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Chromosome-scale genomes of commercial timber trees (Ochroma pyramidale, Mesua ferrea, and Tectona grandis)

Wood is the most important natural and endlessly renewable source of energy. Despite the ecological and economic importance of wood, many aspects of its formation have not yet been investigated. We performed chromosome-scale genome assemblies of three timber trees (Ochroma pyramidale, Mesua ferrea,...

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Autores principales: Sahu, Sunil Kumar, Liu, Min, Chen, Yewen, Gui, Jinshan, Fang, Dongming, Chen, Xiaoli, Yang, Ting, He, Chengzhong, Cheng, Le, Yang, Jinlong, Sahu, Durgesh Nandini, Li, Linzhou, Wang, Hongli, Mu, Weixue, Wei, Jinpu, Liu, Jie, Zhao, Yuxian, Zhang, Shouzhou, Lisby, Michael, Liu, Xin, Xu, Xun, Li, Laigeng, Wang, Sibo, Liu, Huan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10400565/
https://www.ncbi.nlm.nih.gov/pubmed/37537171
http://dx.doi.org/10.1038/s41597-023-02420-8
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author Sahu, Sunil Kumar
Liu, Min
Chen, Yewen
Gui, Jinshan
Fang, Dongming
Chen, Xiaoli
Yang, Ting
He, Chengzhong
Cheng, Le
Yang, Jinlong
Sahu, Durgesh Nandini
Li, Linzhou
Wang, Hongli
Mu, Weixue
Wei, Jinpu
Liu, Jie
Zhao, Yuxian
Zhang, Shouzhou
Lisby, Michael
Liu, Xin
Xu, Xun
Li, Laigeng
Wang, Sibo
Liu, Huan
author_facet Sahu, Sunil Kumar
Liu, Min
Chen, Yewen
Gui, Jinshan
Fang, Dongming
Chen, Xiaoli
Yang, Ting
He, Chengzhong
Cheng, Le
Yang, Jinlong
Sahu, Durgesh Nandini
Li, Linzhou
Wang, Hongli
Mu, Weixue
Wei, Jinpu
Liu, Jie
Zhao, Yuxian
Zhang, Shouzhou
Lisby, Michael
Liu, Xin
Xu, Xun
Li, Laigeng
Wang, Sibo
Liu, Huan
author_sort Sahu, Sunil Kumar
collection PubMed
description Wood is the most important natural and endlessly renewable source of energy. Despite the ecological and economic importance of wood, many aspects of its formation have not yet been investigated. We performed chromosome-scale genome assemblies of three timber trees (Ochroma pyramidale, Mesua ferrea, and Tectona grandis) which exhibit different wood properties such as wood density, hardness, growth rate, and fiber cell wall thickness. The combination of 10X, stLFR, Hi-Fi sequencing and HiC data led us to assemble high-quality genomes evident by scaffold N50 length of 55.97 Mb (O. pyramidale), 22.37 Mb (M. ferrea) and 14.55 Mb (T. grandis) with >97% BUSCO completeness of the assemblies. A total of 35774, 24027, and 44813 protein-coding genes were identified in M. ferrea, T. grandis and O. pyramidale, respectively. The data generated in this study is anticipated to serve as a valuable genetic resource and will promote comparative genomic analyses, and it is of practical importance in gaining a further understanding of the wood properties in non-model woody species.
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spelling pubmed-104005652023-08-05 Chromosome-scale genomes of commercial timber trees (Ochroma pyramidale, Mesua ferrea, and Tectona grandis) Sahu, Sunil Kumar Liu, Min Chen, Yewen Gui, Jinshan Fang, Dongming Chen, Xiaoli Yang, Ting He, Chengzhong Cheng, Le Yang, Jinlong Sahu, Durgesh Nandini Li, Linzhou Wang, Hongli Mu, Weixue Wei, Jinpu Liu, Jie Zhao, Yuxian Zhang, Shouzhou Lisby, Michael Liu, Xin Xu, Xun Li, Laigeng Wang, Sibo Liu, Huan Sci Data Data Descriptor Wood is the most important natural and endlessly renewable source of energy. Despite the ecological and economic importance of wood, many aspects of its formation have not yet been investigated. We performed chromosome-scale genome assemblies of three timber trees (Ochroma pyramidale, Mesua ferrea, and Tectona grandis) which exhibit different wood properties such as wood density, hardness, growth rate, and fiber cell wall thickness. The combination of 10X, stLFR, Hi-Fi sequencing and HiC data led us to assemble high-quality genomes evident by scaffold N50 length of 55.97 Mb (O. pyramidale), 22.37 Mb (M. ferrea) and 14.55 Mb (T. grandis) with >97% BUSCO completeness of the assemblies. A total of 35774, 24027, and 44813 protein-coding genes were identified in M. ferrea, T. grandis and O. pyramidale, respectively. The data generated in this study is anticipated to serve as a valuable genetic resource and will promote comparative genomic analyses, and it is of practical importance in gaining a further understanding of the wood properties in non-model woody species. Nature Publishing Group UK 2023-08-03 /pmc/articles/PMC10400565/ /pubmed/37537171 http://dx.doi.org/10.1038/s41597-023-02420-8 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Data Descriptor
Sahu, Sunil Kumar
Liu, Min
Chen, Yewen
Gui, Jinshan
Fang, Dongming
Chen, Xiaoli
Yang, Ting
He, Chengzhong
Cheng, Le
Yang, Jinlong
Sahu, Durgesh Nandini
Li, Linzhou
Wang, Hongli
Mu, Weixue
Wei, Jinpu
Liu, Jie
Zhao, Yuxian
Zhang, Shouzhou
Lisby, Michael
Liu, Xin
Xu, Xun
Li, Laigeng
Wang, Sibo
Liu, Huan
Chromosome-scale genomes of commercial timber trees (Ochroma pyramidale, Mesua ferrea, and Tectona grandis)
title Chromosome-scale genomes of commercial timber trees (Ochroma pyramidale, Mesua ferrea, and Tectona grandis)
title_full Chromosome-scale genomes of commercial timber trees (Ochroma pyramidale, Mesua ferrea, and Tectona grandis)
title_fullStr Chromosome-scale genomes of commercial timber trees (Ochroma pyramidale, Mesua ferrea, and Tectona grandis)
title_full_unstemmed Chromosome-scale genomes of commercial timber trees (Ochroma pyramidale, Mesua ferrea, and Tectona grandis)
title_short Chromosome-scale genomes of commercial timber trees (Ochroma pyramidale, Mesua ferrea, and Tectona grandis)
title_sort chromosome-scale genomes of commercial timber trees (ochroma pyramidale, mesua ferrea, and tectona grandis)
topic Data Descriptor
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10400565/
https://www.ncbi.nlm.nih.gov/pubmed/37537171
http://dx.doi.org/10.1038/s41597-023-02420-8
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