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Characterization of Alternative Splicing Events in Porcine Skeletal Muscles with Different Intramuscular Fat Contents
Meat quality is one of the most important economic traits in pig breeding and production. Intramuscular fat (IMF) is a major factor that improves meat quality. To better understand the alternative splicing (AS) events underlying meat quality, long-read isoform sequencing (Iso-seq) was used to identi...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8961525/ https://www.ncbi.nlm.nih.gov/pubmed/35204660 http://dx.doi.org/10.3390/biom12020154 |
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author | Hao, Wanjun Yang, Zewei Sun, Yuanlu Li, Jiaxin Zhang, Dongjie Liu, Di Yang, Xiuqin |
author_facet | Hao, Wanjun Yang, Zewei Sun, Yuanlu Li, Jiaxin Zhang, Dongjie Liu, Di Yang, Xiuqin |
author_sort | Hao, Wanjun |
collection | PubMed |
description | Meat quality is one of the most important economic traits in pig breeding and production. Intramuscular fat (IMF) is a major factor that improves meat quality. To better understand the alternative splicing (AS) events underlying meat quality, long-read isoform sequencing (Iso-seq) was used to identify differential (D)AS events between the longissimus thoracis (LT) and semitendinosus (ST), which differ in IMF content, together with short-read RNA-seq. Through Iso-seq analysis, we identified a total of 56,789 novel transcripts covering protein-coding genes, lncRNA, and fusion transcripts that were not previously annotated in pigs. We also identified 456,965 AS events, among which 3930 were DAS events, corresponding to 2364 unique genes. Through integrative analysis of Iso-seq and RNA-seq, we identified 1174 differentially expressed genes (DEGs), among which 122 were DAS genes, i.e., DE-DAS genes. There are 12 overlapped pathways between the top 20 DEGs and DE-DAS genes, as revealed by KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis, indicating that DE-DAS genes play important roles in the differential phenotype of LT and ST. Further analysis showed that upregulated DE-DAS genes are more important than downregulated ones in IMF deposition. Fatty acid degradation and the PPAR (peroxisome proliferator-activated receptor) signaling pathway were found to be the most important pathways regulating the differential fat deposition of the two muscles. The results update the existing porcine genome annotations and provide data for the in-depth exploration of the mechanisms underlying meat quality and IMF deposition. |
format | Online Article Text |
id | pubmed-8961525 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-89615252022-03-30 Characterization of Alternative Splicing Events in Porcine Skeletal Muscles with Different Intramuscular Fat Contents Hao, Wanjun Yang, Zewei Sun, Yuanlu Li, Jiaxin Zhang, Dongjie Liu, Di Yang, Xiuqin Biomolecules Article Meat quality is one of the most important economic traits in pig breeding and production. Intramuscular fat (IMF) is a major factor that improves meat quality. To better understand the alternative splicing (AS) events underlying meat quality, long-read isoform sequencing (Iso-seq) was used to identify differential (D)AS events between the longissimus thoracis (LT) and semitendinosus (ST), which differ in IMF content, together with short-read RNA-seq. Through Iso-seq analysis, we identified a total of 56,789 novel transcripts covering protein-coding genes, lncRNA, and fusion transcripts that were not previously annotated in pigs. We also identified 456,965 AS events, among which 3930 were DAS events, corresponding to 2364 unique genes. Through integrative analysis of Iso-seq and RNA-seq, we identified 1174 differentially expressed genes (DEGs), among which 122 were DAS genes, i.e., DE-DAS genes. There are 12 overlapped pathways between the top 20 DEGs and DE-DAS genes, as revealed by KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis, indicating that DE-DAS genes play important roles in the differential phenotype of LT and ST. Further analysis showed that upregulated DE-DAS genes are more important than downregulated ones in IMF deposition. Fatty acid degradation and the PPAR (peroxisome proliferator-activated receptor) signaling pathway were found to be the most important pathways regulating the differential fat deposition of the two muscles. The results update the existing porcine genome annotations and provide data for the in-depth exploration of the mechanisms underlying meat quality and IMF deposition. MDPI 2022-01-18 /pmc/articles/PMC8961525/ /pubmed/35204660 http://dx.doi.org/10.3390/biom12020154 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Hao, Wanjun Yang, Zewei Sun, Yuanlu Li, Jiaxin Zhang, Dongjie Liu, Di Yang, Xiuqin Characterization of Alternative Splicing Events in Porcine Skeletal Muscles with Different Intramuscular Fat Contents |
title | Characterization of Alternative Splicing Events in Porcine Skeletal Muscles with Different Intramuscular Fat Contents |
title_full | Characterization of Alternative Splicing Events in Porcine Skeletal Muscles with Different Intramuscular Fat Contents |
title_fullStr | Characterization of Alternative Splicing Events in Porcine Skeletal Muscles with Different Intramuscular Fat Contents |
title_full_unstemmed | Characterization of Alternative Splicing Events in Porcine Skeletal Muscles with Different Intramuscular Fat Contents |
title_short | Characterization of Alternative Splicing Events in Porcine Skeletal Muscles with Different Intramuscular Fat Contents |
title_sort | characterization of alternative splicing events in porcine skeletal muscles with different intramuscular fat contents |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8961525/ https://www.ncbi.nlm.nih.gov/pubmed/35204660 http://dx.doi.org/10.3390/biom12020154 |
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