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Christopoulou M, McHale LK, Kozik A, Reyes-Chin Wo S, Wroblewski T, Michelmore RW. Dissection of Two Complex Clusters of Resistance Genes in Lettuce (Lactuca sativa). MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2015; 28:751-65. [PMID: 25650829 DOI: 10.1094/mpmi-06-14-0175-r] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Of the over 50 phenotypic resistance genes mapped in lettuce, 25 colocalize to three major resistance clusters (MRC) on chromosomes 1, 2, and 4. Similarly, the majority of candidate resistance genes encoding nucleotide binding-leucine rich repeat (NLR) proteins genetically colocalize with phenotypic resistance loci. MRC1 and MRC4 span over 66 and 63 Mb containing 84 and 21 NLR-encoding genes, respectively, as well as 765 and 627 genes that are not related to NLR genes. Forward and reverse genetic approaches were applied to dissect MRC1 and MRC4. Transgenic lines exhibiting silencing were selected using silencing of β-glucuronidase as a reporter. Silencing of two of five NLR-encoding gene families resulted in abrogation of nine of 14 tested resistance phenotypes mapping to these two regions. At MRC1, members of the coiled coil-NLR-encoding RGC1 gene family were implicated in host and nonhost resistance through requirement for Dm5/8- and Dm45-mediated resistance to downy mildew caused by Bremia lactucae as well as the hypersensitive response to effectors AvrB, AvrRpm1, and AvrRpt2 of the nonpathogen Pseudomonas syringae. At MRC4, RGC12 family members, which encode toll interleukin receptor-NLR proteins, were implicated in Dm4-, Dm7-, Dm11-, and Dm44-mediated resistance to B. lactucae. Lesions were identified in the sequence of a candidate gene within dm7 loss-of-resistance mutant lines, confirming that RGC12G confers Dm7.
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Affiliation(s)
- Marilena Christopoulou
- Genome Center and Department of Plant Sciences, University of California-Davis, CA 95616, U.S.A
| | - Leah K McHale
- Genome Center and Department of Plant Sciences, University of California-Davis, CA 95616, U.S.A
| | - Alex Kozik
- Genome Center and Department of Plant Sciences, University of California-Davis, CA 95616, U.S.A
| | - Sebastian Reyes-Chin Wo
- Genome Center and Department of Plant Sciences, University of California-Davis, CA 95616, U.S.A
| | - Tadeusz Wroblewski
- Genome Center and Department of Plant Sciences, University of California-Davis, CA 95616, U.S.A
| | - Richard W Michelmore
- Genome Center and Department of Plant Sciences, University of California-Davis, CA 95616, U.S.A
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Kumari A, Kumar A, Wany A, Prajapati GK, Pandey DM. Identification and annotation of abiotic stress responsive candidate genes in peanut ESTs. Bioinformation 2012; 8:1211-9. [PMID: 23275722 PMCID: PMC3530874 DOI: 10.6026/97320630081211] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Accepted: 11/11/2012] [Indexed: 11/23/2022] Open
Abstract
Peanut (Arachis hypogaea L.) ranks fifth among the world oil crops and is widely grown in India and neighbouring countries. Due to its large and unknown genome size, studies on genomics and genetic modification of peanut are still scanty as compared to other model crops like Arabidopsis, rice, cotton and soybean. Because of its favourable cultivation in semi-arid regions, study on abiotic stress responsive genes and its regulation in peanut is very much important. Therefore, we aim to identify and annotate the abiotic stress responsive candidate genes in peanut ESTs. Expression data of drought stress responsive corresponding genes and EST sequences were screened from dot blot experiments shown as heat maps and supplementary tables, respectively as reported by Govind et al. (2009). Some of the screened genes having no information about their ESTs in above mentioned supplementary tables were retrieved from NCBI. A phylogenetic analysis was performed to find a group of utmost similar ESTs for each selected gene. Individual EST of the said group were further searched in peanut ESTs (1,78,490 whole EST sequences) using stand alone BLAST. For the prediction as well as annotation of abiotic stress responsive selected genes, various tools (like Vec-Screen, Repeat Masker, EST-Trimmer, DNA Baser, WISE2 and I-TASSER) were used. Here we report the predicted result of Contigs, domain as well as 3D structure for HSP 17.3KDa protein, DnaJ protein and Type 2 Metallothionein protein.
