Draft genome sequence of first monocot-halophytic species Oryza coarctata reveals stress-specific genes

Oryza coarctata (KKLL; 2n = 4x = 48, 665 Mb) also known as Porteresia coarctata is an extreme halophyte species of the genus Oryza. Using Illumina and Nanopore reads, we achieved an assembled genome size of 569.9 Mb, accounting for 85.69% of the estimated genome size, with N50 of 1.85 Mb and comprising 19.89% repeats. 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 the salt overly sensitive (SOS) signalling 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 the Oryza taxon.