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Dolatabadian A, Patel DA, Edwards D, Batley J. Copy number variation and disease resistance in plants. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:2479-2490. [PMID: 29043379 DOI: 10.1007/s00122-017-2993-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 09/27/2017] [Indexed: 05/06/2023]
Abstract
Plant genome diversity varies from single nucleotide polymorphisms to large-scale deletions, insertions, duplications, or re-arrangements. These re-arrangements of sequences resulting from duplication, gains or losses of DNA segments are termed copy number variations (CNVs). During the last decade, numerous studies have emphasized the importance of CNVs as a factor affecting human phenotype; in particular, CNVs have been associated with risks for several severe diseases. In plants, the exploration of the extent and role of CNVs in resistance against pathogens and pests is just beginning. Since CNVs are likely to be associated with disease resistance in plants, an understanding of the distribution of CNVs could assist in the identification of novel plant disease-resistance genes. In this paper, we review existing information about CNVs; their importance, role and function, as well as their association with disease resistance in plants.
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Affiliation(s)
- Aria Dolatabadian
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Crawley, WA, 6009, Australia
| | - Dhwani Apurva Patel
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Crawley, WA, 6009, Australia
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Crawley, WA, 6009, Australia
| | - Jacqueline Batley
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Crawley, WA, 6009, Australia.
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Kachroo A, Vincelli P, Kachroo P. Signaling Mechanisms Underlying Resistance Responses: What Have We Learned, and How Is It Being Applied? PHYTOPATHOLOGY 2017; 107:1452-1461. [PMID: 28609156 DOI: 10.1094/phyto-04-17-0130-rvw] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Plants have evolved highly specific mechanisms to resist pathogens including preformed barriers and the induction of elaborate signaling pathways. Induced signaling requires recognition of the pathogen either via conserved pathogen-derived factors or specific pathogen-encoded proteins called effectors. Recognition of these factors by host encoded receptor proteins can result in the elicitation of different tiers of resistance at the site of pathogen infection. In addition, plants induce a type of systemic immunity which is effective at the whole plant level and protects against a broad spectrum of pathogens. Advances in our understanding of pathogen-recognition mechanisms, identification of the underlying molecular components, and their significant conservation across diverse plant species has enabled the development of novel strategies to combat plant diseases. This review discusses key advances in plant defense signaling that have been adapted or have the potential to be adapted for plant protection against microbial diseases.
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Affiliation(s)
- Aardra Kachroo
- Department of Plant Pathology, University of Kentucky, Lexington 40546
| | - Paul Vincelli
- Department of Plant Pathology, University of Kentucky, Lexington 40546
| | - Pradeep Kachroo
- Department of Plant Pathology, University of Kentucky, Lexington 40546
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Shen C, Li X, Zhang R, Lin Z. Genome-wide recombination rate variation in a recombination map of cotton. PLoS One 2017; 12:e0188682. [PMID: 29176878 PMCID: PMC5703465 DOI: 10.1371/journal.pone.0188682] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 11/10/2017] [Indexed: 01/03/2023] Open
Abstract
Recombination is crucial for genetic evolution, which not only provides new allele combinations but also influences the biological evolution and efficacy of natural selection. However, recombination variation is not well understood outside of the complex species’ genomes, and it is particularly unclear in Gossypium. Cotton is the most important natural fibre crop and the second largest oil-seed crop. Here, we found that the genetic and physical maps distances did not have a simple linear relationship. Recombination rates were unevenly distributed throughout the cotton genome, which showed marked changes along the chromosome lengths and recombination was completely suppressed in the centromeric regions. Recombination rates significantly varied between A-subgenome (At) (range = 1.60 to 3.26 centimorgan/megabase [cM/Mb]) and D-subgenome (Dt) (range = 2.17 to 4.97 cM/Mb), which explained why the genetic maps of At and Dt are similar but the physical map of Dt is only half that of At. The translocation regions between A02 and A03 and between A04 and A05, and the inversion regions on A10, D10, A07 and D07 indicated relatively high recombination rates in the distal regions of the chromosomes. Recombination rates were positively correlated with the densities of genes, markers and the distance from the centromere, and negatively correlated with transposable elements (TEs). The gene ontology (GO) categories showed that genes in high recombination regions may tend to response to environmental stimuli, and genes in low recombination regions are related to mitosis and meiosis, which suggested that they may provide the primary driving force in adaptive evolution and assure the stability of basic cell cycle in a rapidly changing environment. Global knowledge of recombination rates will facilitate genetics and breeding in cotton.
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Affiliation(s)
- Chao Shen
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Ximei Li
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, Hubei, China
- College of Agronomy and Plant Protection, Qingdao Agricultural University/Shandong Key Laboratory of Dryland Farming Technology, Qingdao, Shandong, China
| | - Ruiting Zhang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Zhongxu Lin
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, Hubei, China
- * E-mail:
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Lv Q, Huang Z, Xu X, Tang L, Liu H, Wang C, Zhou Z, Xin Y, Xing J, Peng Z, Li X, Zheng T, Zhu L. Allelic variation of the rice blast resistance gene Pid3 in cultivated rice worldwide. Sci Rep 2017; 7:10362. [PMID: 28871108 PMCID: PMC5583387 DOI: 10.1038/s41598-017-10617-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 08/11/2017] [Indexed: 11/12/2022] Open
Abstract
In this study, the re-sequencing data from 3,000 rice genomes project (3 K RGP) was used to analyze the allelic variation at the rice blast resistance (R) Pid3 locus. A total of 40 haplotypes were identified based on 71 nucleotide polymorphic sites among 2621 Pid3 homozygous alleles in the 3k genomes. Pid3 alleles in most japonica rice accessions were pseudogenes due to premature stop mutations, while those in most indica rice accessions were identical to the functional haplotype Hap_6, which had a similar resistance spectrum as the previously reported Pid3 gene. By sequencing and CAPS marker analyzing the Pid3 alleles in widespread cultivars in China, we verified that Hap_6 had been widely deployed in indica rice breeding of China. Thus, we suggest that the priority for utilization of the Pid3 locus in rice breeding should be on introducing the functional Pid3 alleles into japonica rice cultivars and the functional alleles of non-Hap_6 haplotypes into indica rice cultivars for increasing genetic diversity.
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Affiliation(s)
- Qiming Lv
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, 410125, China.,State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhiyuan Huang
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, 410125, China
| | - Xiao Xu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Li Tang
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, 410125, China
| | - Hai Liu
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, 410125, China
| | - Chunchao Wang
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhuangzhi Zhou
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yeyun Xin
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, 410125, China
| | - Junjie Xing
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, 410125, China
| | - Zhirong Peng
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, 410125, China
| | - Xiaobing Li
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Tianqing Zheng
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Lihuang Zhu
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, 410125, China. .,State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
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Liu J, Sniezko RA, Zamany A, Williams H, Wang N, Kegley A, Savin DP, Chen H, Sturrock RN. Saturated genic SNP mapping identified functional candidates and selection tools for the Pinus monticola Cr2 locus controlling resistance to white pine blister rust. PLANT BIOTECHNOLOGY JOURNAL 2017; 15:1149-1162. [PMID: 28176454 PMCID: PMC5552481 DOI: 10.1111/pbi.12705] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2016] [Revised: 01/11/2017] [Accepted: 02/02/2017] [Indexed: 05/17/2023]
Abstract
Molecular breeding incorporates efficient tools to increase rust resistance in five-needle pines. Susceptibility of native five-needle pines to white pine blister rust (WPBR), caused by the non-native invasive fungus Cronartium ribicola (J.C. Fisch.), has significantly reduced wild populations of these conifers in North America. Major resistance (R) genes against specific avirulent pathotypes have been found in several five-needle pine species. In this study, we screened genic SNP markers by comparative transcriptome and genetic association analyses and constructed saturated linkage maps for the western white pine (Pinus monticola) R locus (Cr2). Phenotypic segregation was measured by a hypersensitive reaction (HR)-like response on the needles and disease symptoms of cankered stems post inoculation by the C. ribicola avcr2 race. SNP genotypes were determined by HRM- and TaqMan-based SNP genotyping. Saturated maps of the Cr2-linkage group (LG) were constructed in three seed families using a total of 34 SNP markers within 21 unique genes. Cr2 was consistently flanked by contig_2142 (encoding a ruvb-like protein) and contig_3772 (encoding a delta-fatty acid desaturase) across the three seed families. Cr2 was anchored to the Pinus consensus LG-1, which differs from LGs where other R loci of Pinus species were mapped. GO annotation identified a set of NBS-LRR and other resistance-related genes as R candidates in the Cr2 region. Association of one nonsynonymous SNP locus of an NBS-LRR gene with Cr2-mediated phenotypes provides a valuable tool for marker-assisted selection (MAS), which will shorten the breeding cycle of resistance screening and aid in the restoration of WPBR-disturbed forest ecosystems.
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Affiliation(s)
- Jun‐Jun Liu
- Canadian Forest ServiceNatural Resources CanadaVictoriaCanada
| | | | - Arezoo Zamany
- Canadian Forest ServiceNatural Resources CanadaVictoriaCanada
| | - Holly Williams
- Canadian Forest ServiceNatural Resources CanadaVictoriaCanada
| | - Ning Wang
- Canadian Forest ServiceNatural Resources CanadaVictoriaCanada
- Academy of Agriculture and Forestry ScienceQinghai UniversityXiningChina
| | - Angelia Kegley
- Dorena Genetic Resource CenterUSDA Forest ServiceCottage GroveORUSA
| | - Douglas P. Savin
- Dorena Genetic Resource CenterUSDA Forest ServiceCottage GroveORUSA
| | - Hao Chen
- Canadian Forest ServiceNatural Resources CanadaVictoriaCanada
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Evidence for Adaptive Introgression of Disease Resistance Genes Among Closely Related Arabidopsis Species. G3-GENES GENOMES GENETICS 2017. [PMID: 28630104 PMCID: PMC5555472 DOI: 10.1534/g3.117.043984] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The generation and maintenance of functional variation in the pathogen defense system of plants is central to the constant evolutionary battle between hosts and parasites. If a species is susceptible to a given pathogen, hybridization and subsequent introgression of a resistance allele from a related species can potentially be an important source of new immunity and is therefore expected to be selected for in a process referred to as adaptive introgression. Here, we survey sequence variation in 10 resistance (R-) genes and compare them with 37 reference genes in natural populations of the two closely related and interfertile species: Arabidopsis lyrata and A. halleri. The R-genes are highly polymorphic in both species and show clear signs of trans-species polymorphisms. We show that A. lyrata and A. halleri have had a history of limited introgression for the reference genes. For the R-genes, the introgression rate has been significantly higher than for the reference genes, resulting in fewer fixed differences between species and a higher sharing of identical haplotypes. We conclude that R-genes likely cross the species boundaries at a higher rate than reference genes and therefore also that some of the increased diversity and trans-specific polymorphisms in R-genes is due to adaptive introgression.
