Abstract
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.
Highlights
Soil salinity is a major abiotic stress reducing the yield of rice cultivated globally and is increasing gradually due to surface irrigation, high cropping intensity and cultivation of high yielding variety[1]
Apart from these, some BAC end sequences and repeat libraries for O. coarctata were reported as part of The Oryza Map Alignment Project (OMAP)[11,12,13] but no efforts seems to be reported to decode the genome assembly of O. coarctata, which is the pre-requisite to harness its genetic potential for salinity tolerance
There are 3 main genes in the salt overly sensitive (SOS) signal pathway, i.e. SOS1, SOS2 and SOS3 but as SOS2 gets activated by SOS3 after interaction, and their complex is required to fully activate SOS1, we focused on the identification of SOS1 gene, a set of genes with most important role in plant salt-tolerance, to get an overlay of the abundance of SOS pathway related genes in the assembled genome[47,48,49,50]
Summary
Soil salinity is a major abiotic stress reducing the yield of rice cultivated globally and is increasing gradually due to surface irrigation, high cropping intensity and cultivation of high yielding variety[1]. O. coarctata, an allo-tetraploid species (chromosome number of 2n = 4X = 48, KKLL genome)[4,5] is popularly known as Asian wild rice, grows naturally in the coastal region of South-East Asian countries, where this plant experiences the lunar tide and is exposed to submerge saline sea water in every alternative 12 h. It set flowers and seeds under high saline conditions of upto 40 E.CedS m−1 saline soil[6]. The genomic resources developed in this sequencing effort should contribute in advancing molecular breeding programmes against salinity and to investigate the Oryza genome evolution
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