Oryza coarctata (KKLL; 2n = 4x = 48, 665 Mb) also known as Porteresia coarctata is an extreme halophyte species of genus Oryza. Using Illumina and Nanopore reads, we achieved the assembled genome size of 569.9 Mb, accounting 85.69% of the estimated genome size with N50 of 1.85 Mb and 19.89% repetitive region. We also found 230,968 simple sequence repeats (SSRs) and 5,512 non-coding RNAs (ncRNAs). The functional annotation of predicted 33,627 protein-coding genes and 4,916 transcription factors revealed that high salinity adaptation of this species is due to the exclusive or excessive presence of stress-specific genes as compared to rice. We have identified 8 homologs to salt-tolerant SOS1 genes, one of the three main components of salt overly sensitive (SOS) signal pathway. On the other hand, the phylogenetic analysis of the assembled chloroplast (134.75 kb) and mitochondrial genome (491.06 kb) favours the conservative nature of these organelle genomes within Oryza taxon.

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Oryza coarctata Roxb. is a wild halophytic species found mostly on South Asian seashore. It can tolerate salinity up to 4 S m-1 , which is equivalent to 479 mM NaCl. This species has unique morphological, anatomical, as well as physiological adaptations, which helps it to survive under high salinity and submerged conditions. Thus, it is considered to be a reservoir of salinity and submergence tolerance genes. For quantification of gene expressions, it is necessary to identify stable reference genes and validate stress responsive genes by real time quantitative PCR. The present study deals with the expression analyses of eight candidate reference genes, namely, ubiquitin 2, histone 3, β-tubulin, α-tubulin, glyceraldehyde-3-phosphate dehydrogenase, eukaryotic initiation factor 4-α (eIF4-α), cyclophilin, and actin (ACT) under different abiotic stresses such as salinity, cold, drought, heat, submergence, submergence with saline water (dual stress), and abscisic acid treatment. The four different statistical algorithms, namely, Bestkeeper, NormFinder, geNorm, and RefFinder were used to rank the genes in order of stability. The analysis revealed that ACT and eIF4-α were the two most stable reference genes, which was further validated by determining the expressions of two well-known stress responsive genes alcohol dehydrogenase and dehydration responsive element binding protein 2A under submergence and drought stress, respectively. This study is the first report to analyse the reference genes for O. coarctata.

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Three gene families in plants viz. Argonaute (AGOs), Dicer-like (DCLs) and RNA dependent RNA polymerase (RDRs) constitute the core components of small RNA mediated gene silencing machinery. The present study endeavours to identify members of these gene families in tea and to investigate their expression patterns in different tissues and various stress regimes. Using genome-wide analysis, we have identified 18 AGOs, 5 DCLs and 9 RDRs in tea, and analyzed their phylogenetic relationship with orthologs of Arabidopsis thaliana. Gene expression analysis revealed constitutive expression of CsAGO1 in all the studied tissues and stress conditions, whereas CsAGO10c showed most variable expression among all the genes. CsAGO10c gene was found to be upregulated in tissues undergoing high meristematic activity such as buds and roots, as well as in Exobasidium vexans infected samples. CsRDR2 and two paralogs of CsAGO4, which are known to participate in biogenesis of hc-siRNAs, showed similarities in their expression levels in most of the tea plant tissues. This report provides first ever insight into the important gene families involved in biogenesis of small RNAs in tea. The comprehensive knowledge of these small RNA biogenesis purveyors can be utilized for tea crop improvement aimed at stress tolerance and quality enhancement.