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Sharpee W, Oh Y, Yi M, Franck W, Eyre A, Okagaki LH, Valent B, Dean RA. Identification and characterization of suppressors of plant cell death (SPD) effectors from Magnaporthe oryzae. MOLECULAR PLANT PATHOLOGY 2017; 18:850-863. [PMID: 27301772 PMCID: PMC6638229 DOI: 10.1111/mpp.12449] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Revised: 06/09/2016] [Accepted: 06/10/2016] [Indexed: 05/04/2023]
Abstract
Phytopathogenic microorganisms, including the fungal pathogen Magnaporthe oryzae, secrete a myriad of effector proteins to facilitate infection. Utilizing the transient expression of candidate effectors in the leaves of the model plant Nicotiana benthamiana, we identified 11 suppressors of plant cell death (SPD) effectors from M. oryzae that were able to block the host cell death reaction induced by Nep1. Ten of these 11 were also able to suppress BAX-mediated plant cell death. Five of the 11 SPD genes have been identified previously as either essential for the pathogenicity of M. oryzae, secreted into the plant during disease development, or as suppressors or homologues of other characterized suppressors. In addition, of the remaining six, we showed that SPD8 (previously identified as BAS162) was localized to the rice cytoplasm in invaded and surrounding uninvaded cells during biotrophic invasion. Sequence analysis of the 11 SPD genes across 43 re-sequenced M. oryzae genomes revealed that SPD2, SPD4 and SPD7 have nucleotide polymorphisms amongst the isolates. SPD4 exhibited the highest level of nucleotide diversity of any currently known effector from M. oryzae in addition to the presence/absence polymorphisms, suggesting that this gene is potentially undergoing selection to avoid recognition by the host. Taken together, we have identified a series of effectors, some of which were previously unknown or whose function was unknown, that probably act at different stages of the infection process and contribute to the virulence of M. oryzae.
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Affiliation(s)
- William Sharpee
- Center for Integrated Fungal Research, Department of Entomology and Plant PathologyNorth Carolina State UniversityRaleighNC27606USA
| | - Yeonyee Oh
- Center for Integrated Fungal Research, Department of Entomology and Plant PathologyNorth Carolina State UniversityRaleighNC27606USA
| | - Mihwa Yi
- Department of Plant PathologyKansas State UniversityManhattanKS66506USA
- Present address:
Noble FoundationArdmoreOK73401USA
| | - William Franck
- Center for Integrated Fungal Research, Department of Entomology and Plant PathologyNorth Carolina State UniversityRaleighNC27606USA
- Present address:
USDA‐ARS Northern Plains Agricultural Research ServiceSidneyMT59270USA
| | - Alex Eyre
- Center for Integrated Fungal Research, Department of Entomology and Plant PathologyNorth Carolina State UniversityRaleighNC27606USA
| | - Laura H. Okagaki
- Center for Integrated Fungal Research, Department of Entomology and Plant PathologyNorth Carolina State UniversityRaleighNC27606USA
- Present address:
Department of Microbiology and ImmunologyUniversity of MinnesotaMN55455USA
| | - Barbara Valent
- Department of Plant PathologyKansas State UniversityManhattanKS66506USA
| | - Ralph A. Dean
- Center for Integrated Fungal Research, Department of Entomology and Plant PathologyNorth Carolina State UniversityRaleighNC27606USA
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Agrawal AA. Toward a Predictive Framework for Convergent Evolution: Integrating Natural History, Genetic Mechanisms, and Consequences for the Diversity of Life. Am Nat 2017; 190:S1-S12. [PMID: 28731831 DOI: 10.1086/692111] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
A charm of biology as a scientific discipline is the diversity of life. Although this diversity can make laws of biology challenging to discover, several repeated patterns and general principles govern evolutionary diversification. Convergent evolution, the independent evolution of similar phenotypes, has been at the heart of one approach to understand generality in the evolutionary process. Yet understanding when and why organismal traits and strategies repeatedly evolve has been a central challenge. These issues were the focus of the American Society of Naturalists Vice Presidential Symposium in 2016 and are the subject of this collection of articles. Although naturalists have long made inferences about convergent evolution and its importance, there has been confusion in the interpretation of the pattern of convergence. Does convergence primarily indicate adaptation or constraint? How often should convergence be expected? Are there general principles that would allow us to predict where and when and by what mechanisms convergent evolution should occur? What role does natural history play in advancing our understanding of general evolutionary principles? In this introductory article, I address these questions, review several generalizations about convergent evolution that have emerged over the past 15 years, and present a framework for advancing the study and interpretation of convergence. Perhaps the most important emerging conclusion is that the genetic mechanisms of convergent evolution are phylogenetically conserved; that is, more closely related species tend to share the same genetic basis of traits, even when independently evolved. Finally, I highlight how the articles in this special issue further develop concepts, methodologies, and case studies at the frontier of our understanding of the causes and consequences of convergent evolution.
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Distinct Patterns of Gene Gain and Loss: Diverse Evolutionary Modes of NBS-Encoding Genes in Three Solanaceae Crop Species. G3-GENES GENOMES GENETICS 2017; 7:1577-1585. [PMID: 28364035 PMCID: PMC5427506 DOI: 10.1534/g3.117.040485] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Plant resistance conferred by nucleotide binding site (NBS)-encoding resistance genes plays a key role in the defense against various pathogens throughout the entire plant life cycle. However, comparative analyses for the systematic evaluation and determination of the evolutionary modes of NBS-encoding genes among Solanaceae species are rare. In this study, 447, 255, and 306 NBS-encoding genes were identified from the genomes of potato, tomato, and pepper, respectively. These genes usually clustered as tandem arrays on chromosomes; few existed as singletons. Phylogenetic analysis indicated that three subclasses [TNLs (TIR-NBS-LRR), CNLs (CC-NBS-LRR), and RNLs (RPW8-NBS-LRR)] each formed a monophyletic clade and were distinguished by unique exon/intron structures and amino acid motif sequences. By comparing phylogenetic and systematic relationships, we inferred that the NBS-encoding genes in the present genomes of potato, tomato, and pepper were derived from 150 CNL, 22 TNL, and 4 RNL ancestral genes, and underwent independent gene loss and duplication events after speciation. The NBS-encoding genes therefore exhibit diverse and dynamic evolutionary patterns in the three Solanaceae species, giving rise to the discrepant gene numbers observed today. Potato shows a “consistent expansion” pattern, tomato exhibits a pattern of “first expansion and then contraction,” and pepper presents a “shrinking” pattern. The earlier expansion of CNLs in the common ancestor led to the dominance of this subclass in gene numbers. However, RNLs remained at low copy numbers due to their specific functions. Along the evolutionary process of NBS-encoding genes in Solanaceae, species-specific tandem duplications contributed the most to gene expansions.
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Karasov TL, Chae E, Herman JJ, Bergelson J. Mechanisms to Mitigate the Trade-Off between Growth and Defense. THE PLANT CELL 2017; 29:666-680. [PMID: 28320784 PMCID: PMC5435432 DOI: 10.1105/tpc.16.00931] [Citation(s) in RCA: 255] [Impact Index Per Article: 36.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 02/23/2017] [Accepted: 03/16/2017] [Indexed: 05/03/2023]
Abstract
Plants have evolved an array of defenses against pathogens. However, mounting a defense response frequently comes with the cost of a reduction in growth and reproduction, carrying critical implications for natural and agricultural populations. This review focuses on how costs are generated and whether and how they can be mitigated. Most well-characterized growth-defense trade-offs stem from antagonistic crosstalk among hormones rather than an identified metabolic expenditure. A primary way plants mitigate such costs is through restricted expression of resistance; this can be achieved through inducible expression of defense genes or by the concentration of defense to particular times or tissues. Defense pathways can be primed for more effective induction, and primed states can be transmitted to offspring. We examine the resistance (R) genes as a case study of how the toll of defense can be generated and ameliorated. The fine-scale regulation of R genes is critical to alleviate the burden of their expression, and the genomic organization of R genes into coregulatory modules reduces costs. Plants can also recruit protection from other species. Exciting new evidence indicates that a plant's genotype influences the microbiome composition, lending credence to the hypothesis that plants shape their microbiome to enhance defense.
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Affiliation(s)
- Talia L Karasov
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany
| | - Eunyoung Chae
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany
| | - Jacob J Herman
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637
| | - Joy Bergelson
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637
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Song H, Wang P, Li C, Han S, Zhao C, Xia H, Bi Y, Guo B, Zhang X, Wang X. Comparative analysis of NBS-LRR genes and their response to Aspergillus flavus in Arachis. PLoS One 2017; 12:e0171181. [PMID: 28158222 PMCID: PMC5291535 DOI: 10.1371/journal.pone.0171181] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 01/17/2017] [Indexed: 12/31/2022] Open
Abstract
Studies have demonstrated that nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes respond to pathogen attack in plants. Characterization of NBS-LRR genes in peanut is not well documented. The newly released whole genome sequences of Arachis duranensis and Arachis ipaënsis have allowed a global analysis of this important gene family in peanut to be conducted. In this study, we identified 393 (AdNBS) and 437 (AiNBS) NBS-LRR genes from A. duranensis and A. ipaënsis, respectively, using bioinformatics approaches. Full-length sequences of 278 AdNBS and 303 AiNBS were identified. Fifty-one orthologous, four AdNBS paralogous, and six AiNBS paralogous gene pairs were predicted. All paralogous gene pairs were located in the same chromosomes, indicating that tandem duplication was the most likely mechanism forming these paralogs. The paralogs mainly underwent purifying selection, but most LRR 8 domains underwent positive selection. More gene clusters were found in A. ipaënsis than in A. duranensis, possibly owing to tandem duplication events occurring more frequently in A. ipaënsis. The expression profile of NBS-LRR genes was different between A. duranensis and A. hypogaea after Aspergillus flavus infection. The up-regulated expression of NBS-LRR in A. duranensis was continuous, while these genes responded to the pathogen temporally in A. hypogaea.
