Data from: A genome for gnetophytes and early evolution of seed plants

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.