Crop pangenomes.

A Yu Pronozin,E A Salina,M K Bragina

doi:10.18699/vj21.007

Abstract

Progress in genome sequencing, assembly and analysis allows for a deeper study of agricultural plants’ chromosome structures, gene identification 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 specific 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

Highlights

The genome sequence is the basis for a chromosome structure studying, a distribution of repetitive and coding sequences, and genes identification and annotation (Bragina et al, 2019)
The analysis identified more than two thousand sequences that were not represented in the maize reference genome, including genes responsible for the biotic stress response
Pangenome analysis and annotation methods Based on a comparison of sequences, genome annotation allows identifying gene sequences in taxon representatives’ genomes, to determine orthologous genes and universal and variable genes families

Summary

Introduction

The genome sequence is the basis for a chromosome structure studying, a distribution of repetitive and coding sequences, and genes identification and annotation (Bragina et al, 2019). При исследовании сельскохозяйственных растений это позволяет анализировать функции генов, разрабатывать маркеры для поиска ассоциаций с фенотипическими признаками. В работе представлен краткий обзор исследования пангеномов сельскохозяйственных растений, описаны их структурные особенности, методы и программы биоинформатического анализа пангеномных данных.

Results

Conclusion