Application of third-generation sequencing to herbal genomics
There is a long history of traditional medicine use. However, little genetic information is available for the plants used in traditional medicine, which limits the exploitation of these natural resources. Third-generation sequencing (TGS) techniques have made it possible to gather invaluable genetic...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2023-03-01
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| Series: | Frontiers in Plant Science |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2023.1124536/full |
| _version_ | 1811159013124997120 |
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| author | Longlong Gao Wenjie Xu Tianyi Xin Jingyuan Song |
| author_facet | Longlong Gao Wenjie Xu Tianyi Xin Jingyuan Song |
| author_sort | Longlong Gao |
| collection | DOAJ |
| description | There is a long history of traditional medicine use. However, little genetic information is available for the plants used in traditional medicine, which limits the exploitation of these natural resources. Third-generation sequencing (TGS) techniques have made it possible to gather invaluable genetic information and develop herbal genomics. In this review, we introduce two main TGS techniques, PacBio SMRT technology and Oxford Nanopore technology, and compare the two techniques against Illumina, the predominant next-generation sequencing technique. In addition, we summarize the nuclear and organelle genome assemblies of commonly used medicinal plants, choose several examples from genomics, transcriptomics, and molecular identification studies to dissect the specific processes and summarize the advantages and disadvantages of the two TGS techniques when applied to medicinal organisms. Finally, we describe how we expect that TGS techniques will be widely utilized to assemble telomere-to-telomere (T2T) genomes and in epigenomics research involving medicinal plants. |
| first_indexed | 2024-04-10T05:33:58Z |
| format | Article |
| id | doaj.art-e3b57aeafa634520bd410bd7750a0641 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-04-10T05:33:58Z |
| publishDate | 2023-03-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-e3b57aeafa634520bd410bd7750a06412023-03-07T04:39:56ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2023-03-011410.3389/fpls.2023.11245361124536Application of third-generation sequencing to herbal genomicsLonglong GaoWenjie XuTianyi XinJingyuan SongThere is a long history of traditional medicine use. However, little genetic information is available for the plants used in traditional medicine, which limits the exploitation of these natural resources. Third-generation sequencing (TGS) techniques have made it possible to gather invaluable genetic information and develop herbal genomics. In this review, we introduce two main TGS techniques, PacBio SMRT technology and Oxford Nanopore technology, and compare the two techniques against Illumina, the predominant next-generation sequencing technique. In addition, we summarize the nuclear and organelle genome assemblies of commonly used medicinal plants, choose several examples from genomics, transcriptomics, and molecular identification studies to dissect the specific processes and summarize the advantages and disadvantages of the two TGS techniques when applied to medicinal organisms. Finally, we describe how we expect that TGS techniques will be widely utilized to assemble telomere-to-telomere (T2T) genomes and in epigenomics research involving medicinal plants.https://www.frontiersin.org/articles/10.3389/fpls.2023.1124536/fullthird-generation sequencingPacBionanoporeherbal genomicsmedicinal plantmolecular identification |
| spellingShingle | Longlong Gao Wenjie Xu Tianyi Xin Jingyuan Song Application of third-generation sequencing to herbal genomics Frontiers in Plant Science third-generation sequencing PacBio nanopore herbal genomics medicinal plant molecular identification |
| title | Application of third-generation sequencing to herbal genomics |
| title_full | Application of third-generation sequencing to herbal genomics |
| title_fullStr | Application of third-generation sequencing to herbal genomics |
| title_full_unstemmed | Application of third-generation sequencing to herbal genomics |
| title_short | Application of third-generation sequencing to herbal genomics |
| title_sort | application of third generation sequencing to herbal genomics |
| topic | third-generation sequencing PacBio nanopore herbal genomics medicinal plant molecular identification |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2023.1124536/full |
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