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1.
Shaowu Meng Douglas E Brown Daniel J Ebbole Trudy Torto-Alalibo Yeon Yee Oh Jixin Deng Thomas K Mitchell Ralph A Dean 《BMC microbiology》2009,9(Z1):S8
Background
Magnaporthe oryzae, the causal agent of blast disease of rice, is the most destructive disease of rice worldwide. The genome of this fungal pathogen has been sequenced and an automated annotation has recently been updated to Version 6 http://www.broad.mit.edu/annotation/genome/magnaporthe_grisea/MultiDownloads.html. However, a comprehensive manual curation remains to be performed. Gene Ontology (GO) annotation is a valuable means of assigning functional information using standardized vocabulary. We report an overview of the GO annotation for Version 5 of M. oryzae genome assembly.Methods
A similarity-based (i.e., computational) GO annotation with manual review was conducted, which was then integrated with a literature-based GO annotation with computational assistance. For similarity-based GO annotation a stringent reciprocal best hits method was used to identify similarity between predicted proteins of M. oryzae and GO proteins from multiple organisms with published associations to GO terms. Significant alignment pairs were manually reviewed. Functional assignments were further cross-validated with manually reviewed data, conserved domains, or data determined by wet lab experiments. Additionally, biological appropriateness of the functional assignments was manually checked.Results
In total, 6,286 proteins received GO term assignment via the homology-based annotation, including 2,870 hypothetical proteins. Literature-based experimental evidence, such as microarray, MPSS, T-DNA insertion mutation, or gene knockout mutation, resulted in 2,810 proteins being annotated with GO terms. Of these, 1,673 proteins were annotated with new terms developed for Plant-Associated Microbe Gene Ontology (PAMGO). In addition, 67 experiment-determined secreted proteins were annotated with PAMGO terms. Integration of the two data sets resulted in 7,412 proteins (57%) being annotated with 1,957 distinct and specific GO terms. Unannotated proteins were assigned to the 3 root terms. The Version 5 GO annotation is publically queryable via the GO site http://amigo.geneontology.org/cgi-bin/amigo/go.cgi. Additionally, the genome of M. oryzae is constantly being refined and updated as new information is incorporated. For the latest GO annotation of Version 6 genome, please visit our website http://scotland.fgl.ncsu.edu/smeng/GoAnnotationMagnaporthegrisea.html. The preliminary GO annotation of Version 6 genome is placed at a local MySql database that is publically queryable via a user-friendly interface Adhoc Query System.Conclusion
Our analysis provides comprehensive and robust GO annotations of the M. oryzae genome assemblies that will be solid foundations for further functional interrogation of M. oryzae.2.
Shigeyuki Tanaka Akari Ichikawa Kaori Yamada Gento Tsuji Takumi Nishiuchi Masashi Mori Hironori Koga Yoko Nishizawa Richard O'Connell Yasuyuki Kubo 《BMC plant biology》2010,10(1):288
Background
Rice CEBiP recognizes chitin oligosaccharides on the fungal cell surface or released into the plant apoplast, leading to the expression of plant disease resistance against fungal infection. However, it has not yet been reported whether CEBiP is actually required for restricting the growth of fungal pathogens. Here we evaluated the involvement of a putative chitin receptor gene in the basal resistance of barley to the ssd1 mutant of Magnaporthe oryzae, which induces multiple host defense responses. 相似文献3.
Emilie Vergne Xavier Grand Elsa Ballini Véronique Chalvon P Saindrenan D Tharreau J-L Nottéghem J-B Morel 《BMC plant biology》2010,10(1):206
Background
Partial resistance to plant pathogens is extensively used in breeding programs since it could contribute to resistance durability. Partial resistance often builds up during plant development and confers quantitative and usually broad-spectrum resistance. However, very little is known on the mechanisms underlying partial resistance. Partial resistance is often explained by poorly effective induction of plant defense systems. By exploring rice natural diversity, we asked whether expression of defense systems before infection could explain partial resistance towards the major fungal pathogen Magnaporthe oryzae. The constitutive expression of 21 defense-related genes belonging to the defense system was monitored in 23 randomly sampled rice cultivars for which partial resistance was measured. 相似文献4.
Background
Rice blast disease is caused by the filamentous Ascomycetous fungus Magnaporthe oryzae and results in significant annual rice yield losses worldwide. Infection by this and many other fungal plant pathogens requires the development of a specialized infection cell called an appressorium. The molecular processes regulating appressorium formation are incompletely understood. 相似文献5.
