The MIR gene is not an Oryza sativa orphan gene, but an Oryza genus-specific gene that evolved before AA lineage speciation by a complex origination process. Rice (Oryza sativa L.) is a model species and an economically relevant crop. The Oryza genus comprises 25 species, with genomic data available for several Oryza species, making it a model for genetics and evolution. The Mitochondrial Iron-Regulated (MIR) gene was previously implicated in the O. sativa Fe deficiency response, and was considered an orphan gene present only in rice. Here we show that MIR is also found in other Oryza species that belong to the Oryza sativa complex, which have AA genome type and constitute the primary gene pool for O. sativa breeding. Our data suggest that MIR originated in a stepwise process, in which sequences derived from an exon fragment of the raffinose synthase gene were pseudogenized into non-coding, which in turn originated the MIR gene de novo. All species with a putative functional MIR gene conserve their regulation by Fe deficiency, with the exception of Oryza barthii. In O. barthii, the MIR coding sequence was translocated to a different chromosomal position and separated from its regulatory region, leading to a lack of Fe deficiency responsiveness. Moreover, the MIR co-expression subnetwork cluster in O. sativa is responsive to Fe deficiency, evidencing the importance of the newly originated gene in Fe uptake. This work establishes that MIR is not an orphan gene as previously proposed, but a de novo originated gene within the genus Oryza. We also showed that MIR is undergoing genomic changes in one species (O. barthii), with an impact on Fe deficiency response.

中文翻译：

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线粒体铁调节 (MIR) 基因是稻属特异性的，在稻复合物中的物种形成之前进化

MIR基因不是水稻孤儿基因，而是在AA谱系物种形成之前通过复杂的起源过程进化的水稻属特异性基因。水稻 (Oryza sativa L.) 是一种模式物种和经济相关作物。Oryza 属包括 25 个物种，有几个 Oryza 物种的基因组数据，使其成为遗传学和进化的模型。线粒体铁调节 (MIR) 基因先前与水稻缺铁反应有关，并被认为是仅存在于水稻中的孤儿基因。在这里，我们表明 MIR 也存在于属于 Oryza sativa 复合体的其他 Oryza 物种中，它们具有 AA 基因组类型并构成 O. sativa 育种的主要基因库。我们的数据表明 MIR 起源于一个逐步的过程，其中来自棉子糖合酶基因的外显子片段的序列被假基因化为非编码序列，这反过来又从头产生了 MIR 基因。除 Oryza barthii 外，所有具有假定功能性 MIR 基因的物种都因缺铁而保持其调控。在 O. barthii 中，MIR 编码序列易位到不同的染色体位置并与其调节区分离，导致缺乏缺铁反应。此外，水稻中的 MIR 共表达子网络簇对缺铁有反应，证明了新起源的基因在铁吸收中的重要性。这项工作确定 MIR 不是先前提出的孤儿基因，而是稻属中的从头起源的基因。我们还表明，MIR 正在一个物种（O. barthii）中发生基因组变化，