Transcriptome Analysis Reveals Long Intergenic Noncoding RNAs Contributed to Growth and Meat Quality Differences between Yorkshire and Wannanhua Pig
Abstract
:1. Introduction
2. Materials and Methods
2.1. Ethics Statement and Data Acquisition
2.2. Publicly Available Annotations
2.3. RNA-Seq Reads Mapping and Transcriptome Assembly
2.4. Pipeline for lincRNA Identification
2.5. Differentially Expressed lincRNAs and mRNA Analysis
2.6. Prediction of PTGs of lincRNAs
2.7. Gene Ontology and Pathway Analysis
2.8. Correlation Validation between lincRNAs and Their PTGs
3. Results
3.1. Transcripts Assembly and lincRNAs Identification
3.2. Characterization of Identified lincRNAs
3.3. Differential Expression Analysis of lincRNAs and mRNA
3.4. Prediction of Differentially Expressed lincRNA Target Gene
3.5. Gene Ontology and Pathway Analysis of PTGs and mRNA
3.6. Expression Regulation Analysis of DELs and Their Differentially Expressed Potential Target Genes
3.7. Validation of the Correlation between lincRNAs and Their Potential Target Genes
4. Discussion
Supplementary Materials
Acknowledgments
Author Contributions
Conflicts of Interest
References
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Sample | Accession Number | Raw Reads | Clean Reads | Mapped Reads | Mapping Ratio |
---|---|---|---|---|---|
WH03 | SRR2919657 | 64,584,126 | 61,821,920 | 49,030,410 | 79.3% |
WH05 | SRR2919658 | 64,327,738 | 61,484,062 | 48,584,612 | 79.0% |
WH12 | SRR2919659 | 59,244,502 | 56,584,368 | 43,757,304 | 77.3% |
YY01 | SRR2919660 | 57,969,134 | 55,324,162 | 41,665,620 | 75.3% |
YY02 | SRR2919661 | 68,254,168 | 64,955,554 | 49,480,266 | 76.2% |
YY06 | SRR2919662 | 72,298,142 | 68,884,390 | 50,825,220 | 73.8% |
DELs | Number | DELs | Number | ||||
---|---|---|---|---|---|---|---|
DEPTGs | UpRegulated PTGs | DownRegulated PTGs | DEPTGs | UpRegulated PTGs | DownRegulated PTGs | ||
TCONS_00000089 | 41 | 34 | 7 | TCONS_00021915 | 71 | 27 | 44 |
TCONS_00000134 | 4 | 4 | 0 | TCONS_00034774 | 4 | 4 | 0 |
TCONS_00000742 | 53 | 37 | 16 | TCONS_00044733 | 80 | 76 | 4 |
TCONS_00005771 | 7 | 7 | 0 | TCONS_00056305 | 5 | 5 | 0 |
TCONS_00006963 | 31 | 26 | 5 | TCONS_00059011 | 14 | 3 | 11 |
TCONS_00007946 | 46 | 42 | 4 | TCONS_00061360 | 110 | 79 | 31 |
TCONS_00013076 | 3 | 2 | 1 | TCONS_00061633 | 13 | 13 | 0 |
TCONS_00021480 | 12 | 11 | 1 | TCONS_00064940 | 11 | 10 | 1 |
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Zou, C.; Li, S.; Deng, L.; Guan, Y.; Chen, D.; Yuan, X.; Xia, T.; He, X.; Shan, Y.; Li, C. Transcriptome Analysis Reveals Long Intergenic Noncoding RNAs Contributed to Growth and Meat Quality Differences between Yorkshire and Wannanhua Pig. Genes 2017, 8, 203. https://doi.org/10.3390/genes8080203
Zou C, Li S, Deng L, Guan Y, Chen D, Yuan X, Xia T, He X, Shan Y, Li C. Transcriptome Analysis Reveals Long Intergenic Noncoding RNAs Contributed to Growth and Meat Quality Differences between Yorkshire and Wannanhua Pig. Genes. 2017; 8(8):203. https://doi.org/10.3390/genes8080203
Chicago/Turabian StyleZou, Cheng, Sha Li, Lulu Deng, Yang Guan, Dake Chen, Xiongkun Yuan, Tianrui Xia, Xinglin He, Yawei Shan, and Changchun Li. 2017. "Transcriptome Analysis Reveals Long Intergenic Noncoding RNAs Contributed to Growth and Meat Quality Differences between Yorkshire and Wannanhua Pig" Genes 8, no. 8: 203. https://doi.org/10.3390/genes8080203