... and 10 different genome types (i.e., the AA, BB, CC, BBCC, CCDD, EE, FF, GG, JJHH, ... al. 1999). Asian cultivated rice has the diploid AA genome. Oryza species with different genome types have ... ...
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A genomic region (~247kb) from an FF genome, wild Oryza species, O. brachyantha L., was sequenced and compared to the orthologous region (~450 kb) from AA genome rice, O. sativa L. ssp japonica ¬ the first such comparison reported between cultivated Oryza and a distantly ...
Technology Transfer Automated Retrieval System (TEKTRAN)
, September 29, 1999 (received for review May 24, 1999) The rice genus, Oryza, which comprises 23 species genome. An additional genome type, HHKK, was recognized for Oryza schlechteri and Porteresia coarc- tata, suggesting that P. coarctata is an Oryza species. The AA ...
E-print Network
physical map, BES alignment, rice genome sequence, Oryza. punctata, SyMAP, FPC, SNaPshot fingerprinting within a single genus at the whole-genome level. The annual type of Oryza punctata is a diploid wild rice species belonging to the BB genome group of the genus Oryza and ...
from 357 Mbp in Oryza glaberrima [AA] to 1283 Mbp in the polyploid Oryza ridleyi [HHJJ]. Because they tag the highest value of hits in the three AA genome species: O. glaberrima (17% of reads), O. nivara could introduce a certain degree of uncertainty and so the following values should be ...
Retrotransposons are ubiquitous in higher plant genomes. The presence or absence of retrotransposons in whole genome and high throughput genomic sequence (HTGS) from cultivated and wild rice was investigated to understand the organization and evolution of retrotransposon insertions in promoter regions. Approximately half of the ...
PubMed
). These resources, coupled with enormous genetic and functional experimental re- sources alreadyinplaceforO. sativaSeq) from the short arm of chromosome 11 of O. sativa ssp japonica (pseudo molecule build 4; Rice Annotation Genome Clone Address Insert Size (bp) Total Length of the Sequenced Regiona O. sativa ssp indica AA OSI9
The Pi-ta gene in rice confers resistance to the fungus Magnaporthe oryzae containing AVR-Pita. Pi-ta is predicted to encode a cytoplasmic receptor protein with nucleotide binding sites and leucine rich domain. A panel of 51 oryza accessions consisting of the AA genome species, O. sativa, O. glabe...
Comparative genomics is a powerful tool to decipher gene and genome evolution. Placing multiple genome comparisons in a phylogenetic context improves the sensitivity of evolutionary inferences. In the genus Oryza, this comparative approach can be used to investigate gene function, genome ...
PubMed Central
Wild species of rice with many valuable agronomic traits are an important genetic resource for improving cultivated rice by wide hybridization. Genome- or chromosome-specific markers are useful for monitoring genome introgression and for identifying genome components. From 47 random amplified polymorphic DNAs (RAPDs) of nine ...
The Pi-ta gene in rice has been predicted to directly detect the pathogen signaling molecule in preventing blast disease. The resistance Pi-ta allale (alanine at 918) has been introgressed between cultivated rice to confer blast resistance. To understand the evolutionary dynamics present of Pi-ta, w...
BackgroundExtensive DNA rearrangement of genic colinearity, as revealed by comparison of orthologous genomic regions, has been shown to be a general concept describing evolutionary dynamics of plant genomes. However, the nature, timing, lineages and adaptation of local genomic rearrangement in closely related species (e.g., within a ...
MUG1 is a MULE transposon-related domesticated gene in plants. We assessed the sequence diversity, neutrality, expression, and phylogenetics of the MUG1 gene among Oryza ssp. We found MUG1 expression in all tissues analyzed, with different levels in O. sativa. There were 408 variation sites in the 3886 bp of MUG1 locus. The nucleotide diversity of the MUG1 was higher than ...
The rice genus, Oryza, which comprises 23 species and 9 recognized genome types, represents an enormous gene pool for genetic improvement of rice cultivars. Clarification of phylogenetic relationships of rice genomes is critical for effective utilization of the wild rice germ plasm. By generating and comparing two nuclear gene (Adh1 ...
BackgroundPlant genomes contain various kinds of repetitive sequences such as transposable elements, microsatellites, tandem repeats and virus-like sequences. Most of them, with the exception of virus-like sequences, do not allow us to trace their origins nor to follow the process of their integration into the host genome. Recent discoveries of virus-like ...
Rice blast, caused by the fungal pathogen Magnaporthe oryzae, is a devastating disease of rice worldwide. Among the 85 mapped resistance (R) genes against blast, 13 have been cloned and characterized. However, how these genes originated and how they evolved in the Oryza genus remains unclear. We previously cloned the rice blast R-genes Pi2, Pi9, and Piz-t, ...
RiceGenes is a Database of the Rice (Oryza sativa) genome. It also contains extensive information in References....
to 11 genomes including the Oryza sativa (rice) [2] and Homo sapiens [3] genomes. The current version to the Oryza sativa genome as well as 10 other eukaryotic and prokaryotic genomes. Our framework is built://www.python.org>. [2] Yu J., Hu S., Wang J., Wong G., et. al. ...
Hybrid incompatibility in F1 hybrids or later generations is often observed as sterility or inviability. This incompatibility acts as postzygotic reproductive isolation, which results in the irreversible divergence of species. Here, we show that the reciprocal loss of duplicated genes encoding mitochondrial ribosomal protein L27 causes hybrid pollen sterility in ...
