Cargando…

Building pan-genome infrastructures for crop plants and their use in association genetics

Pan-genomic studies aim at representing the entire sequence diversity within a species to provide useful resources for evolutionary studies, functional genomics and breeding of cultivated plants. Cost reductions in high-throughput sequencing and advances in sequence assembly algorithms have made it...

Descripción completa

Detalles Bibliográficos
Autores principales: Jayakodi, Murukarthick, Schreiber, Mona, Stein, Nils, Mascher, Martin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7934568/
https://www.ncbi.nlm.nih.gov/pubmed/33484244
http://dx.doi.org/10.1093/dnares/dsaa030
_version_ 1783660841806069760
author Jayakodi, Murukarthick
Schreiber, Mona
Stein, Nils
Mascher, Martin
author_facet Jayakodi, Murukarthick
Schreiber, Mona
Stein, Nils
Mascher, Martin
author_sort Jayakodi, Murukarthick
collection PubMed
description Pan-genomic studies aim at representing the entire sequence diversity within a species to provide useful resources for evolutionary studies, functional genomics and breeding of cultivated plants. Cost reductions in high-throughput sequencing and advances in sequence assembly algorithms have made it possible to create multiple reference genomes along with a catalogue of all forms of genetic variations in plant species with large and complex or polyploid genomes. In this review, we summarize the current approaches to building pan-genomes as an in silico representation of plant sequence diversity and outline relevant methods for their effective utilization in linking structural with phenotypic variation. We propose as future research avenues (i) transcriptomic and epigenomic studies across multiple reference genomes and (ii) the development of user-friendly and feature-rich pan-genome browsers.
format Online
Article
Text
id pubmed-7934568
institution National Center for Biotechnology Information
language English
publishDate 2021
publisher Oxford University Press
record_format MEDLINE/PubMed
spelling pubmed-79345682021-03-10 Building pan-genome infrastructures for crop plants and their use in association genetics Jayakodi, Murukarthick Schreiber, Mona Stein, Nils Mascher, Martin DNA Res Invited Review Pan-genomic studies aim at representing the entire sequence diversity within a species to provide useful resources for evolutionary studies, functional genomics and breeding of cultivated plants. Cost reductions in high-throughput sequencing and advances in sequence assembly algorithms have made it possible to create multiple reference genomes along with a catalogue of all forms of genetic variations in plant species with large and complex or polyploid genomes. In this review, we summarize the current approaches to building pan-genomes as an in silico representation of plant sequence diversity and outline relevant methods for their effective utilization in linking structural with phenotypic variation. We propose as future research avenues (i) transcriptomic and epigenomic studies across multiple reference genomes and (ii) the development of user-friendly and feature-rich pan-genome browsers. Oxford University Press 2021-01-22 /pmc/articles/PMC7934568/ /pubmed/33484244 http://dx.doi.org/10.1093/dnares/dsaa030 Text en © The Author(s) 2021. Published by Oxford University Press on behalf of Kazusa DNA Research Institute. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) ), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Invited Review
Jayakodi, Murukarthick
Schreiber, Mona
Stein, Nils
Mascher, Martin
Building pan-genome infrastructures for crop plants and their use in association genetics
title Building pan-genome infrastructures for crop plants and their use in association genetics
title_full Building pan-genome infrastructures for crop plants and their use in association genetics
title_fullStr Building pan-genome infrastructures for crop plants and their use in association genetics
title_full_unstemmed Building pan-genome infrastructures for crop plants and their use in association genetics
title_short Building pan-genome infrastructures for crop plants and their use in association genetics
title_sort building pan-genome infrastructures for crop plants and their use in association genetics
topic Invited Review
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7934568/
https://www.ncbi.nlm.nih.gov/pubmed/33484244
http://dx.doi.org/10.1093/dnares/dsaa030
work_keys_str_mv AT jayakodimurukarthick buildingpangenomeinfrastructuresforcropplantsandtheiruseinassociationgenetics
AT schreibermona buildingpangenomeinfrastructuresforcropplantsandtheiruseinassociationgenetics
AT steinnils buildingpangenomeinfrastructuresforcropplantsandtheiruseinassociationgenetics
AT maschermartin buildingpangenomeinfrastructuresforcropplantsandtheiruseinassociationgenetics