Abstract

The gymnosperm Welwitschia mirabilis belongs to the ancient, enigmatic gnetophyte lineage. It is a unique desert plant with extreme longevity and two ever-elongating leaves. We present a chromosome-level assembly of its genome (6.8 Gb/1 C) together with methylome and transcriptome data to explore its astonishing biology. We also present a refined, high-quality assembly of Gnetum montanum to enhance our understanding of gnetophyte genome evolution. The Welwitschia genome has been shaped by a lineage-specific ancient, whole genome duplication (~86 million years ago) and more recently (1-2 million years) by bursts of retrotransposon activity. High levels of cytosine methylation (particularly at CHH motifs) are associated with retrotransposons, whilst long-term deamination has resulted in an exceptionally GC-poor genome. Changes in copy number and/or expression of gene families and transcription factors (e.g. R2R3MYB, SAUR) controlling cell growth, differentiation and metabolism underpin the plant’s longevity and tolerance to temperature, nutrient and water stress.

Welwitschia mirabilis is a unique plant that only has two leaves, but it can survive in hostile conditions of the African desert. Here, the authors report its chromosome-level genome assembly and discuss how gene function and regulation have given rise to its unique morphology and environmental adaptions.

Details

Title
The Welwitschia genome reveals a unique biology underpinning extreme longevity in deserts
Author
Wan, Tao 1 ; Liu, Zhiming 2 ; Leitch, Ilia J 3   VIAFID ORCID Logo  ; Xin Haiping 4 ; Maggs-Kölling Gillian 5 ; Gong Yanbing 6   VIAFID ORCID Logo  ; Li, Zhen 7 ; Marais, Eugene 5   VIAFID ORCID Logo  ; Liao Yiying 8 ; Dai, Can 9   VIAFID ORCID Logo  ; Liu, Fan 10 ; Wu Qijia 11 ; Song, Chi 12 ; Zhou, Yadong 4 ; Huang, Weichang 13 ; Jiang, Kai 13   VIAFID ORCID Logo  ; Wang, Qi 13 ; Yang, Yong 14 ; Zhong Zhixiang 4 ; Yang, Ming 2 ; Xue, Yan 15 ; Hu Guangwan 4 ; Hou, Chen 16   VIAFID ORCID Logo  ; Su Yingjuan 17 ; Feng Shixiu 18 ; Yang, Ji 19 ; Yan, Jijun 20 ; Chu Jinfang 20 ; Chen, Fan 20   VIAFID ORCID Logo  ; Ran Jinhua 21 ; Wang, Xiaoquan 21   VIAFID ORCID Logo  ; Van de Peer Yves 22   VIAFID ORCID Logo  ; Leitch, Andrew R 23   VIAFID ORCID Logo  ; Wang, Qingfeng 4   VIAFID ORCID Logo 