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Affiliation(s)
- Hui Song
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
| | - Pengfei Wang
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
| | - Changsheng Li
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
- College of Life Science, Shandong Normal University, Jinan, China
| | - Suoyi Han
- Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Chuanzhi Zhao
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
| | - Han Xia
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
| | - Yuping Bi
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
| | - Baozhu Guo
- Crop Protection and Management Research Unit, USDA-ARS, Tifton, Georgia, United States of America
| | - Xinyou Zhang
- Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Xingjun Wang
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
- College of Life Science, Shandong Normal University, Jinan, China
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Holdsworth WL, LaPlant KE, Bell DC, Jahn MM, Mazourek M. Cultivar-Based Introgression Mapping Reveals Wild Species-Derived Pm-0, the Major Powdery Mildew Resistance Locus in Squash. PLoS One 2016; 11:e0167715. [PMID: 27936008 PMCID: PMC5147965 DOI: 10.1371/journal.pone.0167715] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 11/18/2016] [Indexed: 11/19/2022] Open
Abstract
Powdery mildew is a major fungal disease on squash and pumpkin (Cucurbita spp.) in the US and throughout the world. Genetic resistance to the disease is not known to occur naturally within Cucurbita pepo and only infrequently in Cucurbita moschata, but has been achieved in both species through the introgression of a major resistance gene from the wild species Cucurbita okeechobeensis subsp. martinezii. At present, this gene, Pm-0, is used extensively in breeding, and is found in nearly all powdery mildew-resistant C. pepo and C. moschata commercial cultivars. In this study, we mapped C. okeechobeensis subsp. martinezii-derived single nucleotide polymorphism (SNP) alleles in a set of taxonomically and morphologically diverse and resistant C. pepo and C. moschata cultivars bred at Cornell University that, by common possession of Pm-0, form a shared-trait introgression panel. High marker density was achieved using genotyping-by-sequencing, which yielded over 50,000 de novo SNP markers in each of the three Cucurbita species genotyped. A single 516.4 kb wild-derived introgression was present in all of the resistant cultivars and absent in a diverse set of heirlooms that predated the Pm-0 introgression. The contribution of this interval to powdery mildew resistance was confirmed by association mapping in a C. pepo cultivar panel that included the Cornell lines, heirlooms, and 68 additional C. pepo cultivars and with an independent F2 population derived from C. okeechobeensis subsp. martinezii x C. moschata. The interval was refined to a final candidate interval of 76.4 kb and CAPS markers were developed inside this interval to facilitate marker-assisted selection.
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Affiliation(s)
- William L. Holdsworth
- Section of Plant Breeding and Genetics, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, United States of America
- Rupp Seeds, Inc., Wauseon, OH, United States of America
| | - Kyle E. LaPlant
- Section of Plant Breeding and Genetics, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, United States of America
| | - Duane C. Bell
- Rupp Seeds, Inc., Wauseon, OH, United States of America
| | - Molly M. Jahn
- Department of Agronomy, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Michael Mazourek
- Section of Plant Breeding and Genetics, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, United States of America
- * E-mail:
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Cantalapiedra CP, Contreras-Moreira B, Silvar C, Perovic D, Ordon F, Gracia MP, Igartua E, Casas AM. A Cluster of Nucleotide-Binding Site-Leucine-Rich Repeat Genes Resides in a Barley Powdery Mildew Resistance Quantitative Trait Loci on 7HL. THE PLANT GENOME 2016; 9. [PMID: 27898833 DOI: 10.3835/plantgenome2015.10.0101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Powdery mildew causes severe yield losses in barley production worldwide. Although many resistance genes have been described, only a few have already been cloned. A strong QTL (quantitative trait locus) conferring resistance to a wide array of powdery mildew isolates was identified in a Spanish barley landrace on the long arm of chromosome 7H. Previous studies narrowed down the QTL position, but were unable to identify candidate genes or physically locate the resistance. In this study, the exome of three recombinant lines from a high-resolution mapping population was sequenced and analyzed, narrowing the position of the resistance down to a single physical contig. Closer inspection of the region revealed a cluster of closely related NBS-LRR (nucleotide-binding site-leucine-rich repeat containing protein) genes. Large differences were found between the resistant lines and the reference genome of cultivar Morex, in the form of PAV (presence-absence variation) in the composition of the NBS-LRR cluster. Finally, a template-guided assembly was performed and subsequent expression analysis revealed that one of the new assembled candidate genes is transcribed. In summary, the results suggest that NBS-LRR genes, absent from the reference and the susceptible genotypes, could be functional and responsible for the powdery mildew resistance. The procedure followed is an example of the use of NGS (next-generation sequencing) tools to tackle the challenges of gene cloning when the target gene is absent from the reference genome.
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Stam R, Scheikl D, Tellier A. Pooled Enrichment Sequencing Identifies Diversity and Evolutionary Pressures at NLR Resistance Genes within a Wild Tomato Population. Genome Biol Evol 2016; 8:1501-15. [PMID: 27189991 PMCID: PMC4898808 DOI: 10.1093/gbe/evw094] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/16/2016] [Indexed: 12/13/2022] Open
Abstract
Nod-like receptors (NLRs) are nucleotide-binding domain and leucine-rich repeats containing proteins that are important in plant resistance signaling. Many of the known pathogen resistance (R) genes in plants are NLRs and they can recognize pathogen molecules directly or indirectly. As such, divergence and copy number variants at these genes are found to be high between species. Within populations, positive and balancing selection are to be expected if plants coevolve with their pathogens. In order to understand the complexity of R-gene coevolution in wild nonmodel species, it is necessary to identify the full range of NLRs and infer their evolutionary history. Here we investigate and reveal polymorphism occurring at 220 NLR genes within one population of the partially selfing wild tomato species Solanum pennellii. We use a combination of enrichment sequencing and pooling ten individuals, to specifically sequence NLR genes in a resource and cost-effective manner. We focus on the effects which different mapping and single nucleotide polymorphism calling software and settings have on calling polymorphisms in customized pooled samples. Our results are accurately verified using Sanger sequencing of polymorphic gene fragments. Our results indicate that some NLRs, namely 13 out of 220, have maintained polymorphism within our S. pennellii population. These genes show a wide range of πN/πS ratios and differing site frequency spectra. We compare our observed rate of heterozygosity with expectations for this selfing and bottlenecked population. We conclude that our method enables us to pinpoint NLR genes which have experienced natural selection in their habitat.
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Affiliation(s)
- Remco Stam
- Section of Population Genetics, Technische Universität München, Freising, Germany
| | - Daniela Scheikl
- Section of Population Genetics, Technische Universität München, Freising, Germany
| | - Aurélien Tellier
- Section of Population Genetics, Technische Universität München, Freising, Germany
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Genetic Engineering and Sustainable Crop Disease Management: Opportunities for Case-by-Case Decision-Making. SUSTAINABILITY 2016. [DOI: 10.3390/su8050495] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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Mahesh HB, Shirke MD, Singh S, Rajamani A, Hittalmani S, Wang GL, Gowda M. Indica rice genome assembly, annotation and mining of blast disease resistance genes. BMC Genomics 2016; 17:242. [PMID: 26984283 PMCID: PMC4793524 DOI: 10.1186/s12864-016-2523-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 02/24/2016] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Rice is a major staple food crop in the world. Over 80% of rice cultivation area is under indica rice. Currently, genomic resources are lacking for indica as compared to japonica rice. In this study, we generated deep-sequencing data (Illumina and Pacific Biosciences sequencing) for one of the indica rice cultivars, HR-12 from India. RESULTS We assembled over 86% (389 Mb) of rice genome and annotated 56,284 protein-coding genes from HR-12 genome using Illumina and PacBio sequencing. Comprehensive comparative analyses between indica and japonica subspecies genomes revealed a large number of indica specific variants including SSRs, SNPs and InDels. To mine disease resistance genes, we sequenced few indica rice cultivars that are reported to be highly resistant (Tetep and Tadukan) and susceptible (HR-12 and Co-39) against blast fungal isolates in many countries including India. Whole genome sequencing of rice genotypes revealed high rate of mutations in defense related genes (NB-ARC, LRR and PK domains) in resistant cultivars as compared to susceptible. This study has identified R-genes Pi-ta and Pi54 from durable indica resistant cultivars; Tetep and Tadukan, which can be used in marker assisted selection in rice breeding program. CONCLUSIONS This is the first report of whole genome sequencing approach to characterize Indian rice germplasm. The genomic resources from our work will have a greater impact in understanding global rice diversity, genetics and molecular breeding.
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Affiliation(s)
- H. B. Mahesh
- />Genomics Laboratory, Centre for Cellular and Molecular Platforms (C-CAMP), National Centre for Biological Sciences (NCBS), Bengaluru, 560065 India
- />Marker Assisted Selection Laboratory, Department of Genetics and Plant Breeding, University of Agricultural Sciences, Bengaluru, 560065 India
- />Department of Plant Pathology, College of Food, Agricultural and Environmental Sciences, Ohio State University, Columbus, 43210 USA
| | - Meghana Deepak Shirke
- />Genomics Laboratory, Centre for Cellular and Molecular Platforms (C-CAMP), National Centre for Biological Sciences (NCBS), Bengaluru, 560065 India
- />Manipal University, Manipal, 576104 India
| | - Siddarth Singh
- />Pacific Biosciences, Boon Lay Way, Singapore, 609964 Singapore
| | - Anantharamanan Rajamani
- />Genomics Laboratory, Centre for Cellular and Molecular Platforms (C-CAMP), National Centre for Biological Sciences (NCBS), Bengaluru, 560065 India
| | - Shailaja Hittalmani
- />Marker Assisted Selection Laboratory, Department of Genetics and Plant Breeding, University of Agricultural Sciences, Bengaluru, 560065 India
| | - Guo-Liang Wang
- />Department of Plant Pathology, College of Food, Agricultural and Environmental Sciences, Ohio State University, Columbus, 43210 USA
| | - Malali Gowda
- />Genomics Laboratory, Centre for Cellular and Molecular Platforms (C-CAMP), National Centre for Biological Sciences (NCBS), Bengaluru, 560065 India
- />Genomics Discovery Program, School of Conservation, Life Science and Health Sciences, TransDisciplinary University, Foundation of Revitalization of Local Health Traditions, Bengaluru, 560064 India
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Dramatic Number Variation of R Genes in Solanaceae Species Accounted for by a Few R Gene Subfamilies. PLoS One 2016; 11:e0148708. [PMID: 26849045 PMCID: PMC4743996 DOI: 10.1371/journal.pone.0148708] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 01/20/2016] [Indexed: 11/30/2022] Open
Abstract
Most disease resistance genes encode nucleotide-binding-site (NBS) and leucine-rich-repeat (LRR) domains, and the NBS-LRR encoding genes are often referred to as R genes. Using newly developed approach, 478, 485, 1,194, 1,665, 2,042 and 374 R genes were identified from the genomes of tomato Heinz1706, wild tomato LA716, potato DM1-3, pepper Zunla-1 and wild pepper Chiltepin and tobacco TN90, respectively. The majority of R genes from Solanaceae were grouped into 87 subfamilies, including 16 TIR-NBS-LRR (TNL) and 71 non-TNL subfamilies. Each subfamily was annotated manually, including identification of intron/exon structure and intron phase. Interestingly, TNL subfamilies have similar intron phase patterns, while the non-TNL subfamilies have diverse intron phase due to frequent gain of introns. Prevalent presence/absence polymorphic R gene loci were found among Solanaceae species, and an integrated map with 427 R loci was constructed. The pepper genome (2,042 in Chiltepin) has at least four times of R genes as in tomato (478 in Heinz1706). The high number of R genes in pepper genome is due to the amplification of R genes in a few subfamilies, such as the Rpi-blb2 and BS2 subfamilies. The mechanism underlying the variation of R gene number among different plant genomes is discussed.
