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Whole-genome sequence of synthetically derived Brassica napus inbred cultivar Da-Ae

Brassica napus, a globally important oilseed crop, is an allotetraploid hybrid species with two subgenomes originating from Brassica rapa and Brassica oleracea. The presence of two highly similar subgenomes has made the assembly of a complete draft genome challenging and has also resulted in natural...

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Autores principales: Davis, John T, Li, Ruijuan, Kim, Seungmo, Michelmore, Richard, Kim, Shinje, Maloof, Julin N
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10085753/
https://www.ncbi.nlm.nih.gov/pubmed/36724115
http://dx.doi.org/10.1093/g3journal/jkad026
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author Davis, John T
Li, Ruijuan
Kim, Seungmo
Michelmore, Richard
Kim, Shinje
Maloof, Julin N
author_facet Davis, John T
Li, Ruijuan
Kim, Seungmo
Michelmore, Richard
Kim, Shinje
Maloof, Julin N
author_sort Davis, John T
collection PubMed
description Brassica napus, a globally important oilseed crop, is an allotetraploid hybrid species with two subgenomes originating from Brassica rapa and Brassica oleracea. The presence of two highly similar subgenomes has made the assembly of a complete draft genome challenging and has also resulted in natural homoeologous exchanges between the genomes, resulting in variations in gene copy number, which further complicates assigning sequences to correct chromosomes. Despite these challenges, high-quality draft genomes of this species have been released. Using third generation sequencing and assembly technologies, we generated a new genome assembly for the synthetic B. napus cultivar Da-Ae. Through the use of long reads, linked-reads, and Hi-C proximity data, we assembled a new draft genome that provides a high-quality reference genome of a synthetic B. napus. In addition, we identified potential hotspots of homoeologous exchange between subgenomes within Da-Ae, based on their presence in other independently derived lines. The occurrence of these hotspots may provide insight into the genetic rearrangements required for B. napus to be viable following the hybridization of B. rapa and B. oleracea.
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spelling pubmed-100857532023-04-12 Whole-genome sequence of synthetically derived Brassica napus inbred cultivar Da-Ae Davis, John T Li, Ruijuan Kim, Seungmo Michelmore, Richard Kim, Shinje Maloof, Julin N G3 (Bethesda) Genome Report Brassica napus, a globally important oilseed crop, is an allotetraploid hybrid species with two subgenomes originating from Brassica rapa and Brassica oleracea. The presence of two highly similar subgenomes has made the assembly of a complete draft genome challenging and has also resulted in natural homoeologous exchanges between the genomes, resulting in variations in gene copy number, which further complicates assigning sequences to correct chromosomes. Despite these challenges, high-quality draft genomes of this species have been released. Using third generation sequencing and assembly technologies, we generated a new genome assembly for the synthetic B. napus cultivar Da-Ae. Through the use of long reads, linked-reads, and Hi-C proximity data, we assembled a new draft genome that provides a high-quality reference genome of a synthetic B. napus. In addition, we identified potential hotspots of homoeologous exchange between subgenomes within Da-Ae, based on their presence in other independently derived lines. The occurrence of these hotspots may provide insight into the genetic rearrangements required for B. napus to be viable following the hybridization of B. rapa and B. oleracea. Oxford University Press 2023-02-01 /pmc/articles/PMC10085753/ /pubmed/36724115 http://dx.doi.org/10.1093/g3journal/jkad026 Text en © The Author(s) 2023. Published by Oxford University Press on behalf of the Genetics Society of America. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (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 Genome Report
Davis, John T
Li, Ruijuan
Kim, Seungmo
Michelmore, Richard
Kim, Shinje
Maloof, Julin N
Whole-genome sequence of synthetically derived Brassica napus inbred cultivar Da-Ae
title Whole-genome sequence of synthetically derived Brassica napus inbred cultivar Da-Ae
title_full Whole-genome sequence of synthetically derived Brassica napus inbred cultivar Da-Ae
title_fullStr Whole-genome sequence of synthetically derived Brassica napus inbred cultivar Da-Ae
title_full_unstemmed Whole-genome sequence of synthetically derived Brassica napus inbred cultivar Da-Ae
title_short Whole-genome sequence of synthetically derived Brassica napus inbred cultivar Da-Ae
title_sort whole-genome sequence of synthetically derived brassica napus inbred cultivar da-ae
topic Genome Report
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10085753/
https://www.ncbi.nlm.nih.gov/pubmed/36724115
http://dx.doi.org/10.1093/g3journal/jkad026
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