The rice disease resistance (R) gene Xa3/Xa26 (having also been named Xa3 and Xa26) against Xanthomonas oryzae pv. oryzae (Xoo), which causes bacterial blight disease, belongs to a multiple gene family clustered in chromosome 11 and is from an AA genome rice cultivar (Oryza sativa L.). This ...
Rice and rice gene pool Asian cultivated rice (Oryza sativa L., referred to hereafter as rice) is an important world crop, providing staple foods for nearly one half of the global population. Achieving high productivity, including improved breeding methods, is always the challenge in meeting the demand for food security and nutritional sufficiency, particularly for the ...
The genome sequence of Aspergillus oryzae, a fungus used in the production of the traditional Japanese fermentation foods sake (rice wine), shoyu (soy sauce), and miso (soybean paste), has revealed prominent features in its gene composition as compared to those of Saccharomyces cerevisiae and Neurospora crassa. The A. oryzae ...
cDNA and genomic DNA for two nearly identical genes, AmyI and AmyII, coding for the enzyme Taka-amylase A (TA-A) of the fungus Aspergillus oryzae have been cloned and characterized. These genes are apparently unlinked, differing by only 3 nucleotides (nt) out of the 2720 nt that span the coding regions. The 617-nt 5'-flanking regions differ only at nt -372 ...
Background With the completion of the genome sequence for rice (Oryza sativa L.), the focus of rice genomics research has shifted to the comparison of the rice genome with genomes of other species for gene cloning, breeding, and evolutionary studies. The genus Oryza ...
polyploidization events. Apart from Arabidopsis thaliana, rice (Oryza sativa) is currently the only plant species dating of duplicated segments 1. The genome sequence of Oryza sativa - assembly1. The genome sequence of Oryza sativa - assembly � Input: 2,987 IRGSP genomic ...
p-SINE1 was the first plant SINE element identified in the Waxy gene in Oryza sativa, and since then a large number of p-SINE1-family members have been identified from rice species with the AA or non-AA genome. In this paper, we report two new rice SINE elements, designated p-SINE2 and p-SINE3, which form distinct ...
The Oryza Map Alignment Project: the golden path to unlocking the genetic potential of wild rice, comparative genomics, physical mapping, rice, wild species Abstract The wild species of the genus Oryza offer Oryza sativa and Oryza glaberrima. To unlock the genetic potential of wild rice we have ...
Vol. 45 No. 5 SCIENCE IN CHINA (Series C) October 2002 The transfer RNA genes in Oryza sativa L@itp.ac.cn) Received July 26, 2002 Abstract The availability of the draft genome sequence of Oryza sativa L. ssp tRNA genes is discovered in the complete chloroplast genome of Oryza sativa L. ssp. ...
The race-specific resistance gene Pi-ta has been effectively used to control blast disease, one of the most destructive plant diseases worldwide. A single amino acid change at the 918 position of the Pi-ta protein was known to determine resistance specificity. To understand the evolutionary dynamics present, we examined sequences of the Pi-ta locus and its flanking regions in 159 accessions ...
Aspergillus flavus is a plant and animal pathogen that also produces the potent carcinogen aflatoxin. Aspergillus oryzae is a closely related species that has been used for centuries in the food fermentation industry and is generally regarded as safe (GRAS). Whole genome sequences for these two fu...
Rhizopus oryzae is the primary etiologic agent of mucormycosis, an emerging lifethreatening infection. The rapid growth and angioinvasive nature of mucormycotic infections in humans result in an overall mortality rate that exceeds 50%, even with combined surgical and antifungal therapies. As part ...
Aspergillus flavus produces aflatoxins and is the second leading cause of aspergillosis in immunocompromised individuals. Aspergillus oryzae, on the other hand, has been used for centuries in Japan for the fermentation of food. The recently available whole genome sequences of Aspergillus flavus an...
Research article Transposable element distribution, abundance and role in genome size variation in the genus Oryza
] and between the species of the rice genus, Oryza [7,8]. To take full advantage of rice genome resources of the rice genus. The genus Oryza consists of 2 cultivated and approximately 22 wild species distributed pairing in interspecific hybrids, traditional genome analyses grouped the majority of ...
of genome size in the genus Oryza Jetty S. S. Ammiraju1, , Andrea Zuccolo1, , Yeisoo Yu1 , Xiang Song1 to detect ancestrally related retrotransposons. The genus Oryza, with 24 species, ten genome types of an LTR retrotrans- poson family named RWG in the genus Oryza. Comparative analysis of ...
BackgroundOryza longistaminata, an AA genome type (2 n = 24), originates from Africa and is closely related to Asian cultivated rice (O. sativa L.). It contains various valuable traits with respect to tolerance to biotic and abiotic stress, QTLs with agronomically important traits and high ability to use nitrogen efficiently (NUE). ...
This is an Open Access article distributed under the terms of the Creative Commons Attribution License
Rice blast, caused by Magnaporthe oryzae, is one of the most devastating diseases. The two major subspecies of Asian cultivated rice (Oryza sativa L.), indica and japonica, have shown obvious differences in rice blast resistance, but the genomic basis that underlies the difference is not clear. We performed a genomewide comparison of ...
