Cheng Li, David Wickell, Li-Yaung Kuo, Xueqing Chen, Bao Nie, Xuezhu Liao, Dan Peng, Jiaojiao Ji, Jerry Jenkins, Mellissa Williams, Shengqiang Shu, Christopher Plott, Kerrie Barry, Shanmugam Rajasekar, Jane Grimwood, Xiaoxu Han, Shichao Sun, Zhuangwei Hou, Weijun He, Guanhua Dai, Cheng Sun, Jeremy Schmutz, James H Leebens-Mack, Fay-Wei Li, Li Wang
{"title":"Extraordinary preservation of gene collinearity over three hundred million years revealed in homosporous lycophytes.","authors":"Cheng Li, David Wickell, Li-Yaung Kuo, Xueqing Chen, Bao Nie, Xuezhu Liao, Dan Peng, Jiaojiao Ji, Jerry Jenkins, Mellissa Williams, Shengqiang Shu, Christopher Plott, Kerrie Barry, Shanmugam Rajasekar, Jane Grimwood, Xiaoxu Han, Shichao Sun, Zhuangwei Hou, Weijun He, Guanhua Dai, Cheng Sun, Jeremy Schmutz, James H Leebens-Mack, Fay-Wei Li, Li Wang","doi":"10.1073/pnas.2312607121","DOIUrl":null,"url":null,"abstract":"<p><p>Homosporous lycophytes (Lycopodiaceae) are a deeply diverged lineage in the plant tree of life, having split from heterosporous lycophytes (<i>Selaginella</i> and <i>Isoetes</i>) ~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 <i>Huperzia asiatica</i> and the diploid <i>Diphasiastrum complanatum</i>. Remarkably, despite that the two species diverged ~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 <i>H. asiatica</i> and <i>D. complanatum</i> not only fill a crucial gap in the plant genomic landscape but also highlight a potentially meaningful genomic contrast between homosporous and heterosporous species.</p>","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":null,"pages":null},"PeriodicalIF":9.4000,"publicationDate":"2024-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10823260/pdf/","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Proceedings of the National Academy of Sciences of the United States of America","FirstCategoryId":"103","ListUrlMain":"https://doi.org/10.1073/pnas.2312607121","RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2024/1/18 0:00:00","PubModel":"Epub","JCR":"Q1","JCRName":"MULTIDISCIPLINARY SCIENCES","Score":null,"Total":0}
引用次数: 0
Abstract
Homosporous lycophytes (Lycopodiaceae) are a deeply diverged lineage in the plant tree of life, having split from heterosporous lycophytes (Selaginella and Isoetes) ~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 ~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.
期刊介绍:
The Proceedings of the National Academy of Sciences (PNAS), a peer-reviewed journal of the National Academy of Sciences (NAS), serves as an authoritative source for high-impact, original research across the biological, physical, and social sciences. With a global scope, the journal welcomes submissions from researchers worldwide, making it an inclusive platform for advancing scientific knowledge.