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A genome for gnetophytes and early evolution of seed plants

(2018) NATURE PLANTS. 4(2). p.82-89
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Bioinformatics: from nucleotids to networks (N2N)
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.
Keywords
COLD STRESS, FLOWERING PLANTS, GNETUM GNETALES, GENE FAMILY, ANGIOSPERMS, ORIGIN, POLYPLOIDY, EXPRESSION, SEQUENCE, GYMNOSPERMS

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Citation

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Chicago
Wan, Tao, Zhi-Ming Liu, Ling-Fei Li, Andrew R Leitch, Ilia J Leitch, Rolf Lohaus, Zhong-Jian Liu, et al. 2018. “A Genome for Gnetophytes and Early Evolution of Seed Plants.” Nature Plants 4 (2): 82–89.
APA
Wan, T., Liu, Z.-M., Li, L.-F., Leitch, A. R., Leitch, I. J., Lohaus, R., Liu, Z.-J., et al. (2018). A genome for gnetophytes and early evolution of seed plants. NATURE PLANTS, 4(2), 82–89.
Vancouver
1.
Wan T, Liu Z-M, Li L-F, Leitch AR, Leitch IJ, Lohaus R, et al. A genome for gnetophytes and early evolution of seed plants. NATURE PLANTS. 2018;4(2):82–9.
MLA
Wan, Tao, Zhi-Ming Liu, Ling-Fei Li, et al. “A Genome for Gnetophytes and Early Evolution of Seed Plants.” NATURE PLANTS 4.2 (2018): 82–89. Print.
@article{8558174,
  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 {\textrangle}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.},
  author       = {Wan, Tao and Liu, Zhi-Ming and Li, Ling-Fei and Leitch, Andrew R and Leitch, Ilia J and Lohaus, Rolf and Liu, Zhong-Jian and Xin, Hai-Ping and Gong, Yan-Bing and Liu, Yang and Wang, Wen-Cai and Chen, Ling-Yun and Yang, Yong and Kelly, Laura J and Yang, Ji and Huang, Jin-Ling and Li, Zhen and Liu, Ping and Zhang, Li and Liu, Hong-Mei and Wang, Hui and Deng, Shu-Han and Liu, Meng and Li, Ji and Ma, Lu and Liu, Yan and Lei, Yang and Xu, Wei and Wu, Ling-Qing and Liu, Fan and Ma, Qian and Yu, Xin-Ran and Jiang, Zhi and Zhang, Guo-Qiang and Li, Shao-Hua and Li, Rui-Qiang and Zhang, Shou-Zhou and Wang, Qing-Feng and Van de Peer, Yves and Zhang, Jin-Bo and Wang, Xiao-Ming},
  issn         = {2055-026X},
  journal      = {NATURE PLANTS},
  keyword      = {COLD STRESS,FLOWERING PLANTS,GNETUM GNETALES,GENE FAMILY,ANGIOSPERMS,ORIGIN,POLYPLOIDY,EXPRESSION,SEQUENCE,GYMNOSPERMS},
  language     = {eng},
  number       = {2},
  pages        = {82--89},
  title        = {A genome for gnetophytes and early evolution of seed plants},
  url          = {http://dx.doi.org/10.1038/s41477-017-0097-2},
  volume       = {4},
  year         = {2018},
}

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