© 2018 Macmillan Publishers Limited, part of Springer Nature. All rights reserved. © 2018 Macmillan Publishers Limited, part of Springer Nature. All rights reserved.
Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China.
Sino-Africa Joint Research Centre, Chinese Academy of Science, Wuhan, China.
Novogene Bioinformatics Institute, Beijing, China.
School of Biological
and Chemical Sciences, Queen Mary University of London, London, UK.
Jodrell Laboratory, Royal Botanic Gardens, Kew, UK.
Department of Plant
Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
Centre for Plant Systems Biology, VIB, Ghent, Belgium.
Shenzhen Key Laboratory
for Orchid Conservation and Utilization, National Orchid Conservation Centre of China and Orchid Conservation and Research Centre, Shenzhen, China.
Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.
State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China.
Key Laboratory of Aquatic Botany and Watershed
Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.
State Key Laboratory of Systematic and Evolutionary Botany,
Institute of Botany, Chinese Academy of Sciences, Beijing, China.
Education Key Laboratory for Biodiversity Science and Ecological Engineering,
Fudan University, Shanghai, China.
Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Henan University, Kaifeng, China.
Department of Biology, East Carolina University, Greenville NC, USA.
Beijing Key Laboratory of Grape Sciences and Enology, Institute of Botany, Chinese
Academy of Sciences, Beijing, China.
Genomics Research Institute, University of Pretoria, Pretoria, South Africa.
These authors contributed equally:
Tao Wan, Zhi-Ming Liu, Ling-Fei Li, Andrew R. Leitch, Ilia J. Leitch and Zhong-Jian Liu. *e-mail: email@example.com; firstname.lastname@example.org;
he seed plants today are represented by five distinct lineages:
the species-rich angiosperms (flowering plants, approxi
mately 352,000 species) and four gymnosperm lineages
(which together comprise approximately 1,000 species and encom
pass cycads, Ginkgo biloba, conifers and gnetophytes). It is appar-
ent from their long fossil record (dating back to the Late Devonian
approximately 360 million years ago (Ma)) that considerably greater
seed plant diversity existed in the past
. Nevertheless, widespread
extinctions among many gymnosperm lineages mean that today’s
gymnosperms are only a relic of their former diversity, and this
has presented a major challenge for reconstructing evolution
ary relationships between the extant lineages
. Probably the most
controversial outstanding question in plant evolution is the phylo-
genetic position of gnetophytes
(comprising the genera Gnetum,
Welwitschia and Ephedra, Fig. 1) in relation to the other seed plant
lineages. Apparent morphological similarities with angiosperms,
such as vessel-like water-conducting cells, double fertilization and
leaf morphologies with reticulate venation, have historically led
to the proposition that gnetophytes form a group that is sister to
angiosperms (termed the ‘Anthophyte hypothesis’)
. That hypoth-
esis has, however, largely been rejected by molecular phylogenetic
data and a deeper understanding of the developmental pathways
that lead to similar morphological features. Nevertheless, the use
of molecular data has also been problematic in inferring the exact
A genome for gnetophytes and early evolution of
, Zhi-Ming Liu
, Ling-Fei Li
, Andrew R. Leitch
, Ilia J. Leitch
, Rolf Lohaus
, Hai-Ping Xin
, Yan-Bing Gong
, Yang Liu
, Wen-Cai Wang
, Ling-Yun Chen
, Laura J. Kelly
, Ji Yang
, Jin-Ling Huang
, Zhen Li
, Ping Liu
, Li Zhang
, Hui Wang
, Shu-Han Deng
, Meng Liu
, Ji Li
, Lu Ma
, Yan Liu
, Yang Lei
, Wei Xu
, Fan Liu
, Qian Ma
, Xin-Ran Yu
, Zhi Jiang
, Guo-Qiang Zhang
, Shao-Hua Li
, Shou-Zhou Zhang
, Qing-Feng Wang
*, Yves Van de Peer
*, Jin-Bo Zhang
and Xiao-Ming Wang
Gnetophytes are an enigmatic gymnosperm lineage comprising three genera, Gnetum, Welwitschia and Ephedra, which are mor-
phologically 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 rela-
tion to other seed plants, we report here a high-quality draft genome sequence for Gnetum montanum, the first for any gneto-
phyte. 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 dis-
tinctive 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 charac-
ters that distinguish Gnetum from other gymnosperms.
NATURE PLANTS | VOL 4 | FEBRUARY 2018 | 82–89 | www.nature.com/natureplants