Academic Journal
Haplotype-resolved autotetraploid genome of Dioscorea nipponica provides insights into recent polyploidization, metabolic rewiring, and environmental adaptation.
| Τίτλος: | Haplotype-resolved autotetraploid genome of Dioscorea nipponica provides insights into recent polyploidization, metabolic rewiring, and environmental adaptation. |
|---|---|
| Συγγραφείς: | Li SS; Jiangsu Provincial Key Laboratory for Plant Taxonomy, Resource Conservation and Utilization, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China., Sun XQ; Jiangsu Provincial Key Laboratory for Plant Taxonomy, Resource Conservation and Utilization, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China., Feng Y; Key Laboratory of Mountain Ecological Rehabilitation and Biological Resource Utilization, Chengdu Institute of Biology, Chinese Academy of Sciences (CAS), Chengdu, 610041, China., Hu K; Jiangsu Provincial Key Laboratory for Plant Taxonomy, Resource Conservation and Utilization, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China., Li P; College of Life Sciences, Zhejiang University, Hangzhou, 310058, China., Liu Y; Jiangsu Provincial Key Laboratory for Plant Taxonomy, Resource Conservation and Utilization, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China., Gu JH; Jiangsu Provincial Key Laboratory for Plant Taxonomy, Resource Conservation and Utilization, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China., Chen M; Jiangsu Provincial Key Laboratory for Plant Taxonomy, Resource Conservation and Utilization, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China., Lu RS; Jiangsu Provincial Key Laboratory for Plant Taxonomy, Resource Conservation and Utilization, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China. |
| Πηγή: | The Plant journal : for cell and molecular biology [Plant J] 2026 Sep; Vol. 127 (6), pp. e71153. |
| Τύπος έκδοσης: | Journal Article |
| Γλώσσα: | English |
| Στοιχεία περιοδικού: | Publisher: Blackwell Scientific Publishers and BIOS Scientific Publishers in association with the Society for Experimental Biology Country of Publication: England NLM ID: 9207397 Publication Model: Print Cited Medium: Internet ISSN: 1365-313X (Electronic) Linking ISSN: 09607412 NLM ISO Abbreviation: Plant J Subsets: MEDLINE |
| Imprint Name(s): | Original Publication: Oxford : Blackwell Scientific Publishers and BIOS Scientific Publishers in association with the Society for Experimental Biology, c1991- |
| Ιατρικοί όροι (MeSH): | Dioscorea*/genetics , Dioscorea*/metabolism , Dioscorea*/physiology , Genome, Plant*/genetics, Haplotypes/genetics ; Adaptation, Physiological/genetics ; Tetraploidy ; Polyploidy |
| Περίληψη: | Whole-genome duplication (WGD, or polyploidization) is a major evolutionary force in plants, yet the genomic, transcriptional, and metabolic consequences of autopolyploidy remain less understood than those of allopolyploidy. Dioscorea nipponica, a medicinal species producing diosgenin-type steroidal saponins, harbors both diploid and autopolyploid populations, providing a unique system to investigate these processes. Here, we present a haplotype-resolved, chromosome-scale genome assembly of autotetraploid D. nipponica (2n = 4x = 40). Comparative and population genomic analyses indicate a single, recent autotetraploid origin (<1.63 Ma), after the divergence of its diploid ancestors (~2.5-2.9 Ma), coinciding with Pliocene-Pleistocene climatic shifts that may have promoted population isolation and genome duplication. The four haplotypes exhibit high average nucleotide identity, extensive synteny and similar global gene expression, with pervasive allele loss (~32% of genes) and widespread allelic transcriptional suppression (~60% of expressed tetrads), together buffering dosage effects. Metabolomic