The evolution of ultraconserved elements in vertebrates.

IF 11 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY
Mitchell Cummins, Cadel Watson, Richard J Edwards, John S Mattick
{"title":"The evolution of ultraconserved elements in vertebrates.","authors":"Mitchell Cummins, Cadel Watson, Richard J Edwards, John S Mattick","doi":"10.1093/molbev/msae146","DOIUrl":null,"url":null,"abstract":"<p><p>Ultraconserved elements (UCEs) were discovered two decades ago, arbitrarily defined as sequences that are identical over a length ≥200 bp in the human, mouse and rat genomes. The definition was subsequently extended to sequences ≥100 bp identical in at least three of five mammalian genomes (including dog and cow), and shown to have undergone rapid expansion from ancestors in fish and strong negative selection in birds and mammals. Since then, many more genomes have become available, allowing better definition and more thorough examination of UCE distribution and evolutionary history. We developed a fast and flexible analytical pipeline for identifying UCEs in multiple genomes, dedUCE, which allows manipulation of minimum length, sequence identity, and number of species with a detectable UCE according to specified parameters. We suggest an updated definition of UCEs as sequences ≥100 bp and ≥97% sequence identity in ≥50% of placental mammal orders (12813 UCEs). By mapping UCEs to ∼200 species we find that placental UCEs appeared early in vertebrate evolution, well before land colonisation, suggesting the evolutionary pressures driving UCE selection were present in aquatic environments in the Cambrian-Devonian periods. Most (>90%) UCEs likely appeared after the divergence of gnathostomes from jawless predecessors, were largely established in sequence identity by early Sarcopterygii evolution - before the divergence of lobe-finned fishes from tetrapods - and became near fixed in the amniotes. UCEs are mainly located in the introns of protein-coding and non-coding genes involved in neurological and skeletomuscular development, enriched in regulatory elements, and dynamically expressed throughout embryonic development.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":null,"pages":null},"PeriodicalIF":11.0000,"publicationDate":"2024-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Molecular biology and evolution","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1093/molbev/msae146","RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"BIOCHEMISTRY & MOLECULAR BIOLOGY","Score":null,"Total":0}
引用次数: 0

Abstract

Ultraconserved elements (UCEs) were discovered two decades ago, arbitrarily defined as sequences that are identical over a length ≥200 bp in the human, mouse and rat genomes. The definition was subsequently extended to sequences ≥100 bp identical in at least three of five mammalian genomes (including dog and cow), and shown to have undergone rapid expansion from ancestors in fish and strong negative selection in birds and mammals. Since then, many more genomes have become available, allowing better definition and more thorough examination of UCE distribution and evolutionary history. We developed a fast and flexible analytical pipeline for identifying UCEs in multiple genomes, dedUCE, which allows manipulation of minimum length, sequence identity, and number of species with a detectable UCE according to specified parameters. We suggest an updated definition of UCEs as sequences ≥100 bp and ≥97% sequence identity in ≥50% of placental mammal orders (12813 UCEs). By mapping UCEs to ∼200 species we find that placental UCEs appeared early in vertebrate evolution, well before land colonisation, suggesting the evolutionary pressures driving UCE selection were present in aquatic environments in the Cambrian-Devonian periods. Most (>90%) UCEs likely appeared after the divergence of gnathostomes from jawless predecessors, were largely established in sequence identity by early Sarcopterygii evolution - before the divergence of lobe-finned fishes from tetrapods - and became near fixed in the amniotes. UCEs are mainly located in the introns of protein-coding and non-coding genes involved in neurological and skeletomuscular development, enriched in regulatory elements, and dynamically expressed throughout embryonic development.

脊椎动物超保守元素的进化。
超保守元件(UCE)发现于二十年前,在人类、小鼠和大鼠基因组中被任意定义为长度≥200 bp的相同序列。随后,这一定义被扩展到五个哺乳动物基因组(包括狗和牛)中至少三个基因组中长度≥100 bp的相同序列,并证明这些序列从鱼类的祖先迅速扩展而来,在鸟类和哺乳动物中经历了强烈的负选择。从那时起,有更多的基因组可供使用,从而可以对 UCE 的分布和进化史进行更好的定义和更全面的研究。我们开发了一种快速而灵活的分析管道,用于识别多基因组中的 UCE,即 dedUCE,它可以根据指定参数对最小长度、序列同一性和可检测到 UCE 的物种数量进行操作。我们建议更新 UCE 的定义,即在≥50% 的胎盘哺乳动物目(12813 个 UCE)中≥100 bp 且序列同一性≥97% 的序列。通过绘制 200 个物种的 UCEs 图谱,我们发现胎盘类 UCEs 出现在脊椎动物进化的早期,远早于陆地殖民时期,这表明在寒武纪-德文纪时期,驱动 UCE 选择的进化压力已经出现在水生环境中。大多数(>90%)UCEs可能出现在无颌类从无颌类的前身分化之后,在早期猿类进化(在叶鳍鱼类从四足类分化之前)中基本确定了序列特征,并在羊膜动物中接近固定。UCEs 主要位于涉及神经和骨骼肌肉发育的编码蛋白和非编码基因的内含子中,富含调控元件,并在整个胚胎发育过程中动态表达。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
求助全文
约1分钟内获得全文 求助全文
来源期刊
Molecular biology and evolution
Molecular biology and evolution 生物-进化生物学
CiteScore
19.70
自引率
3.70%
发文量
257
审稿时长
1 months
期刊介绍: Molecular Biology and Evolution Journal Overview: Publishes research at the interface of molecular (including genomics) and evolutionary biology Considers manuscripts containing patterns, processes, and predictions at all levels of organization: population, taxonomic, functional, and phenotypic Interested in fundamental discoveries, new and improved methods, resources, technologies, and theories advancing evolutionary research Publishes balanced reviews of recent developments in genome evolution and forward-looking perspectives suggesting future directions in molecular evolution applications.
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
copy
已复制链接
快去分享给好友吧!
我知道了
右上角分享
点击右上角分享
0
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术官方微信