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Beyond genomic variation - comparison and functional annotation of three Brassica rapa genomes: a turnip, a rapid cycling and a Chinese cabbage

BACKGROUND: Brassica rapa is an economically important crop species. During its long breeding history, a large number of morphotypes have been generated, including leafy vegetables such as Chinese cabbage and pakchoi, turnip tuber crops and oil crops. RESULTS: To investigate the genetic variation un...

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Autores principales: Lin, Ke, Zhang, Ningwen, Severing, Edouard I, Nijveen, Harm, Cheng, Feng, Visser, Richard GF, Wang, Xiaowu, de Ridder, Dick, Bonnema, Guusje
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4230417/
https://www.ncbi.nlm.nih.gov/pubmed/24684742
http://dx.doi.org/10.1186/1471-2164-15-250
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author Lin, Ke
Zhang, Ningwen
Severing, Edouard I
Nijveen, Harm
Cheng, Feng
Visser, Richard GF
Wang, Xiaowu
de Ridder, Dick
Bonnema, Guusje
author_facet Lin, Ke
Zhang, Ningwen
Severing, Edouard I
Nijveen, Harm
Cheng, Feng
Visser, Richard GF
Wang, Xiaowu
de Ridder, Dick
Bonnema, Guusje
author_sort Lin, Ke
collection PubMed
description BACKGROUND: Brassica rapa is an economically important crop species. During its long breeding history, a large number of morphotypes have been generated, including leafy vegetables such as Chinese cabbage and pakchoi, turnip tuber crops and oil crops. RESULTS: To investigate the genetic variation underlying this morphological variation, we re-sequenced, assembled and annotated the genomes of two B. rapa subspecies, turnip crops (turnip) and a rapid cycling. We then analysed the two resulting genomes together with the Chinese cabbage Chiifu reference genome to obtain an impression of the B. rapa pan-genome. The number of genes with protein-coding changes between the three genotypes was lower than that among different accessions of Arabidopsis thaliana, which can be explained by the smaller effective population size of B. rapa due to its domestication. Based on orthology to a number of non-brassica species, we estimated the date of divergence among the three B. rapa morphotypes at approximately 250,000 YA, far predating Brassica domestication (5,000-10,000 YA). CONCLUSIONS: By analysing genes unique to turnip we found evidence for copy number differences in peroxidases, pointing to a role for the phenylpropanoid biosynthesis pathway in the generation of morphological variation. The estimated date of divergence among three B. rapa morphotypes implies that prior to domestication there was already considerably divergence among B. rapa genotypes. Our study thus provides two new B. rapa reference genomes, delivers a set of computer tools to analyse the resulting pan-genome and uses these to shed light on genetic drivers behind the rich morphological variation found in B. rapa. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1471-2164-15-250) contains supplementary material, which is available to authorized users.
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spelling pubmed-42304172014-11-14 Beyond genomic variation - comparison and functional annotation of three Brassica rapa genomes: a turnip, a rapid cycling and a Chinese cabbage Lin, Ke Zhang, Ningwen Severing, Edouard I Nijveen, Harm Cheng, Feng Visser, Richard GF Wang, Xiaowu de Ridder, Dick Bonnema, Guusje BMC Genomics Research Article BACKGROUND: Brassica rapa is an economically important crop species. During its long breeding history, a large number of morphotypes have been generated, including leafy vegetables such as Chinese cabbage and pakchoi, turnip tuber crops and oil crops. RESULTS: To investigate the genetic variation underlying this morphological variation, we re-sequenced, assembled and annotated the genomes of two B. rapa subspecies, turnip crops (turnip) and a rapid cycling. We then analysed the two resulting genomes together with the Chinese cabbage Chiifu reference genome to obtain an impression of the B. rapa pan-genome. The number of genes with protein-coding changes between the three genotypes was lower than that among different accessions of Arabidopsis thaliana, which can be explained by the smaller effective population size of B. rapa due to its domestication. Based on orthology to a number of non-brassica species, we estimated the date of divergence among the three B. rapa morphotypes at approximately 250,000 YA, far predating Brassica domestication (5,000-10,000 YA). CONCLUSIONS: By analysing genes unique to turnip we found evidence for copy number differences in peroxidases, pointing to a role for the phenylpropanoid biosynthesis pathway in the generation of morphological variation. The estimated date of divergence among three B. rapa morphotypes implies that prior to domestication there was already considerably divergence among B. rapa genotypes. Our study thus provides two new B. rapa reference genomes, delivers a set of computer tools to analyse the resulting pan-genome and uses these to shed light on genetic drivers behind the rich morphological variation found in B. rapa. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1471-2164-15-250) contains supplementary material, which is available to authorized users. BioMed Central 2014-03-31 /pmc/articles/PMC4230417/ /pubmed/24684742 http://dx.doi.org/10.1186/1471-2164-15-250 Text en © Lin et al.; licensee BioMed Central Ltd. 2014 This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited.
spellingShingle Research Article
Lin, Ke
Zhang, Ningwen
Severing, Edouard I
Nijveen, Harm
Cheng, Feng
Visser, Richard GF
Wang, Xiaowu
de Ridder, Dick
Bonnema, Guusje
Beyond genomic variation - comparison and functional annotation of three Brassica rapa genomes: a turnip, a rapid cycling and a Chinese cabbage
title Beyond genomic variation - comparison and functional annotation of three Brassica rapa genomes: a turnip, a rapid cycling and a Chinese cabbage
title_full Beyond genomic variation - comparison and functional annotation of three Brassica rapa genomes: a turnip, a rapid cycling and a Chinese cabbage
title_fullStr Beyond genomic variation - comparison and functional annotation of three Brassica rapa genomes: a turnip, a rapid cycling and a Chinese cabbage
title_full_unstemmed Beyond genomic variation - comparison and functional annotation of three Brassica rapa genomes: a turnip, a rapid cycling and a Chinese cabbage
title_short Beyond genomic variation - comparison and functional annotation of three Brassica rapa genomes: a turnip, a rapid cycling and a Chinese cabbage
title_sort beyond genomic variation - comparison and functional annotation of three brassica rapa genomes: a turnip, a rapid cycling and a chinese cabbage
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4230417/
https://www.ncbi.nlm.nih.gov/pubmed/24684742
http://dx.doi.org/10.1186/1471-2164-15-250
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