Extraordinary preservation of gene collinearity over three hundred million years revealed in homosporous lycophytes

• 成果类型: Article
• 署名作者: Li, Cheng; Wickell, David; Kuo, Li-Yaung; Chen, Xueqing; Nie, Bao; Liao, Xuezhu; Peng, Dan; Ji, Jiaojiao; Jenkins, Jerry; Williams, Mellissa; Shu, Shengqiang; Plott, Christopher; Barry, Kerrie; Rajasekar, Shanmugam; Grimwood, Jane; Han, Xiaoxu; Sun, Shichao; Hou, Zhuangwei; He, Weijun; Dai, Guanhua; Sun, Cheng; Schmutz, Jeremy; Leebens-Mack, James H.; Li, Fay-Wei; Wang, Li
• 署名单位: Guangdong Laboratory for Lingnan Modern Agriculture; Chinese Academy of Agricultural Sciences; Cornell University; Boyce Thompson Institute for Plant Research; Cornell University; National Tsing Hua University; HudsonAlpha Institute for Biotechnology; United States Department of Energy (DOE); Lawrence Berkeley National Laboratory; University of Arizona; Chinese Academy of Sciences; Capital Normal University; University System of Georgia; University of Georgia
• 刊物名称: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
• ISSN/ISSBN: 0027-11417
• DOI: 10.1073/pnas.2312607121
• 发表日期: 2024-01-23
• 关键词: phylogenetic analysis; genome; EVOLUTION; patterns; biology; origin; plants; ferns

摘要

Homosporous lycophytes (Lycopodiaceae) are a deeply diverged lineage in the plant tree of life, having split from heterosporous lycophytes (Selaginella and Isoetes) similar to 400 Mya. Compared to the heterosporous lineage, Lycopodiaceae has markedly larger genome sizes and remains the last major plant clade for which no chromosome-level assembly has been available. Here, we present chromosomal genome assemblies for two homosporous lycophyte species, the allotetraploid Huperzia asiatica and the diploid Diphasiastrum complanatum. Remarkably, despite that the two species diverged similar to 350 Mya, around 30% of the genes are still in syntenic blocks. Furthermore, both genomes had undergone independent whole genome duplications, and the resulting intragenomic syntenies have likewise been preserved relatively well. Such slow genome evolution over deep time is in stark contrast to heterosporous lycophytes and is correlated with a decelerated rate of nucleotide substitution. Together, the genomes of H. asiatica and D. complanatum not only fill a crucial gap in the plant genomic landscape but also highlight a potentially meaningful genomic contrast between homosporous and heterosporous species.