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| A chromosome-scale genome and transcriptomic analysis of the endangered tropical tree Vatica mangachapoi (Dipterocarpaceae) | |
Tang, Liang; Liao, Xuezhu1; Tembrock, Luke R.; Ge, Song3 ; Wu, Zhiqiang1
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| 2022 | |
| Source Publication | DNA RESEARCH
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| ISSN | 1340-2838 |
| Volume | 29Issue:2 |
| Abstract | 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. |
| Keyword | dipterocarp forests genome assembly whole-genome duplication tree genomics conservation biology |
| Subject Area | Genetics & Heredity |
| DOI | 10.1093/dnares/dsac005 |
| Indexed By | SCI |
| Language | 英语 |
| WOS Keyword | MULTIPLE SEQUENCE ALIGNMENT ; PHYLOGENETIC ANALYSIS ; TERPENE SYNTHASES ; EMISSIONS ; PROGRAM ; TOOL ; BIOSYNTHESIS ; EVOLUTIONARY ; ANNOTATION ; POLYPLOIDY |
| WOS Research Area | Science Citation Index Expanded (SCI-EXPANDED) |
| WOS ID | WOS:000761968100001 |
| Publisher | OXFORD UNIV PRESS |
| Subtype | Article |
| Publication Place | OXFORD |
| EISSN | 1756-1663 |
| Funding Organization | 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] |
| Corresponding Author Email | ecotang@163.com ; wuzhiqiang@caas.cn |
| OA | gold, Green Published |
| Citation statistics | |
| Document Type | 期刊论文 |
| Identifier | http://ir.ibcas.ac.cn/handle/2S10CLM1/28763 |
| Collection | 系统与进化植物学国家重点实验室 |
| Affiliation | 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 |
| Recommended Citation 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). |
| Files in This Item: | ||||||
| File Name/Size | DocType | Version | Access | License | ||
| Tang-2022-A chromoso（910KB） | 期刊论文 | 出版稿 | 开放获取 | CC BY-NC-SA | View Application Full Text | |
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