Comparative Analysis of Rice Genome Sequence to Understand the Molecular Basis of Genome Evolution

Wu, Jianzhong; Mizuno, Hiroshi; Sasaki, Takuji; Matsumoto, Takashi

doi:10.1007/s12284-008-9021-8

Cited by 6 publications

(7 citation statements)

References 46 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Recent researches from multiple gene loci reported that the average nucleotide diversity of O. sativa ranged 0.0023∼0.0024 [4,43]. Obviously, the nucleotide diversity of Hd6 gene calculated using 398 bp PCR-amplified sequences from the both populations of O. sativa (π= 0.00016) and its wild relatives of O. rufipogon (π=0.00024) in this study was much lower than that of the above researches (Supplementary Table 3).…”

Section: Genome Diversity Within the Hd6 Regions Of Different Speciescontrasting

confidence: 64%

“…In plants, the alcohol dehydrogenase gene (Adh1) has been reported to be one of the most highly conserved genes [10,11,41]. For comparison, we also sequenced and calculated Ka and Ks from the coding sequences of Adh1 between all the species used in this study [38] and found a Ka value ≤0.013 and a Ka/Ks ratio ≤0.605. This demonstrates that the nonsynonymous substitution rate in Hd6 is even slower than that in Adh1.…”

Section: Molecular Evolution Of Hd6mentioning

confidence: 96%

See 1 more Smart Citation

Molecular and Evolutionary Analysis of the Hd6 Photoperiod Sensitivity Gene Within Genus Oryza

Yamane¹,

Ito²,

Ishikubo³

et al. 2008

Rice

Self Cite

View full text Add to dashboard Cite

Heading date determines rice's adaptation to its area and cropping season. We analyzed the molecular evolution of the Hd6 quantitative trait locus for photoperiod sensitivity in a total of 20 cultivated varieties and wild rice species and found 74 polymorphic sites within its coding region (1,002 bp), of which five were nonsynonymous substitutions. Thus, natural mutations and modifications of the coding region of Hd6 within the genus Oryza have been suppressed during its evolution; this is supported by low Ka (≤0.003) and Ka/Ks (≤0.576) values between species, indicating purifying selection for a protein-coding gene. A nonsynonymous substitution detected in the japonica variety "Nipponbare" (a premature stop codon and nonfunctional allele) was found within only some local Japanese japonica varieties, which suggests that this point mutation happened recently, probably after the introduction of Chinese rice to Japan, and is likely involved in rice adaptation to high latitudes. Phylogenetic analysis and genome divergence using the entire Hd6 genomic region confirmed the current taxonomic sections of Oryza and supported the hypothesis of independent domestication of indica and japonica rice.

show abstract

Section: Genome Diversity Within the Hd6 Regions Of Different Speciescontrasting

confidence: 64%

Section: Molecular Evolution Of Hd6mentioning

confidence: 96%

Molecular and Evolutionary Analysis of the Hd6 Photoperiod Sensitivity Gene Within Genus Oryza

Yamane¹,

Ito²,

Ishikubo³

et al. 2008

Rice

Self Cite

View full text Add to dashboard Cite

show abstract

“…Although BAC libraries have been constructed from various rice cultivars for the purpose of gene isolation, BAC physical maps covering the whole genome have been reported only in indica ‘Teqing’ and japonica ‘ZH11’ (Tao et al ., ; Wu et al ., ; Lin et al ., ). The ‘Kasalath’ MTP BAC clones and the accompanying map information provide not only genomic resources for confirming gene functions directly through complementary transformation with candidate BACs of interest, but also provide valuable tools to demonstrate the diversity of chromosomal structures between the two rice cultivars in a given genomic region.…”

Section: Discussionmentioning

confidence: 99%

“…A similarity analysis of genomic sequences within large indel sites was performed by BLAST search against the following public databases: the Oryza Repeat Database, containing rice repetitive sequences (http://rice.plantbiology.msu.edu/annotation_oryza.shtml), KOME, containing rice full‐length cDNA sequences (http://cdna01.dna.affrc.go.jp/cDNA/), and the NCBI non‐redundant protein database (ftp://ftp.ncbi.nlm.nih.gov/blast/db/) on demand. Characterization of TE elements within the large indel sites was performed as described previously (Ma et al ., ; Wu et al ., ).…”