profiling reveals a metabolic trade-off in rhizomes, with autotetraploids accumulating higher flavonoids but lower diosgenin-type steroidal saponins than diploids, potentially enhancing reproductive fitness and adaptation to marginal environments. This shift is supported by expanded flavonoid gene families (e.g., PAL, CHS), some exhibiting positive dosage effects, whereas diosgenin pathway genes (e.g., CYP90, CYP94) remain copy number stable and mostly show negative dosage effects in autotetraploids. Selective sweep analysis further identified genes linked to genome stability (e.g., AtTOP3α, AtDMC1) and abiotic stress response, crucial for polyploid establishment. Overall, these findings offer novel insights into how autopolyploidy shapes gene expression, metabolic evolution, and ecological adaptation, with implications for the conservation and utilization of this medicinally important species. (© 2026 The Author(s). The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd.) |
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| Grant Information: | 32570444 National Natural Science Foundation of China; 32671990 National Natural Science Foundation of China; 32200192 National Natural Science Foundation of China; JSPKLB202401 Open Fund of the Jiangsu Provincial Key Laboratory for Plant Taxonomy, Resource Conservation and Utilization; JSTJ-2025-004 Jiangsu Provincial Science and Technology Association Youth Talent Support Project |
| Contributed Indexing: | Keywords: Dioscorea nipponica; autopolyploidy; haplotype‐resolved genome; metabolic trade‐off; population genomics |
| Entry Date(s): | Date Created: 20260928 Date Completed: 20260928 Latest Revision: 20260930 |
| Update Code: | 20260930 |
| PubMed Central ID: | PMC13618807 |
| DOI: | 10.1111/tpj.71153 |
| PMID: | 42804372 |
| Βάση Δεδομένων: | MEDLINE |
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| Items | – Name: Title Label: Title Group: Ti Data: Haplotype-resolved autotetraploid genome of Dioscorea nipponica provides insights into recent polyploidization, metabolic rewiring, and environmental adaptation. – Name: Author Label: Authors Group: Au Data: <searchLink fieldCode="AU" term="%22Li+SS%22">Li SS</searchLink>; Jiangsu Provincial Key Laboratory for Plant Taxonomy, Resource Conservation and Utilization, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China.<br /><searchLink fieldCode="AU" term="%22Sun+XQ%22">Sun XQ</searchLink>; Jiangsu Provincial Key Laboratory for Plant Taxonomy, Resource Conservation and Utilization, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China.<br /><searchLink fieldCode="AU" term="%22Feng+Y%22">Feng Y</searchLink>; Key Laboratory of Mountain Ecological Rehabilitation and Biological Resource Utilization, Chengdu Institute of Biology, Chinese Academy of Sciences (CAS), Chengdu, 610041, China.<br /><searchLink fieldCode="AU" term="%22Hu+K%22">Hu K</searchLink>; Jiangsu Provincial Key Laboratory for Plant Taxonomy, Resource Conservation and Utilization, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China.<br /><searchLink fieldCode="AU" term="%22Li+P%22">Li P</searchLink>; College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.<br /><searchLink fieldCode="AU" term="%22Liu+Y%22">Liu Y</searchLink>; Jiangsu Provincial Key Laboratory for Plant Taxonomy, Resource Conservation and Utilization, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China.<br /><searchLink fieldCode="AU" term="%22Gu+JH%22">Gu JH</searchLink>; Jiangsu Provincial Key Laboratory for Plant Taxonomy, Resource Conservation and Utilization, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China.<br /><searchLink fieldCode="AU" term="%22Chen+M%22">Chen M</searchLink>; Jiangsu Provincial Key Laboratory for Plant Taxonomy, Resource Conservation and Utilization, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China.