Wen-Xiang Liu, Guo-Bo Li, Zhuo Zhou, Jia-Fu Chen, An-Min Yu, Ai-Zhong Liu, Bin Tian, Jun-Wei Ye
{"title":"用质体组和转录组系统基因组学揭示了部落蓖麻属间和种间的关系。","authors":"Wen-Xiang Liu, Guo-Bo Li, Zhuo Zhou, Jia-Fu Chen, An-Min Yu, Ai-Zhong Liu, Bin Tian, Jun-Wei Ye","doi":"10.3389/fpls.2025.1544247","DOIUrl":null,"url":null,"abstract":"<p><strong>Introduction: </strong>The taxonomy of Euphorbiaceae is extremely difficult, especially the phylogeny of closely related genera. In <i>Ricinus</i>, which embraces an important non-food oil-seed crop worldwide, <i>Discocleidion</i> and <i>Speranskia</i> are closely related genera based on molecular evidence (tribe Ricineae), however the intergeneric and interspecific relationship of the tribe is not well-resolved.</p><p><strong>Methods: </strong>Plastome and transcriptome were sequenced and assembled before maximum likelihood and Bayesian inference phylogenetic trees were reconstructed. Plastome features and comparative analyses were conducted. Morphological traits of the tribe were explored as supplement to the molecular data.</p><p><strong>Results: </strong>The newly sequenced plastomes ranged from 167,327 to 190,093 bp with typical circular quadripartite structures. The longest genome of <i>S. tuberculata</i> may due to higher number of simple sequence repeats. Natural selection pressure on chloroplast genes was relatively small and the tribe likely experienced a population contraction. The transcriptome assembly contig N50 of the tribe ranged from 1506 (<i>D. rufescens</i>) to 2489 bp (<i>S. tuberculata</i>). A total of 50,513 genes (<i>S. cantonensis</i>) to 78,048 genes (<i>D. ulmifolium</i>) were detected, and the GC content varied between 38.17% (<i>S. cantonensis</i>) and 40.01% (<i>R. communis</i>). The three genera formed a well-supported monophyletic lineage, confirmed by different genomic data using different methods. <i>Discocleidion</i> and <i>Ricinus</i> were supported to be closely related. In <i>Speranskia</i>, <i>S. yunnanensis</i> diverged first and the divergence of <i>S. tuberculata</i> and <i>S. cantonensis</i> was followed. Further, morphological similarities supported the monophyletic lineage and intergeneric and interspecific relationship.</p><p><strong>Discussion: </strong>The relationship in the tribe Ricineae is clearly revealed by genomic and morphological data, providing a genetic basis for future comparative genomic investigations and phylogeny reconstruction of Euphorbiaceae.</p>","PeriodicalId":12632,"journal":{"name":"Frontiers in Plant Science","volume":"16 ","pages":"1544247"},"PeriodicalIF":4.1000,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12078312/pdf/","citationCount":"0","resultStr":"{\"title\":\"Intergeneric and interspecific relationships in tribe Ricineae revealed by phylogenomics of the plastome and transcriptome.\",\"authors\":\"Wen-Xiang Liu, Guo-Bo Li, Zhuo Zhou, Jia-Fu Chen, An-Min Yu, Ai-Zhong Liu, Bin Tian, Jun-Wei Ye\",\"doi\":\"10.3389/fpls.2025.1544247\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><strong>Introduction: </strong>The taxonomy of Euphorbiaceae is extremely difficult, especially the phylogeny of closely related genera. In <i>Ricinus</i>, which embraces an important non-food oil-seed crop worldwide, <i>Discocleidion</i> and <i>Speranskia</i> are closely related genera based on molecular evidence (tribe Ricineae), however the intergeneric and interspecific relationship of the tribe is not well-resolved.</p><p><strong>Methods: </strong>Plastome and transcriptome were sequenced and assembled before maximum likelihood and Bayesian inference phylogenetic trees were reconstructed. Plastome features and comparative analyses were conducted. Morphological traits of the tribe were explored as supplement to the molecular data.</p><p><strong>Results: </strong>The newly sequenced plastomes ranged from 167,327 to 190,093 bp with typical circular quadripartite structures. The longest genome of <i>S. tuberculata</i> may due to higher number of simple sequence repeats. Natural selection pressure on chloroplast genes was relatively small and the tribe likely experienced a population contraction. The transcriptome assembly contig N50 of the tribe ranged from 1506 (<i>D. rufescens</i>) to 2489 bp (<i>S. tuberculata</i>). A total of 50,513 genes (<i>S. cantonensis</i>) to 78,048 genes (<i>D. ulmifolium</i>) were detected, and the GC content varied between 38.17% (<i>S. cantonensis</i>) and 40.01% (<i>R. communis</i>). The three genera formed a well-supported monophyletic lineage, confirmed by different genomic data using different methods. <i>Discocleidion</i> and <i>Ricinus</i> were supported to be closely related. In <i>Speranskia</i>, <i>S. yunnanensis</i> diverged first and the divergence of <i>S. tuberculata</i> and <i>S. cantonensis</i> was followed. Further, morphological similarities supported the monophyletic lineage and intergeneric and interspecific relationship.