Oryza rufipogon and O. longistaminata are important wild relatives of cultivated rice, harboring a promising source of novel genes for rice breeding programs. Here, we present de novo assembled draft genomes and annotation of O. rufipogon and O. longistaminata. Our analysis reveals a considerable number of lineage‐specific gene families associated with the self‐incompatibility (SI) and formation of reproductive separation. We show how lineage‐specific expansion or contraction of gene families with functional enrichment of the recognition of pollen, thus enlightening their reproductive diversification. We documented a large number of lineage‐specific gene families enriched in salt stress, antifungal response, and disease resistance. Our comparative analysis further shows a genome‐wide expansion of genes encoding NBS‐LRR proteins in these two outcrossing wild species in contrast to six other selfing rice species. Conserved noncoding sequences (CNSs) in the two wild rice genomes rapidly evolve relative to selfing rice species, resulting in the reduction of genomic variation owing to shifts of mating systems. We find that numerous genes related to these rapidly evolving CNSs are enriched in reproductive structure development, flower development, and postembryonic development, which may associate with SI in O. rufipogon and O. longistaminata.

中文翻译：

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两种异型杂交野生稻（Oryza rufipogon 和 O. longistaminata）的基因组草图揭示了与交配系统进化相关的基因组特征。


普通野生稻和长雄野生稻是栽培稻的重要野生近缘种，为水稻育种项目提供了有前景的新基因来源。在这里，我们展示了O. rufipogon和O. longistaminata的从头组装的基因组草图和注释。我们的分析揭示了相当多的谱系特异性基因家族与自交不亲和性（SI）和生殖分离的形成相关。我们展示了基因家族的谱系特异性扩张或收缩如何丰富花粉识别的功能，从而启发其生殖多样化。我们记录了大量富含盐胁迫、抗真菌反应和抗病性的谱系特异性基因家族。我们的比较分析进一步表明，与其他六种自交水稻品种相比，这两个异交野生物种中编码 NBS-LRR 蛋白的基因在全基因组范围内扩展。两种野生稻基因组中的保守非编码序列（CNS）相对于自交水稻物种迅速进化，导致由于交配系统的变化而导致的基因组变异减少。我们发现与这些快速进化的中枢神经系统相关的许多基因在生殖结构发育、花发育和胚胎后发育中富集，这可能与普通野生稻和长雄野生稻的SI有关。