<br /><searchLink fieldCode="AU" term="%22Lu+RS%22">Lu RS</searchLink>; Jiangsu Provincial Key Laboratory for Plant Taxonomy, Resource Conservation and Utilization, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China. – Name: TitleSource Label: Source Group: Src Data: <searchLink fieldCode="JN" term="%229207397%22">The Plant journal : for cell and molecular biology</searchLink> [Plant J] 2026 Sep; Vol. 127 (6), pp. e71153. – Name: TypePub Label: Publication Type Group: TypPub Data: Journal Article – Name: Language Label: Language Group: Lang Data: English – Name: TitleSource Label: Journal Info Group: Src Data: <i>Publisher: </i><searchLink fieldCode="PB" term="%22Blackwell+Scientific+Publishers+and+BIOS+Scientific+Publishers+in+association+with+the+Society+for+Experimental+Biology%22">Blackwell Scientific Publishers and BIOS Scientific Publishers in association with the Society for Experimental Biology </searchLink><i>Country of Publication: </i>England <i>NLM ID: </i>9207397 <i>Publication Model: </i>Print <i>Cited Medium: </i>Internet <i>ISSN: </i>1365-313X (Electronic) <i>Linking ISSN: </i><searchLink fieldCode="IS" term="%2209607412%22">09607412 </searchLink><i>NLM ISO Abbreviation: </i>Plant J <i>Subsets: </i>MEDLINE – Name: PublisherInfo Label: Imprint Name(s) Group: PubInfo Data: <i>Original Publication</i>: Oxford : Blackwell Scientific Publishers and BIOS Scientific Publishers in association with the Society for Experimental Biology, c1991- – Name: SubjectMESH Label: MeSH Terms Group: Su Data: <searchLink fieldCode="MM" term="%22Dioscorea%22">Dioscorea*</searchLink>/<searchLink fieldCode="MM" term="%22Dioscorea+genetics%22">genetics</searchLink> <br /><searchLink fieldCode="MM" term="%22Dioscorea%22">Dioscorea*</searchLink>/<searchLink fieldCode="MM" term="%22Dioscorea+metabolism%22">metabolism</searchLink> <br /><searchLink fieldCode="MM" term="%22Dioscorea%22">Dioscorea*</searchLink>/<searchLink fieldCode="MM" term="%22Dioscorea+physiology%22">physiology</searchLink> <br /><searchLink fieldCode="MM" term="%22Genome%2C+Plant%22">Genome, Plant*</searchLink>/<searchLink fieldCode="MM" term="%22Genome%2C+Plant+genetics%22">genetics</searchLink><br /><searchLink fieldCode="MH" term="%22Haplotypes%22">Haplotypes</searchLink>/<searchLink fieldCode="MH" term="%22Haplotypes+genetics%22">genetics</searchLink> ; <searchLink fieldCode="MH" term="%22Adaptation%2C+Physiological%22">Adaptation, Physiological</searchLink>/<searchLink fieldCode="MH" term="%22Adaptation%2C+Physiological+genetics%22">genetics</searchLink> ; <searchLink fieldCode="MH" term="%22Tetraploidy%22">Tetraploidy</searchLink> ; <searchLink fieldCode="MH" term="%22Polyploidy%22">Polyploidy</searchLink> – Name: Abstract Label: Abstract Group: Ab Data: Whole-genome duplication (WGD, or polyploidization) is a major evolutionary force in plants, yet the genomic, transcriptional, and metabolic consequences of autopolyploidy remain less understood than those of allopolyploidy. Dioscorea nipponica, a medicinal species producing diosgenin-type steroidal saponins, harbors both diploid and autopolyploid populations, providing a unique system to investigate these processes. Here, we present a haplotype-resolved, chromosome-scale genome assembly of autotetraploid D. nipponica (2n = 4x = 40). Comparative and population genomic analyses indicate a single, recent autotetraploid origin (&lt;1.63 Ma), after the divergence of its diploid ancestors (~2.5-2.9 Ma), coinciding with Pliocene-Pleistocene climatic shifts that may have promoted population isolation and genome duplication. The four haplotypes exhibit high average nucleotide identity, extensive synteny and similar global gene expression, with pervasive allele loss (~32% of genes) and widespread allelic transcriptional suppression (~60% of expressed tetrads), together buffering dosage effects. Metabolomic profiling reveals a metabolic trade-off in rhizomes, with autotetraploids accumulating higher flavonoids but lower diosgenin-type steroidal saponins than diploids, potentially enhancing reproductive fitness and adaptation to marginal environments. This shift is supported by expanded flavonoid gene families (e.g., PAL, CHS), some exhibiting positive dosage effects, whereas diosgenin pathway genes (e.g., CYP90, CYP94) remain copy number stable and mostly show negative dosage effects in autotetraploids. Selective sweep analysis further identified genes linked to genome stability (e.g., AtTOP3α, AtDMC1) and abiotic stress response, crucial for polyploid establishment. Overall, these findings offer novel insights into how autopolyploidy shapes gene expression, metabolic evolution, and ecological adaptation, with implications for the conservation and utilization of this medicinally important species.<br /> (© 2026 The Author(s). 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(PMID: <searchLink fieldCode="PM" term="%2226744215%22">26744215)</searchLink> – Name: GrantInfo Label: Grant Information Group: Grant Data: 32570444 National Natural Science Foundation of China; 32671990 National Natural Science Foundation of China; 32200192 National Natural Science Foundation of China; JSPKLB202401 Open Fund of the Jiangsu Provincial Key Laboratory for Plant Taxonomy, Resource Conservation and Utilization; JSTJ-2025-004 Jiangsu Provincial Science and Technology Association Youth Talent Support Project – Name: SubjectMinor Label: Contributed Indexing Group: Data: <i>Keywords: </i>Dioscorea nipponica; autopolyploidy; haplotype‐resolved genome; metabolic trade‐off; population genomics – Name: DateEntry Label: Entry Date(s) Group: Date Data: <i>Date Created: </i>20260928 <i>Date Completed: </i>20260928 <i>Latest Revision: </i>20260930 – Name: DateUpdate Label: Update Code Group: Date Data: 20260930 – Name: PubmedCentralID Label: PubMed Central ID Group: ID Data: PMC13618807 – Name: DOI Label: DOI Group: ID Data: 10.1111/tpj.71153 – Name: AN Label: PMID Group: ID Data: 42804372 |
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| RecordInfo | BibRecord: BibEntity: Identifiers: – Type: doi Value: 10.1111/tpj.71153 Languages: – Code: eng Text: English PhysicalDescription: Pagination: StartPage: e71153 Subjects: – SubjectFull: Haplotypes genetics Type: general – SubjectFull: Adaptation, Physiological genetics Type: general – SubjectFull: Tetraploidy Type: general – SubjectFull: Polyploidy Type: general – SubjectFull: Dioscorea genetics Type: general – SubjectFull: Dioscorea metabolism Type: general – SubjectFull: Dioscorea physiology Type: general – SubjectFull: Genome, Plant genetics Type: general Titles: – TitleFull: Haplotype-resolved autotetraploid genome of Dioscorea nipponica provides insights into recent polyploidization, metabolic rewiring, and environmental adaptation. Type: main BibRelationships: HasContributorRelationships: – PersonEntity: Name: NameFull: Li SS – PersonEntity: Name: NameFull: Sun XQ – PersonEntity: Name: NameFull: Feng Y – PersonEntity: Name: NameFull: Hu K – PersonEntity: Name: NameFull: Li P – PersonEntity: Name: NameFull: Liu Y – PersonEntity: Name: NameFull: Gu JH – PersonEntity: Name: NameFull: Chen M – PersonEntity: Name: NameFull: Lu RS IsPartOfRelationships: – BibEntity: Dates: – D: 01 M: 09 Text: 2026 Sep Type: published Y: 2026 Identifiers: – Type: issn-electronic Value: 1365-313X Numbering: – Type: volume Value: 127 – Type: issue Value: 6 Titles: – TitleFull: The Plant journal : for cell and molecular biology Type: main |
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