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Author Zhang,T., Hu,S., Zhang,G., Pan,L., Zhang,X., Al-Mssallem,I.S. and Yu,J.
Title 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.
Journal PLoS ONE
Country China
Volume 7 (7)
Pages E42041
Year 2012
PubMed ID 22870184
PubMed Central ID -
DOI 10.1371/journal.pone.0042041
URL -
Relation
Gene 16S rRNA 16S rRNA 23S rRNA 23S rRNA 26S rRNA 26S rRNA 3'RPS12 4.5S rRNA 4.5S rRNA 5S rRNA 5S rRNA 5S rRNA CLPP GSLm INFA NAD1 NAD2 NAD3 NAD4 NAD4L NAD5 NAD6 NAD7 NAD9 NDHA NDHB NDHB NDHC NDHD NDHE NDHF NDHG NDHH NDHI NDHJ NDHK PETA PETD PETE PSAA PSAB PSAC PSBA PSBC PSBD PSBE PSBF PSBH PSBI PSBK PSBL PSBM PSBN PSBZ RBCL RPL14 RPL16 RPL16 RPL2 RPL2 RPL2 RPL22 RPL23 RPL23 RPL32 RPL33 RPL36 RPOA RPOB RPOC1 RPOC2 RPS1 RPS11 RPS12 RPS12 RPS12 RPS13 RPS14 RPS15 RPS15 RPS16 RPS18 RPS19 RPS19 RPS19 RPS2 RPS2 RPS3 RPS3 RPS4 RPS4 RPS7 RPS7 RPS7 RPS8 YCF4 _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
INSD JN861110 JN861111 JN861112 JN861109
Strain Wild Core Collection -
Sterile Seed Strain -
Lethal Embryo
Mutantion Strain
-
Stages in Each Organ
- Muant Lines (Gene)
-
Cultivated Varieties(NIG Collection) -
Stages in Each Organ -
/rice/oryzabase