{"title":"蔷薇科植物中的可转座元件:对基因组进化、表达动态和同源基因调控的见解。","authors":"Ze Yu, Jiale Li, Hanyu Wang, Boya Ping, Xinchu Li, Zhiguang Liu, Bocheng Guo, Qiaoming Yu, Yangjun Zou, Yaqiang Sun, Fengwang Ma, Tao Zhao","doi":"10.1093/hr/uhae118","DOIUrl":null,"url":null,"abstract":"<p><p>Transposable elements (TEs) exert significant influence on plant genomic structure and gene expression. Here, we explored TE-related aspects across 14 Rosaceae genomes, investigating genomic distribution, transposition activity, expression patterns, and nearby differentially expressed genes (DEGs). Analyses unveiled distinct long terminal repeat retrotransposon (LTR-RT) evolutionary patterns, reflecting varied genome size changes among nine species over the past million years. In the past 2.5 million years, <i>Rubus idaeus</i> showed a transposition rate twice as fast as <i>Fragaria vesca</i>, while <i>Pyrus bretschneideri</i> displayed significantly faster transposition compared with <i>Crataegus pinnatifida</i>. Genes adjacent to recent TE insertions were linked to adversity resistance, while those near previous insertions were functionally enriched in morphogenesis, enzyme activity, and metabolic processes. Expression analysis revealed diverse responses of LTR-RTs to internal or external conditions. Furthermore, we identified 3695 pairs of syntenic DEGs proximal to TEs in <i>Malus domestica</i> cv. 'Gala' and <i>M. domestica</i> (GDDH13), suggesting TE insertions may contribute to varietal trait differences in these apple varieties. Our study across representative Rosaceae species underscores the pivotal role of TEs in plant genome evolution within this diverse family. It elucidates how these elements regulate syntenic DEGs on a genome-wide scale, offering insights into Rosaceae-specific genomic evolution.</p>","PeriodicalId":57479,"journal":{"name":"园艺研究(英文)","volume":"11 6","pages":"uhae118"},"PeriodicalIF":7.6000,"publicationDate":"2024-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11197308/pdf/","citationCount":"0","resultStr":"{\"title\":\"Transposable elements in Rosaceae: insights into genome evolution, expression dynamics, and syntenic gene regulation.\",\"authors\":\"Ze Yu, Jiale Li, Hanyu Wang, Boya Ping, Xinchu Li, Zhiguang Liu, Bocheng Guo, Qiaoming Yu, Yangjun Zou, Yaqiang Sun, Fengwang Ma, Tao Zhao\",\"doi\":\"10.1093/hr/uhae118\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>Transposable elements (TEs) exert significant influence on plant genomic structure and gene expression. Here, we explored TE-related aspects across 14 Rosaceae genomes, investigating genomic distribution, transposition activity, expression patterns, and nearby differentially expressed genes (DEGs). Analyses unveiled distinct long terminal repeat retrotransposon (LTR-RT) evolutionary patterns, reflecting varied genome size changes among nine species over the past million years. In the past 2.5 million years, <i>Rubus idaeus</i> showed a transposition rate twice as fast as <i>Fragaria vesca</i>, while <i>Pyrus bretschneideri</i> displayed significantly faster transposition compared with <i>Crataegus pinnatifida</i>. Genes adjacent to recent TE insertions were linked to adversity resistance, while those near previous insertions were functionally enriched in morphogenesis, enzyme activity, and metabolic processes. Expression analysis revealed diverse responses of LTR-RTs to internal or external conditions. Furthermore, we identified 3695 pairs of syntenic DEGs proximal to TEs in <i>Malus domestica</i> cv. 'Gala' and <i>M. domestica</i> (GDDH13), suggesting TE insertions may contribute to varietal trait differences in these apple varieties. Our study across representative Rosaceae species underscores the pivotal role of TEs in plant genome evolution within this diverse family. It elucidates how these elements regulate syntenic DEGs on a genome-wide scale, offering insights into Rosaceae-specific genomic evolution.</p>\",\"PeriodicalId\":57479,\"journal\":{\"name\":\"园艺研究(英文)\",\"volume\":\"11 6\",\"pages\":\"uhae118\"},\"PeriodicalIF\":7.6000,\"publicationDate\":\"2024-04-26\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11197308/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"园艺研究(英文)\",\"FirstCategoryId\":\"1091\",\"ListUrlMain\":\"https://doi.org/10.1093/hr/uhae118\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"2024/6/1 0:00:00\",\"PubModel\":\"eCollection\",\"JCR\":\"Q1\",\"JCRName\":\"GENETICS & HEREDITY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"园艺研究(英文)","FirstCategoryId":"1091","ListUrlMain":"https://doi.org/10.1093/hr/uhae118","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2024/6/1 0:00:00","PubModel":"eCollection","JCR":"Q1","JCRName":"GENETICS & HEREDITY","Score":null,"Total":0}
引用次数: 0
摘要
可转座元素(TE)对植物基因组结构和基因表达有重大影响。在这里,我们探索了 14 个蔷薇科植物基因组中与 TE 相关的方面,研究了基因组分布、转座活性、表达模式和附近的差异表达基因(DEGs)。分析揭示了不同的长末端重复反转座子(LTR-RT)进化模式,反映了过去一百万年中九个物种基因组大小的变化。在过去 250 万年中,Rubus idaeus 的转座速度是 Fragaria vesca 的两倍,而 Pyrus bretschneideri 的转座速度明显快于 Crataegus pinnatifida。与最近的TE插入相邻的基因与抗逆境有关,而与以前的插入相邻的基因则在形态发生、酶活性和代谢过程中具有丰富的功能。表达分析揭示了 LTR-RT 对内部或外部条件的不同反应。此外,我们在 Malus domestica cv. 'Gala' 和 M. domestica (GDDH13) 中发现了 3695 对与 TEs 邻近的同源 DEGs,这表明 TE 插入可能导致了这些苹果品种的性状差异。我们对代表性蔷薇科物种的研究强调了 TE 在这一多样化家族中植物基因组进化中的关键作用。它阐明了这些元素如何在全基因组范围内调控同源 DEGs,为了解蔷薇科特有的基因组进化提供了见解。
Transposable elements in Rosaceae: insights into genome evolution, expression dynamics, and syntenic gene regulation.
Transposable elements (TEs) exert significant influence on plant genomic structure and gene expression. Here, we explored TE-related aspects across 14 Rosaceae genomes, investigating genomic distribution, transposition activity, expression patterns, and nearby differentially expressed genes (DEGs). Analyses unveiled distinct long terminal repeat retrotransposon (LTR-RT) evolutionary patterns, reflecting varied genome size changes among nine species over the past million years. In the past 2.5 million years, Rubus idaeus showed a transposition rate twice as fast as Fragaria vesca, while Pyrus bretschneideri displayed significantly faster transposition compared with Crataegus pinnatifida. Genes adjacent to recent TE insertions were linked to adversity resistance, while those near previous insertions were functionally enriched in morphogenesis, enzyme activity, and metabolic processes. Expression analysis revealed diverse responses of LTR-RTs to internal or external conditions. Furthermore, we identified 3695 pairs of syntenic DEGs proximal to TEs in Malus domestica cv. 'Gala' and M. domestica (GDDH13), suggesting TE insertions may contribute to varietal trait differences in these apple varieties. Our study across representative Rosaceae species underscores the pivotal role of TEs in plant genome evolution within this diverse family. It elucidates how these elements regulate syntenic DEGs on a genome-wide scale, offering insights into Rosaceae-specific genomic evolution.