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.买麻藤类（Gnetophytes）是一类神秘的裸子植物（gymnosperm）谱系，包含买麻藤属（Gnetum）、百岁兰属（Welwitschia）与麻黄属（Ephedra）三个属，其形态特征与所有其他种子植物均存在显著差异。这类植物的独特性引发了学界关于其起源、演化以及在种子植物系统发育框架中位置的广泛争议。为加深我们对买麻藤类演化历程及其与其他种子植物亲缘关系的理解，本研究报道了山买麻藤（Gnetum montanum）的高质量草图基因组序列，这是首个针对买麻藤类植物的基因组测序成果。研究团队采用了一种应对高杂合度水平的新型基因组组装策略，最终组装得到超过4Gb的基因组序列，共编码27491个蛋白编码基因。通过将山买麻藤基因组与其他裸子植物基因组进行比较分析，研究揭示了多项显著且独特的基因组特征：例如，一类多样化的逆转录转座子（retrotransposons）群体，相关证据表明其在基因组中的消除频率显著高于积累频率；内含子结构存在显著差异，具体涵盖内含子长度分布以及（逆转录）转座元件占比两个维度；以及功能蛋白结构域呈现独特的扩增模式。此外，部分基因家族呈现出买麻藤属特有的拷贝数扩张（如纤维素合酶）或收缩（如胚胎发育晚期丰富蛋白（Late Embryogenesis Abundant protein）），这或与买麻藤属为适应温暖中生环境而演化出的独特形态创新性状相关。总体而言，山买麻藤的基因组序列有助于更清晰地解析种子植物的祖先基因组特征，并鉴定出区分买麻藤属与其他裸子植物的基因组性状。