</p><p><strong>Discussion: </strong>The relationship in the tribe Ricineae is clearly revealed by genomic and morphological data, providing a genetic basis for future comparative genomic investigations and phylogeny reconstruction of Euphorbiaceae.</p>\",\"PeriodicalId\":12632,\"journal\":{\"name\":\"Frontiers in Plant Science\",\"volume\":\"16 \",\"pages\":\"1544247\"},\"PeriodicalIF\":4.1000,\"publicationDate\":\"2025-05-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12078312/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Frontiers in Plant Science\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://doi.org/10.3389/fpls.2025.1544247\",\"RegionNum\":2,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"2025/1/1 0:00:00\",\"PubModel\":\"eCollection\",\"JCR\":\"Q1\",\"JCRName\":\"PLANT SCIENCES\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Frontiers in Plant Science","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.3389/fpls.2025.1544247","RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2025/1/1 0:00:00","PubModel":"eCollection","JCR":"Q1","JCRName":"PLANT SCIENCES","Score":null,"Total":0}
Intergeneric and interspecific relationships in tribe Ricineae revealed by phylogenomics of the plastome and transcriptome.
Introduction: The taxonomy of Euphorbiaceae is extremely difficult, especially the phylogeny of closely related genera. In Ricinus, which embraces an important non-food oil-seed crop worldwide, Discocleidion and Speranskia are closely related genera based on molecular evidence (tribe Ricineae), however the intergeneric and interspecific relationship of the tribe is not well-resolved.
Methods: Plastome and transcriptome were sequenced and assembled before maximum likelihood and Bayesian inference phylogenetic trees were reconstructed. Plastome features and comparative analyses were conducted. Morphological traits of the tribe were explored as supplement to the molecular data.
Results: The newly sequenced plastomes ranged from 167,327 to 190,093 bp with typical circular quadripartite structures. The longest genome of S. tuberculata may due to higher number of simple sequence repeats. Natural selection pressure on chloroplast genes was relatively small and the tribe likely experienced a population contraction. The transcriptome assembly contig N50 of the tribe ranged from 1506 (D. rufescens) to 2489 bp (S. tuberculata). A total of 50,513 genes (S. cantonensis) to 78,048 genes (D. ulmifolium) were detected, and the GC content varied between 38.17% (S. cantonensis) and 40.01% (R. communis). The three genera formed a well-supported monophyletic lineage, confirmed by different genomic data using different methods. Discocleidion and Ricinus were supported to be closely related. In Speranskia, S. yunnanensis diverged first and the divergence of S. tuberculata and S. cantonensis was followed. Further, morphological similarities supported the monophyletic lineage and intergeneric and interspecific relationship.
Discussion: The relationship in the tribe Ricineae is clearly revealed by genomic and morphological data, providing a genetic basis for future comparative genomic investigations and phylogeny reconstruction of Euphorbiaceae.
期刊介绍：
In an ever changing world, plant science is of the utmost importance for securing the future well-being of humankind. Plants provide oxygen, food, feed, fibers, and building materials. In addition, they are a diverse source of industrial and pharmaceutical chemicals. Plants are centrally important to the health of ecosystems, and their understanding is critical for learning how to manage and maintain a sustainable biosphere. Plant science is extremely interdisciplinary, reaching from agricultural science to paleobotany, and molecular physiology to ecology. It uses the latest developments in computer science, optics, molecular biology and genomics to address challenges in model systems, agricultural crops, and ecosystems. Plant science research inquires into the form, function, development, diversity, reproduction, evolution and uses of both higher and lower plants and their interactions with other organisms throughout the biosphere. Frontiers in Plant Science welcomes outstanding contributions in any field of plant science from basic to applied research, from organismal to molecular studies, from single plant analysis to studies of populations and whole ecosystems, and from molecular to biophysical to computational approaches.
Frontiers in Plant Science publishes articles on the most outstanding discoveries across a wide research spectrum of Plant Science. The mission of Frontiers in Plant Science is to bring all relevant Plant Science areas together on a single platform.
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