The HTIRDB: A resource containing a transcriptional atlas for 105 different tissues from each of seven species of domestic herbivore.
Abstract: Here, we describe the Herbivore Transcriptome Integrated Resource Database (HTIRDB, https://yanglab.hzau.edu.cn/HTIRDB#/). The HTIRDB comprises the self-generated transcriptomic data from 100 to 105 tissues from two female domestic herbivores from six species (cattle, donkey, goat, horse, rabbit, and sika deer) and two breeds of sheep, and an extra 28,710 related published datasets. The HTIRDB user-friendly interface provides tools and functionalities that facilitate the exploration of gene expression between tissues and species. The tools for comparative transcriptomics can be used to identify housekeeping genes, tissue-specific genes, species-specific genes, and species-conserved genes. To date, the HTIRDB is the most extensive transcriptome data resource for domestic herbivores that is freely available.
© 2025 The Author(s). iMeta published by John Wiley & Sons Australia, Ltd on behalf of iMeta Science.
Publication Date: 2025-01-28 PubMed ID: 40027488PubMed Central: PMC11865344DOI: 10.1002/imt2.267Google Scholar: Lookup
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Summary
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The research introduces the Herbivore Transcriptome Integrated Resource Database (HTIRDB), an extensive database with gene expression data from multiple tissues across seven domestic herbivore species.
Overview of the Herbivore Transcriptome Integrated Resource Database
- The HTIRDB is a comprehensive resource that holds transcriptomic data for various tissues from seven domestic herbivore species. The species include cattle, donkey, goat, horse, rabbit, sika deer, and two breeds of sheep.
- The researchers gathered data from 100 to 105 tissues from two females of each species and combined it with an extra 28,710 related datasets sourced from published studies.
Database Interface and Functionality
- The HTIRDB has a user-friendly interface that provides tools for exploring gene expression across different tissues and species.
- Users can employ comparative transcriptomics tools to identify housekeeping genes (genes that are necessary for the maintenance of basic cellular functions and are expressed in all cells), tissue-specific genes, species-specific genes, and species-conserved genes (genes that remain unchanged across different species).
Significance of the HTIRDB
- At the time of the study, the HTIRDB was the most extensive transcriptome data resource freely available for domestic herbivores.
- The database is not only useful for study in domestic herbivore genetics but also serves as a comparative resource for those studying gene expression in other animals or humans.
- Given the importance of these species in agriculture, the database can also aid in agricultural research and improve understanding of genetic expression, diseases, and the breeding of these animals.
Cite This Article
APA
Ding L, Wang Y, Zhang L, Luo C, Wu F, Huang Y, Zhen Y, Chen N, Wang L, Song L, Pool K, Blache D, Maloney SK, Liu D, Yang Z, Huang X, Li C, Yu X, Zhang Z, Chen Y, Xue C, Gu Y, Huang W, Yan L, Wei W, Wang Y, Zhang J, Zhang Y, Sun Y, Dai R, Wang S, Zhao X, Wang H, Zhou P, Yang QY, Wang M.
(2025).
The HTIRDB: A resource containing a transcriptional atlas for 105 different tissues from each of seven species of domestic herbivore.
Imeta, 4(1), e267.
https://doi.org/10.1002/imt2.267 Publication
Researcher Affiliations
- Laboratory of Metabolic Manipulation of Herbivorous Animal Nutrition, College of Animal Science and Technology Yangzhou University Yangzhou China.
- Laboratory of Metabolic Manipulation of Herbivorous Animal Nutrition, College of Animal Science and Technology Yangzhou University Yangzhou China.
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production Xinjiang Academy of Agricultural Reclamation Sciences Shihezi China.
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production Xinjiang Academy of Agricultural Reclamation Sciences Shihezi China.
- Key Laboratory of Smart Farming for Agricultural Animals, Engineering Technology Research Center of Agricultural Big Data, College of Informatics Huazhong Agricultural University Wuhan China.
- Key Laboratory of Smart Farming for Agricultural Animals, Engineering Technology Research Center of Agricultural Big Data, College of Informatics Huazhong Agricultural University Wuhan China.
- Laboratory of Metabolic Manipulation of Herbivorous Animal Nutrition, College of Animal Science and Technology Yangzhou University Yangzhou China.
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production Xinjiang Academy of Agricultural Reclamation Sciences Shihezi China.
- Key Laboratory of Smart Farming for Agricultural Animals, Engineering Technology Research Center of Agricultural Big Data, College of Informatics Huazhong Agricultural University Wuhan China.
- Laboratory of Metabolic Manipulation of Herbivorous Animal Nutrition, College of Animal Science and Technology Yangzhou University Yangzhou China.
