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A chromosome-level genome assembly and annotation of the maize elite breeding line Dan340
BACKGROUND: Maize is an important model organism for genetics and genomics research. Though reference genomes of maize are available, some genomes of important genetic germplasms for maize breeding are still lacking, for instance, the cultivar Dan340, which is a backbone inbred line of the LvDa Red...
Autores principales: | , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
GigaScience Press
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9694154/ https://www.ncbi.nlm.nih.gov/pubmed/36824505 http://dx.doi.org/10.46471/gigabyte.63 |
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author | Zhao, Yikun Wang, Yuancong Ma, De Feng, Guang Huo, Yongxue Liu, Zhihao Zhou, Ling Zhang, Yunlong Xu, Liwen Wang, Liang Zhao, Han Zhao, Jiuran Wang, Fengge |
author_facet | Zhao, Yikun Wang, Yuancong Ma, De Feng, Guang Huo, Yongxue Liu, Zhihao Zhou, Ling Zhang, Yunlong Xu, Liwen Wang, Liang Zhao, Han Zhao, Jiuran Wang, Fengge |
author_sort | Zhao, Yikun |
collection | PubMed |
description | BACKGROUND: Maize is an important model organism for genetics and genomics research. Though reference genomes of maize are available, some genomes of important genetic germplasms for maize breeding are still lacking, for instance, the cultivar Dan340, which is a backbone inbred line of the LvDa Red Cob Group with several desirable characteristics. In this study, we constructed a high-quality chromosome-level reference genome for Dan340 by using long HiFi reads, short reads, and Hi-C. The final assembly of the Dan340 genome was 2348.72 Mb, which was anchored to 10 chromosomes. Repeat sequences accounted for 73.40% of the genome and 39,733 protein-coding genes were annotated. Comparative genomic analysis between Dan340 and other maize lines identified that 1806 genes from 359 gene families were specific to Dan340. CONCLUSIONS: Our genome assembly and annotation provide a valuable resource for improving maize breeding and further understanding the intraspecific genome diversity in maize. |
format | Online Article Text |
id | pubmed-9694154 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | GigaScience Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-96941542023-02-22 A chromosome-level genome assembly and annotation of the maize elite breeding line Dan340 Zhao, Yikun Wang, Yuancong Ma, De Feng, Guang Huo, Yongxue Liu, Zhihao Zhou, Ling Zhang, Yunlong Xu, Liwen Wang, Liang Zhao, Han Zhao, Jiuran Wang, Fengge GigaByte Data Release BACKGROUND: Maize is an important model organism for genetics and genomics research. Though reference genomes of maize are available, some genomes of important genetic germplasms for maize breeding are still lacking, for instance, the cultivar Dan340, which is a backbone inbred line of the LvDa Red Cob Group with several desirable characteristics. In this study, we constructed a high-quality chromosome-level reference genome for Dan340 by using long HiFi reads, short reads, and Hi-C. The final assembly of the Dan340 genome was 2348.72 Mb, which was anchored to 10 chromosomes. Repeat sequences accounted for 73.40% of the genome and 39,733 protein-coding genes were annotated. Comparative genomic analysis between Dan340 and other maize lines identified that 1806 genes from 359 gene families were specific to Dan340. CONCLUSIONS: Our genome assembly and annotation provide a valuable resource for improving maize breeding and further understanding the intraspecific genome diversity in maize. GigaScience Press 2022-06-14 /pmc/articles/PMC9694154/ /pubmed/36824505 http://dx.doi.org/10.46471/gigabyte.63 Text en © The Author(s) 2022. 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 | Data Release Zhao, Yikun Wang, Yuancong Ma, De Feng, Guang Huo, Yongxue Liu, Zhihao Zhou, Ling Zhang, Yunlong Xu, Liwen Wang, Liang Zhao, Han Zhao, Jiuran Wang, Fengge A chromosome-level genome assembly and annotation of the maize elite breeding line Dan340 |
title | A chromosome-level genome assembly and annotation of the maize elite breeding line Dan340 |
title_full | A chromosome-level genome assembly and annotation of the maize elite breeding line Dan340 |
title_fullStr | A chromosome-level genome assembly and annotation of the maize elite breeding line Dan340 |
title_full_unstemmed | A chromosome-level genome assembly and annotation of the maize elite breeding line Dan340 |
title_short | A chromosome-level genome assembly and annotation of the maize elite breeding line Dan340 |
title_sort | chromosome-level genome assembly and annotation of the maize elite breeding line dan340 |
topic | Data Release |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9694154/ https://www.ncbi.nlm.nih.gov/pubmed/36824505 http://dx.doi.org/10.46471/gigabyte.63 |
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