The Mitochondrial Iron-Regulated (MIR) gene is Oryza genus specific and evolved before speciation within the Oryza sativa complex.

Abstract

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. TheOryzagenus comprises 25 species, with genomic data available for several Oryzaspecies, making it a model for genetics and evolution. TheMitochondrial Iron-Regulated(MIR) gene was previously implicated inthe O. sativaFe deficiency response, and was considered an orphan gene present only in rice. Here we show that MIR is also found in otherOryzaspecies 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 thatMIRoriginated 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 functionalMIRgene conserve their regulation by Fe deficiency, with the exception ofOryza barthii. InO. 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 inO. sativais responsive to Fe deficiency, evidencing the importance of the newly originated gene in Fe uptake. This work establishes thatMIRis not an orphan gene as previously proposed, but a de novo originated gene within thegenus Oryza. We also showed that MIR is undergoing genomic changes in one species (O. barthii), with an impact onFe deficiency response.