Yuan B Zhai C Wang W Zeng X Xu X Hu H Lin F Wang L Pan Q 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2011,122(5):1017-1028
The blast resistance gene Pik-p, mapping to the Pik locus on the long arm of rice chromosome 11, was isolated by map-based in silico cloning. Four NBS-LRR genes are present in the target region of cv. Nipponbare, and a presence/absence analysis in the Pik-p carrier cv. K60 excluded two of these as candidates for Pik-p. The other two candidates (KP3 and KP4) were expressed in cv. K60. A loss-of-function experiment by RNAi showed that both KP3 and KP4 are required for Pik-p function, while a gain-of-function experiment by complementation test revealed that neither KP3 nor KP4 on their own can impart resistance, but that resistance was expressed when both were introduced simultaneously. Both Pikp-1 (KP3) and Pikp-2 (KP4) encode coiled-coil NBS-LRR proteins and share, respectively, 95 and 99% peptide identity with the two alleles, Pikm1-TS and Pikm2-TS. The Pikp-1 and Pikp-2 sequences share only limited homology. Their sequence allowed Pik-p to be distinguished from Pik, Pik-s, Pik-m and Pik-h. Both Pikp-1 and Pikp-2 were constitutively expressed in cv. K60 and only marginally induced by blast infection. 相似文献
6.
Lim SH So BH Wang JC Song ES Park YJ Lee BM Kang HW 《Journal of microbiology (Seoul, Korea)》2008,46(2):214-220
Bacterial blight (BB) of rice, caused by Xanthomonas oryzae pv. oryzae (Xoo), is the most devastating bacterial disease in rice. A virulence-attenuated mutant strain HNU89K9 of X. oryzae pv. oryzae (KACC10331), with a transposon insertion in the pilQ gene was used for this study. The pilQ was involved in the gene cluster pilMNOPQ of the Xoo genome. Growth rate of the pilQ mutant was similar to that of wild-type. At level of amino acids, PilQ of Xoo showed that a high sequence identities more than 94% and 70% to Xanthomonas species and to Xyllela fastidiosa, respectively but a low sequence homology less than 30% to other bacterial species. The twitching motility forming a marginal fringe on PSA media was observed on colony of the wild-type strain KACC10331, but not in mutant HNU89K9. Wild-type Xoo cells formed a biofilm on the surface of the PVC plastic test tube, while the mutant strain HNU89K9 did not form a biofilm. The results suggest that the pilQ gene of X. oryzae pv. oryzae plays a critical role in pathogenicity, twitching motility, and biofilm formation. 相似文献
7.
Cao Y Duan L Li H Sun X Zhao Y Xu C Li X Wang S 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2007,115(7):887-895
Plant disease resistant (R) genes are frequently clustered in the genome. The diversity of members in a complex R-gene family may provide variation in resistance specificity. Rice Xa3/Xa26, conferring resistance to Xanthomonas
oryzae pv. oryzae (Xoo) encodes a leucine-rich repeat (LRR) receptor kinase-type protein and belongs to a multigene family, consisting of Xa3/Xa26, MRKa, MRKc and MRKd in rice cultivar Minghui 63. MRKa and MRKc are intact genes, while MRKd is a pseudogene. Complementary analyses showed that MRKa and MRKc could not mediate resistance to Xoo when regulated by their native promoters, but MRKa not MRKc conferred partial resistance to Xoo when regulated by a strong constitutive promoter. Plants carrying truncated XA3/XA26, which lacked the kinase domain, were
compromised in their resistance to Xoo. However, the kinase domain of MRKa could partially restore the function of the truncated XA3/XA26 in resistance. MRKa and MRKc showed similar expression pattern as Xa3/Xa26, which expressed only in the vascular systems of different tissues. The expressional characteristic of MRKa and MRKc perfectly fits the function of genes conferring resistance to Xoo, a vascular pathogen. These results suggest that although MRKa and MRKc cannot mediate bacterial blight resistance nowadays, they may be once effective genes for Xoo resistance. Their expressional characteristic and sequence similarity to Xa3/Xa26 will provide templates for generating novel recognition specificity to face the evolution of Xoo. In addition, both LRR and kinase domains encoded by Xa3/Xa26 and MRKa are the functional determinants and MRKa-mediated resistance is dosage-dependent.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
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Wu X Li X Xu C Wang S 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2008,118(1):185-191
