A genome for gnetophytes and early evolution of seed plants

Tao Wan, Zhi Ming Liu, Ling Fei Li, Andrew R. Leitch, Ilia J. Leitch, Rolf Lohaus, Zhong Jian Liu, Hai Ping Xin, Yan Bing Gong, Yang Liu, Wen Cai Wang, Ling Yun Chen, Yong Yang, Laura J. Kelly, Ji Yang, Jin Ling Huang, Zhen Li, Ping Liu, Li Zhang, Hong Mei LiuHui Wang, Shu Han Deng, Meng Liu, Ji Li, Lu Ma, Yang Lei, Wei Xu, Ling Qing Wu, Fan Liu, Qian Ma, Xin Ran Yu, Zhi Jiang, Guo Qiang Zhang, Shao Hua Li, Rui Qiang Li, Shou Zhou Zhang, Qing Feng Wang, Yves Van De Peer, Jin Bo Zhang, Xiao Ming Wang

Research output: Contribution to journalArticlepeer-review

40 Scopus citations

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.

Original languageEnglish (US)
Pages (from-to)82-89
Number of pages8
JournalNature plants
Volume4
Issue number2
DOIs
StatePublished - Feb 1 2018

Bibliographical note

Funding Information:
Genome sequencing, assembly and annotation were conducted by the Novogene Bioinformatics Institute, Beijing, China; mutual contracts were No. NHT140016 and NVT140016004. This work was supported by funding from the Scientific Project of Shenzhen Urban Administration (201519) and a Major Technical Research Project of the Innovation of Science and Technology Commission of Shenzhen (JSGG20140515164852417). Additional funding was provided in particular by the Scientific Research Program of Sino-Africa Joint Research Center (SAJL201607). We thank X.Q. Wang, G.W. Hu, Z.D. Chen and Y.H. Guo for comments on gnetophyte phylogenetic relationships and ecological issues; H. Wu and X.P. Ning for discussion of related organ development; K.K. Wan and S. Sun for additional help on the analysis of repeats. We also thank X.Y. for support of funding coordination. Y.V.d.P. acknowledges the Multidisciplinary Research Partnership ‘Bioinformatics: from nucleotides to networks’ Project (no. 01MR0310W) of Ghent University, and funding from the European Union Seventh Framework Programme (FP7/2007-2013) under European Research Council Advanced Grant Agreement 322739-DOUBLEUP.

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