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Zhang YM, Shao ZQ, Wang Q, Hang YY, Xue JY, Wang B, Chen JQ. Uncovering the dynamic evolution of nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes in Brassicaceae. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2016; 58:165-77. [PMID: 25926337 DOI: 10.1111/jipb.12365] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 04/24/2015] [Indexed: 05/22/2023]
Abstract
Plant genomes harbor dozens to hundreds of nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes; however, the long-term evolutionary history of these resistance genes has not been fully understood. This study focuses on five Brassicaceae genomes and the Carica papaya genome to explore changes in NBS-LRR genes that have taken place in this Rosid II lineage during the past 72 million years. Various numbers of NBS-LRR genes were identified from Arabidopsis lyrata (198), A. thaliana (165), Brassica rapa (204), Capsella rubella (127), Thellungiella salsuginea (88), and C. papaya (51). In each genome, the identified NBS-LRR genes were found to be unevenly distributed among chromosomes and most of them were clustered together. Phylogenetic analysis revealed that, before and after Brassicaceae speciation events, both toll/interleukin-1 receptor-NBS-LRR (TNL) genes and non-toll/interleukin-1 receptor-NBS-LRR (nTNL) genes exhibited a pattern of first expansion and then contraction, suggesting that both subclasses of NBS-LRR genes were responding to pathogen pressures synchronically. Further, by examining the gain/loss of TNL and nTNL genes at different evolutionary nodes, this study revealed that both events often occurred more drastically in TNL genes. Finally, the phylogeny of nTNL genes suggested that this NBS-LRR subclass is composed of two separate ancient gene types: RPW8-NBS-LRR and Coiled-coil-NBS-LRR.
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Affiliation(s)
- Yan-Mei Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, Center of Plant Genetics and Molecular Evolution, School of Life Sciences, Nanjing University, Nanjing 210023, China
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
| | - Zhu-Qing Shao
- State Key Laboratory of Pharmaceutical Biotechnology, Center of Plant Genetics and Molecular Evolution, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Qiang Wang
- State Key Laboratory of Pharmaceutical Biotechnology, Center of Plant Genetics and Molecular Evolution, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Yue-Yu Hang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
| | - Jia-Yu Xue
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
| | - Bin Wang
- State Key Laboratory of Pharmaceutical Biotechnology, Center of Plant Genetics and Molecular Evolution, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Jian-Qun Chen
- State Key Laboratory of Pharmaceutical Biotechnology, Center of Plant Genetics and Molecular Evolution, School of Life Sciences, Nanjing University, Nanjing 210023, China
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Wang D, Wang X, Mei Y, Dong H. The wheat homolog of putative nucleotide-binding site-leucine-rich repeat resistance gene TaRGA contributes to resistance against powdery mildew. Funct Integr Genomics 2016; 16:115-26. [PMID: 26815536 DOI: 10.1007/s10142-015-0471-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2015] [Revised: 11/20/2015] [Accepted: 12/21/2015] [Indexed: 01/20/2023]
Abstract
Powdery mildew, one of the most destructive wheat diseases worldwide, is caused by Blumeria graminis f. sp. tritici (Bgt), a fungal species with a consistently high mutation rate that makes individual resistance (R) genes ineffective. Therefore, effective resistance-related gene cloning is vital for breeding and studying the resistance mechanisms of the disease. In this study, a putative nucleotide-binding site-leucine-rich repeat (NBS-LRR) R gene (TaRGA) was cloned using a homology-based cloning strategy and analyzed for its effect on powdery mildew disease and wheat defense responses. Real-time reverse transcription-PCR (RT-PCR) analyses revealed that a Bgt isolate 15 and salicylic acid stimulation significantly induced TaRGA in the resistant variety. Furthermore, the silencing of TaRGA in powdery mildew-resistant plants increased susceptibility to Bgt15 and prompted conidia propagation at the infection site. However, the expression of TaRGA in leaf segments after single-cell transient expression assay highly increased the defense responses to Bgt15 by enhancing callose deposition and phenolic autofluorogen accumulation at the pathogen invading sites. Meanwhile, the expression of pathogenesis-related genes decreased in the TaRGA-silenced plants and increased in the TaRGA-transient-overexpressing leaf segments. These results implied that the TaRGA gene positively regulates the defense response to powdery mildew disease in wheat.
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Affiliation(s)
- Defu Wang
- College of Life Science, Shanxi Agricultural University, Taigu, Shanxi, 030801, China.,National Ministry of Education Key Laboratory of Integrated Management of Crop Diseases and Insect Pests, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaobing Wang
- National Ministry of Education Key Laboratory of Integrated Management of Crop Diseases and Insect Pests, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yu Mei
- National Ministry of Education Key Laboratory of Integrated Management of Crop Diseases and Insect Pests, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hansong Dong
- National Ministry of Education Key Laboratory of Integrated Management of Crop Diseases and Insect Pests, Nanjing Agricultural University, Nanjing, 210095, China.
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Yang J, Ma Q, Zhang Y, Wang X, Zhang G, Ma Z. Molecular cloning and functional analysis of GbRVd, a gene in Gossypium barbadense that plays an important role in conferring resistance to Verticillium wilt. Gene 2016; 575:687-94. [DOI: 10.1016/j.gene.2015.09.046] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2015] [Revised: 09/19/2015] [Accepted: 09/19/2015] [Indexed: 02/01/2023]
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Wu J, Zheng S, Feng G, Yi H. Comparative Analysis of miRNAs and Their Target Transcripts between a Spontaneous Late-Ripening Sweet Orange Mutant and Its Wild-Type Using Small RNA and Degradome Sequencing. FRONTIERS IN PLANT SCIENCE 2016; 7:1416. [PMID: 27708662 PMCID: PMC5030777 DOI: 10.3389/fpls.2016.01416] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 09/06/2016] [Indexed: 05/04/2023]
Abstract
Fruit ripening in citrus is not well-understood at the molecular level. Knowledge of the regulatory mechanism of citrus fruit ripening at the post-transcriptional level in particular is lacking. Here, we comparatively analyzed the miRNAs and their target genes in a spontaneous late-ripening mutant, "Fengwan" sweet orange (MT) (Citrus sinensis L. Osbeck), and its wild-type counterpart ("Fengjie 72-1," WT). Using high-throughput sequencing of small RNAs and RNA degradome tags, we identified 107 known and 21 novel miRNAs, as well as 225 target genes. A total of 24 miRNAs (16 known miRNAs and 8 novel miRNAs) were shown to be differentially expressed between MT and WT. The expression pattern of several key miRNAs and their target genes during citrus fruit development and ripening stages was examined. Csi-miR156k, csi-miR159, and csi-miR166d suppressed specific transcription factors (GAMYBs, SPLs, and ATHBs) that are supposed to be important regulators involved in citrus fruit development and ripening. In the present study, miRNA-mediated silencing of target genes was found under complicated and sensitive regulation in citrus fruit. The identification of miRNAs and their target genes provide new clues for future investigation of mechanisms that regulate citrus fruit ripening.
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Guo C, Sun X, Chen X, Yang S, Li J, Wang L, Zhang X. Cloning of novel rice blast resistance genes from two rapidly evolving NBS-LRR gene families in rice. PLANT MOLECULAR BIOLOGY 2016; 90:95-105. [PMID: 26530637 DOI: 10.1007/s11103-015-0398-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 10/24/2015] [Indexed: 05/28/2023]
Abstract
Most rice blast resistance genes (R-genes) encode proteins with nucleotide-binding site (NBS) and leucine-rich repeat (LRR) domains. Our previous study has shown that more rice blast R-genes can be cloned in rapidly evolving NBS-LRR gene families. In the present study, two rapidly evolving R-gene families in rice were selected for cloning a subset of genes from their paralogs in three resistant rice lines. A total of eight functional blast R-genes were identified among nine NBS-LRR genes, and some of these showed resistance to three or more blast strains. Evolutionary analysis indicated that high nucleotide diversity of coding regions served as important parameters in the determination of gene resistance. We also observed that amino-acid variants (nonsynonymous mutations, insertions, or deletions) in essential motifs of the NBS domain contribute to the blast resistance capacity of NBS-LRR genes. These results suggested that the NBS regions might also play an important role in resistance specificity determination. On the other hand, different splicing patterns of introns were commonly observed in R-genes. The results of the present study contribute to improving the effectiveness of R-gene identification by using evolutionary analysis method and acquisition of novel blast resistance genes.
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Affiliation(s)
- Changjiang Guo
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Xiaoguang Sun
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Xiao Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Sihai Yang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Jing Li
- Institute for Research on Cancer and Ageing, Nice (IRCAN), University of Nice, Nice, France
| | - Long Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China.
| | - Xiaohui Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China.
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Species-specific duplications of NBS-encoding genes in Chinese chestnut (Castanea mollissima). Sci Rep 2015; 5:16638. [PMID: 26559332 PMCID: PMC4642323 DOI: 10.1038/srep16638] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 10/19/2015] [Indexed: 11/22/2022] Open
Abstract
The disease resistance (R) genes play an important role in protecting plants from infection by diverse pathogens in the environment. The nucleotide-binding site (NBS)-leucine-rich repeat (LRR) class of genes is one of the largest R gene families. Chinese chestnut (Castanea mollissima) is resistant to Chestnut Blight Disease, but relatively little is known about the resistance mechanism. We identified 519 NBS-encoding genes, including 374 NBS-LRR genes and 145 NBS-only genes. The majority of Ka/Ks were less than 1, suggesting the purifying selection operated during the evolutionary history of NBS-encoding genes. A minority (4/34) of Ka/Ks in non-TIR gene families were greater than 1, showing that some genes were under positive selection pressure. Furthermore, Ks peaked at a range of 0.4 to 0.5, indicating that ancient duplications arose during the evolution. The relationship between Ka/Ks and Ks indicated greater selective pressure on the newer and older genes with the critical value of Ks = 0.4–0.5. Notably, species-specific duplications were detected in NBS-encoding genes. In addition, the group of RPW8-NBS-encoding genes clustered together as an independent clade located at a relatively basal position in the phylogenetic tree. Many cis-acting elements related to plant defense responses were detected in promoters of NBS-encoding genes.
