The reference genome and organelle genomes of wasabi (Eutrema japoniacum)

Wasabi (Eutrema japonicum) is one of the most famous vegetable crops in the family Brassicaceae. However, a limited genomic resource is available, which hinders genomic breeding and understanding of the genetic basis of vital traits. Here, we generated the genome assembly of wasabi using the hybrid...

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Autores principales: Liu, Hexia, Qiao, Qinghua, Ye, Xiaoxia, Guo, Yipeng, Ye, Baojian, Xu, Qiuyuan, Zhou, Xingwen, Li, Bo
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Genetics
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9661192/
https://www.ncbi.nlm.nih.gov/pubmed/36386825
http://dx.doi.org/10.3389/fgene.2022.1048264
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author Liu, Hexia
Qiao, Qinghua
Ye, Xiaoxia
Guo, Yipeng
Ye, Baojian
Xu, Qiuyuan
Zhou, Xingwen
Li, Bo
author_facet Liu, Hexia
Qiao, Qinghua
Ye, Xiaoxia
Guo, Yipeng
Ye, Baojian
Xu, Qiuyuan
Zhou, Xingwen
Li, Bo
author_sort Liu, Hexia
collection PubMed
description Wasabi (Eutrema japonicum) is one of the most famous vegetable crops in the family Brassicaceae. However, a limited genomic resource is available, which hinders genomic breeding and understanding of the genetic basis of vital traits. Here, we generated the genome assembly of wasabi using the hybrid genome assembly strategy, which combined the Nanopore long reads and Illumina reads. The genome assembly contains 687M bp and 39,534 high-quality annotated gene models. Besides, we annotated 68.85% of the genomic sequences as repetitive elements, including 43.72% of retrotransposons and 18.99% of DNA transposons. Using the customized pipeline, we also generated the complete organelle genomes of wasabi. This reference genome could provide essential genomic resources for evolution, breeding, and exploring the unique biological traits of wasabi.
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spelling pubmed-96611922022-11-15 The reference genome and organelle genomes of wasabi (Eutrema japoniacum) Liu, Hexia Qiao, Qinghua Ye, Xiaoxia Guo, Yipeng Ye, Baojian Xu, Qiuyuan Zhou, Xingwen Li, Bo Front Genet Genetics Wasabi (Eutrema japonicum) is one of the most famous vegetable crops in the family Brassicaceae. However, a limited genomic resource is available, which hinders genomic breeding and understanding of the genetic basis of vital traits. Here, we generated the genome assembly of wasabi using the hybrid genome assembly strategy, which combined the Nanopore long reads and Illumina reads. The genome assembly contains 687M bp and 39,534 high-quality annotated gene models. Besides, we annotated 68.85% of the genomic sequences as repetitive elements, including 43.72% of retrotransposons and 18.99% of DNA transposons. Using the customized pipeline, we also generated the complete organelle genomes of wasabi. This reference genome could provide essential genomic resources for evolution, breeding, and exploring the unique biological traits of wasabi. Frontiers Media S.A. 2022-10-31 /pmc/articles/PMC9661192/ /pubmed/36386825 http://dx.doi.org/10.3389/fgene.2022.1048264 Text en Copyright © 2022 Liu, Qiao, Ye, Guo, Ye, Xu, Zhou and Li. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Genetics
Liu, Hexia
Qiao, Qinghua
Ye, Xiaoxia
Guo, Yipeng
Ye, Baojian
Xu, Qiuyuan
Zhou, Xingwen
Li, Bo
The reference genome and organelle genomes of wasabi (Eutrema japoniacum)
title The reference genome and organelle genomes of wasabi (Eutrema japoniacum)
title_full The reference genome and organelle genomes of wasabi (Eutrema japoniacum)
title_fullStr The reference genome and organelle genomes of wasabi (Eutrema japoniacum)
title_full_unstemmed The reference genome and organelle genomes of wasabi (Eutrema japoniacum)
title_short The reference genome and organelle genomes of wasabi (Eutrema japoniacum)
title_sort reference genome and organelle genomes of wasabi (eutrema japoniacum)
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9661192/
https://www.ncbi.nlm.nih.gov/pubmed/36386825
http://dx.doi.org/10.3389/fgene.2022.1048264
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