Juan Pablo Marczuk-Rojas, Ana D Maldonado, Lorenzo Carretero-Paulet
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By modeling the distribution of ages and sizes, examining their linear arrangement across the plastid genome, and statistically assessing spatial biases with respect to other genomic features, we showed that NUPTs are i) formed by both continuous and episodic mechanisms; ii) unevenly represented across the plastid genome; iii) consistently associated with certain classes of RNA genes, in particular rRNA, tRNA and regulatory RNA genes; iv) differentially contributing to structural genes; and v) closer than expected to different superfamilies of transposons in a species-specific manner. Our results reveal the unexpected complexity in the mechanisms driving the origin of NUPTs, which do not only involve their continuous formation but also episodic, highlight their role as a major source of non-coding RNA genes and other genomic features and provide a more complete picture of the different drivers of evolutionary change at the genome level.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":2.8000,"publicationDate":"2025-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Episodic and ongoing mechanisms drive plastid-derived nuclear DNA evolution in angiosperms.\",\"authors\":\"Juan Pablo Marczuk-Rojas, Ana D Maldonado, Lorenzo Carretero-Paulet\",\"doi\":\"10.1093/gbe/evaf194\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>NUPTs are DNA sequences of plastid origin present in plant nuclear genomes to varying, though typically low, amounts. It is assumed that they are continuously formed and, due to their potentially mutagenic effect, removed at a constant turnover rate, which should result in an exponential decay of their age distributions and a negative correlation between age and size. However, these assumptions are based on analysis from a limited number of species and have never been explicitly tested. To gain insight into the mechanisms driving the origin and evolution of NUPTs, here we surveyed the plastid and nuclear genomes of 30 species representing the main angiosperm (flowering plants) lineages. By modeling the distribution of ages and sizes, examining their linear arrangement across the plastid genome, and statistically assessing spatial biases with respect to other genomic features, we showed that NUPTs are i) formed by both continuous and episodic mechanisms; ii) unevenly represented across the plastid genome; iii) consistently associated with certain classes of RNA genes, in particular rRNA, tRNA and regulatory RNA genes; iv) differentially contributing to structural genes; and v) closer than expected to different superfamilies of transposons in a species-specific manner. Our results reveal the unexpected complexity in the mechanisms driving the origin of NUPTs, which do not only involve their continuous formation but also episodic, highlight their role as a major source of non-coding RNA genes and other genomic features and provide a more complete picture of the different drivers of evolutionary change at the genome level.</p>\",\"PeriodicalId\":12779,\"journal\":{\"name\":\"Genome Biology and Evolution\",\"volume\":\" \",\"pages\":\"\"},\"PeriodicalIF\":2.8000,\"publicationDate\":\"2025-10-13\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Genome Biology and Evolution\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://doi.org/10.1093/gbe/evaf194\",\"RegionNum\":2,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q2\",\"JCRName\":\"EVOLUTIONARY BIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Genome Biology and Evolution","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1093/gbe/evaf194","RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"EVOLUTIONARY BIOLOGY","Score":null,"Total":0}
Episodic and ongoing mechanisms drive plastid-derived nuclear DNA evolution in angiosperms.
NUPTs are DNA sequences of plastid origin present in plant nuclear genomes to varying, though typically low, amounts. It is assumed that they are continuously formed and, due to their potentially mutagenic effect, removed at a constant turnover rate, which should result in an exponential decay of their age distributions and a negative correlation between age and size. However, these assumptions are based on analysis from a limited number of species and have never been explicitly tested. To gain insight into the mechanisms driving the origin and evolution of NUPTs, here we surveyed the plastid and nuclear genomes of 30 species representing the main angiosperm (flowering plants) lineages. By modeling the distribution of ages and sizes, examining their linear arrangement across the plastid genome, and statistically assessing spatial biases with respect to other genomic features, we showed that NUPTs are i) formed by both continuous and episodic mechanisms; ii) unevenly represented across the plastid genome; iii) consistently associated with certain classes of RNA genes, in particular rRNA, tRNA and regulatory RNA genes; iv) differentially contributing to structural genes; and v) closer than expected to different superfamilies of transposons in a species-specific manner. Our results reveal the unexpected complexity in the mechanisms driving the origin of NUPTs, which do not only involve their continuous formation but also episodic, highlight their role as a major source of non-coding RNA genes and other genomic features and provide a more complete picture of the different drivers of evolutionary change at the genome level.
期刊介绍:
About the journal
Genome Biology and Evolution (GBE) publishes leading original research at the interface between evolutionary biology and genomics. Papers considered for publication report novel evolutionary findings that concern natural genome diversity, population genomics, the structure, function, organisation and expression of genomes, comparative genomics, proteomics, and environmental genomic interactions. Major evolutionary insights from the fields of computational biology, structural biology, developmental biology, and cell biology are also considered, as are theoretical advances in the field of genome evolution. GBE’s scope embraces genome-wide evolutionary investigations at all taxonomic levels and for all forms of life — within populations or across domains. Its aims are to further the understanding of genomes in their evolutionary context and further the understanding of evolution from a genome-wide perspective.