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

Abstract

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 complete chloroplast genome provides insight into the evolution and polymorphism of Panax ginseng

“…Minor allele frequency (MAF) refers to the frequency of the least common allele occurs in a given population and is usually used for conducting evolutionary analyses of genetic markers (Zhang et al, 2012a ; McPherson et al, 2013 ). Diversity in the MAF has been widely employed for evolutionary and genetic analyses between domestic and wild species in both plants and animals (Vasemagi et al, 2012 ; Alhaddad et al, 2013 ; Iorizzo et al, 2013 ; Petersen et al, 2013 ).…”

Whole Mitochondrial Genome Sequencing and Re-Examination of a Cytoplasmic Male Sterility-Associated Gene in Boro-Taichung-Type Cytoplasmic Male Sterile Rice

“…CMS-associated gene candidates have been selected based on whether they carry chimeric structures with known mitochondrial genes or encode proteins with a transmembrane domain, and whether or not they exhibit different expression patterns in the presence or absence of Rf genes. Whole mitochondrial genome sequences have been reported for Nipponbare [ 21 ], PA64S [ 22 ], indica cultivars 93–11 [ 22 ], IR6888B [ 17 ], and Hassawai [ 23 ], and several CMS lines such as LD-type CMS derived from Oryza sativa , WA-type CMS, Chinese wild rice (CW)-type CMS, RT98-type CMS, and RT102-type CMS derived from Oryza rufipogon [ 17 – 20 ]. Whole genome sequences of Boro-type mitochondria, however, have not been reported to date despite its economic importance in the production of F 1 hybrid seeds.…”

Molecular Diversity of Tidal Swamp Rice (Oryza sativa L.) in South Kalimantan, Indonesia

“…Furthermore, studies on phylogenetic relationships are indispensable to support rice breeding programs in the future [40], particularly in choosing the parents for developing new rice cultivars. These studies are extensively conducted by many researchers-such as Kim et al [22], Choudhury et al [41], Liu et al [11], Zhang et al [42], etc.-using different molecular markers, both in a local and a global scale. Nevertheless, such studies are still limited to the tidal swamp rice germplasm.…”