IGTCM: An integrative genome database of traditional Chinese medicine plants
Abstract Fully understanding traditional Chinese medicines (TCMs) is still challenging because of the extreme complexity of their chemical components and mechanisms of action. The TCM Plant Genome Project aimed to obtain genetic information, determine gene functions, discover regulatory networks of...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Wiley
2023-06-01
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| Series: | The Plant Genome |
| Online Access: | https://doi.org/10.1002/tpg2.20317 |
| _version_ | 1797800539689320448 |
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| author | Yuan‐Nong Ye Ding‐Fa Liang Jia‐Hao Yi Shuai Jin Zhu Zeng |
| author_facet | Yuan‐Nong Ye Ding‐Fa Liang Jia‐Hao Yi Shuai Jin Zhu Zeng |
| author_sort | Yuan‐Nong Ye |
| collection | DOAJ |
| description | Abstract Fully understanding traditional Chinese medicines (TCMs) is still challenging because of the extreme complexity of their chemical components and mechanisms of action. The TCM Plant Genome Project aimed to obtain genetic information, determine gene functions, discover regulatory networks of herbal species, and elucidate the molecular mechanisms involved in the disease prevention and treatment, thereby accelerating the modernization of TCMs. A comprehensive database that contains TCM‐related information will provide a vital resource. Here, we present an integrative genome database of TCM plants (IGTCM) that contains 14,711,220 records of 83 annotated TCM‐related herb genomes, including 3,610,350 genes, 3,534,314 proteins and corresponding coding sequences, and 4,032,242 RNAs, as well as 1033 non‐redundant component records for 68 herbs, downloaded and integrated from the GenBank and RefSeq databases. For minimal interconnectivity, each gene, protein, and component was annotated using the eggNOG‐mapper tool and Kyoto Encyclopedia of Genes and Genomes database to acquire pathway information and enzyme classifications. These features can be linked across several species and different components. The IGTCM database also provides visualization and sequence similarity search tools for data analyses. These annotated herb genome sequences in IGTCM database are a necessary resource for systematically exploring genes related to the biosynthesis of compounds that have significant medicinal activities and excellent agronomic traits that can be used to improve TCM‐related varieties through molecular breeding. It also provides valuable data and tools for future research on drug discovery and the protection and rational use of TCM plant resources. The IGTCM database is freely available at http://yeyn.group:96/. |
| first_indexed | 2024-03-13T04:36:48Z |
| format | Article |
| id | doaj.art-f1c2d752f91a4778a8c6e6ad1cc0a553 |
| institution | Directory Open Access Journal |
| issn | 1940-3372 |
| language | English |
| last_indexed | 2024-03-13T04:36:48Z |
| publishDate | 2023-06-01 |
| publisher | Wiley |
| record_format | Article |
| series | The Plant Genome |
| spelling | doaj.art-f1c2d752f91a4778a8c6e6ad1cc0a5532023-06-19T06:48:03ZengWileyThe Plant Genome1940-33722023-06-01162n/an/a10.1002/tpg2.20317IGTCM: An integrative genome database of traditional Chinese medicine plantsYuan‐Nong Ye0Ding‐Fa Liang1Jia‐Hao Yi2Shuai Jin3Zhu Zeng4Cells and Antibody Engineering Research Center of Guizhou Province Key Laboratory of Biology and Medical Engineering School of Biology and Engineering Guizhou Medical University Guiyang ChinaCells and Antibody Engineering Research Center of Guizhou Province Key Laboratory of Biology and Medical Engineering School of Biology and Engineering Guizhou Medical University Guiyang ChinaBioinformatics and Biomedical Big Data Mining Laboratory Department of Medical Informatics School of Big Health Guizhou Medical University Guiyang ChinaBioinformatics and Biomedical Big Data Mining Laboratory Department of Medical Informatics School of Big Health Guizhou Medical University Guiyang ChinaCells and Antibody Engineering Research Center of Guizhou Province Key Laboratory of Biology and Medical Engineering School of Biology and Engineering Guizhou Medical University Guiyang ChinaAbstract Fully understanding traditional Chinese medicines (TCMs) is still challenging because of the extreme complexity of their chemical components and mechanisms of action. The TCM Plant Genome Project aimed to obtain genetic information, determine gene functions, discover regulatory networks of herbal species, and elucidate the molecular mechanisms involved in the disease prevention and treatment, thereby accelerating the modernization of TCMs. A comprehensive database that contains TCM‐related information will provide a vital resource. Here, we present an integrative genome database of TCM plants (IGTCM) that contains 14,711,220 records of 83 annotated TCM‐related herb genomes, including 3,610,350 genes, 3,534,314 proteins and corresponding coding sequences, and 4,032,242 RNAs, as well as 1033 non‐redundant component records for 68 herbs, downloaded and integrated from the GenBank and RefSeq databases. For minimal interconnectivity, each gene, protein, and component was annotated using the eggNOG‐mapper tool and Kyoto Encyclopedia of Genes and Genomes database to acquire pathway information and enzyme classifications. These features can be linked across several species and different components. The IGTCM database also provides visualization and sequence similarity search tools for data analyses. These annotated herb genome sequences in IGTCM database are a necessary resource for systematically exploring genes related to the biosynthesis of compounds that have significant medicinal activities and excellent agronomic traits that can be used to improve TCM‐related varieties through molecular breeding. It also provides valuable data and tools for future research on drug discovery and the protection and rational use of TCM plant resources. The IGTCM database is freely available at http://yeyn.group:96/.https://doi.org/10.1002/tpg2.20317 |
| spellingShingle | Yuan‐Nong Ye Ding‐Fa Liang Jia‐Hao Yi Shuai Jin Zhu Zeng IGTCM: An integrative genome database of traditional Chinese medicine plants The Plant Genome |
| title | IGTCM: An integrative genome database of traditional Chinese medicine plants |
| title_full | IGTCM: An integrative genome database of traditional Chinese medicine plants |
| title_fullStr | IGTCM: An integrative genome database of traditional Chinese medicine plants |
| title_full_unstemmed | IGTCM: An integrative genome database of traditional Chinese medicine plants |
| title_short | IGTCM: An integrative genome database of traditional Chinese medicine plants |
| title_sort | igtcm an integrative genome database of traditional chinese medicine plants |
| url | https://doi.org/10.1002/tpg2.20317 |
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