Section: Methodsmentioning

confidence: 97%

A BAC physical map of aus rice cultivar ‘Kasalath’, and the map‐based genomic sequence of ‘Kasalath’ chromosome 1

et al. 2013

Self Cite

View full text Add to dashboard Cite

SUMMARYComparative analysis using available genomic resources within closely related species is an effective way to investigate genomic sequence and structural diversity. Rice (Oryza sativa L.) has undergone significant physiological and morphological changes during its domestication and local adaptation. We present a complete bacterial artificial chromosome (BAC) physical map for the aus rice cultivar 'Kasalath', which covers 90% of the sequence of temperate japonica rice cultivar 'Nipponbare'. Examination of physical distances between computational and experimental measurements of 'Kasalath' BAC insert size revealed the presence of more than 500 genomic regions that appear to have significant chromosome structural changes between the two cultivars. In particular, a genomic region on the long arm of 'Kasalath' chromosome 11 carrying a disease-resistance gene cluster was greatly expanded relative to the 'Nipponbare' genome. We also decoded 41.37 Mb of high-quality genomic sequence from 'Kasalath' chromosome 1. Extensive comparisons of chromosome 1 between 'Kasalath' and 'Nipponbare' led to the discovery of 317 843 single-nucleotide polymorphisms (SNPs) and 66 331 insertion/deletion (indel) sites. Nearly two-thirds of the expressed genes on rice chromosome 1 carried natural variations involving SNPs and/or indels that resulted in substitutions, insertions or deletions of amino acids in one cultivar relative to the other. We also observed gain and loss of genes caused by large indels. This study provides an important framework and an invaluable dataset for further understanding of the molecular mechanisms underlying the evolution and functions of the rice genome.

show abstract

“…W1588, Cameroon). The close genetic relationships of the cultivated rices with their wild ancestors have been confirmed both at the gene level [41][42][43] and at a population structure level, as analysed by using genome-wide retrotransposon markers (in preparation). BAC libraries of each cultivar or accession were constructed as described before 41,44 .…”

Section: Differences Between Amplifiable and Difficult-to-amplify R-gmentioning

confidence: 93%

Evolutionary dynamics and impacts of chromosome regions carrying R-gene clusters in rice

Mizuno

Katagiri

Kanamori

et al. 2020

Sci Rep

Self Cite

View full text Add to dashboard Cite

to elucidate R-gene evolution, we compared the genomic compositions and structures of chromosome regions carrying R-gene clusters among cultivated and wild rice species. Map-based sequencing and gene annotation of orthologous genomic regions (1.2 to 1.9 Mb) close to the terminal end of the long arm of rice chromosome 11 revealed R-gene clusters within six cultivated and ancestral wild rice accessions. nBS-LRR R-genes were much more abundant in Asian cultivated rice (O. sativa L.) than in its ancestors, indicating that homologs of functional genes involved in the same pathway likely increase in number because of tandem duplication of chromosomal segments and were selected during cultivation. phylogenetic analysis using amino acid sequences indicated that homologs of paired Pikm1-Pikm2 (NBS-LRR) genes conferring rice-blast resistance were likely conserved among all cultivated and wild rice species we examined, and the homolog of Xa3/Xa26 (LRR-RLK) conferring bacterial blight resistance was lacking only in Kasalath. Resistance genes (R-genes) confer disease resistance on plants, often forming clusters and showing frequent changes in copy number among genomes 1-3. As the sequences of cluster members are highly homologous, it is believable that the individual genes have evolved possibly through duplication events 4,5. Considerably, clustering of similar R-genes with the highly conserved sequences may lead to the creation of new resistance specificities via unequal crossing-over, gene conversion, or both which can be an important genetic resource 4,6. Models including the birth-and-death model and the balancing model are often used to explain the evolutionary process of R-genes. Based on a prediction that defeated R-genes get lost rapidly from the host population due to a metabolic cost associated with the gene maintenance, the birth-and-death model proposes that new disease-resistance genes are born by gene duplication 4,7. In plants, several R-genes such as wheat Pm3, Arabidopsis thaliana RPP13, flax L and capsicum eIF4E, for example, seem to have evolved in this way since they are likely involved in co-evolutionary relationships with pathogens 8-11. The balancing model suggests that genetic variation in disease resistance is maintained, even though there exists a fitness cost associated with the preservation of temporarily non-functional R-genes 12. R-genes of RPM1, RPS2 and RPS5 in Arabidopsis and Lr21 in wheat have been studied, revealing that both functional and non-functional alleles show the coexistence over a long period of evolutionary time in wild populations 12-15. Factors that explain the differences about the evolutionary patterns of R-genes in these two distinct models are still not well known. Cultivated rice varieties are either Asian or African in origin. The Asian cultivated rice Oryza sativa L. consists of two main subspecies, indica and japonica, each of which has a wild rice as its ancestor. The wild rice that was the source of O. sativa ssp. japonica is O. rufipogon (a perennial wild rice); the o...

show abstract

Comparative Analysis of Rice Genome Sequence to Understand the Molecular Basis of Genome Evolution

Cited by 6 publications

References 46 publications

Molecular and Evolutionary Analysis of the Hd6 Photoperiod Sensitivity Gene Within Genus Oryza

Molecular and Evolutionary Analysis of the Hd6 Photoperiod Sensitivity Gene Within Genus Oryza

A BAC physical map of aus rice cultivar ‘Kasalath’, and the map‐based genomic sequence of ‘Kasalath’ chromosome 1

Evolutionary dynamics and impacts of chromosome regions carrying R-gene clusters in rice

Contact Info

Product

Resources

About