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Zhang X, Yang S, Wang J, Jia Y, Huang J, Tan S, Zhong Y, Wang L, Gu L, Chen JQ, Pan Q, Bergelson J, Tian D. A genome-wide survey reveals abundant rice blast R genes in resistant cultivars. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 84:20-28. [PMID: 26248689 PMCID: PMC4591205 DOI: 10.1111/tpj.12955] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 07/17/2015] [Accepted: 07/22/2015] [Indexed: 05/18/2023]
Abstract
Plant resistance genes (R genes) harbor tremendous allelic diversity, constituting a robust immune system effective against microbial pathogens. Nevertheless, few functional R genes have been identified for even the best-studied pathosystems. Does this limited repertoire reflect specificity, with most R genes having been defeated by former pests, or do plants harbor a rich diversity of functional R genes, the composite behavior of which is yet to be characterized? Here, we survey 332 NBS-LRR genes cloned from five resistant Oryza sativa (rice) cultivars for their ability to confer recognition of 12 rice blast isolates when transformed into susceptible cultivars. Our survey reveals that 48.5% of the 132 NBS-LRR loci tested contain functional rice blast R genes, with most R genes deriving from multi-copy clades containing especially diversified loci. Each R gene recognized, on average, 2.42 of the 12 isolates screened. The abundant R genes identified in resistant genomes provide extraordinary redundancy in the ability of host genotypes to recognize particular isolates. If the same is true for other pathogens, many extant NBS-LRR genes retain functionality. Our success at identifying rice blast R genes also validates a highly efficient cloning and screening strategy.
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Affiliation(s)
- Xiaohui Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Biology, Nanjing Agricultural University, Nanjing 210023, China
| | - Sihai Yang
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Biology, Nanjing Agricultural University, Nanjing 210023, China
| | - Jiao Wang
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Yanxiao Jia
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Biology, Nanjing Agricultural University, Nanjing 210023, China
| | - Ju Huang
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Biology, Nanjing Agricultural University, Nanjing 210023, China
| | - Shengjun Tan
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Biology, Nanjing Agricultural University, Nanjing 210023, China
| | - Yan Zhong
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Ling Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, China
| | - Longjiang Gu
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Biology, Nanjing Agricultural University, Nanjing 210023, China
| | - Jian-Qun Chen
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Biology, Nanjing Agricultural University, Nanjing 210023, China
| | - Qinghua Pan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, China
- Corresponding author: Dacheng Tian, State Key Laboratory of Pharmaceutical Biotechnology, Department of Biology, School of Life Sciences, Nanjing University, 210023, Nanjing, China. Phone: +86-25-89686406. Fax: +86-25-89686406. . Joy Bergelson, Department of Ecology & Evolution, University of Chicago, Chicago, USA. Phone: 773-702-3855. Fax: 773-702-9740. . Qinghua Pan, State Key Laboratory for Conservation and Utilization of Subtropical Agrobioresources, South China Agricultural University, Guangzhou, China. Phone:+86-20-85288315.
| | - Joy Bergelson
- Department of Ecology & Evolution, University of Chicago, Chicago, USA
- Corresponding author: Dacheng Tian, State Key Laboratory of Pharmaceutical Biotechnology, Department of Biology, School of Life Sciences, Nanjing University, 210023, Nanjing, China. Phone: +86-25-89686406. Fax: +86-25-89686406. . Joy Bergelson, Department of Ecology & Evolution, University of Chicago, Chicago, USA. Phone: 773-702-3855. Fax: 773-702-9740. . Qinghua Pan, State Key Laboratory for Conservation and Utilization of Subtropical Agrobioresources, South China Agricultural University, Guangzhou, China. Phone:+86-20-85288315.
| | - Dacheng Tian
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Biology, Nanjing Agricultural University, Nanjing 210023, China
- Corresponding author: Dacheng Tian, State Key Laboratory of Pharmaceutical Biotechnology, Department of Biology, School of Life Sciences, Nanjing University, 210023, Nanjing, China. Phone: +86-25-89686406. Fax: +86-25-89686406. . Joy Bergelson, Department of Ecology & Evolution, University of Chicago, Chicago, USA. Phone: 773-702-3855. Fax: 773-702-9740. . Qinghua Pan, State Key Laboratory for Conservation and Utilization of Subtropical Agrobioresources, South China Agricultural University, Guangzhou, China. Phone:+86-20-85288315.
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Zhao L, Zhang Q, Gao R, Yang S, Liu H, Zhang X. High genetic abundance of Rpi-blb2/Mi-1.2/Cami gene family in Solanaceae. BMC Evol Biol 2015; 15:215. [PMID: 26424005 PMCID: PMC4590265 DOI: 10.1186/s12862-015-0493-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 09/21/2015] [Indexed: 11/29/2022] Open
Abstract
Background Three NBS-LRR genes, Rpi-blb2, Mi-1.2, and Cami, constitute a very special plant resistance gene family. These genes confer resistance against 4 distantly related pathogen species in 3 different Solanaceae hosts. To characterize this noted resistance, we conducted a series of studies on this gene family. Results First, homologs of this gene family were identified in the pepper, tomato and potato genomes. This revealed a large variation in copy number within this gene family among species and a great divergence was found both between and within species. To gain more information pertaining to gene resistance within this family, 121 LRR regions were cloned in 16 different wild/cultivated potato accessions. Again, frequent copy number variations and a high level of divergence between homolog were observed common among accessions. The divergence within species was so high that it reaches the level of divergence between species. Also, frequent frameshift mutations and abundant gene conversion events were identified in these LRR regions. Conclusions Our findings suggest that this family harbors an unusually high level of genetic abundance, making it of particular interest. Together with other reported examples, our study also provides evidence that multi-resistance is a common trait in R gene families like this. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0493-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lina Zhao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210000, China.
| | - Qijun Zhang
- Jiangsu Academy of Agricultural Sciences, Nanjing, 210000, China.
| | - Rongchao Gao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210000, China.
| | - Sihai Yang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210000, China.
| | - Haoxuan Liu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210000, China.
| | - Xiaohui Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210000, China.
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76
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Cokus SJ, Gugger PF, Sork VL. Evolutionary insights from de novo transcriptome assembly and SNP discovery in California white oaks. BMC Genomics 2015. [PMID: 26215102 PMCID: PMC4517385 DOI: 10.1186/s12864-015-1761-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Background Reference transcriptomes provide valuable resources for understanding evolution within and among species. We de novo assembled and annotated a reference transcriptome for Quercus lobata and Q. garryana and identified single-nucleotide polymorphisms (SNPs) to provide resources for forest genomicists studying this ecologically and economically important genus. We further performed preliminary analyses of genes important in interspecific divergent (positive) selection that might explain ecological differences among species, estimating rates of nonsynonymous to synonymous substitutions (dN/dS) and Fay and Wu’s H. Functional classes of genes were tested for unusually high dN/dS or low H consistent with divergent positive selection. Results Our draft transcriptome is among the most complete for oaks, including 83,644 contigs (23,329 ≥ 1 kbp), 14,898 complete and 13,778 partial gene models, and functional annotations for 9,431 Arabidopsis orthologs and 19,365 contigs with Pfam hits. We identified 1.7 million possible sequence variants including 1.1 million high-quality diallelic SNPs — among the largest sets identified in any tree. 11 of 18 functional categories with significantly elevated dN/dS are involved in disease response, including 50+ genes with dN/dS > 1. Other high-dN/dS genes are involved in biotic response, flowering and growth, or regulatory processes. In contrast, median dN/dS was low (0.22), suggesting that purifying selection influences most genes. No functional categories have unusually low H. Conclusions These results offer preliminary support for the hypothesis that divergent selection at pathogen resistance are important factors in species divergence in these hybridizing California oaks. Our transcriptome provides a solid foundation for future studies of gene expression, natural selection, and speciation in Quercus. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1761-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shawn J Cokus
- Molecular, Cell, and Developmental Biology, University of California, 3000 Terasaki Life Sciences Building, 610 Charles E. Young Drive East, Los Angeles, CA, 90095-7239, USA
| | - Paul F Gugger
- Ecology and Evolutionary Biology, University of California, 4140 Terasaki Life Sciences Building, 610 Charles E. Young Drive East, Los Angeles, CA, 90095-7239, USA.
| | - Victoria L Sork
- Ecology and Evolutionary Biology, University of California, 4140 Terasaki Life Sciences Building, 610 Charles E. Young Drive East, Los Angeles, CA, 90095-7239, USA.,Institute of the Environment and Sustainability, University of California, 300 La Kretz Hall, 619 Charles E. Young Drive East, Los Angeles, CA, 90095-1496, USA
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77
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Si W, Yuan Y, Huang J, Zhang X, Zhang Y, Zhang Y, Tian D, Wang C, Yang Y, Yang S. Widely distributed hot and cold spots in meiotic recombination as shown by the sequencing of rice F2 plants. THE NEW PHYTOLOGIST 2015; 206:1491-502. [PMID: 25664766 DOI: 10.1111/nph.13319] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 12/29/2014] [Indexed: 05/02/2023]
Abstract
Numerous studies have argued that environmental variations may contribute to evolution through the generation of novel heritable variations via meiotic recombination, which plays a crucial role in crop domestication and improvement. Rice is one of the most important staple crops, but no direct estimate of recombination events has yet been made at a fine scale. Here, we address this limitation by sequencing 41 rice individuals with high sequencing coverage and c. 900 000 accurate markers. An average of 33.9 crossover (c. 4.53 cM Mb(-1) ) and 2.47 non-crossover events were detected per F2 plant, which is similar to the values in Arabidopsis. Although not all samples in the stress treatment group showed an increased number of crossover events, environmental stress increased the recombination rate in c. 28.5% of samples. Interestingly, the crossovers showed a highly uneven distribution among and along chromosomes, with c. 13.9% of the entire genome devoid of crossovers, including 11 of the 12 centromere regions, and c. 0.72% of the genome containing large numbers of crossovers (> 50 cM Mb(-1) ). The gene ontology (GO) categories showed that genes clustered within the recombination hot spot regions primarily tended to be involved in responses to environmental stimuli, suggesting that recombination plays an important role for adaptive evolution in rapidly changing environments.