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Affiliation(s)
- Archana Kumari
- Department of Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand-835215, India
| | - Ashutosh Kumar
- Department of Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand-835215, India
| | - Aakanksha Wany
- Department of Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand-835215, India
| | - Gopal Kumar Prajapati
- Department of Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand-835215, India
| | - Dev Mani Pandey
- Department of Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand-835215, India
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Fossdal CG, Yaqoob N, Krokene P, Kvaalen H, Solheim H, Yakovlev IA. Local and systemic changes in expression of resistance genes, NB-LRR genes and their putative microRNAs in Norway spruce after wounding and inoculation with the pathogen Ceratocystis polonica. BMC PLANT BIOLOGY 2012; 12:105. [PMID: 22776433 PMCID: PMC3431983 DOI: 10.1186/1471-2229-12-105] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Accepted: 07/09/2012] [Indexed: 05/24/2023]
Abstract
BACKGROUND NB-LRR resistance proteins are involved in recognizing pathogens and other exogenous stressors in plants. Resistance proteins are the first step in induced defence responses and a better understanding of their regulation is important to understand the mechanisms of plant defence. Much of the post-transcriptional regulation in plants is controlled by microRNAs (miRNA). We examined the expression of five Norway spruce miRNA that may regulate NB-LRR related transcripts in secondary phloem (bark) of resistant Norway spruce after wounding and inoculation with the necrotrophic blue stain fungus Ceratocystis polonica. RESULTS The plants of this clone recovered from both the pathogen inoculations and wounding alone. We found local and systemic induction of the resistance marker genes PaChi4, PaPAL and PaPX3 indicative of an effective induced host defence response. There were minor local and systemic changes in the expression of five miRNAs and 21 NB-LRRs between healthy and treated plants. Only five putative NB-LRRs (PaLRR1, PaLRR3, PaLRR14, PaLRR15 and PaLRR16) showed significant increases greater than two-fold as a local response to C. polonica. Of all NB-LRRs only PaLRR3, the most highly differentially regulated NB-LRR, showed a significant increase also due to wounding. The five miRNAs showed indications of an initial local and systemic down-regulation at day 1, followed by a later increase up to and beyond the constitutive levels at day 6. However, the initial down-regulation was significant only for miR3693 and miR3705. CONCLUSIONS Overall, local and systemic expression changes were evident only for the established resistance marker genes and PaLRR3. The minor expression changes observed both for the followed miRNAs and their predicted NB-LRR targets suggest that the expression of most NB-LRR genes are maintained close to their constitutive levels in stressed and healthy Norway spruce plants.
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Affiliation(s)
- Carl Gunnar Fossdal
- Norwegian Forest and Landscape Institute, Høgskoleveien 8, As, NO-1431, Norway
| | - Nadeem Yaqoob
- Norwegian Forest and Landscape Institute, Høgskoleveien 8, As, NO-1431, Norway
- Department of Ecology and Natural Resource Management, Norwegian University of Life Sciences, Høgskoleveien 12, As, NO-1432, Norway
| | - Paal Krokene
- Norwegian Forest and Landscape Institute, Høgskoleveien 8, As, NO-1431, Norway
| | - Harald Kvaalen
- Norwegian Forest and Landscape Institute, Høgskoleveien 8, As, NO-1431, Norway
| | - Halvor Solheim
- Norwegian Forest and Landscape Institute, Høgskoleveien 8, As, NO-1431, Norway
| | - Igor A Yakovlev
- Norwegian Forest and Landscape Institute, Høgskoleveien 8, As, NO-1431, Norway
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Tan S, Wu S. Genome Wide Analysis of Nucleotide-Binding Site Disease Resistance Genes in Brachypodium distachyon. Comp Funct Genomics 2012; 2012:418208. [PMID: 22693425 PMCID: PMC3368180 DOI: 10.1155/2012/418208] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Revised: 02/20/2012] [Accepted: 02/27/2012] [Indexed: 02/07/2023] Open
Abstract
Nucleotide-binding site (NBS) disease resistance genes play an important role in defending plants from a variety of pathogens and insect pests. Many R-genes have been identified in various plant species. However, little is known about the NBS-encoding genes in Brachypodium distachyon. In this study, using computational analysis of the B. distachyon genome, we identified 126 regular NBS-encoding genes and characterized them on the bases of structural diversity, conserved protein motifs, chromosomal locations, gene duplications, promoter region, and phylogenetic relationships. EST hits and full-length cDNA sequences (from Brachypodium database) of 126 R-like candidates supported their existence. Based on the occurrence of conserved protein motifs such as coiled-coil (CC), NBS, leucine-rich repeat (LRR), these regular NBS-LRR genes were classified into four subgroups: CC-NBS-LRR, NBS-LRR, CC-NBS, and X-NBS. Further expression analysis of the regular NBS-encoding genes in Brachypodium database revealed that these genes are expressed in a wide range of libraries, including those constructed from various developmental stages, tissue types, and drought challenged or nonchallenged tissue.