1  Chinese Academy of Sciences, Core Botanical Gardens/Wuhan Botanical Garden, Wuhan, China (GRID:grid.9227.e) (ISNI:0000000119573309); Chinese Academy of Sciences, Sino-Africa Joint Research Centre, Wuhan, China (GRID:grid.9227.e) (ISNI:0000000119573309); FairyLake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Key Laboratory of Southern Subtropical Plant Diversity, Shenzhen, China (GRID:grid.9227.e) 
2  FairyLake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Key Laboratory of Southern Subtropical Plant Diversity, Shenzhen, China (GRID:grid.9227.e) 
3  Royal Botanic Gardens, Kew, Surrey, UK (GRID:grid.4903.e) (ISNI:0000 0001 2097 4353) 
4  Chinese Academy of Sciences, Core Botanical Gardens/Wuhan Botanical Garden, Wuhan, China (GRID:grid.9227.e) (ISNI:0000000119573309); Chinese Academy of Sciences, Sino-Africa Joint Research Centre, Wuhan, China (GRID:grid.9227.e) (ISNI:0000000119573309) 
5  Gobabeb Research and Training Centre, Walvis Bay, Namibia (GRID:grid.500209.e) (ISNI:0000 0004 6006 169X) 
6  Wuhan University, State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan, China (GRID:grid.49470.3e) (ISNI:0000 0001 2331 6153) 
7  Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium (GRID:grid.5342.0) (ISNI:0000 0001 2069 7798); Center for Plant Systems Biology, VIB, Ghent, Belgium (GRID:grid.11486.3a) (ISNI:0000000104788040) 
8  FairyLake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Key Laboratory of Southern Subtropical Plant Diversity, Shenzhen, China (GRID:grid.500209.e) 
9  Hubei University, School of Resources and Environmental Science, Wuhan, China (GRID:grid.34418.3a) (ISNI:0000 0001 0727 9022) 
10  Chinese Academy of Sciences, Sino-Africa Joint Research Centre, Wuhan, China (GRID:grid.9227.e) (ISNI:0000000119573309); Wuhan Botanical Garden, Chinese Academy of Sciences, Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan, China (GRID:grid.458515.8) (ISNI:0000 0004 1770 1110) 
11  Seqhealth Technology, Wuhan, China (GRID:grid.458515.8) 
12  China Academy of Chinese Medical Sciences, Institute of Chinese Materia Medica, Beijing, China (GRID:grid.410318.f) (ISNI:0000 0004 0632 3409) 
13  Shanghai Chenshan Botanical Garden, Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai, China (GRID:grid.452763.1) (ISNI:0000 0004 1777 8361) 
14  Nanjing Forestry University, College of Biology and Environment, Nanjing, China (GRID:grid.410625.4) (ISNI:0000 0001 2293 4910) 
15  Chinese Academy of Sciences, Core Botanical Gardens/Wuhan Botanical Garden, Wuhan, China (GRID:grid.9227.e) (ISNI:0000000119573309); Wuhan Botanical Garden, Chinese Academy of Sciences, Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan, China (GRID:grid.458515.8) (ISNI:0000 0004 1770 1110) 
16  Protection and Utilization, Guangdong Academy of Forestry, Guangdong Provincial Key Laboratory of Silviculture, Guangzhou, China (GRID:grid.464300.5) (ISNI:0000 0001 0373 5991) 
17  Sun Yat-Sen University, School of Life Sciences, Guangzhou, China (GRID:grid.12981.33) (ISNI:0000 0001 2360 039X) 
18  FairyLake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Key Laboratory of Southern Subtropical Plant Diversity, Shenzhen, China (GRID:grid.12981.33) 
19  Fudan University, Education Key Laboratory for Biodiversity Science and Ecological Engineering, Shanghai, China (GRID:grid.8547.e) (ISNI:0000 0001 0125 2443) 
20  Chinese Academy of Sciences, Institute of Genetics and Developmental Biology, Beijing, China (GRID:grid.9227.e) (ISNI:0000000119573309) 
21  Institute of Botany, Chinese Academy of Sciences, State Key Laboratory of Systematic and Evolutionary Botany, Beijing, China (GRID:grid.435133.3) (ISNI:0000 0004 0596 3367) 
22  Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium (GRID:grid.5342.0) (ISNI:0000 0001 2069 7798); Center for Plant Systems Biology, VIB, Ghent, Belgium (GRID:grid.11486.3a) (ISNI:0000000104788040); University of Pretoria, Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, Hatfield, South Africa (GRID:grid.49697.35) (ISNI:0000 0001 2107 2298); Nanjing Agricultural University, College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing, China (GRID:grid.27871.3b) (ISNI:0000 0000 9750 7019) 
23  Queen Mary University of London, School of Biological and Chemical Sciences, London, UK (GRID:grid.4868.2) (ISNI:0000 0001 2171 1133) 
Publication year
2021
Publication date
2021
Publisher
Nature Publishing Group
e-ISSN
20411723
Source type
Scholarly Journal
Language of publication
English
DOI
https://doi.org/10.1038/s41467-021-24528-4
ProQuest document ID
2550573358
Copyright
© The Author(s) 2021. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.