A genome for gnetophytes and early evolution of seed plants
Wan, Tao; Liu, Zhi-Ming; Li, Ling-Fei; Leitch, Andrew R.; Leitch, Ilia J.; Lohaus, Rolf; Liu, Zhong-Jian; Xin, Hai-Ping; Gong, Yan-Bing; Liu, Yang; Wang, Wen-Cai; Chen, Ling-Yun; Yang, Yong; Kelly, Laura J.; Yang, Ji; Huang, Jin-Ling; Zhen, Li; Liu, Ping; Zhang, Li; Liu, Hong-Mei; Wang, Hui; Deng, Shu-Han; Liu, Meng; Li, Ji; Ma, Lu; Liu, Yan; Lei, Yang; Xu, Wei; Wu, Ling-Qing; Liu, Fan; Ma, Qian; Yu, Xin-Ran; Jiang, Zhi; Zhang, Guo-Qiang; Li, Shao-Hua; Li, Rui-Qiang; Zhang, Shou-Zhou; Wang, Qing-Feng; Van de Peer, Yves; Zhang, Jin-Bo; Wang, Xiao-Ming
Date:
2018-02
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.