A chromosome-scale genome and transcriptomic analysis of the endangered tropical tree Vatica mangachapoi (Dipterocarpaceae)

doi:10.1093/dnares/dsac005

	A chromosome-scale genome and transcriptomic analysis of the endangered tropical tree Vatica mangachapoi (Dipterocarpaceae)
	Tang, Liang ; Liao, Xuezhu 1; Tembrock, Luke R.; Ge, Song3 ; Wu, Zhiqiang 1
	2022
发表期刊	DNA RESEARCH
ISSN	1340-2838
卷号	29 期号:2
摘要	Vatica mangachapoi is a tropical tree species native to Southeast Asia. It has long been valued as a timber species because the wood resists decay, but it is now considered vulnerable to extinction due to habitat loss and overexploitation. Here, we present the first chromosome-level genome assembly of V. mangachapoi that we created by combining data from PacBio long read sequencing with Hi-C proximity ligation and Illumina short-read sequencing. The assembled genome was 456.21 Mb, containing 11 chromosome and a BUSCO score of 93.4%. From the newly assembled genome, 46,811 protein-coding genes were predicted. Repetitive DNA accounted for 53% of the genome. Phylogenomic and gene family analyses showed that V. mangachapoi diverged from a common ancestor of Gossypium raimondii 70 million years ago. Transcriptome analyses found 227 genes that were differentially expressed in the leaves of plants grown in normal soil relative to plants grown in dry, coastal, sandy soil. For these genes, we identified three significantly enriched with GO terms: responses to organonitrogen compounds, chitin-triggered immunity, and wound response. This genome provides an important comparative benchmark not only for future conservation work on V. mangachapoi but also for phylogenomics work on Dipterocarpaceae.
关键词	dipterocarp forests genome assembly whole-genome duplication tree genomics conservation biology
学科领域	Genetics & Heredity
DOI	10.1093/dnares/dsac005
收录类别	SCI
语种	英语
WOS关键词	MULTIPLE SEQUENCE ALIGNMENT ; PHYLOGENETIC ANALYSIS ; TERPENE SYNTHASES ; EMISSIONS ; PROGRAM ; TOOL ; BIOSYNTHESIS ; EVOLUTIONARY ; ANNOTATION ; POLYPLOIDY
WOS研究方向	Science Citation Index Expanded (SCI-EXPANDED)
WOS记录号	WOS:000761968100001
出版者	OXFORD UNIV PRESS
文献子类	Article
出版地	OXFORD
EISSN	1756-1663
资助机构	Hainan Natural Science Foundation of High-Level Talents Project [2019RC066] ; National Natural Science Foundation of China [32060236, 41661010, 32170238] ; Science, Technology and Innovation Commission of Shenzhen Municipality [RCYX20200714114538196]
作者邮箱	ecotang@163.com ; wuzhiqiang@caas.cn
作品OA属性	gold, Green Published
引用统计	被引频次：3[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://ir.ibcas.ac.cn/handle/2S10CLM1/28763
专题	系统与进化植物学国家重点实验室
作者单位	1.Hainan Univ, Ctr Terr Biodivers South China Sea, Haikou 570228, Hainan, Peoples R China 2.Agr Genom Inst Shenzhen, Shenzhen Branch, Guangdong Lab Lingnan Modern Agr, Genome Anal Lab Minist Agr, Shenzhen 518120, Peoples R China 3.Tembrock, Luke R.] Colorado State Univ, Dept Agr Biol, Ft Collins, CO 80523 USA 4.Chinese Acad Sci, Inst Bot, State Key Lab Systemat & Evolutionary Bot, Beijing 100093, Peoples R China
推荐引用方式 GB/T 7714	Tang, Liang,Liao, Xuezhu,Tembrock, Luke R.,et al. A chromosome-scale genome and transcriptomic analysis of the endangered tropical tree Vatica mangachapoi (Dipterocarpaceae)[J]. DNA RESEARCH,2022,29(2).
APA	Tang, Liang,Liao, Xuezhu,Tembrock, Luke R.,Ge, Song,&Wu, Zhiqiang.(2022).A chromosome-scale genome and transcriptomic analysis of the endangered tropical tree Vatica mangachapoi (Dipterocarpaceae).DNA RESEARCH,29(2).
MLA	Tang, Liang,et al."A chromosome-scale genome and transcriptomic analysis of the endangered tropical tree Vatica mangachapoi (Dipterocarpaceae)".DNA RESEARCH 29.2(2022).

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