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Affiliation(s)
- Shenglong Tan
- Services Computing Technology and System Laboratory, Cluster and Grid Computing Laboratory, School of Computer Science and Technology, Huazhong University of Science & Technology (HUST), Luoyu Road 1037, Wuhan 430074, China
- School of Information Management, Hubei University of Economics, Wuhan 430205, China
| | - Song Wu
- Services Computing Technology and System Laboratory, Cluster and Grid Computing Laboratory, School of Computer Science and Technology, Huazhong University of Science & Technology (HUST), Luoyu Road 1037, Wuhan 430074, China
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Sturbois B, Dubrana-Ourabah MP, Gombert J, Lasseur B, Macquet A, Faure C, Bendahmane A, Baurès I, Candresse T. Identification and characterization of tomato mutants affected in the Rx-mediated resistance to PVX isolates. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2012; 25:341-54. [PMID: 22088194 DOI: 10.1094/mpmi-07-11-0181] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Five tomato mutants affected in the Rx-mediated resistance against Potato virus X (PVX) were identified by screening a mutagenized population derived from a transgenic, Rx1-expressing 'Micro-Tom' line. Contrary to their parental line, they failed to develop lethal systemic necrosis upon infection with the virulent PVX-KH2 isolate. Sequence analysis and quantitative reverse-transcription polymerase chain reaction experiments indicated that the mutants are not affected in the Rx1 transgene or in the Hsp90, RanGap1 and RanGap2, Rar1 and Sgt1 genes. Inoculation with the PVX-CP4 avirulent isolate demonstrated that the Rx1 resistance was still effective in the mutants. In contrast, the virulent PVX-KH2 isolate accumulation was readily detectable in all mutants, which could further be separated in two groups depending on their ability to restrict the accumulation of PVX-RR, a mutant affected at two key positions for Rx1 elicitor activity. Finally, transient expression of the viral capsid protein elicitor indicated that the various mutants have retained the ability to mount an Rx1-mediated hypersensitive response. Taken together, the results obtained are consistent with a modification of the specificity or intensity of the Rx1-mediated response. The five Micro-Tom mutants should provide very valuable resources for the identification of novel tomato genes affecting the functioning of the Rx gene.
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Affiliation(s)
- Bénédicte Sturbois
- URGV, Unité de Recherche en Génomique Végétale, Université d'Evry d'Essonne, INRA, France.
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Host specificity determinants as a genetic continuum. Trends Microbiol 2011; 20:88-93. [PMID: 22196375 DOI: 10.1016/j.tim.2011.11.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Revised: 11/10/2011] [Accepted: 11/15/2011] [Indexed: 01/22/2023]
Abstract
Host specificity is an important concept that underlies the interaction of all clinically and agriculturally relevant microbes with their hosts. Changes in the host specificity of animal pathogens, in particular, are often of greatest concern due to their immediate and unexpected impact on human health. Host switching or host jumps can often be traced to modification of key microbial pathogenicity factors that facilitate the formation of particular host associations. An increase in the number of genome-level studies has begun revealing that almost any type of change, from the simplest to the most complex, can potentially impact host specificity. This review highlights examples of host specificity determinants of viruses, bacteria and fungi, and presents them from within a genetic continuum that spans from the single residue through to entire genomic islands.
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