CAULIFINDER: a pipeline for the automated detection and annotation of caulimovirid endogenous viral elements in plant genomes.

IF 4.7 2区 生物学 Q1 GENETICS & HEREDITY
Héléna Vassilieff, Sana Haddad, Véronique Jamilloux, Nathalie Choisne, Vikas Sharma, Delphine Giraud, Mariène Wan, Saad Serfraz, Andrew D W Geering, Pierre-Yves Teycheney, Florian Maumus
{"title":"CAULIFINDER: a pipeline for the automated detection and annotation of caulimovirid endogenous viral elements in plant genomes.","authors":"Héléna Vassilieff,&nbsp;Sana Haddad,&nbsp;Véronique Jamilloux,&nbsp;Nathalie Choisne,&nbsp;Vikas Sharma,&nbsp;Delphine Giraud,&nbsp;Mariène Wan,&nbsp;Saad Serfraz,&nbsp;Andrew D W Geering,&nbsp;Pierre-Yves Teycheney,&nbsp;Florian Maumus","doi":"10.1186/s13100-022-00288-w","DOIUrl":null,"url":null,"abstract":"<p><p>Plant, animal and protist genomes often contain endogenous viral elements (EVEs), which correspond to partial and sometimes entire viral genomes that have been captured in the genome of their host organism through a variety of integration mechanisms. While the number of sequenced eukaryotic genomes is rapidly increasing, the annotation and characterization of EVEs remains largely overlooked. EVEs that derive from members of the family Caulimoviridae are widespread across tracheophyte plants, and sometimes they occur in very high copy numbers. However, existing programs for annotating repetitive DNA elements in plant genomes are poor at identifying and then classifying these EVEs. Other than accurately annotating plant genomes, there is intrinsic value in a tool that could identify caulimovirid EVEs as they testify to recent or ancient host-virus interactions and provide valuable insights into virus evolution. In response to this research need, we have developed CAULIFINDER, an automated and sensitive annotation software package. CAULIFINDER consists of two complementary workflows, one to reconstruct, annotate and group caulimovirid EVEs in a given plant genome and the second to classify these genetic elements into officially recognized or tentative genera in the Caulimoviridae. We have benchmarked the CAULIFINDER package using the Vitis vinifera reference genome, which contains a rich assortment of caulimovirid EVEs that have previously been characterized using manual methods. The CAULIFINDER package is distributed in the form of a Docker image.</p>","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":null,"pages":null},"PeriodicalIF":4.7000,"publicationDate":"2022-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9719215/pdf/","citationCount":"1","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Mobile DNA","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1186/s13100-022-00288-w","RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"GENETICS & HEREDITY","Score":null,"Total":0}
引用次数: 1

Abstract

Plant, animal and protist genomes often contain endogenous viral elements (EVEs), which correspond to partial and sometimes entire viral genomes that have been captured in the genome of their host organism through a variety of integration mechanisms. While the number of sequenced eukaryotic genomes is rapidly increasing, the annotation and characterization of EVEs remains largely overlooked. EVEs that derive from members of the family Caulimoviridae are widespread across tracheophyte plants, and sometimes they occur in very high copy numbers. However, existing programs for annotating repetitive DNA elements in plant genomes are poor at identifying and then classifying these EVEs. Other than accurately annotating plant genomes, there is intrinsic value in a tool that could identify caulimovirid EVEs as they testify to recent or ancient host-virus interactions and provide valuable insights into virus evolution. In response to this research need, we have developed CAULIFINDER, an automated and sensitive annotation software package. CAULIFINDER consists of two complementary workflows, one to reconstruct, annotate and group caulimovirid EVEs in a given plant genome and the second to classify these genetic elements into officially recognized or tentative genera in the Caulimoviridae. We have benchmarked the CAULIFINDER package using the Vitis vinifera reference genome, which contains a rich assortment of caulimovirid EVEs that have previously been characterized using manual methods. The CAULIFINDER package is distributed in the form of a Docker image.

Abstract Image

Abstract Image

Abstract Image

CAULIFINDER:用于植物基因组中caulimovirid内源病毒元件的自动检测和注释的管道。
植物、动物和原生生物基因组通常含有内源性病毒元件(EVEs),这些内源性病毒元件对应于通过各种整合机制在宿主基因组中捕获的部分甚至整个病毒基因组。虽然测序的真核生物基因组数量正在迅速增加,但EVEs的注释和表征在很大程度上仍然被忽视。来源于Caulimoviridae家族成员的eve广泛存在于气管植物中,有时它们的拷贝数非常高。然而,现有的用于植物基因组中重复DNA元素注释的程序在识别和分类这些eve方面很差。除了准确地注释植物基因组外,这种工具具有内在价值,因为它们可以证明最近或古老的宿主-病毒相互作用,并为病毒进化提供有价值的见解。为了应对这一研究需求,我们开发了CAULIFINDER,一个自动化和敏感的注释软件包。CAULIFINDER包括两个互补的工作流程,一个是在给定的植物基因组中重建、注释和分组caulimovirid eve,第二个是将这些遗传元件分类为正式认可的或初步确定的Caulimoviridae属。我们使用葡萄参考基因组对CAULIFINDER包进行了基准测试,该基因组包含丰富的caulimovirid EVEs,这些EVEs以前已使用手动方法进行了表征。CAULIFINDER包以Docker镜像的形式分发。
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
Mobile DNA
Mobile DNA GENETICS & HEREDITY-
CiteScore
8.20
自引率
6.10%
发文量
26
审稿时长
11 weeks
期刊介绍: Mobile DNA is an online, peer-reviewed, open access journal that publishes articles providing novel insights into DNA rearrangements in all organisms, ranging from transposition and other types of recombination mechanisms to patterns and processes of mobile element and host genome evolution. In addition, the journal will consider articles on the utility of mobile genetic elements in biotechnological methods and protocols.
×
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