
@article {124206,
	title = {A conserved SNP variation in the pre-miR396c flanking region in Oryza sativa indica landraces correlates with mature miRNA abundance.},
	journal = {Sci Rep},
	volume = {13},
	year = {2023},
	month = {2023 Feb 07},
	pages = {2195},
	abstract = {<p>Plant precursor miRNAs (pre-miRNA) have conserved evolutionary footprints that correlate with mode of miRNA biogenesis. In plants, base to loop and loop to base modes of biogenesis have been reported. Conserved structural element(s) in pre-miRNA play a major role in turn over and abundance of mature miRNA. Pre-miR396c sequences and secondary structural characteristics across Oryza species are presented. Based on secondary structure, twelve Oryza pre-miR396c sequences are divided into three groups, with the precursor from halophytic Oryza coarctata forming a distinct group.\&nbsp;The miRNA-miRNA* duplex region is completely conserved across eleven\&nbsp;Oryza\&nbsp;species as are other structural elements in the pre-miRNA, suggestive of an evolutionarily conserved base-to-loop mode of miRNA biogenesis. SNPs within O. coarctata mature miR396c sequence and miRNA* region have the potential to alter target specificity and association with the RNA-induced silencing complex. A conserved SNP variation, rs10234287911 (G/A), identified in O. sativa pre-miR396c sequences alters base pairing above the miRNA-miRNA* duplex. The more stable structure conferred by the {\textquoteright}A{\textquoteright} allele may promote better processing vis-{\`a}-vis the structure conferred by {\textquoteright}G{\textquoteright} allele. We also examine pri- and pre-miR396c expression in cultivated rice under heat and salinity and their correlation with miR396c expression.</p>
},
	keywords = {MicroRNAs, Oryza, Polymorphism, Single Nucleotide, Salt-Tolerant Plants},
	issn = {2045-2322},
	doi = {10.1038/s41598-023-28836-1},
	author = {Jaganathan, Deepa and Rajakani, Raja and Doddamani, Dadakhalandar and Saravanan, Divya and Pulipati, Shalini and Vivek Hari Sundar G and Sellamuthu, Gothandapani and Jayabalan, Shilpha and Kumari, Kumkum and Parthasarathy, Pavithra and S, Punitha and Ramalingam, Sivaprakash and Shivaprasad, Padubidri V and Venkataraman, Gayatri}
}
@article {77381,
	title = {Distinct Evolutionary Origins of Intron Retention Splicing Events in  Antiporter Transcripts Relate to Sequence Specific Distinctions in  Species.},
	journal = {Front Plant Sci},
	volume = {11},
	year = {2020},
	month = {2020},
	pages = {267},
	abstract = {<p>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{\textquoteright} 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{\textquoteright} and 3{\textquoteright} ends of the NHX1 transcripts. We demonstrate that the IR event involving the 5{\textquoteright} 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{\textquoteright} UTR/13th intron-retaining splice variants under salinity was observed. The implications of IR on mRNA stability and ORF diversity in spp. is discussed.</p>
},
	issn = {1664-462X},
	doi = {10.3389/fpls.2020.00267},
	author = {Sellamuthu, Gothandapani and Jegadeeson, Vidya and Sajeevan, Radha Sivarajan and Rajakani, Raja and Parthasarathy, Pavithra and Raju, Kalaimani and Shabala, Lana and Chen, Zhong-Hua and Zhou, Meixue and Sowdhamini, Ramanathan and Shabala, Sergey and Venkataraman, Gayatri}
}