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Affiliation(s)
- Weina Si
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210093, China
| | - Yang Yuan
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210093, China
| | - Ju Huang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210093, China
| | - Xiaohui Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210093, China
| | - Yanchun Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210093, China
| | - Yadong Zhang
- Institute of Food Crops, Jiangsu Academy of Agricultural Science, Nanjing, 210014, China
| | - Dacheng Tian
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210093, China
| | - Cailin Wang
- Institute of Food Crops, Jiangsu Academy of Agricultural Science, Nanjing, 210014, China
| | - Yonghua Yang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210093, China
| | - Sihai Yang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210093, China
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78
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Stuart J. Insect effectors and gene-for-gene interactions with host plants. CURRENT OPINION IN INSECT SCIENCE 2015; 9:56-61. [PMID: 32846709 DOI: 10.1016/j.cois.2015.02.010] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Revised: 02/17/2015] [Accepted: 02/20/2015] [Indexed: 06/11/2023]
Abstract
Within the context of the four-phase model of plant immunity, gene-for-gene interactions have gained new relevance. Genes conferring resistance to the Asian rice gall midge (Orseolia oryzae) and the small brown planthopper (Nilaparvata lugens) have been cloned in rice (Oryza sativa). Mutations in insect avirulence genes that defeat plant resistance have been identified and cloned. Results are consistent with both the gene-for-gene hypothesis and the new model of plant immunity. Insect resistance genes encode proteins with nucleotide binding sites and leucine-rich repeats. Insects use effectors that elicit effector-triggered immunity. At least seven-percent of Hessian fly genes are effector encoding.
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Affiliation(s)
- Jeff Stuart
- Department of Entomology, Purdue University, West Lafayette, IN 47907, United States.
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79
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Xie Z, Si W, Gao R, Zhang X, Yang S. Evolutionary analysis of RB/Rpi-blb1 locus in the Solanaceae family. Mol Genet Genomics 2015; 290:2173-86. [PMID: 26008792 DOI: 10.1007/s00438-015-1068-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 05/12/2015] [Indexed: 11/28/2022]
Abstract
Late blight caused by the oomycete Phytophthora infestans is one of the most severe threats to potato production worldwide. Numerous studies suggest that the most effective protective strategy against the disease would be to provide potato cultivars with durable resistance (R) genes. However, little is known about the origin and evolutional history of these durable R-genes in potato. Addressing this might foster better understanding of the dynamics of these genes in nature and provide clues for identifying potential candidate R-genes. Here, a systematic survey was executed at RB/Rpi-blb1 locus, an exclusive broad-spectrum R-gene locus in potato. As indicated by synteny analysis, RB/Rpi-blb1 homologs were identified in all tested genomes, including potato, tomato, pepper, and Nicotiana, suggesting that the RB/Rpi-blb1 locus has an ancient origin. Two evolutionary patterns, similar to those reported on RGC2 in Lactuca, and Pi2/9 in rice, were detected at this locus. Type I RB/Rpi-blb1 homologs have frequent copy number variations and sequence exchanges, obscured orthologous relationships, considerable nucleotide divergence, and high non-synonymous to synonymous substitutions (Ka/Ks) between or within species, suggesting rapid diversification and balancing selection in response to rapid changes in the oomycete pathogen genomes. These characteristics may serve as signatures for cloning of late blight resistance genes.
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Affiliation(s)
- Zhengqing Xie
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210093, China
| | - Weina Si
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210093, China
| | - Rongchao Gao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210093, China
| | - Xiaohui Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210093, China.
| | - Sihai Yang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210093, China.
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80
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Schaper E, Anisimova M. The evolution and function of protein tandem repeats in plants. THE NEW PHYTOLOGIST 2015; 206:397-410. [PMID: 25420631 DOI: 10.1111/nph.13184] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 10/18/2014] [Indexed: 05/27/2023]
Abstract
Sequence tandem repeats (TRs) are abundant in proteomes across all domains of life. For plants, little is known about their distribution or contribution to protein function. We exhaustively annotated TRs and studied the evolution of TR unit variations for all Ensembl plants. Using phylogenetic patterns of TR units, we detected conserved TRs with unit number and order preserved during evolution, and those TRs that have diverged via recent TR unit gains/losses. We correlated the mode of evolution of TRs to protein function. TR number was strongly correlated with proteome size, with about one-half of all TRs recognized as common protein domains. The majority of TRs have been highly conserved over long evolutionary distances, some since the separation of red algae and green plants c. 1.6 billion yr ago. Conversely, recurrent recent TR unit mutations were rare. Our results suggest that the first TRs by far predate the first plants, and that TR appearance is an ongoing process with similar rates across the plant kingdom. Interestingly, the few detected highly mutable TRs might provide a source of variation for rapid adaptation. In particular, such TRs are enriched in leucine-rich repeats (LRRs) commonly found in R genes, where TR unit gain/loss may facilitate resistance to emerging pathogens.
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Affiliation(s)
- Elke Schaper
- Department of Computer Science, ETH Zürich, Zürich, 8092, Switzerland
- Institute of Integrative Biology, ETH Zürich, Zürich, 8092, Switzerland
- Vital-IT Competency Center, Swiss Institute for Bioinformatics (SIB), Lausanne, 1015, Switzerland
| | - Maria Anisimova
- Institute of Applied Simulation (IAS), School of Life Sciences and Facility Management, Zürich University of Applied Sciences (ZHAW), Wädenswil, 8820, Switzerland
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81
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Wang Y, Zhou L, Li D, Dai L, Lawton-Rauh A, Srimani PK, Duan Y, Luo F. Genome-wide comparative analysis reveals similar types of NBS genes in hybrid Citrus sinensis genome and original Citrus clementine genome and provides new insights into non-TIR NBS genes. PLoS One 2015; 10:e0121893. [PMID: 25811466 PMCID: PMC4374887 DOI: 10.1371/journal.pone.0121893] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 02/04/2015] [Indexed: 11/19/2022] Open
Abstract
In this study, we identified and compared nucleotide-binding site (NBS) domain-containing genes from three Citrus genomes (C. clementina, C. sinensis from USA and C. sinensis from China). Phylogenetic analysis of all Citrus NBS genes across these three genomes revealed that there are three approximately evenly numbered groups: one group contains the Toll-Interleukin receptor (TIR) domain and two different Non-TIR groups in which most of proteins contain the Coiled Coil (CC) domain. Motif analysis confirmed that the two groups of CC-containing NBS genes are from different evolutionary origins. We partitioned NBS genes into clades using NBS domain sequence distances and found most clades include NBS genes from all three Citrus genomes. This suggests that three Citrus genomes have similar numbers and types of NBS genes. We also mapped the re-sequenced reads of three pomelo and three mandarin genomes onto the C. sinensis genome. We found that most NBS genes of the hybrid C. sinensis genome have corresponding homologous genes in both pomelo and mandarin genomes. The homologous NBS genes in pomelo and mandarin suggest that the parental species of C. sinensis may contain similar types of NBS genes. This explains why the hybrid C. sinensis and original C. clementina have similar types of NBS genes in this study. Furthermore, we found that sequence variation amongst Citrus NBS genes were shaped by multiple independent and shared accelerated mutation accumulation events among different groups of NBS genes and in different Citrus genomes. Our comparative analyses yield valuable insight into the structure, organization and evolution of NBS genes in Citrus genomes. Furthermore, our comprehensive analysis showed that the non-TIR NBS genes can be divided into two groups that come from different evolutionary origins. This provides new insights into non-TIR genes, which have not received much attention.
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Affiliation(s)
- Yunsheng Wang
- College of Plant Protection, Hunan Agricultural University, Changsha, China
- School of Computing, Clemson University, Clemson, South Carolina, United States of America
| | - Lijuan Zhou
- Agricultural Research Service, U.S. Horticultural Research Laboratory, Fort Pierce, Florida, United States of America
| | - Dazhi Li
- National Center for Citrus Improvement, Hunan Agricultural University, Changsha, China
| | - Liangying Dai
- College of Plant Protection, Hunan Agricultural University, Changsha, China
| | - Amy Lawton-Rauh
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, United States of America
| | - Pradip K. Srimani
- School of Computing, Clemson University, Clemson, South Carolina, United States of America
| | - Yongping Duan
- Agricultural Research Service, U.S. Horticultural Research Laboratory, Fort Pierce, Florida, United States of America
| | - Feng Luo
- School of Computing, Clemson University, Clemson, South Carolina, United States of America
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82
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Gu L, Si W, Zhao L, Yang S, Zhang X. Dynamic evolution of NBS-LRR genes in bread wheat and its progenitors. Mol Genet Genomics 2014. [PMID: 25475390 DOI: 10.1007/s00438‐014‐0948‐8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Extensive studies have focused on the largest class of disease resistance genes (nucleotide binding site-leucine-rich repeat, NBS-LRR) in various plants. However, no research on the dynamic evolution of these genes in domesticated species and their progenitors has been reported. Recently published genome sequences of bread wheat and its two ancestors provide a good opportunity for comparing NBS-encoding genes between ancestors and their progeny. Over 2000 NBS-encoding genes have been identified in bread wheat, which is the largest number having been reported so far. Compared with other grass species, its two progenitors also contained more NBS-encoding genes, indicating that there was an expansion of these genes in their common ancestor. Interestingly, the inherited relationships of NBS-LRR genes among the bread wheat and its two progenitors were ambiguous and only 3 % single-copy orthologues retained gene order in three-way genome comparisons of the three genomes. Lots of NBS-encoding genes present in the either ancestor could not be found in the bread wheat. These results indicated that NBS-LRR genes in bread wheat might have evolved rapidly through a rapid loss of ancestor genes.
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Affiliation(s)
- Longjiang Gu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
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83
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Gu L, Si W, Zhao L, Yang S, Zhang X. Dynamic evolution of NBS-LRR genes in bread wheat and its progenitors. Mol Genet Genomics 2014; 290:727-38. [PMID: 25475390 DOI: 10.1007/s00438-014-0948-8] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Accepted: 10/30/2014] [Indexed: 12/25/2022]
Abstract
Extensive studies have focused on the largest class of disease resistance genes (nucleotide binding site-leucine-rich repeat, NBS-LRR) in various plants. However, no research on the dynamic evolution of these genes in domesticated species and their progenitors has been reported. Recently published genome sequences of bread wheat and its two ancestors provide a good opportunity for comparing NBS-encoding genes between ancestors and their progeny. Over 2000 NBS-encoding genes have been identified in bread wheat, which is the largest number having been reported so far. Compared with other grass species, its two progenitors also contained more NBS-encoding genes, indicating that there was an expansion of these genes in their common ancestor. Interestingly, the inherited relationships of NBS-LRR genes among the bread wheat and its two progenitors were ambiguous and only 3 % single-copy orthologues retained gene order in three-way genome comparisons of the three genomes. Lots of NBS-encoding genes present in the either ancestor could not be found in the bread wheat. These results indicated that NBS-LRR genes in bread wheat might have evolved rapidly through a rapid loss of ancestor genes.
