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Insights from the first genome assembly of Onion (Allium cepa)

Onion is an important vegetable crop with an estimated genome size of 16 Gb. We describe the de novo assembly and ab initio annotation of the genome of a doubled haploid onion line DHCU066619, which resulted in a final assembly of 14.9 Gb with an N50 of 464 Kb. Of this, 2.4 Gb was ordered into eight...

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Autores principales: Finkers, Richard, van Kaauwen, Martijn, Ament, Kai, Burger-Meijer, Karin, Egging, Raymond, Huits, Henk, Kodde, Linda, Kroon, Laurens, Shigyo, Masayoshi, Sato, Shusei, Vosman, Ben, van Workum, Wilbert, Scholten, Olga
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8496297/
https://www.ncbi.nlm.nih.gov/pubmed/34544132
http://dx.doi.org/10.1093/g3journal/jkab243
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author Finkers, Richard
van Kaauwen, Martijn
Ament, Kai
Burger-Meijer, Karin
Egging, Raymond
Huits, Henk
Kodde, Linda
Kroon, Laurens
Shigyo, Masayoshi
Sato, Shusei
Vosman, Ben
van Workum, Wilbert
Scholten, Olga
author_facet Finkers, Richard
van Kaauwen, Martijn
Ament, Kai
Burger-Meijer, Karin
Egging, Raymond
Huits, Henk
Kodde, Linda
Kroon, Laurens
Shigyo, Masayoshi
Sato, Shusei
Vosman, Ben
van Workum, Wilbert
Scholten, Olga
author_sort Finkers, Richard
collection PubMed
description Onion is an important vegetable crop with an estimated genome size of 16 Gb. We describe the de novo assembly and ab initio annotation of the genome of a doubled haploid onion line DHCU066619, which resulted in a final assembly of 14.9 Gb with an N50 of 464 Kb. Of this, 2.4 Gb was ordered into eight pseudomolecules using four genetic linkage maps. The remainder of the genome is available in 89.6 K scaffolds. Only 72.4% of the genome could be identified as repetitive sequences and consist, to a large extent, of (retro) transposons. In addition, an estimated 20% of the putative (retro) transposons had accumulated a large number of mutations, hampering their identification, but facilitating their assembly. These elements are probably already quite old. The ab initio gene prediction indicated 540,925 putative gene models, which is far more than expected, possibly due to the presence of pseudogenes. Of these models, 47,066 showed RNASeq support. No gene rich regions were found, genes are uniformly distributed over the genome. Analysis of synteny with Allium sativum (garlic) showed collinearity but also major rearrangements between both species. This assembly is the first high-quality genome sequence available for the study of onion and will be a valuable resource for further research.
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spelling pubmed-84962972021-10-07 Insights from the first genome assembly of Onion (Allium cepa) Finkers, Richard van Kaauwen, Martijn Ament, Kai Burger-Meijer, Karin Egging, Raymond Huits, Henk Kodde, Linda Kroon, Laurens Shigyo, Masayoshi Sato, Shusei Vosman, Ben van Workum, Wilbert Scholten, Olga G3 (Bethesda) Genome Report Onion is an important vegetable crop with an estimated genome size of 16 Gb. We describe the de novo assembly and ab initio annotation of the genome of a doubled haploid onion line DHCU066619, which resulted in a final assembly of 14.9 Gb with an N50 of 464 Kb. Of this, 2.4 Gb was ordered into eight pseudomolecules using four genetic linkage maps. The remainder of the genome is available in 89.6 K scaffolds. Only 72.4% of the genome could be identified as repetitive sequences and consist, to a large extent, of (retro) transposons. In addition, an estimated 20% of the putative (retro) transposons had accumulated a large number of mutations, hampering their identification, but facilitating their assembly. These elements are probably already quite old. The ab initio gene prediction indicated 540,925 putative gene models, which is far more than expected, possibly due to the presence of pseudogenes. Of these models, 47,066 showed RNASeq support. No gene rich regions were found, genes are uniformly distributed over the genome. Analysis of synteny with Allium sativum (garlic) showed collinearity but also major rearrangements between both species. This assembly is the first high-quality genome sequence available for the study of onion and will be a valuable resource for further research. Oxford University Press 2021-07-13 /pmc/articles/PMC8496297/ /pubmed/34544132 http://dx.doi.org/10.1093/g3journal/jkab243 Text en © The Author(s) 2021. Published by Oxford University Press on behalf of 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 (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 Genome Report
Finkers, Richard
van Kaauwen, Martijn
Ament, Kai
Burger-Meijer, Karin
Egging, Raymond
Huits, Henk
Kodde, Linda
Kroon, Laurens
Shigyo, Masayoshi
Sato, Shusei
Vosman, Ben
van Workum, Wilbert
Scholten, Olga
Insights from the first genome assembly of Onion (Allium cepa)
title Insights from the first genome assembly of Onion (Allium cepa)
title_full Insights from the first genome assembly of Onion (Allium cepa)
title_fullStr Insights from the first genome assembly of Onion (Allium cepa)
title_full_unstemmed Insights from the first genome assembly of Onion (Allium cepa)
title_short Insights from the first genome assembly of Onion (Allium cepa)
title_sort insights from the first genome assembly of onion (allium cepa)
topic Genome Report
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8496297/
https://www.ncbi.nlm.nih.gov/pubmed/34544132
http://dx.doi.org/10.1093/g3journal/jkab243
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