Transcriptome Atlas of 16 Donkey Tissues
Donkeys (Equus asinus) are important livestock with great economic value in meat, skin, and milk production. However, a lack of knowledge of the transcriptome landscape across a wide range of donkey tissues limits genetic selective breeding and conservation. Here we used transcriptomics to describe...
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2021-08-01
|
| Series: | Frontiers in Genetics |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2021.682734/full |
| _version_ | 1818916057288540160 |
|---|---|
| author | Yinan Wang Yinan Wang Xinyao Miao Xinyao Miao Zicheng Zhao Yonghui Wang Shuaicheng Li Changfa Wang |
| author_facet | Yinan Wang Yinan Wang Xinyao Miao Xinyao Miao Zicheng Zhao Yonghui Wang Shuaicheng Li Changfa Wang |
| author_sort | Yinan Wang |
| collection | DOAJ |
| description | Donkeys (Equus asinus) are important livestock with great economic value in meat, skin, and milk production. However, a lack of knowledge of the transcriptome landscape across a wide range of donkey tissues limits genetic selective breeding and conservation. Here we used transcriptomics to describe the transcriptome landscape, classify the tissue-specific gene expression across all primary donkey tissues, and present supplementary analyses on the protein level of additional donkey milk samples. Overall, 16,013 protein-coding genes and 21,983 transcripts were mapped to the reference genome, including 6,778 ubiquitously expressed genes and 2,601 tissue-enriched genes. Functional analysis revealed that the function of the tissue-enriched genes was highly tissue specific. Tissue-elevated genes that could be associated with unique phenotypes in donkey were analyzed. The results showed that, compared with those in human and other livestock, the lysozyme gene in donkey breast was specifically and highly expressed. The calcium-binding lysozyme, encoded by the lysozyme gene, was also detected in high amounts in donkey milk. Given those intact lysozyme genes that predict potentially functional calcium-binding lysozyme found in only a few species (e.g., donkey and horse), the high expression of the lysozyme gene in donkey breast may contribute to the high lysozyme content in donkey milk. Furthermore, 71% of the proteins in donkey milk overlapped with human milk protein, higher than the overlapping rates of bovine, sheep, and swine with humans. The donkey transcriptomic resource contributes to the available genomic resources to interpret the molecular mechanisms underlying phenotype traits. |
| first_indexed | 2024-12-20T00:12:07Z |
| format | Article |
| id | doaj.art-24ae396e8ce94186a2be770ab8b255df |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-12-20T00:12:07Z |
| publishDate | 2021-08-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-24ae396e8ce94186a2be770ab8b255df2022-12-21T20:00:28ZengFrontiers Media S.A.Frontiers in Genetics1664-80212021-08-011210.3389/fgene.2021.682734682734Transcriptome Atlas of 16 Donkey TissuesYinan Wang0Yinan Wang1Xinyao Miao2Xinyao Miao3Zicheng Zhao4Yonghui Wang5Shuaicheng Li6Changfa Wang7Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng, ChinaCollege of Forensic Medicine, Xi’an Jiaotong University, Xi’an, ChinaCollege of Forensic Medicine, Xi’an Jiaotong University, Xi’an, ChinaDepartment of Computer Science, City University of Hong Kong, Hong Kong, ChinaShenzhen Byoryn Technology Co., Ltd, Shenzhen, ChinaLiaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng, ChinaDepartment of Computer Science, City University of Hong Kong, Hong Kong, ChinaLiaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng, ChinaDonkeys (Equus asinus) are important livestock with great economic value in meat, skin, and milk production. However, a lack of knowledge of the transcriptome landscape across a wide range of donkey tissues limits genetic selective breeding and conservation. Here we used transcriptomics to describe the transcriptome landscape, classify the tissue-specific gene expression across all primary donkey tissues, and present supplementary analyses on the protein level of additional donkey milk samples. Overall, 16,013 protein-coding genes and 21,983 transcripts were mapped to the reference genome, including 6,778 ubiquitously expressed genes and 2,601 tissue-enriched genes. Functional analysis revealed that the function of the tissue-enriched genes was highly tissue specific. Tissue-elevated genes that could be associated with unique phenotypes in donkey were analyzed. The results showed that, compared with those in human and other livestock, the lysozyme gene in donkey breast was specifically and highly expressed. The calcium-binding lysozyme, encoded by the lysozyme gene, was also detected in high amounts in donkey milk. Given those intact lysozyme genes that predict potentially functional calcium-binding lysozyme found in only a few species (e.g., donkey and horse), the high expression of the lysozyme gene in donkey breast may contribute to the high lysozyme content in donkey milk. Furthermore, 71% of the proteins in donkey milk overlapped with human milk protein, higher than the overlapping rates of bovine, sheep, and swine with humans. The donkey transcriptomic resource contributes to the available genomic resources to interpret the molecular mechanisms underlying phenotype traits.https://www.frontiersin.org/articles/10.3389/fgene.2021.682734/fulldonkeyRNA sequencingproteomicsiBAQlysozyme |
| spellingShingle | Yinan Wang Yinan Wang Xinyao Miao Xinyao Miao Zicheng Zhao Yonghui Wang Shuaicheng Li Changfa Wang Transcriptome Atlas of 16 Donkey Tissues Frontiers in Genetics donkey RNA sequencing proteomics iBAQ lysozyme |
| title | Transcriptome Atlas of 16 Donkey Tissues |
| title_full | Transcriptome Atlas of 16 Donkey Tissues |
| title_fullStr | Transcriptome Atlas of 16 Donkey Tissues |
| title_full_unstemmed | Transcriptome Atlas of 16 Donkey Tissues |
| title_short | Transcriptome Atlas of 16 Donkey Tissues |
| title_sort | transcriptome atlas of 16 donkey tissues |
| topic | donkey RNA sequencing proteomics iBAQ lysozyme |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2021.682734/full |
| work_keys_str_mv | AT yinanwang transcriptomeatlasof16donkeytissues AT yinanwang transcriptomeatlasof16donkeytissues AT xinyaomiao transcriptomeatlasof16donkeytissues AT xinyaomiao transcriptomeatlasof16donkeytissues AT zichengzhao transcriptomeatlasof16donkeytissues AT yonghuiwang transcriptomeatlasof16donkeytissues AT shuaichengli transcriptomeatlasof16donkeytissues AT changfawang transcriptomeatlasof16donkeytissues |