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Affiliation(s)
- Longjiang Gu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
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84
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Piquerez SJM, Harvey SE, Beynon JL, Ntoukakis V. Improving crop disease resistance: lessons from research on Arabidopsis and tomato. FRONTIERS IN PLANT SCIENCE 2014; 5:671. [PMID: 25520730 PMCID: PMC4253662 DOI: 10.3389/fpls.2014.00671] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 11/10/2014] [Indexed: 05/04/2023]
Abstract
One of the great challenges for food security in the 21st century is to improve yield stability through the development of disease-resistant crops. Crop research is often hindered by the lack of molecular tools, growth logistics, generation time and detailed genetic annotations, hence the power of model plant species. Our knowledge of plant immunity today has been largely shaped by the use of models, specifically through the use of mutants. We examine the importance of Arabidopsis and tomato as models in the study of plant immunity and how they help us in revealing a detailed and deep understanding of the various layers contributing to the immune system. Here we describe examples of how knowledge from models can be transferred to economically important crops resulting in new tools to enable and accelerate classical plant breeding. We will also discuss how models, and specifically transcriptomics and effectoromics approaches, have contributed to the identification of core components of the defense response which will be key to future engineering of durable and sustainable disease resistance in plants.
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Affiliation(s)
| | | | - Jim L. Beynon
- School of Life Sciences, University of WarwickCoventry, UK
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85
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Chae E, Bomblies K, Kim ST, Karelina D, Zaidem M, Ossowski S, Martín-Pizarro C, Laitinen RAE, Rowan BA, Tenenboim H, Lechner S, Demar M, Habring-Müller A, Lanz C, Rätsch G, Weigel D. Species-wide genetic incompatibility analysis identifies immune genes as hot spots of deleterious epistasis. Cell 2014; 159:1341-51. [PMID: 25467443 DOI: 10.1016/j.cell.2014.10.049] [Citation(s) in RCA: 193] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Revised: 07/22/2014] [Accepted: 10/07/2014] [Indexed: 01/07/2023]
Abstract
Intraspecific genetic incompatibilities prevent the assembly of specific alleles into single genotypes and influence genome- and species-wide patterns of sequence variation. A common incompatibility in plants is hybrid necrosis, characterized by autoimmune responses due to epistatic interactions between natural genetic variants. By systematically testing thousands of F1 hybrids of Arabidopsis thaliana strains, we identified a small number of incompatibility hot spots in the genome, often in regions densely populated by nucleotide-binding domain and leucine-rich repeat (NLR) immune receptor genes. In several cases, these immune receptor loci interact with each other, suggestive of conflict within the immune system. A particularly dangerous locus is a highly variable cluster of NLR genes, DM2, which causes multiple independent incompatibilities with genes that encode a range of biochemical functions, including NLRs. Our findings suggest that deleterious interactions of immune receptors limit the combinations of favorable disease resistance alleles accessible to plant genomes.
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Affiliation(s)
- Eunyoung Chae
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Kirsten Bomblies
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Sang-Tae Kim
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Darya Karelina
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany; Friedrich Miescher Laboratory, Max Planck Society, 72076 Tübingen, Germany
| | - Maricris Zaidem
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Stephan Ossowski
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Carmen Martín-Pizarro
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Roosa A E Laitinen
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Beth A Rowan
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Hezi Tenenboim
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Sarah Lechner
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Monika Demar
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Anette Habring-Müller
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Christa Lanz
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Gunnar Rätsch
- Friedrich Miescher Laboratory, Max Planck Society, 72076 Tübingen, Germany
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.
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86
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Guo HM, Li HC, Zhou SR, Xue HW, Miao XX. Cis-12-oxo-phytodienoic acid stimulates rice defense response to a piercing-sucking insect. MOLECULAR PLANT 2014; 7:1683-1692. [PMID: 25239066 DOI: 10.1093/mp/ssu098] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The brown planthopper (BPH, Nilaparvata lugens) is a destructive, monophagous, piercing-sucking insect pest of rice. Previous studies indicated that jasmonic acid (JA) positively regulates rice defense against chewing insect pests but negatively regulates it against the piercing-sucking insect of BPH. We here demonstrated that overexpression of allene oxide cyclase (AOC) but not OPR3 (cis-12-oxo-phytodienoic acid (OPDA) reductase 3, an enzyme adjacent to AOC in the JA synthetic pathway) significantly increased rice resistance to BPH, mainly by reducing the feeding activity and survival rate. Further analysis revealed that plant response to BPH under AOC overexpression was independent of the JA pathway and that significantly higher OPDA levels stimulated rice resistance to BPH. Microarray analysis identified multiple candidate resistance-related genes under AOC overexpression. OPDA treatment stimulated the resistance of radish seedlings to green peach aphid Myzus persicae, another piercing-sucking insect. These results imply that rice resistance to chewing insects and to sucking insects can be enhanced simultaneously through AOC-mediated increases of JA and OPDA and provide direct evidence of the potential application of OPDA in stimulating plant defense responses to piercing-sucking insect pests in agriculture.
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Affiliation(s)
- Hui-Min Guo
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Hai-Chao Li
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Shi-Rong Zhou
- National Key Laboratory of Plant Molecular Genetics Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Hong-Wei Xue
- National Key Laboratory of Plant Molecular Genetics Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China.
| | - Xue-Xia Miao
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China.
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87
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Vasudevan K, Vera Cruz CM, Gruissem W, Bhullar NK. Large scale germplasm screening for identification of novel rice blast resistance sources. FRONTIERS IN PLANT SCIENCE 2014; 5:505. [PMID: 25324853 PMCID: PMC4183131 DOI: 10.3389/fpls.2014.00505] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2014] [Accepted: 09/09/2014] [Indexed: 05/02/2023]
Abstract
Rice is a major cereal crop that contributes significantly to global food security. Biotic stresses, including the rice blast fungus, cause severe yield losses that significantly impair rice production worldwide. The rapid genetic evolution of the fungus often overcomes the resistance conferred by major genes after a few years of intensive agricultural use. Therefore, resistance breeding requires continuous efforts of enriching the reservoir of resistance genes/alleles to effectively tackle the disease. Seed banks represent a rich stock of genetic diversity, however, they are still under-explored for identifying novel genes and/or their functional alleles. We conducted a large-scale screen for new rice blast resistance sources in 4246 geographically diverse rice accessions originating from 13 major rice-growing countries. The accessions were selected from a total collection of over 120,000 accessions based on their annotated rice blast resistance information in the International Rice Genebank. A two-step resistance screening protocol was used involving natural infection in a rice uniform blast nursery and subsequent artificial infections with five single rice blast isolates. The nursery-resistant accessions showed varied disease responses when infected with single isolates, suggesting the presence of diverse resistance genes/alleles in this accession collection. In addition, 289 accessions showed broad-spectrum resistance against all five single rice blast isolates. The selected resistant accessions were genotyped for the presence of the Pi2 resistance gene, thereby identifying potential accessions for isolation of allelic variants of this blast resistance gene. Together, the accession collection with broad spectrum and isolate specific blast resistance represent the core material for isolation of previously unknown blast resistance genes and/or their allelic variants that can be deployed in rice breeding programs.
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Affiliation(s)
- Kumar Vasudevan
- Plant Biotechnology, Department of Biology, ETH Zurich (Swiss Federal Institute of Technology)Zurich, Switzerland
| | | | - Wilhelm Gruissem
- Plant Biotechnology, Department of Biology, ETH Zurich (Swiss Federal Institute of Technology)Zurich, Switzerland
| | - Navreet K. Bhullar
- Plant Biotechnology, Department of Biology, ETH Zurich (Swiss Federal Institute of Technology)Zurich, Switzerland
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Mace E, Tai S, Innes D, Godwin I, Hu W, Campbell B, Gilding E, Cruickshank A, Prentis P, Wang J, Jordan D. The plasticity of NBS resistance genes in sorghum is driven by multiple evolutionary processes. BMC PLANT BIOLOGY 2014; 14:253. [PMID: 25928459 PMCID: PMC4189741 DOI: 10.1186/s12870-014-0253-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Accepted: 09/20/2014] [Indexed: 05/20/2023]
Abstract
BACKGROUND Increased disease resistance is a key target of cereal breeding programs, with disease outbreaks continuing to threaten global food production, particularly in Africa. Of the disease resistance gene families, the nucleotide-binding site plus leucine-rich repeat (NBS-LRR) family is the most prevalent and ancient and is also one of the largest gene families known in plants. The sequence diversity in NBS-encoding genes was explored in sorghum, a critical food staple in Africa, with comparisons to rice and maize and with comparisons to fungal pathogen resistance QTL. RESULTS In sorghum, NBS-encoding genes had significantly higher diversity in comparison to non NBS-encoding genes and were significantly enriched in regions of the genome under purifying and balancing selection, both through domestication and improvement. Ancestral genes, pre-dating species divergence, were more abundant in regions with signatures of selection than in regions not under selection. Sorghum NBS-encoding genes were also significantly enriched in the regions of the genome containing fungal pathogen disease resistance QTL; with the diversity of the NBS-encoding genes influenced by the type of co-locating biotic stress resistance QTL. CONCLUSIONS NBS-encoding genes are under strong selection pressure in sorghum, through the contrasting evolutionary processes of purifying and balancing selection. Such contrasting evolutionary processes have impacted ancestral genes more than species-specific genes. Fungal disease resistance hot-spots in the genome, with resistance against multiple pathogens, provides further insight into the mechanisms that cereals use in the "arms race" with rapidly evolving pathogens in addition to providing plant breeders with selection targets for fast-tracking the development of high performing varieties with more durable pathogen resistance.
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Affiliation(s)
- Emma Mace
- Department of Agriculture, Fisheries & Forestry (DAFF), Warwick, QLD, Australia.
| | | | - David Innes
- DAFFQ, Cooper's Plains, Brisbane, QLD, Australia.
| | - Ian Godwin
- The University of Queensland, School of Agriculture and Food Sciences, Brisbane, QLD, Australia.
| | | | | | - Edward Gilding
- The Institute of Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia.
| | - Alan Cruickshank
- Department of Agriculture, Fisheries & Forestry (DAFF), Warwick, QLD, Australia.
| | - Peter Prentis
- Queensland University of Technology, Brisbane, QLD, Australia.
| | - Jun Wang
- BGI-Shenzhen, Shenzhen, China.
- Department of Biology, University of Copenhagen, DK-2200, Copenhagen, Denmark.
- The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, DK-2200, Copenhagen, Denmark.
| | - David Jordan
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Warwick, QLD, Australia.
