Distinct evolutionary origins of intron retention splicing events in NHX1 antiporter transcripts relate to sequence specific distinctions in Oryza species

The genome of Asian cultivated rice (<i>Oryza sativa</i> L.) shows the presence of six organelle-specific and one plasma membrane (<i>OsNHX1-7</i>) NHX-type cation proton antiporters. Of these, vacuolar-localized <i>OsNHX1</i> is extensively characterized. The genus <i>Oryza</i> consists of 27 species and 11 genome-types, with cultivated rice, diploid <i>O. sativa</i>, having an AA-type genome. <i>Oryza NHX1</i> orthologous regions (gene organization, 5′ upstream cis elements, amino acid residues/motifs) from closely related <i>Oryza</i> AA genomes cluster distinctly from <i>NHX1</i> regions from more ancestral <i>Oryza</i> BB, FF and KKLL genomes. These sequence-specific distinctions also extend to two separate intron retention (IR) events involving <i>Oryza NHX1</i> transcripts that occur at the 5′ and 3′ ends of the NHX1 transcripts. We demonstrate that the IR event involving the 5′ UTR is present only in more recently evolved <i>Oryza</i> AA genomes while the IR event governing retention of the 13th intron of <i>Oryza NHX1</i> (terminal intron) is more ancient in origin, also occurring in halophytic wild rice, <i>Oryza coarctata</i> (KKLL). We also report presence of a retro-copy of the <i>OcNHX1</i> cDNA in the genome of <i>O. coarctata</i> (<i>rOcNHX1</i>). Preferential species and tissue specific up- or down-regulation of the correctly spliced <i>NHX1</i> transcript/5′ UTR/13th intron-retaining splice variants under salinity was observed. The implications of IR on <i>NHX1</i> mRNA stability and ORF diversity in <i>Oryza</i> spp. is discussed.