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Pseudomolecule-level assembly of the Chinese oil tree yellowhorn (Xanthoceras sorbifolium) genome

BACKGROUND: Yellowhorn (Xanthoceras sorbifolium) is a species of the Sapindaceae family native to China and is an oil tree that can withstand cold and drought conditions. A pseudomolecule-level genome assembly for this species will not only contribute to understanding the evolution of its genes and...

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Autores principales: Bi, Quanxin, Zhao, Yang, Du, Wei, Lu, Ying, Gui, Lang, Zheng, Zhimin, Yu, Haiyan, Cui, Yifan, Liu, Zhi, Cui, Tianpeng, Cui, Deshi, Liu, Xiaojuan, Li, Yingchao, Fan, Siqi, Hu, Xiaoyu, Fu, Guanghui, Ding, Jian, Ruan, Chengjiang, Wang, Libing
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6593361/
https://www.ncbi.nlm.nih.gov/pubmed/31241154
http://dx.doi.org/10.1093/gigascience/giz070
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author Bi, Quanxin
Zhao, Yang
Du, Wei
Lu, Ying
Gui, Lang
Zheng, Zhimin
Yu, Haiyan
Cui, Yifan
Liu, Zhi
Cui, Tianpeng
Cui, Deshi
Liu, Xiaojuan
Li, Yingchao
Fan, Siqi
Hu, Xiaoyu
Fu, Guanghui
Ding, Jian
Ruan, Chengjiang
Wang, Libing
author_facet Bi, Quanxin
Zhao, Yang
Du, Wei
Lu, Ying
Gui, Lang
Zheng, Zhimin
Yu, Haiyan
Cui, Yifan
Liu, Zhi
Cui, Tianpeng
Cui, Deshi
Liu, Xiaojuan
Li, Yingchao
Fan, Siqi
Hu, Xiaoyu
Fu, Guanghui
Ding, Jian
Ruan, Chengjiang
Wang, Libing
author_sort Bi, Quanxin
collection PubMed
description BACKGROUND: Yellowhorn (Xanthoceras sorbifolium) is a species of the Sapindaceae family native to China and is an oil tree that can withstand cold and drought conditions. A pseudomolecule-level genome assembly for this species will not only contribute to understanding the evolution of its genes and chromosomes but also bring yellowhorn breeding into the genomic era. FINDINGS: Here, we generated 15 pseudomolecules of yellowhorn chromosomes, on which 97.04% of scaffolds were anchored, using the combined Illumina HiSeq, Pacific Biosciences Sequel, and Hi-C technologies. The length of the final yellowhorn genome assembly was 504.2 Mb with a contig N50 size of 1.04 Mb and a scaffold N50 size of 32.17 Mb. Genome annotation revealed that 68.67% of the yellowhorn genome was composed of repetitive elements. Gene modelling predicted 24,672 protein-coding genes. By comparing orthologous genes, the divergence time of yellowhorn and its close sister species longan (Dimocarpus longan) was estimated at ∼33.07 million years ago. Gene cluster and chromosome synteny analysis demonstrated that the yellowhorn genome shared a conserved genome structure with its ancestor in some chromosomes. CONCLUSIONS: This genome assembly represents a high-quality reference genome for yellowhorn. Integrated genome annotations provide a valuable dataset for genetic and molecular research in this species. We did not detect whole-genome duplication in the genome. The yellowhorn genome carries syntenic blocks from ancient chromosomes. These data sources will enable this genome to serve as an initial platform for breeding better yellowhorn cultivars.
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spelling pubmed-65933612019-07-01 Pseudomolecule-level assembly of the Chinese oil tree yellowhorn (Xanthoceras sorbifolium) genome Bi, Quanxin Zhao, Yang Du, Wei Lu, Ying Gui, Lang Zheng, Zhimin Yu, Haiyan Cui, Yifan Liu, Zhi Cui, Tianpeng Cui, Deshi Liu, Xiaojuan Li, Yingchao Fan, Siqi Hu, Xiaoyu Fu, Guanghui Ding, Jian Ruan, Chengjiang Wang, Libing Gigascience Data Note BACKGROUND: Yellowhorn (Xanthoceras sorbifolium) is a species of the Sapindaceae family native to China and is an oil tree that can withstand cold and drought conditions. A pseudomolecule-level genome assembly for this species will not only contribute to understanding the evolution of its genes and chromosomes but also bring yellowhorn breeding into the genomic era. FINDINGS: Here, we generated 15 pseudomolecules of yellowhorn chromosomes, on which 97.04% of scaffolds were anchored, using the combined Illumina HiSeq, Pacific Biosciences Sequel, and Hi-C technologies. The length of the final yellowhorn genome assembly was 504.2 Mb with a contig N50 size of 1.04 Mb and a scaffold N50 size of 32.17 Mb. Genome annotation revealed that 68.67% of the yellowhorn genome was composed of repetitive elements. Gene modelling predicted 24,672 protein-coding genes. By comparing orthologous genes, the divergence time of yellowhorn and its close sister species longan (Dimocarpus longan) was estimated at ∼33.07 million years ago. Gene cluster and chromosome synteny analysis demonstrated that the yellowhorn genome shared a conserved genome structure with its ancestor in some chromosomes. CONCLUSIONS: This genome assembly represents a high-quality reference genome for yellowhorn. Integrated genome annotations provide a valuable dataset for genetic and molecular research in this species. We did not detect whole-genome duplication in the genome. The yellowhorn genome carries syntenic blocks from ancient chromosomes. These data sources will enable this genome to serve as an initial platform for breeding better yellowhorn cultivars. Oxford University Press 2019-06-26 /pmc/articles/PMC6593361/ /pubmed/31241154 http://dx.doi.org/10.1093/gigascience/giz070 Text en © The Author(s) 2019. Published by Oxford University Press. http://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/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Data Note
Bi, Quanxin
Zhao, Yang
Du, Wei
Lu, Ying
Gui, Lang
Zheng, Zhimin
Yu, Haiyan
Cui, Yifan
Liu, Zhi
Cui, Tianpeng
Cui, Deshi
Liu, Xiaojuan
Li, Yingchao
Fan, Siqi
Hu, Xiaoyu
Fu, Guanghui
Ding, Jian
Ruan, Chengjiang
Wang, Libing
Pseudomolecule-level assembly of the Chinese oil tree yellowhorn (Xanthoceras sorbifolium) genome
title Pseudomolecule-level assembly of the Chinese oil tree yellowhorn (Xanthoceras sorbifolium) genome
title_full Pseudomolecule-level assembly of the Chinese oil tree yellowhorn (Xanthoceras sorbifolium) genome
title_fullStr Pseudomolecule-level assembly of the Chinese oil tree yellowhorn (Xanthoceras sorbifolium) genome
title_full_unstemmed Pseudomolecule-level assembly of the Chinese oil tree yellowhorn (Xanthoceras sorbifolium) genome
title_short Pseudomolecule-level assembly of the Chinese oil tree yellowhorn (Xanthoceras sorbifolium) genome
title_sort pseudomolecule-level assembly of the chinese oil tree yellowhorn (xanthoceras sorbifolium) genome
topic Data Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6593361/
https://www.ncbi.nlm.nih.gov/pubmed/31241154
http://dx.doi.org/10.1093/gigascience/giz070
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