Distinct Evolutionary Origins of Intron Retention Splicing Events in Antiporter Transcripts Relate to Sequence Specific Distinctions in Species.

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