{"title":"不同性染色体系统鱼类可转座元件动态对比分析","authors":"Carolina Crepaldi, Diogo Cavalcanti Cabral-de-Mello, Patricia Pasquali Parise-Maltempi","doi":"10.1139/gen-2023-0134","DOIUrl":null,"url":null,"abstract":"<p><p>Transposable elements (TEs) are widespread genomic components with substantial roles in genome evolution and sex chromosome differentiation. In this study, we compared the TE composition of three closely related fish with different sex chromosome systems: <i>Megaleporinus elongatus</i> (Z1Z1Z2Z2/Z1W1Z2W2), <i>Megaleporinus macrocephalus</i> (ZZ/ZW) (both with highly differentiated W sex chromosomes), and <i>Leporinus friderici</i> (without heteromorphic sex chromosomes). We created custom TE libraries for each species using clustering methods and manual annotation and prediction, and we predicted TE temporal dynamics through divergence-based analysis. The TE abundance ranged from 16% to 21% in the three mobilomes, with <i>L. friderici</i> having the lowest overall. Despite the recent amplification of TEs in all three species, we observed differing expansion activities, particularly between the two genera. Both <i>Megaleporinus</i> recently experienced high retrotransposon activity, with a reduction in DNA TEs, which could have implications in sex chromosome composition. In contrast, <i>L. friderici</i> showed the opposite pattern. Therefore, despite having similar TE compositions, <i>Megaleporinus</i> and <i>Leporinus</i> exhibit distinct TE histories that likely evolved after their separation, highlighting a rapid TE expansion over short evolutionary periods.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"339-350"},"PeriodicalIF":2.3000,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Comparative analysis of transposable elements dynamics in fish with different sex chromosome systems.\",\"authors\":\"Carolina Crepaldi, Diogo Cavalcanti Cabral-de-Mello, Patricia Pasquali Parise-Maltempi\",\"doi\":\"10.1139/gen-2023-0134\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>Transposable elements (TEs) are widespread genomic components with substantial roles in genome evolution and sex chromosome differentiation. In this study, we compared the TE composition of three closely related fish with different sex chromosome systems: <i>Megaleporinus elongatus</i> (Z1Z1Z2Z2/Z1W1Z2W2), <i>Megaleporinus macrocephalus</i> (ZZ/ZW) (both with highly differentiated W sex chromosomes), and <i>Leporinus friderici</i> (without heteromorphic sex chromosomes). We created custom TE libraries for each species using clustering methods and manual annotation and prediction, and we predicted TE temporal dynamics through divergence-based analysis. The TE abundance ranged from 16% to 21% in the three mobilomes, with <i>L. friderici</i> having the lowest overall. Despite the recent amplification of TEs in all three species, we observed differing expansion activities, particularly between the two genera. Both <i>Megaleporinus</i> recently experienced high retrotransposon activity, with a reduction in DNA TEs, which could have implications in sex chromosome composition. In contrast, <i>L. friderici</i> showed the opposite pattern. Therefore, despite having similar TE compositions, <i>Megaleporinus</i> and <i>Leporinus</i> exhibit distinct TE histories that likely evolved after their separation, highlighting a rapid TE expansion over short evolutionary periods.</p>\",\"PeriodicalId\":12809,\"journal\":{\"name\":\"Genome\",\"volume\":\" \",\"pages\":\"339-350\"},\"PeriodicalIF\":2.3000,\"publicationDate\":\"2024-10-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Genome\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://doi.org/10.1139/gen-2023-0134\",\"RegionNum\":3,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"2024/5/13 0:00:00\",\"PubModel\":\"Epub\",\"JCR\":\"Q3\",\"JCRName\":\"BIOTECHNOLOGY & APPLIED MICROBIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Genome","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1139/gen-2023-0134","RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2024/5/13 0:00:00","PubModel":"Epub","JCR":"Q3","JCRName":"BIOTECHNOLOGY & APPLIED MICROBIOLOGY","Score":null,"Total":0}
引用次数: 0
摘要
可转座元件(TE)是一种广泛存在的基因组成分,在基因组进化和性染色体分化中发挥着重要作用。在这项研究中,我们比较了三种性染色体系统不同的近缘鱼类的可转座元件组成:Megaleporinus elongatus(Z1Z1Z2Z2/Z1W1Z2W2)、Megaleporinus macrocephalus(ZZ/ZW)(均具有高度分化的 W 性染色体)和 Leporinus friderici(无异形性染色体)。我们利用聚类方法和人工注释与预测为每个物种创建了定制的 TE 库,并通过基于分化的分析预测了 TE 的时间动态。在三个动员组中,TE丰度从16%到21%不等,其中L. friderici的总体丰度最低。尽管这三个物种中的 TEs 最近都在扩大,但我们观察到了不同的扩展活动,尤其是在两个属之间。Megaleporinus和L. friderici最近都经历了较高的反转座子活动,DNA TEs减少,这可能对性染色体的组成有影响。相比之下,L. friderici则表现出相反的模式。因此,尽管Megaleporinus和Leporinus具有相似的TE组成,但它们的TE历史却截然不同,很可能是在它们分离后进化而来的,这凸显了TE在短进化期内的快速扩张。
Comparative analysis of transposable elements dynamics in fish with different sex chromosome systems.
Transposable elements (TEs) are widespread genomic components with substantial roles in genome evolution and sex chromosome differentiation. In this study, we compared the TE composition of three closely related fish with different sex chromosome systems: Megaleporinus elongatus (Z1Z1Z2Z2/Z1W1Z2W2), Megaleporinus macrocephalus (ZZ/ZW) (both with highly differentiated W sex chromosomes), and Leporinus friderici (without heteromorphic sex chromosomes). We created custom TE libraries for each species using clustering methods and manual annotation and prediction, and we predicted TE temporal dynamics through divergence-based analysis. The TE abundance ranged from 16% to 21% in the three mobilomes, with L. friderici having the lowest overall. Despite the recent amplification of TEs in all three species, we observed differing expansion activities, particularly between the two genera. Both Megaleporinus recently experienced high retrotransposon activity, with a reduction in DNA TEs, which could have implications in sex chromosome composition. In contrast, L. friderici showed the opposite pattern. Therefore, despite having similar TE compositions, Megaleporinus and Leporinus exhibit distinct TE histories that likely evolved after their separation, highlighting a rapid TE expansion over short evolutionary periods.
期刊介绍:
Genome is a monthly journal, established in 1959, that publishes original research articles, reviews, mini-reviews, current opinions, and commentaries. Areas of interest include general genetics and genomics, cytogenetics, molecular and evolutionary genetics, developmental genetics, population genetics, phylogenomics, molecular identification, as well as emerging areas such as ecological, comparative, and functional genomics.