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Chromosome-level genome assembly and population genetic analysis of a near-threatened rosewood species (Dalbergia cultrata Pierre Graham ex Benth) provide insights into its evolutionary and cold stress responses

Dalbergia cultrata Pierre Graham ex Benth (D. cultrata) is a precious rosewood tree species that grows in the tropical and subtropical regions of Asia. In this study, we used PacBio long-reading sequencing technology and Hi-C assistance to sequence and assemble the reference genome of D. cultrata. W...

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Autores principales: Huang, Ping, Li, Changhong, Lin, Furong, Liu, Yu, Zong, Yichen, Li, Bin, Zheng, Yongqi
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10552272/
https://www.ncbi.nlm.nih.gov/pubmed/37810393
http://dx.doi.org/10.3389/fpls.2023.1212967
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author Huang, Ping
Li, Changhong
Lin, Furong
Liu, Yu
Zong, Yichen
Li, Bin
Zheng, Yongqi
author_facet Huang, Ping
Li, Changhong
Lin, Furong
Liu, Yu
Zong, Yichen
Li, Bin
Zheng, Yongqi
author_sort Huang, Ping
collection PubMed
description Dalbergia cultrata Pierre Graham ex Benth (D. cultrata) is a precious rosewood tree species that grows in the tropical and subtropical regions of Asia. In this study, we used PacBio long-reading sequencing technology and Hi-C assistance to sequence and assemble the reference genome of D. cultrata. We generated 171.47 Gb PacBio long reads and 72.43 Gb Hi-C data and yielded an assembly of 10 pseudochromosomes with a total size of 690.99 Mb and Scaffold N50 of 65.76 Mb. The analysis of specific genes revealed that the triterpenoids represented by lupeol may play an important role in D. cultrata’s potential medicinal value. Using the new reference genome, we analyzed the resequencing of 19 Dalbergia accessions and found that D. cultrata and D. cochinchinensis have the latest genetic relationship. Transcriptome sequencing of D. cultrata leaves grown under cold stress revealed that MYB transcription factor and E3 ubiquitin ligase may be playing an important role in the cold response of D. cultrata. Genome resources and identified genetic variation, especially those genes related to the biosynthesis of phytochemicals and cold stress response, will be helpful for the introduction, domestication, utilization, and further breeding of Dalbergia species.
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spelling pubmed-105522722023-10-06 Chromosome-level genome assembly and population genetic analysis of a near-threatened rosewood species (Dalbergia cultrata Pierre Graham ex Benth) provide insights into its evolutionary and cold stress responses Huang, Ping Li, Changhong Lin, Furong Liu, Yu Zong, Yichen Li, Bin Zheng, Yongqi Front Plant Sci Plant Science Dalbergia cultrata Pierre Graham ex Benth (D. cultrata) is a precious rosewood tree species that grows in the tropical and subtropical regions of Asia. In this study, we used PacBio long-reading sequencing technology and Hi-C assistance to sequence and assemble the reference genome of D. cultrata. We generated 171.47 Gb PacBio long reads and 72.43 Gb Hi-C data and yielded an assembly of 10 pseudochromosomes with a total size of 690.99 Mb and Scaffold N50 of 65.76 Mb. The analysis of specific genes revealed that the triterpenoids represented by lupeol may play an important role in D. cultrata’s potential medicinal value. Using the new reference genome, we analyzed the resequencing of 19 Dalbergia accessions and found that D. cultrata and D. cochinchinensis have the latest genetic relationship. Transcriptome sequencing of D. cultrata leaves grown under cold stress revealed that MYB transcription factor and E3 ubiquitin ligase may be playing an important role in the cold response of D. cultrata. Genome resources and identified genetic variation, especially those genes related to the biosynthesis of phytochemicals and cold stress response, will be helpful for the introduction, domestication, utilization, and further breeding of Dalbergia species. Frontiers Media S.A. 2023-09-21 /pmc/articles/PMC10552272/ /pubmed/37810393 http://dx.doi.org/10.3389/fpls.2023.1212967 Text en Copyright © 2023 Huang, Li, Lin, Liu, Zong, Li and Zheng 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 Plant Science
Huang, Ping
Li, Changhong
Lin, Furong
Liu, Yu
Zong, Yichen
Li, Bin
Zheng, Yongqi
Chromosome-level genome assembly and population genetic analysis of a near-threatened rosewood species (Dalbergia cultrata Pierre Graham ex Benth) provide insights into its evolutionary and cold stress responses
title Chromosome-level genome assembly and population genetic analysis of a near-threatened rosewood species (Dalbergia cultrata Pierre Graham ex Benth) provide insights into its evolutionary and cold stress responses
title_full Chromosome-level genome assembly and population genetic analysis of a near-threatened rosewood species (Dalbergia cultrata Pierre Graham ex Benth) provide insights into its evolutionary and cold stress responses
title_fullStr Chromosome-level genome assembly and population genetic analysis of a near-threatened rosewood species (Dalbergia cultrata Pierre Graham ex Benth) provide insights into its evolutionary and cold stress responses
title_full_unstemmed Chromosome-level genome assembly and population genetic analysis of a near-threatened rosewood species (Dalbergia cultrata Pierre Graham ex Benth) provide insights into its evolutionary and cold stress responses
title_short Chromosome-level genome assembly and population genetic analysis of a near-threatened rosewood species (Dalbergia cultrata Pierre Graham ex Benth) provide insights into its evolutionary and cold stress responses
title_sort chromosome-level genome assembly and population genetic analysis of a near-threatened rosewood species (dalbergia cultrata pierre graham ex benth) provide insights into its evolutionary and cold stress responses
topic Plant Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10552272/
https://www.ncbi.nlm.nih.gov/pubmed/37810393
http://dx.doi.org/10.3389/fpls.2023.1212967
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