10
Alternative splicing events in each stage (XLSX 5462 kb)
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Liu, H., Xi, Y., Liu, G. et al. Comparative transcriptomic analysis of skeletal muscle tissue during prenatal stages in Tongcheng and Yorkshire pig using RNA-seq. Funct Integr Genomics 18, 195–209 (2018). https://doi.org/10.1007/s10142-017-0584-6
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DOI: https://doi.org/10.1007/s10142-017-0584-6