Full-Length Transcriptome and Gene Expression Analysis of Different <i>Ovis aries</i> Adipose Tissues Reveals Transcript Variants Involved in Lipid Biosynthesis
Sheep have historically been bred globally as a vital food source. To explore the transcriptome of adipose tissue and investigate key genes regulating adipose metabolism in sheep, adipose tissue samples were obtained from F1 Dorper × Hu sheep. High-throughput sequencing libraries for second- and thi...
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MDPI AG
2023-12-01
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| Online Access: | https://www.mdpi.com/2076-2615/14/1/7 |
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| author | Lixia An Yangyang Pan Mengjiao Yuan Zhonghao Wen Liying Qiao Weiwei Wang Jianhua Liu Baojun Li Wenzhong Liu |
| author_facet | Lixia An Yangyang Pan Mengjiao Yuan Zhonghao Wen Liying Qiao Weiwei Wang Jianhua Liu Baojun Li Wenzhong Liu |
| author_sort | Lixia An |
| collection | DOAJ |
| description | Sheep have historically been bred globally as a vital food source. To explore the transcriptome of adipose tissue and investigate key genes regulating adipose metabolism in sheep, adipose tissue samples were obtained from F1 Dorper × Hu sheep. High-throughput sequencing libraries for second- and third-generation sequencing were constructed using extracted total RNA. Functional annotation of differentially expressed genes and isoforms facilitated the identification of key regulatory genes and isoforms associated with sheep fat metabolism. SMRT-seq generated 919,259 high-accuracy cDNA sequences after filtering. Full-length sequences were corrected using RNA-seq sequences, and 699,680 high-quality full-length non-chimeric (FLNC) reads were obtained. Upon evaluating the ratio of total lengths based on FLNC sequencing, it was determined that 36,909 out of 56,316 multiple-exon isoforms met the criteria for full-length status. This indicates the identification of 330,375 full-length FLNC transcripts among the 370,114 multiple-exon FLNC transcripts. By comparing the reference genomes, 60,276 loci and 111,302 isoforms were identified. In addition, 43,423 new genes and 44,563 new isoforms were identified. The results identified 185 (3198), 394 (3592), and 83 (3286) differentially expressed genes (transcripts) between tail and subcutaneous, tail and visceral, and subcutaneous and visceral adipose tissues, respectively. Functional annotation and pathway analysis revealed the following observations. (1) Among the differentially expressed genes (DEGs) of TF and SF tissues, the downregulation of <i>ACADL</i>, <i>ACSL6</i>, and <i>NC_056060.1.2536</i> was observed in SF, while <i>FFAR4</i> exhibited upregulation. (2) Among the DEGs of TF and VF tissues, expressions of <i>ACADL</i>, <i>ACSL6</i>, <i>COL1A1</i>, <i>COL1A2</i>, and <i>SCD</i> were downregulated in VF, with upregulation of <i>FFAR4</i>. (3) Among SF and VF expressions of <i>COL1A1</i>, <i>COL1A2,</i> and <i>NC_056060.1.2536</i> were downregulated in VF. Specific differentially expressed genes (<i>ACADL</i>, <i>ACSL6</i>, <i>COL1A1</i>, <i>COL1A2</i>, <i>FFAR4</i>, <i>NC_056060.1.2536</i>, and <i>SCD</i>) and transcripts (NC_056066.1.1866.16 and NC_056066.1.1866.22) were identified as relevant to fat metabolism. These results provide a dataset for further verification of the regulatory pathway associated with fat metabolism in sheep. |
| first_indexed | 2024-03-08T15:13:26Z |
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| last_indexed | 2024-03-08T15:13:26Z |
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| spelling | doaj.art-749619d51e934d489bc6973bb3e317572024-01-10T14:49:51ZengMDPI AGAnimals2076-26152023-12-01141710.3390/ani14010007Full-Length Transcriptome and Gene Expression Analysis of Different <i>Ovis aries</i> Adipose Tissues Reveals Transcript Variants Involved in Lipid BiosynthesisLixia An0Yangyang Pan1Mengjiao Yuan2Zhonghao Wen3Liying Qiao4Weiwei Wang5Jianhua Liu6Baojun Li7Wenzhong Liu8College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, ChinaCollege of Animal Science, Shanxi Agricultural University, Jinzhong 030801, ChinaCollege of Animal Science, Shanxi Agricultural University, Jinzhong 030801, ChinaCollege of Animal Science, Shanxi Agricultural University, Jinzhong 030801, ChinaCollege of Animal Science, Shanxi Agricultural University, Jinzhong 030801, ChinaCollege of Animal Science, Shanxi