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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...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2021
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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 |
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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 |
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