| Chromosome-level assembly of Lindenbergia philippensis and comparative genomic analyses shed light on genome evolution in Lamiales | |
Chen, Bao-Zheng; Li, Da-Wei; Luo, Kai-Yong; Jiu, Song-Tao; Dong, Xiao; Wang, Wei-Bin; Li, Xu-Zhen; Hao, Ting-Ting; Lei, Ya-Hui; Guo, Da-Zhong; Liu, Xu-Tao; Duan, Sheng-Chang; Zhu, Yi-Fan; Chen, Wei; Dong, Yang14; Yu, Wen-Bin
| |
| 2024 | |
| Source Publication | FRONTIERS IN PLANT SCIENCE
 |
| ISSN | 1664-462X |
| Volume | 15Issue:xPages:- |
| Abstract | Lamiales, comprising over 23,755 species across 24 families, stands as a highly diverse and prolific plant group, playing a significant role in the cultivation of horticultural, ornamental, and medicinal plant varieties. Whole-genome duplication (WGD) and its subsequent post-polyploid diploidization (PPD) process represent the most drastic type of karyotype evolution, injecting significant potential for promoting the diversity of this lineage. However, polyploidization histories, as well as genome and subgenome fractionation following WGD events in Lamiales species, are still not well investigated. In this study, we constructed a chromosome-level genome assembly of Lindenbergia philippensis (Orobanchaceae) and conducted comparative genomic analyses with 14 other Lamiales species. L. philippensis is positioned closest to the parasitic lineage within Orobanchaceae and has a conserved karyotype. Through a combination of Ks analysis and syntenic depth analysis, we reconstructed and validated polyploidization histories of Lamiales species. Our results indicated that Primulina huaijiensis underwent three rounds of diploidization events following the gamma-WGT event, rather than two rounds as reported. Besides, we reconfirmed that most Lamiales species shared a common diploidization event (L-WGD). Subsequently, we constructed the Lamiales Ancestral Karyotype (LAK), comprising 11 proto-chromosomes, and elucidated its evolutionary trajectory, highlighting the highly flexible reshuffling of the Lamiales paleogenome. We identified biased fractionation of subgenomes following the L-WGD event across eight species, and highlighted the positive impacts of non-WGD genes on gene family expansion. This study provides novel genomic resources and insights into polyploidy and karyotype remodeling of Lamiales species, essential for advancing our understanding of species diversification and genome evolution. |
| Keyword | HI-C ALIGNMENT DIVERSIFICATION POLYPLOIDY ANNOTATION ACCURATE DIPLOIDIZATION IDENTIFICATION DUPLICATIONS DIVERGENCE |
| Subject Area | Plant Sciences |
| DOI | 10.3389/fpls.2024.1444234 |
| Indexed By | SCI |
| Language | 英语 |
| WOS ID | WOS:001291985600001 |
| Citation statistics | |
| Document Type | 期刊论文 |
| Identifier | https://ir.xtbg.ac.cn/handle/353005/14326 |
| Collection | 2012年后新成立研究组 |
| Affiliation | 1.[Chen, Bao-Zheng 2.Luo, Kai-Yong 3.Guo, Da-Zhong 4.Liu, Xu-Tao 5.Yunnan Agr Univ, Coll Food Sci & Technol, Kunming, Yunnan, Peoples R China 6.Li, Da-Wei 7.Dong, Xiao 8.Wang, Wei-Bin 9.Li, Xu-Zhen 10.Hao, Ting-Ting 11.Lei, Ya-Hui 12.Duan, Sheng-Chang 13.Zhu, Yi-Fan 14.Chen, Wei 15.Yunnan Agr Univ, Yunnan Prov Key Lab Biol Big Data, Kunming, Yunnan, Peoples R China 16.Shanghai Jiao Tong Univ, Sch Agr & Biol, Dept Plant Sci, Shanghai, Peoples R China 17.Chinese Acad Sci, Ctr Integrat Conservat, Mengla, Yunnan, Peoples R China 18.Chinese Acad Sci, Yunnan Key Lab Conservat Trop Rainforests & Asian, Xishuangbanna Trop Bot Garden, Mengla, Yunnan, Peoples R China 19.Chinese Acad Sci, Southeast Asia Biodivers Res Inst, Mengla, Yunnan, Peoples R China |
| Recommended Citation GB/T 7714 | Chen, Bao-Zheng,Li, Da-Wei,Luo, Kai-Yong,et al. Chromosome-level assembly of Lindenbergia philippensis and comparative genomic analyses shed light on genome evolution in Lamiales[J]. FRONTIERS IN PLANT SCIENCE,2024,15(x):-. |
| APA | Chen, Bao-Zheng.,Li, Da-Wei.,Luo, Kai-Yong.,Jiu, Song-Tao.,Dong, Xiao.,...&Yu, Wen-Bin.(2024).Chromosome-level assembly of Lindenbergia philippensis and comparative genomic analyses shed light on genome evolution in Lamiales.FRONTIERS IN PLANT SCIENCE,15(x),-. |
| MLA | Chen, Bao-Zheng,et al."Chromosome-level assembly of Lindenbergia philippensis and comparative genomic analyses shed light on genome evolution in Lamiales".FRONTIERS IN PLANT SCIENCE 15.x(2024):-. |
| Files in This Item: | Download All | |||||
| File Name/Size | DocType | Version | Access | License | ||
| Chromosome-level ass（6951KB） | 期刊论文 | 出版稿 | 开放获取 | CC BY-NC-SA | View Download | |
Items in the repository are protected by copyright, with all rights reserved, unless otherwise indicated.
Edit Comment