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Nat Plants. 2018 Feb;4(2):82-89. doi: 10.1038/s41477-017-0097-2. Epub 2018 Jan 29.

A genome for gnetophytes and early evolution of seed plants.

Author information

1
Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China.
2
Sino-Africa Joint Research Centre, Chinese Academy of Science, Wuhan, China.
3
Novogene Bioinformatics Institute, Beijing, China.
4
School of Biological and Chemical Sciences, Queen Mary University of London, London, UK.
5
Jodrell Laboratory, Royal Botanic Gardens, Kew, UK.
6
Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
7
Centre for Plant Systems Biology, VIB, Ghent, Belgium.
8
Shenzhen Key Laboratory for Orchid Conservation and Utilization, National Orchid Conservation Centre of China and Orchid Conservation and Research Centre, Shenzhen, China.
9
Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.
10
State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China.
11
Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.
12
State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.
13
Education Key Laboratory for Biodiversity Science and Ecological Engineering, Fudan University, Shanghai, China.
14
Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Henan University, Kaifeng, China.
15
Department of Biology, East Carolina University, Greenville, NC, USA.
16
Beijing Key Laboratory of Grape Sciences and Enology, Institute of Botany, Chinese Academy of Sciences, Beijing, China.
17
Sino-Africa Joint Research Centre, Chinese Academy of Science, Wuhan, China. qfwang@wbgcas.cn.
18
Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China. qfwang@wbgcas.cn.
19
Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium. yves.vandepeer@psb.vib-ugent.be.
20
Centre for Plant Systems Biology, VIB, Ghent, Belgium. yves.vandepeer@psb.vib-ugent.be.
21
Genomics Research Institute, University of Pretoria, Pretoria, South Africa. yves.vandepeer@psb.vib-ugent.be.
22
Novogene Bioinformatics Institute, Beijing, China. zhangjinbo@novogene.com.
23
Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China. 719921868@qq.com.

Abstract

Gnetophytes are an enigmatic gymnosperm lineage comprising three genera, Gnetum, Welwitschia and Ephedra, which are morphologically distinct from all other seed plants. Their distinctiveness has triggered much debate as to their origin, evolution and phylogenetic placement among seed plants. To increase our understanding of the evolution of gnetophytes, and their relation to other seed plants, we report here a high-quality draft genome sequence for Gnetum montanum, the first for any gnetophyte. By using a novel genome assembly strategy to deal with high levels of heterozygosity, we assembled >4 Gb of sequence encoding 27,491 protein-coding genes. Comparative analysis of the G. montanum genome with other gymnosperm genomes unveiled some remarkable and distinctive genomic features, such as a diverse assemblage of retrotransposons with evidence for elevated frequencies of elimination rather than accumulation, considerable differences in intron architecture, including both length distribution and proportions of (retro) transposon elements, and distinctive patterns of proliferation of functional protein domains. Furthermore, a few gene families showed Gnetum-specific copy number expansions (for example, cellulose synthase) or contractions (for example, Late Embryogenesis Abundant protein), which could be connected with Gnetum's distinctive morphological innovations associated with their adaptation to warm, mesic environments. Overall, the G. montanum genome enables a better resolution of ancestral genomic features within seed plants, and the identification of genomic characters that distinguish Gnetum from other gymnosperms.

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PMID:
29379155
DOI:
10.1038/s41477-017-0097-2

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