Bacterial blight, caused by Xanthomonas oryzae pv. oryzae (Xoo), is the most devastating plant bacterial disease worldwide. Different bacterial blight resistance (R) genes confer race-specific resistance to different strains of Xoo. We fine mapped a fully recessive gene, xa24, for bacterial blight resistance to a 71-kb DNA fragment in the long arm of rice chromosome 2 using polymerase chain reaction-based
molecular markers. The xa24 gene confers disease resistance at the seedling and adult stages. It mediates resistance to at least the Philippine Xoo races 4, 6 and 10 and Chinese Xoo strains Zhe173, JL691 and KS-1-21. Sequence analysis of the DNA fragment harboring the dominant (susceptible) allele of xa24 suggests that this gene should encode a novel protein that is not homologous to any known R proteins. These results will
greatly facilitate the isolation and characterization of xa24. The markers will be convenient tools for marker-assisted selection of xa24 in breeding programs.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
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Odile Faivre-Rampant Gianluca Bruschi Pamela Abbruscato Stefano Cavigiolo Anna Maria Picco Laetitia Borgo Elisabetta Lupotto Pietro Piffanelli 《Molecular breeding : new strategies in plant improvement》2011,27(2):233-246
Italy is the only country in Europe with a significant land area used for rice production. In this paper, the genetic diversity
of 172 national varieties and 47 foreign accessions (ITALORYZA collection) was investigated using a set of neutral markers
evenly distributed throughout the 12 chromosomes. Out of the 218 alleles detected in our analysis, 17 and 29% were specific
to the Italian and foreign accessions, respectively. From the neighbour-joining tree generated, six sub-groups of temperate
japonica germplasm were identified. Plant height and grain type measured in the source collection were fitted to the phylogenetic
tree, along with the period of variety registration. This integrated genotype–phenotype analysis revealed that specific sub-groups
are characterized by uniform classes of grain type, or by similar plant size, or by period of release in the market. The whole
collection was also evaluated for leaf blast resistance by inoculating the plants with three strains of Magnaporthe oryzae, representing the pathogen genetic diversity existing in Italy. Only 15 out of 172 Italian accessions (8.7%) were resistant
to all three fungal strains. The correlation between genotype and leaf blast phenotype revealed that the most highly resistant
Italian varieties are included in a single germplasm sub-group derived from US varieties. This study represents the starting
point for carrying out detailed phenotype–genotype whole-genome association studies and identification of the genetic basis
of important agronomic traits for rice cultivation in temperate climates. 相似文献
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The major quantitative trait locus qBR9.1 confers broad-spectrum resistance to rice blast, and was mapped to a ~69.1 kb region on chromosome 9 that was inherited from resistant variety Sanhuangzhan No 2 (SHZ-2). Within this region, only one predicted disease resistance gene with nucleotide binding site and leucine-rich repeat (NBS-LRR) domains was found. Specific markers corresponding to this gene cosegregated with blast resistance in F2 and F3 populations derived from crosses of susceptible variety Texianzhan 13 (TXZ-13) to SHZ-2 and the resistant backcross line BC-10. We tentatively designate the gene as Pi56(t). Sequence analysis revealed that Pi56(t) encodes an NBS-LRR protein composed of 743 amino acids. Pi56(t) was highly induced by blast infection in resistant lines SHZ-2 and BC-10. The corresponding allele of Pi56(t) in the susceptible line TXZ-13 encodes a protein with an NBS domain but without LRR domain, and it was not induced by Magnaporthe oryzae infection. Three new cosegregating gene-specific markers, CRG4-1, CRG4-2 and CRG4-3, were developed. In addition, we evaluated polymorphism of the gene-based markers among popular varieties from national breeding programs in Asia and Africa. The presence of the CRG4-2 SHZ-2 allele cosegregated with a blast-resistant phenotype in two BC2F1 families of SHZ-2 crossed to recurrent parents IR64-Sub1 and Swarna-Sub1. CRG4-1 and CRG4-3 showed clear polymorphism among 19 varieties, suggesting that they can be used in marker-assisted breeding to combine Pi56(t) with other target genes in breeding lines. 相似文献
15.
