Intraspecific phylogeny and genomic resources development for an important medical plant Dioscorea nipponica, based on low-coverage whole genome sequencing data
Dioscorea nipponica Makino, a perennial twining herb with medicinal importance, has a disjunctive distribution in the Sino-Japanese Floristic Region. It has a long history in traditional Chinese medicine, with demonstrated efficacy against various health conditions. However, the limited genomic data...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2023-12-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2023.1320473/full |
| _version_ | 1827586572752519168 |
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| author | Ke Hu Min Chen Min Chen Pan Li Xiaoqin Sun Xiaoqin Sun Xiaoqin Sun Ruisen Lu Ruisen Lu |
| author_facet | Ke Hu Min Chen Min Chen Pan Li Xiaoqin Sun Xiaoqin Sun Xiaoqin Sun Ruisen Lu Ruisen Lu |
| author_sort | Ke Hu |
| collection | DOAJ |
| description | Dioscorea nipponica Makino, a perennial twining herb with medicinal importance, has a disjunctive distribution in the Sino-Japanese Floristic Region. It has a long history in traditional Chinese medicine, with demonstrated efficacy against various health conditions. However, the limited genomic data and knowledge of genetic variation have hindered its comprehensive exploration, utilization and conservation. In this study, we undertook low-coverage whole genome sequencing of diverse D. nipponica accessions to develop both plastome (including whole plastome sequences, plastome-derived SSRs and plastome-divergent hotspots) and nuclear genomic resources (including polymorphic nuclear SSRs and single-copy nuclear genes), as well as elucidate the intraspecific phylogeny of this species. Our research revealed 639 plastome-derived SSRs and highlighted six key mutational hotspots (namely CDS ycf1, IGS trnL-rpl32, IGS trnE-trnT, IGS rps16-trnQ, Intron 1 of clpP, and Intron trnG) within these accessions. Besides, three IGS regions (i.e., ndhD-cssA, trnL-rpl32, trnD-trnY), and the intron rps16 were identified as potential markers for distinguishing D. nipponica from its closely related species. In parallel, we successfully developed 988 high-quality candidate polymorphic nuclear SSRs and identified 17 single-copy nuclear genes for D. nipponica, all of which empower us to conduct in-depth investigations into phylogenetics and population genetics of this species. Although our phylogenetic analyses, based on plastome sequences and single-copy nuclear genes revealed cytonuclear discordance within D. nipponica, both findings challenged the current subspecies classification. In summary, this study developed a wealth of genomic resources for D. nipponica and enhanced our understanding of the intraspecific phylogeny of this species, offering valuable insights that can be instrumental in the conservation and strategic utilization of this economically significant plant. |
| first_indexed | 2024-03-09T00:03:32Z |
| format | Article |
| id | doaj.art-f44d558c714d4613a00783e078937b40 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-03-09T00:03:32Z |
| publishDate | 2023-12-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Plant Science |
| spelling | doaj.art-f44d558c714d4613a00783e078937b402023-12-12T14:40:48ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2023-12-011410.3389/fpls.2023.13204731320473Intraspecific phylogeny and genomic resources development for an important medical plant Dioscorea nipponica, based on low-coverage whole genome sequencing dataKe Hu0Min Chen1Min Chen2Pan Li3Xiaoqin Sun4Xiaoqin Sun5Xiaoqin Sun6Ruisen Lu7Ruisen Lu8Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, ChinaInstitute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, ChinaJiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing, ChinaLaboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, ChinaInstitute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, ChinaJiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing, ChinaJiangsu Provincial Science and Technology Resources Coordination Platform (Agricultural Germplasm Resources) Germplasm Resources Nursery of Medicinal Plants, Nanjing, ChinaInstitute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, ChinaJiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing, ChinaDioscorea nipponica Makino, a perennial twining herb with medicinal importance, has a disjunctive distribution in the Sino-Japanese Floristic Region. It has a long history in traditional Chinese medicine, with demonstrated efficacy against various health conditions. However, the limited genomic data and knowledge of genetic variation have hindered its comprehensive exploration, utilization and conservation. In this study, we undertook low-coverage whole genome sequencing of diverse D. nipponica accessions to develop both plastome (including whole plastome sequences, plastome-derived SSRs and plastome-divergent hotspots) and nuclear genomic resources (including polymorphic nuclear SSRs and single-copy nuclear genes), as well as elucidate the intraspecific phylogeny of this species. Our research revealed 639 plastome-derived SSRs and highlighted six key mutational hotspots (namely CDS ycf1, IGS trnL-rpl32, IGS trnE-trnT, IGS rps16-trnQ, Intron 1 of clpP, and Intron trnG) within these accessions. Besides, three IGS regions (i.e., ndhD-cssA, trnL-rpl32, trnD-trnY), and the intron rps16 were identified as potential markers for distinguishing D. nipponica from its closely related species. In parallel, we successfully developed 988 high-quality candidate polymorphic nuclear SSRs and identified 17 single-copy nuclear genes for D. nipponica, all of which empower us to conduct in-depth investigations into phylogenetics and population genetics of this species. Although our phylogenetic analyses, based on plastome sequences and single-copy nuclear genes revealed cytonuclear discordance within D. nipponica, both findings challenged the current subspecies classification. In summary, this study developed a wealth of genomic resources for D. nipponica and enhanced our understanding of the intraspecific phylogeny of this species, offering valuable insights that can be instrumental in the conservation and strategic utilization of this economically significant plant.https://www.frontiersin.org/articles/10.3389/fpls.2023.1320473/fullDioscorea nipponicaplastome-derived markerspolymorphic nSSRsSCNGsintraspecific phylogeny |
| spellingShingle | Ke Hu Min Chen Min Chen Pan Li Xiaoqin Sun Xiaoqin Sun Xiaoqin Sun Ruisen Lu Ruisen Lu Intraspecific phylogeny and genomic resources development for an important medical plant Dioscorea nipponica, based on low-coverage whole genome sequencing data Frontiers in Plant Science Dioscorea nipponica plastome-derived markers polymorphic nSSRs SCNGs intraspecific phylogeny |
| title | Intraspecific phylogeny and genomic resources development for an important medical plant Dioscorea nipponica, based on low-coverage whole genome sequencing data |
| title_full | Intraspecific phylogeny and genomic resources development for an important medical plant Dioscorea nipponica, based on low-coverage whole genome sequencing data |
| title_fullStr | Intraspecific phylogeny and genomic resources development for an important medical plant Dioscorea nipponica, based on low-coverage whole genome sequencing data |
| title_full_unstemmed | Intraspecific phylogeny and genomic resources development for an important medical plant Dioscorea nipponica, based on low-coverage whole genome sequencing data |
| title_short | Intraspecific phylogeny and genomic resources development for an important medical plant Dioscorea nipponica, based on low-coverage whole genome sequencing data |
| title_sort | intraspecific phylogeny and genomic resources development for an important medical plant dioscorea nipponica based on low coverage whole genome sequencing data |
| topic | Dioscorea nipponica plastome-derived markers polymorphic nSSRs SCNGs intraspecific phylogeny |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2023.1320473/full |
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