vavilovВавиловский журнал генетики и селекцииVavilov Journal of Genetics and Breeding2500-3259Institute of Cytology and Genetics of Siberian Branch of the RAS10.18699/VJ21.007vavilov-2916Research ArticleБИОИНФОРМАТИКА И СИСТЕМНАЯ КОМПЬЮТЕРНАЯ БИОЛОГИЯBIOINFORMATICS AND COMPUTATIONAL SYSTEMS BIOLOGYПангеномы сельскохозяйственных растенийCrop pangenomeshttps://orcid.org/0000-0002-3011-6288ПронозинА. Ю.PronozinA. Yu.

Новосибирск

Novosibirsk

pronozinartem95@gmail.comБрагинаМ. К.BraginaM. K.

Новосибирск

Novosibirsk

https://orcid.org/0000-0001-8590-847XСалинаЕ. А.SalinaE. A.

Новосибирск

Novosibirsk

Федеральный исследовательский центр Институт цитологии и генетики Сибирского отделения Российской академии наукРоссияInstitute of Cytology and Genetics of Siberian Branch of the Russian Academy of SciencesRussian FederationФедеральный исследовательский центр Институт цитологии и генетики Сибирского отделения Российской академии наук; Курчатовский геномный центр Института цитологии и генетики Сибирского отделения Российской академии наукРоссияInstitute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences; Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of SciencesRussian Federation2021150320212515763Copyright © Пронозин А.Ю., Брагина М.К., Салина Е.А., 20212021Пронозин А.Ю., Брагина М.К., Салина Е.А.Pronozin A.Y., Bragina M.K., Salina E.A.This work is licensed under a Creative Commons Attribution 4.0 License.https://vavilov.elpub.ru/jour/article/view/2916

Cеквенирование генома организма – важный этап в его генетических исследованиях. Расшифровка геномной последовательности открывает широкие возможности для изучения строения структуры хромосом, распределения повторенных и кодирующих последовательностей, идентификации и аннотации генов. При исследовании сельскохозяйственных растений это позволяет анализировать функции генов, разрабатывать маркеры для поиска ассоциаций с фенотипическими признаками. При решении этих задач геном вида часто представлен последовательностью одного организма (так называемым референсным геномом). В последнее время, однако, появляется много свидетельств в пользу того, что большие структурные изменения генома, включая вариации числа копий генов и вариации наличия/отсутствия генов, преобладают в сельскохозяйственных культурах, играют ключевую роль в генетическом определении агрономически важных признаков и приводят к значительным вариациям функционального набора генов и генного состава у представителей одного вида. Такие структурные вариации не могут быть представлены на основе одной лишь референсной последовательности и описываются исходя из концепции пангенома. Пангеном – это информация о полном наборе генов таксона, среди которых можно выделить набор универсальных генов, общих для всех представителей таксона, и вариабельных генов, которые являются частично или полностью специфичными для его представителей. Анализ пангеномов дает более точное понимание генетического разнообразия генофонда. Технологии секвенирования и анализа пангеномов позволяют обеспечить возможность масштабного изучения геномных вариаций, доступ к более широкому спектру геномных данных в селекционных программах и помогут ускорить селекцию культурных растений для создания сортов со стабильно высокой урожайностью и устойчивостью к стрессам. В работе представлен краткий обзор исследования пангеномов сельскохозяйственных растений, описаны их структурные особенности, методы и программы биоинформатического анализа пангеномных данных.

Progress in genome sequencing, assembly and analysis allows for a deeper study of agricultural plants’ chromosome structures, gene identif ication and annotation. The published genomes of agricultural plants proved to be a valuable tool for studing gene functions and for marker-assisted and genomic selection. However, large structural genome changes, including gene copy number variations (CNVs) and gene presence/absence variations (PAVs), prevail in crops. These genomic variations play an important role in the functional set of genes and the gene composition in individuals of the same species and provide the genetic determination of the agronomically important crops properties. A high degree of genomic variation observed indicates that single reference genomes do not represent the diversity within a species, leading to the pangenome concept. The pangenome represents information about all genes in a taxon: those that are common to all taxon members and those that are variable and are partially or completely specif ic for particular individuals. Pangenome sequencing and analysis technologies provide a large-scale study of genomic variation and resources for an evolutionary research, functional genomics and crop breeding. This review provides an analysis of agricultural plants’ pangenome studies. Pangenome structural features, methods and programs for bioinformatic analysis of pangenomic data are described.

сельскохозяйственные растениягеномыпангеномыгеныэволюциябиоинформатический анализвычислительные конвейерыagricultural plantsgenomespangenomesgenesevolutionbioinformatics analysiscomputational pipelinesThis work was carried out with funding from the Russian Science Foundation, grant No. 18-14-00293. The authors are grateful to N.A. Shmakov and D.A. Afonnikov for their assistance with the text. We consider it our pleasant duty to thank the anonymous reviewers for their valuable comments.ReferencesAlcaraz L.D., Moreno-Hagelsieb G., Eguiarte L.E., Souza V., HerreraEstrella L., Olmedo G. Understanding the evolutionary relationships and major traits of Bacillus through comparative genomics. BMC Genomics. 2010;11(1):332.Alcaraz L.D., Moreno-Hagelsieb G., Eguiarte L.E., Souza V., HerreraEstrella L., Olmedo G. Understanding the evolutionary relationships and major traits of Bacillus through comparative genomics. BMC Genomics. 2010;11(1):332.Bragina M.K., Afonnikov D.A., Salina E.A. 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The authors declare that there are no conflicts of interest present.