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89
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Shao ZQ, Zhang YM, Hang YY, Xue JY, Zhou GC, Wu P, Wu XY, Wu XZ, Wang Q, Wang B, Chen JQ. Long-term evolution of nucleotide-binding site-leucine-rich repeat genes: understanding gained from and beyond the legume family. PLANT PHYSIOLOGY 2014; 166:217-34. [PMID: 25052854 PMCID: PMC4149708 DOI: 10.1104/pp.114.243626] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2014] [Accepted: 07/11/2014] [Indexed: 05/18/2023]
Abstract
Proper utilization of plant disease resistance genes requires a good understanding of their short- and long-term evolution. Here we present a comprehensive study of the long-term evolutionary history of nucleotide-binding site (NBS)-leucine-rich repeat (LRR) genes within and beyond the legume family. The small group of NBS-LRR genes with an amino-terminal RESISTANCE TO POWDERY MILDEW8 (RPW8)-like domain (referred to as RNL) was first revealed as a basal clade sister to both coiled-coil-NBS-LRR (CNL) and Toll/Interleukin1 receptor-NBS-LRR (TNL) clades. Using Arabidopsis (Arabidopsis thaliana) as an outgroup, this study explicitly recovered 31 ancestral NBS lineages (two RNL, 21 CNL, and eight TNL) that had existed in the rosid common ancestor and 119 ancestral lineages (nine RNL, 55 CNL, and 55 TNL) that had diverged in the legume common ancestor. It was shown that, during their evolution in the past 54 million years, approximately 94% (112 of 119) of the ancestral legume NBS lineages experienced deletions or significant expansions, while seven original lineages were maintained in a conservative manner. The NBS gene duplication pattern was further examined. The local tandem duplications dominated NBS gene gains in the total number of genes (more than 75%), which was not surprising. However, it was interesting from our study that ectopic duplications had created many novel NBS gene loci in individual legume genomes, which occurred at a significant frequency of 8% to 20% in different legume lineages. Finally, by surveying the legume microRNAs that can potentially regulate NBS genes, we found that the microRNA-NBS gene interaction also exhibited a gain-and-loss pattern during the legume evolution.
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Affiliation(s)
- Zhu-Qing Shao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210093, China (Z.-Q.S., Y.-M.Z., J.-Y.X., G.-C.Z., P.W., X.-Y.W., X.-Z.W., Q.W., B.W., J.-Q.C.); andJiangsu Province and Chinese Academy of Science, Institute of Botany, Nanjing 210014, China (Y.-M.Z., Y.-Y.H., J.-Y.X.)
| | - Yan-Mei Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210093, China (Z.-Q.S., Y.-M.Z., J.-Y.X., G.-C.Z., P.W., X.-Y.W., X.-Z.W., Q.W., B.W., J.-Q.C.); andJiangsu Province and Chinese Academy of Science, Institute of Botany, Nanjing 210014, China (Y.-M.Z., Y.-Y.H., J.-Y.X.)
| | - Yue-Yu Hang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210093, China (Z.-Q.S., Y.-M.Z., J.-Y.X., G.-C.Z., P.W., X.-Y.W., X.-Z.W., Q.W., B.W., J.-Q.C.); andJiangsu Province and Chinese Academy of Science, Institute of Botany, Nanjing 210014, China (Y.-M.Z., Y.-Y.H., J.-Y.X.)
| | - Jia-Yu Xue
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210093, China (Z.-Q.S., Y.-M.Z., J.-Y.X., G.-C.Z., P.W., X.-Y.W., X.-Z.W., Q.W., B.W., J.-Q.C.); andJiangsu Province and Chinese Academy of Science, Institute of Botany, Nanjing 210014, China (Y.-M.Z., Y.-Y.H., J.-Y.X.)
| | - Guang-Can Zhou
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210093, China (Z.-Q.S., Y.-M.Z., J.-Y.X., G.-C.Z., P.W., X.-Y.W., X.-Z.W., Q.W., B.W., J.-Q.C.); andJiangsu Province and Chinese Academy of Science, Institute of Botany, Nanjing 210014, China (Y.-M.Z., Y.-Y.H., J.-Y.X.)
| | - Ping Wu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210093, China (Z.-Q.S., Y.-M.Z., J.-Y.X., G.-C.Z., P.W., X.-Y.W., X.-Z.W., Q.W., B.W., J.-Q.C.); andJiangsu Province and Chinese Academy of Science, Institute of Botany, Nanjing 210014, China (Y.-M.Z., Y.-Y.H., J.-Y.X.)
| | - Xiao-Yi Wu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210093, China (Z.-Q.S., Y.-M.Z., J.-Y.X., G.-C.Z., P.W., X.-Y.W., X.-Z.W., Q.W., B.W., J.-Q.C.); andJiangsu Province and Chinese Academy of Science, Institute of Botany, Nanjing 210014, China (Y.-M.Z., Y.-Y.H., J.-Y.X.)
| | - Xun-Zong Wu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210093, China (Z.-Q.S., Y.-M.Z., J.-Y.X., G.-C.Z., P.W., X.-Y.W., X.-Z.W., Q.W., B.W., J.-Q.C.); andJiangsu Province and Chinese Academy of Science, Institute of Botany, Nanjing 210014, China (Y.-M.Z., Y.-Y.H., J.-Y.X.)
| | - Qiang Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210093, China (Z.-Q.S., Y.-M.Z., J.-Y.X., G.-C.Z., P.W., X.-Y.W., X.-Z.W., Q.W., B.W., J.-Q.C.); andJiangsu Province and Chinese Academy of Science, Institute of Botany, Nanjing 210014, China (Y.-M.Z., Y.-Y.H., J.-Y.X.)
| | - Bin Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210093, China (Z.-Q.S., Y.-M.Z., J.-Y.X., G.-C.Z., P.W., X.-Y.W., X.-Z.W., Q.W., B.W., J.-Q.C.); andJiangsu Province and Chinese Academy of Science, Institute of Botany, Nanjing 210014, China (Y.-M.Z., Y.-Y.H., J.-Y.X.)
| | - Jian-Qun Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210093, China (Z.-Q.S., Y.-M.Z., J.-Y.X., G.-C.Z., P.W., X.-Y.W., X.-Z.W., Q.W., B.W., J.-Q.C.); andJiangsu Province and Chinese Academy of Science, Institute of Botany, Nanjing 210014, China (Y.-M.Z., Y.-Y.H., J.-Y.X.)
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90
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Huang J, Si W, Deng Q, Li P, Yang S. Rapid evolution of avirulence genes in rice blast fungus Magnaporthe oryzae. BMC Genet 2014; 15:45. [PMID: 24725999 PMCID: PMC4021558 DOI: 10.1186/1471-2156-15-45] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Accepted: 04/07/2014] [Indexed: 11/24/2022] Open
Abstract
Background Rice blast fungus Magnaporthe oryzae is one of the most devastating pathogens in rice. Avirulence genes in this fungus share a gene-for-gene relationship with the resistance genes in its host rice. Although numerous studies have shown that rice blast R-genes are extremely diverse and evolve rapidly in their host populations, little is known about the evolutionary patterns of the Avr-genes in the pathogens. Results Here, six well-characterized Avr-genes and seven randomly selected non-Avr control genes were used to investigate the genetic variations in 62 rice blast strains from different parts of China. Frequent presence/absence polymorphisms, high levels of nucleotide variation (~10-fold higher than non-Avr genes), high non-synonymous to synonymous substitution ratios, and frequent shared non-synonymous substitution were observed in the Avr-genes of these diversified blast strains. In addition, most Avr-genes are closely associated with diverse repeated sequences, which may partially explain the frequent presence/absence polymorphisms in Avr-genes. Conclusion The frequent deletion and gain of Avr-genes and rapid non-synonymous variations might be the primary mechanisms underlying rapid adaptive evolution of pathogens toward virulence to their host plants, and these features can be used as the indicators for identifying additional Avr-genes. The high number of nucleotide polymorphisms among Avr-gene alleles could also be used to distinguish genetic groups among different strains.
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Affiliation(s)
| | | | | | - Ping Li
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210093, China.
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91
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Karasov TL, Horton MW, Bergelson J. Genomic variability as a driver of plant-pathogen coevolution? CURRENT OPINION IN PLANT BIOLOGY 2014; 18:24-30. [PMID: 24491596 PMCID: PMC4696489 DOI: 10.1016/j.pbi.2013.12.003] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Revised: 12/16/2013] [Accepted: 12/20/2013] [Indexed: 05/03/2023]
Abstract
Pathogens apply one of the strongest selective pressures in plant populations. Understanding plant-pathogen coevolution has therefore been a major research focus for at least sixty years [1]. Recent comparative genomic studies have revealed that the genes involved in plant defense and pathogen virulence are among the most polymorphic in the respective genomes. Which fraction of this diversity influences the host-pathogen interaction? Do coevolutionary dynamics maintain variation? Here we review recent literature on the evolutionary and molecular processes that shape this variation, focusing primarily on gene-for-gene interactions. In summarizing theoretical and empirical studies of the processes that shape this variation in natural plant and pathogen populations, we find a disconnect between the complexity of ecological interactions involving hosts and their myriad microbes, and the models that describe them.
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Affiliation(s)
- Talia L Karasov
- University of Chicago, Chicago, IL 60637, USA; Committee on Genetics, Genomics and Systems Biology
| | | | - Joy Bergelson
- University of Chicago, Chicago, IL 60637, USA; Department of Ecology & Evolution.
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92
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Wang D, Guo C, Huang J, Yang S, Tian D, Zhang X. Allele-mining of rice blast resistance genes at AC134922 locus. Biochem Biophys Res Commun 2014; 446:1085-90. [PMID: 24661882 DOI: 10.1016/j.bbrc.2014.03.056] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2014] [Accepted: 03/15/2014] [Indexed: 10/25/2022]
Abstract
The AC134922 locus is one of the most rapidly evolving nucleotide binding site-leucine-rich repeat (NBS-LRR) gene family in rice genome. Six rice blast resistance (R) genes have been cloned from this locus and other two resistance candidate genes, Pi34 and Pi47, are also mapped to this complex locus. Therefore, it seems that more functional R genes could be identified from this locus. In this study, we cloned 22 genes from 12 cultivars based on allele-mining strategy at this locus and identified 6 rice blast R genes with 4 of them recognizing more than one isolates. Our result suggests that gene stacking might be the evolutionary strategy for complex gene locus to interact with rapidly evolving pathogens, which might provide a potential way for the cloning of durable resistance genes. Moreover, the mosaic structure and ambiguous ortholog/paralog relationships of these homologous genes, caused by frequent recombination and gene conversion, indicate that multiple alleles of this complex locus may serve as a reservoir for the evolutionary novelty of these R genes.
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Affiliation(s)
- Dan Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 210093 Nanjing, China
| | - Changjiang Guo
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 210093 Nanjing, China
| | - Ju Huang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 210093 Nanjing, China
| | - Sihai Yang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 210093 Nanjing, China
| | - Dacheng Tian
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 210093 Nanjing, China.
| | - Xiaohui Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 210093 Nanjing, China.
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