Agricultural University, Jinzhong 030801, ChinaCollege of Animal Science, Shanxi Agricultural University, Jinzhong 030801, ChinaCollege of Animal Science, Shanxi Agricultural University, Jinzhong 030801, ChinaCollege of Animal Science, Shanxi Agricultural University, Jinzhong 030801, ChinaSheep have historically been bred globally as a vital food source. To explore the transcriptome of adipose tissue and investigate key genes regulating adipose metabolism in sheep, adipose tissue samples were obtained from F1 Dorper × Hu sheep. High-throughput sequencing libraries for second- and third-generation sequencing were constructed using extracted total RNA. Functional annotation of differentially expressed genes and isoforms facilitated the identification of key regulatory genes and isoforms associated with sheep fat metabolism. SMRT-seq generated 919,259 high-accuracy cDNA sequences after filtering. Full-length sequences were corrected using RNA-seq sequences, and 699,680 high-quality full-length non-chimeric (FLNC) reads were obtained. Upon evaluating the ratio of total lengths based on FLNC sequencing, it was determined that 36,909 out of 56,316 multiple-exon isoforms met the criteria for full-length status. This indicates the identification of 330,375 full-length FLNC transcripts among the 370,114 multiple-exon FLNC transcripts. By comparing the reference genomes, 60,276 loci and 111,302 isoforms were identified. In addition, 43,423 new genes and 44,563 new isoforms were identified. The results identified 185 (3198), 394 (3592), and 83 (3286) differentially expressed genes (transcripts) between tail and subcutaneous, tail and visceral, and subcutaneous and visceral adipose tissues, respectively. Functional annotation and pathway analysis revealed the following observations. (1) Among the differentially expressed genes (DEGs) of TF and SF tissues, the downregulation of <i>ACADL</i>, <i>ACSL6</i>, and <i>NC_056060.1.2536</i> was observed in SF, while <i>FFAR4</i> exhibited upregulation. (2) Among the DEGs of TF and VF tissues, expressions of <i>ACADL</i>, <i>ACSL6</i>, <i>COL1A1</i>, <i>COL1A2</i>, and <i>SCD</i> were downregulated in VF, with upregulation of <i>FFAR4</i>. (3) Among SF and VF expressions of <i>COL1A1</i>, <i>COL1A2,</i> and <i>NC_056060.1.2536</i> were downregulated in VF. Specific differentially expressed genes (<i>ACADL</i>, <i>ACSL6</i>, <i>COL1A1</i>, <i>COL1A2</i>, <i>FFAR4</i>, <i>NC_056060.1.2536</i>, and <i>SCD</i>) and transcripts (NC_056066.1.1866.16 and NC_056066.1.1866.22) were identified as relevant to fat metabolism. These results provide a dataset for further verification of the regulatory pathway associated with fat metabolism in sheep.https://www.mdpi.com/2076-2615/14/1/7adipose tissuefull-length transcriptomenew transcriptRNA sequencingsheep |
| spellingShingle | Lixia An Yangyang Pan Mengjiao Yuan Zhonghao Wen Liying Qiao Weiwei Wang Jianhua Liu Baojun Li Wenzhong Liu Full-Length Transcriptome and Gene Expression Analysis of Different <i>Ovis aries</i> Adipose Tissues Reveals Transcript Variants Involved in Lipid Biosynthesis Animals adipose tissue full-length transcriptome new transcript RNA sequencing sheep |
| title | Full-Length Transcriptome and Gene Expression Analysis of Different <i>Ovis aries</i> Adipose Tissues Reveals Transcript Variants Involved in Lipid Biosynthesis |
| title_full | Full-Length Transcriptome and Gene Expression Analysis of Different <i>Ovis aries</i> Adipose Tissues Reveals Transcript Variants Involved in Lipid Biosynthesis |
| title_fullStr | Full-Length Transcriptome and Gene Expression Analysis of Different <i>Ovis aries</i> Adipose Tissues Reveals Transcript Variants Involved in Lipid Biosynthesis |
| title_full_unstemmed | Full-Length Transcriptome and Gene Expression Analysis of Different <i>Ovis aries</i> Adipose Tissues Reveals Transcript Variants Involved in Lipid Biosynthesis |
| title_short | Full-Length Transcriptome and Gene Expression Analysis of Different <i>Ovis aries</i> Adipose Tissues Reveals Transcript Variants Involved in Lipid Biosynthesis |
| title_sort | full length transcriptome and gene expression analysis of different i ovis aries i adipose tissues reveals transcript variants involved in lipid biosynthesis |
| topic | adipose tissue full-length transcriptome new transcript RNA sequencing sheep |
| url | https://www.mdpi.com/2076-2615/14/1/7 |
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