Academic Journal
Haplotype-resolved genome assembly of a male Dioscorea alata cultivar reveals the structure and evolution of young sex chromosomes.
| Τίτλος: | Haplotype-resolved genome assembly of a male Dioscorea alata cultivar reveals the structure and evolution of young sex chromosomes. |
|---|---|
| Συγγραφείς: | Dossa K; CIRAD, UMR AGAP Institut, 97170, Petit Bourg, Guadeloupe, France.; UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398, Montpellier, France., Su X; Wuhan Benagen Technology Company Limited, 430070, Wuhan, Hubei, China., Zoclanclounon YAB; Rothamsted Research, Harpenden, AL5 2JQ, UK., Chen Y; Wuhan Benagen Technology Company Limited, 430070, Wuhan, Hubei, China., Nawaz MA; Advanced Engineering School (Agrobiotek), National Research Tomsk State University, Lenin Ave, 36, 634050, Tomsk, Tomsk Oblast, Russia.; Laboratory for Research and Application of Supercritical Fluid Technologies in Agro-Food Biotechnology, National Research Tomsk State University, Lenin Ave, 36, 634050, Tomsk, Tomsk Oblast, Russia., Ni P; School of Computer Science and Engineering, Central South University, Changsha, 410083, China.; Hunan Provincial Key Lab on Bioinformatics, Central South University, Changsha, 410083, China., Qiu T; Wuhan Benagen Technology Company Limited, 430070, Wuhan, Hubei, China., Chen G; Wuhan Benagen Technology Company Limited, 430070, Wuhan, Hubei, China., Malédon E; CIRAD, UMR AGAP Institut, 97170, Petit Bourg, Guadeloupe, France.; UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398, Montpellier, France., Gravillon MC; CIRAD, UMR AGAP Institut, 97170, Petit Bourg, Guadeloupe, France.; UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398, Montpellier, France., Perrot C; CIRAD, UMR AGAP Institut, 97170, Petit Bourg, Guadeloupe, France.; UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398, Montpellier, France., Nudol E; CIRAD, UMR AGAP Institut, 97170, Petit Bourg, Guadeloupe, France.; UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398, Montpellier, France., Laurent L; CIRAD, UMR AGAP Institut, 97170, Petit Bourg, Guadeloupe, France.; UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398, Montpellier, France., Diouf M; Département de Mathématiques et Informatique, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, BP 5005, Dakar-Fann, Dakar, 10700, Senegal., Dobrev PI; Institute of Experimental Botany, Czech Academy of Sciences, Laboratory of hormonal regulations in plants, Rozvojova 263, 165 02, Prague 6, Czech Republic., Karikari B; Department of Agricultural Biotechnology, University for Development Studies, Nyankpala campus, Tamale, Ghana., Fouks B; UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398, Montpellier, France.; CIRAD, UMR AGAP Institut, F-34398, Montpellier, France., Arnau G; UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398, Montpellier, France.; CIRAD, UMR AGAP Institut, F-34398, Montpellier, France., Mournet P; UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398, Montpellier, France.; CIRAD, UMR AGAP Institut, F-34398, Montpellier, France., Wang J; School of Computer Science and Engineering, Central South University, Changsha, 410083, China.; Hunan Provincial Key Lab on Bioinformatics, Central South University, Changsha, 410083, China., Chaïr H; UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398, Montpellier, France.; CIRAD, UMR AGAP Institut, F-34398, Montpellier, France. |
| Πηγή: | The Plant journal : for cell and molecular biology [Plant J] 2026 Aug; Vol. 127 (4), pp. e71091. |
| 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): | Chromosomes, Plant*/genetics , Genome, Plant*/genetics , Dioscorea*/genetics , Haplotypes*/genetics , Sex Chromosomes*/genetics, Evolution, Molecular |
| Περίληψη: | Dioscorea alata L., the most widely cultivated yam species, exhibits dioecy (XY system) and a strong male-biased sex ratio. These two major constraints limit parental combinations and hinder breeding progress. To get insight into the sex chromosome structure and evolution in D. alata, we present a haplotype-resolved, near-complete genome assembly of the male cultivar "Kabusa," spanning 958 Mb across 40 chromosomes. DalaChr6A is identified as the Y chromosome which exhibits early signs of heteromorphism, including a slight reduction in size (∼400 Kb difference) and a potential centromere shift relative to the X chromosome. Our findings also reveal a sex chromosome turnover between D. alata and D. rotundata. The sex chromosomes of D. alata are evolutionarily young (approximately 4.32 million years ago) and emerged after the divergence from the D. rotundata lineage. The sex-determining region (SDR) is refined to approximately 7.6 Mb, representing approximately 44% of the Y chromosome. It contains several inversions and a divergence gradient was observed across these inversions. INV4 identified as the oldest pericentric inversion likely marks the early step in D. alata SDR evolution. Despite structural divergence, both X and Y chromosomes remain transcriptionally active. Among the 231 genes annotated in the SDR, 97 are sex-biased and enriched in functions associated with floral organ formation and hormonal signaling pathways. This study enhances our understanding of sex chromosome evolution and sex determination in dioecious plants. It provides a gold-standard reference genome for the Dioscorea genus and lays the foundation for accelerated breeding and genetic improvement in yam. (© 2026 The Author(s). The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd.) |
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| Grant Information: | CGIAR Research Program on Roots, Tubers and Bananas (CRP-RTB; INV-003446 Bill and Melinda Gates Foundation (BMGF); ANR-24-CE20-6201-01 French National Research Agency (ANR); CZ.02.01.01/00/22_008/0004581 ERDF program Johannes Amos Comenius; GPE005599 European Union and Guadeloupe Region (Programme Opérationnel FEDER - Guadeloupe - Conseil Régional 2021-2027) "TAESA" |
| Contributed Indexing: | Keywords: dioecy; genetic gain; genome; root and tuber crops; structural variants |
| Entry Date(s): | Date Created: 20260817 Date Completed: 20260817 Latest Revision: 20260819 |
| Update Code: | 20260819 |
| PubMed Central ID: | PMC13479938 |
| DOI: | 10.1111/tpj.71091 |
| PMID: | 42606221 |
| Βάση Δεδομένων: | MEDLINE |
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