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Hassawi  rice ( Oryza sativa  L.) is a landrace adapted to the climate of Saudi Arabia, characterized by its strong resistance to soil salinity and drought. Using high quality sequencing reads extracted from raw data of a whole genome sequencing project, we assembled both chloroplast (cp) and mitochondrial (mt) genomes of the wild-type  Hassawi  rice ( Hassawi-1 ) and its dwarf hybrid ( Hassawi-2 ). We discovered 16 InDels (insertions and deletions) but no SNP (single nucleotide polymorphism) is present between the two  Hassawi  cp genomes. We identified 48 InDels and 26 SNPs in the two  Hassawi  mt genomes and a new type of sequence variation, termed reverse complementary variation (RCV) in the rice cp genomes. There are two and four RCVs identified in  Hassawi-1  when compared to  93–11  ( indica ) and  Nipponbare  ( japonica ), respectively. Microsatellite sequence analysis showed there are more SSRs in the genic regions of both cp and mt genomes in the  Hassawi  rice than in the other rice varieties. There are also large repeats in the  Hassawi  mt genomes, with the longest length of 96,168 bp and 96,165 bp in  Hassawi-1  and  Hassawi-2 , respectively. We believe that frequent DNA rearrangement in the  Hassawi  mt and cp genomes indicate ongoing dynamic processes to reach genetic stability under strong environmental pressures. Based on sequence variation analysis and the breeding history, we suggest that both  Hassawi-1  and  Hassawi-2  originated from the Indonesian variety  Peta  since genetic diversity between the two  Hassawi  cultivars is very low albeit an unknown historic origin of the wild-type  Hassawi  rice.

The Organelle Genomes of Hassawi Rice (Oryza sativa L.) and Its Hybrid in Saudi Arabia: Genome Variation, Rearrangement, and Origins