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production Xinjiang Academy of Agricultural Reclamation Sciences Shihezi China.
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production Xinjiang Academy of Agricultural Reclamation Sciences Shihezi China.
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production Xinjiang Academy of Agricultural Reclamation Sciences Shihezi China.
- College of Life Science Guizhou University Guiyang China.
- UWA Institute of Agriculture The University of Western Australia Perth Western Australia Australia.
- Laboratory of Metabolic Manipulation of Herbivorous Animal Nutrition, College of Animal Science and Technology Yangzhou University Yangzhou China.
- UWA Institute of Agriculture The University of Western Australia Perth Western Australia Australia.
- UWA Institute of Agriculture The University of Western Australia Perth Western Australia Australia.
- Key Laboratory of Smart Farming for Agricultural Animals, Engineering Technology Research Center of Agricultural Big Data, College of Informatics Huazhong Agricultural University Wuhan China.
- Key Laboratory of Smart Farming for Agricultural Animals, Engineering Technology Research Center of Agricultural Big Data, College of Informatics Huazhong Agricultural University Wuhan China.
- Key Laboratory of Smart Farming for Agricultural Animals, Engineering Technology Research Center of Agricultural Big Data, College of Informatics Huazhong Agricultural University Wuhan China.
- Laboratory of Metabolic Manipulation of Herbivorous Animal Nutrition, College of Animal Science and Technology Yangzhou University Yangzhou China.
- Laboratory of Metabolic Manipulation of Herbivorous Animal Nutrition, College of Animal Science and Technology Yangzhou University Yangzhou China.
- Laboratory of Metabolic Manipulation of Herbivorous Animal Nutrition, College of Animal Science and Technology Yangzhou University Yangzhou China.
- Laboratory of Metabolic Manipulation of Herbivorous Animal Nutrition, College of Animal Science and Technology Yangzhou University Yangzhou China.
- Laboratory of Metabolic Manipulation of Herbivorous Animal Nutrition, College of Animal Science and Technology Yangzhou University Yangzhou China.
- Laboratory of Metabolic Manipulation of Herbivorous Animal Nutrition, College of Animal Science and Technology Yangzhou University Yangzhou China.
- Laboratory of Metabolic Manipulation of Herbivorous Animal Nutrition, College of Animal Science and Technology Yangzhou University Yangzhou China.
- Laboratory of Metabolic Manipulation of Herbivorous Animal Nutrition, College of Animal Science and Technology Yangzhou University Yangzhou China.
- Laboratory of Metabolic Manipulation of Herbivorous Animal Nutrition, College of Animal Science and Technology Yangzhou University Yangzhou China.
- Laboratory of Metabolic Manipulation of Herbivorous Animal Nutrition, College of Animal Science and Technology Yangzhou University Yangzhou China.
- Laboratory of Metabolic Manipulation of Herbivorous Animal Nutrition, College of Animal Science and Technology Yangzhou University Yangzhou China.
- Laboratory of Metabolic Manipulation of Herbivorous Animal Nutrition, College of Animal Science and Technology Yangzhou University Yangzhou China.
- Laboratory of Metabolic Manipulation of Herbivorous Animal Nutrition, College of Animal Science and Technology Yangzhou University Yangzhou China.
- Key Laboratory of Smart Farming for Agricultural Animals, Engineering Technology Research Center of Agricultural Big Data, College of Informatics Huazhong Agricultural University Wuhan China.
- Key Laboratory of Smart Farming for Agricultural Animals, Engineering Technology Research Center of Agricultural Big Data, College of Informatics Huazhong Agricultural University Wuhan China.
- Key Laboratory of Smart Farming for Agricultural Animals, Engineering Technology Research Center of Agricultural Big Data, College of Informatics Huazhong Agricultural University Wuhan China.
- Key Laboratory of Smart Farming for Agricultural Animals, Engineering Technology Research Center of Agricultural Big Data, College of Informatics Huazhong Agricultural University Wuhan China.
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production Xinjiang Academy of Agricultural Reclamation Sciences Shihezi China.
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production Xinjiang Academy of Agricultural Reclamation Sciences Shihezi China.
- Key Laboratory of Smart Farming for Agricultural Animals, Engineering Technology Research Center of Agricultural Big Data, College of Informatics Huazhong Agricultural University Wuhan China.
- Laboratory of Metabolic Manipulation of Herbivorous Animal Nutrition, College of Animal Science and Technology Yangzhou University Yangzhou China.
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production Xinjiang Academy of Agricultural Reclamation Sciences Shihezi China.
Conflict of Interest Statement
The authors declare no conflicts of interest.
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