Wuming Xiao Qiyun Yang Hui Wang Tao Guo Yongzhu Liu Xiaoyuan Zhu Zhiqiang Chen 《Molecular breeding : new strategies in plant improvement》2011,28(3):303-312
Finding novel sources of resistance (R) to rice blast disease should facilitate breeding for improved resistance. The objectives
of the present study were to evaluate reactions to blast and identify in a space-induced mutant an R gene to a representative
isolate of rice blast pathogen. The mutant H4, its parent and twelve monogenic lines were evaluated for their responses to
35 isolates collected from Guangdong Province, China. H4 was found to be resistant to more isolates than its parent and the
twelve monogenic lines, suggesting newly acquired resistance may be a function of one or more R genes. A representative isolate
GD0193 was used to identify and map the R gene from H4. Genetic analysis revealed that resistance to the isolate GD0193 was
controlled by a single dominant gene, designated Pi46(t). Linkage analysis using susceptible F2 individuals showed that Pi46(t) was mapped between the markers RM224 and RM27360 within 1.04 and 1.2 cM on the long arm of chromosome 11. Subsequently,
Pi46(t) was delimited to an interval of approximately 183.7 kb flanked by the markers K67 and T94. These results provide essential
information for the cloning of the Pi46(t) gene and will facilitate marker-assisted selection in rice breeding. 相似文献
16.
Wang GL Wu C Zeng L He C Baraoidan M de Assis Goes da Silva F Williams CE Ronald PC Leung H 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2004,108(3):379-384
The rice gene, Xa21, confers resistance to diverse races of Xanthomonas oryzae pv. oryzae (Xoo) and encodes a receptor-like kinase with leucine-rich repeats in the extra-cellular domain. To identify genes essential for the function of the Xa21 gene, 4,500 IRBB21 (Xa21 isogenic line in IR24 background) mutants, induced by diepoxybutane and fast neutrons, were screened against Philippine race six (PR6) Xoo for a change from resistance to susceptibility. From two greenhouse screens, 23 mutants were identified that had changed from resistant to fully (6) or partially (17) susceptible to PR6. All fully susceptible mutants carried rearrangements at the Xa21 locus as detected by PCR and Southern hybridization. For the partially susceptible mutants, no changes were detected at the Xa21 locus based on Southern and PCR analyses. However, two of these mutants were confirmed via genetic analysis to have mutations at the Xa21 locus. Partially susceptible mutants exhibited variation in level of susceptibility to different Xoo strains, suggesting that they may carry different mutations required for the Xa21-mediated resistance. The mutants identified in this study provide useful materials for dissecting the Xa21-mediated resistance pathway in rice.Communicated by D.J. Mackill 相似文献
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Pathogenesis-related (PR) proteins play an important role in the disease resistance response. To better understand the function
of rice PR proteins, we examined the expressions of ten PR proteins in rice leaves at different developmental stages with
or without the interaction between rice and Xanthomonas oryzae pv. oryzae (Xoo). The results showed that most of the PR proteins were expressed in rice leaves in normal growth conditions, suggesting that
they play a role in rice growth. Six out of ten PR proteins (PR1, PR2, PR3, PR4b, PR8, and PR-pha) showed enhanced expression
in Xa21-mediated resistance responses at late stages after inoculation with Xoo. The remaining four PR proteins (PR5, PR6, PR15, and PR16) did not show changes in expression in the resistance response.
The expressions of PR proteins in the resistance reaction were further compared with those in the susceptible reaction and
a mock treatment. Interestingly, several of the PR proteins were expressed at the highest levels in the susceptible reaction
and at the lowest levels in the mock treatment. Among the other four PR proteins, PR5 and PR16 showed changes in the abundance
only in the susceptible response, while PR6 and PR15 showed no detectable difference in expression. These data provide fundamental
knowledge about the expression of PR proteins in the interaction between rice and Xoo. 相似文献
19.
Genome sequence analysis of Xanthomonas
oryzae pv. oryzae has revealed a cluster of 12 ORFs that are closely related to the gum gene cluster of Xanthomonas campestris pv. campestris. The gum gene cluster of X. oryzae encodes proteins involved in xanthan production; however, there is little experimental evidence supporting this. In this
study, biochemical analyses of xanthan produced by a defined set of X. oryzae
gum mutant strains allowed us to preliminarily assign functions to most of the gum gene products: biosynthesis of the pentasaccharide repeating unit for GumD, GumM, GumH, GumK, and GumI, xanthan polymerization
and transport for GumB, GumC, GumE, and GumJ, and modification of the pentasaccharide repeating unit for GumF, GumG, and GumL.
In addition, we found that the exopolysaccharides are essential but not specific for the virulence of X. oryzae.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.
Sang-Yoon Kim and Jeong-Gu Kim contributed equally to this work. 相似文献
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