The gymnosperm Welwitschia mirabilis belongs to the ancient, enigmatic gnetophyte lineage.
It is a unique desert plant with extreme longevity and two ever-elongating leaves. We present
a chromosome-level assembly of its genome (6.8 Gb/1 C) together with methylome and
transcriptome data to explore its astonishing biology. We also present a refined, high-quality
assembly of Gnetum montanum to enhance our understanding of gnetophyte genome evolution. The Welwitschia genome has been shaped by a lineage-specific ancient, whole genome
duplication (~86 million years ago) and more recently (1-2 million years) by bursts of retrotransposon activity. High levels of cytosine methylation (particularly at CHH motifs) are
associated with retrotransposons, whilst long-term deamination has resulted in an exceptionally GC-poor genome. Changes in copy number and/or expression of gene families and
transcription factors (e.g. R2R3MYB, SAUR) controlling cell growth, differentiation and
metabolism underpin the plant’s longevity and tolerance to temperature, nutrient and water
stress.
