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. 2012;7(7):e42041.
doi: 10.1371/journal.pone.0042041. Epub 2012 Jul 31.

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

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Free PMC article

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

Tongwu Zhang et al. PLoS One. .
Free PMC article

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.

Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1
Figure 1. Circular representation of the cp and mt genome assemblies of both Hassawi-1 and Hassawi-2.
Circle display (from the outside): (1) physical map scale in kilobase pairs (in cp genome, LSC region in blue, SSC region in green, and IRs regions in red); (2) read depths of the 454 sequencing data in plum (step size: 100 bp in cp genome and 200 bp in mt genome; cp assembly: range 200–1325 in Hassawi-1 and range 200–2230 in Hassawi-2; mt assembly: range 0–500); (3) SOLiD mate-pair read validation with the 0.5–1 kb insert library in purple (insert size 600–800 bp and step size 100 bp in the cp assembly and 450 bp in the mt assembly); (4) SOLiD mate-pair read validation with 1–3 kb library in orange (insert size 1400–1600 bp and step size 150 bp in the cp assembly and 700 bp in the mt assembly). The high variance in read depth of the mt genome results from the regions of cp-derived sequences. This figure is generated by the Circos program.
Figure 2
Figure 2. Dot matrix alignment of cp genomes between Hassawi-1 and 93-11 (top) and between Hassawi-1 and Nipponbare (bottom).
The blue and red lines show direct and reverse matches, respectively. The red lines indicate IR regions in cp genomes.
Figure 3
Figure 3. Dot matrix alignment of mt genomes between Hassawi-1 and 93-11 (top) and between Hassawi-1 and Nipponbare (bottom).
The blue and red lines show direct and reverse matches, respectively.
Figure 4
Figure 4. Circos diagram illustrating SNP and InDel distributions in cp genomes of Hassawi-1 and the other three cultivars.
The first circle (from outside) displays genomes (color-coding) and genes (blocks). The second circle displays genomic regions including SSC, LSC, IRA, and IRB. The connecting lines inside the circles show SNPs (blue) and InDels (red) between two genomes.
Figure 5
Figure 5. Detail alignments of reverse complementary variations in four cp genomes.
The forward fragment is shown in green and the reverse fragment is shown in purple.
Figure 6
Figure 6. Circos diagram illustrating genome rearrangement and repeat distribution of mt genomes between Hassawi-1 and 93–11 (A) and between Hassawi-1 and Nipponbare (B).
The first circle (from outside) displays different genomes (color-coding) and genes (blocks). The second circle displays repeat distribution along genomes. The connecting lines inside the circles join syntenic regions with direct (blue) and reversed matches (red) between two genomes.
Figure 7
Figure 7. The origins of Hassawi rice and it’s hybrid.
The blue line predicts the origin of wild-type Hassawi rice from the Indonesian variety Peta.
Figure 8
Figure 8. Phylogenetic relationships of 5 rice cultivars as determined from whole cp genomes.
Support values are shown for nodes as maximum likelihood bootstrap. The scale bar denotes substitutions per site. The histogram presents the variations (Insertion, deletion and SNP) in both cp and mt genomes between Hassawi-1 and Hassawi-2.

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Grant support

The authors thank the Joint Center of Excellence for Genomics, King Abdulaziz City for Science and Technology (KACST) and Chinese Academy of Sciences. KASCT had a role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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