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Wang H, Shi S, Hua W. Advances of herbivore-secreted elicitors and effectors in plant-insect interactions. FRONTIERS IN PLANT SCIENCE 2023; 14:1176048. [PMID: 37404545 PMCID: PMC10317074 DOI: 10.3389/fpls.2023.1176048] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 03/31/2023] [Indexed: 07/06/2023]
Abstract
Diverse molecular processes regulate the interactions between insect herbivores and their host plants. When plants are exposed to insects, elicitors induce plant defenses, and complex physiological and biochemical processes are triggered, such as the activation of the jasmonic acid (JA) and salicylic acid (SA) pathways, Ca2+ flux, reactive oxygen species (ROS) burst, mitogen-activated protein kinase (MAPK) activation, and other responses. For better adaptation, insects secrete a large number of effectors to interfere with plant defenses on multiple levels. In plants, resistance (R) proteins have evolved to recognize effectors and trigger stronger defense responses. However, only a few effectors recognized by R proteins have been identified until now. Multi-omics approaches for high-throughput elicitor/effector identification and functional characterization have been developed. In this review, we mainly highlight the recent advances in the identification of the elicitors and effectors secreted by insects and their target proteins in plants and discuss their underlying molecular mechanisms, which will provide new inspiration for controlling these insect pests.
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Affiliation(s)
- Huiying Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Shaojie Shi
- Hubei Hongshan Laboratory, Wuhan, China
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Key Laboratory of Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs, Institute of Food Crops, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Wei Hua
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
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Gene-rich X chromosomes implicate intragenomic conflict in the evolution of bizarre genetic systems. Proc Natl Acad Sci U S A 2022; 119:e2122580119. [PMID: 35653559 DOI: 10.1073/pnas.2122580119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
SignificanceSex determination systems such as haplodiploidy, in which males' gene transmission is haploid, are surprisingly common, however, the evolutionary paths to these systems are poorly understood. X chromosomes may play a particularly important role, either by increasing survival of males with only maternal genomes, or due to conflicts between X-chromosomal and autosomal genes. We studied X-chromosome gene richness in three arthropod lineages in which males are diploid as adults but only transmit their maternally inherited haploid genome. We find that species with such atypical systems have far more X-chromosomal genes than related diploid species. These results suggest that conflict between genetic elements within the genome drives the evolution of unusual sex determination systems.
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Navarro-Escalante L, Zhao C, Shukle R, Stuart J. BSA-Seq Discovery and Functional Analysis of Candidate Hessian Fly ( Mayetiola destructor) Avirulence Genes. FRONTIERS IN PLANT SCIENCE 2020; 11:956. [PMID: 32670342 PMCID: PMC7330099 DOI: 10.3389/fpls.2020.00956] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 06/10/2020] [Indexed: 05/17/2023]
Abstract
The Hessian fly (HF, Mayetiola destructor) is a plant-galling parasite of wheat (Triticum spp.). Seven percent of its genome is composed of highly diversified signal-peptide-encoding genes that are transcribed in HF larval salivary glands. These observations suggest that they encode effector proteins that are injected into wheat cells to suppress basal wheat immunity and redirect wheat development towards gall formation. Genetic mapping has determined that mutations in four of these genes are associated with HF larval survival (virulence) on plants carrying four different resistance (R) genes. Here, this line of investigation was pursued further using bulked-segregant analysis combined with whole genome resequencing (BSA-seq). Virulence to wheat R genes H6, Hdic, and H5 was examined. Mutations associated with H6 virulence had been mapped previously. Therefore, we used H6 to test the capacity of BSA-seq to map virulence using a field-derived HF population. This was the first time a non-structured HF population had been used to map HF virulence. Hdic virulence had not been mapped previously. Using a structured laboratory population, BSA-seq associated Hdic virulence with mutations in two candidate effector-encoding genes. Using a laboratory population, H5 virulence was previously positioned in a region spanning the centromere of HF autosome 2. BSA-seq resolved H5 virulence to a 1.3 Mb fragment on the same chromosome but failed to identify candidate mutations. Map-based candidate effectors were then delivered to Nicotiana plant cells via the type III secretion system of Burkholderia glumae bacteria. These experiments demonstrated that the genes associated with virulence to wheat R genes H6 and H13 are capable of suppressing plant immunity. Results are consistent with the hypothesis that effector proteins underlie the ability of HFs to survive on wheat.
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Affiliation(s)
| | - Chaoyang Zhao
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, United States
| | - Richard Shukle
- USDA-ARS and Department of Entomology, Purdue University, West Lafayette, IN, United States
| | - Jeffrey Stuart
- Department of Entomology, Purdue University, West Lafayette, IN, United States
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Kaloshian I, Walling LL. Hemipteran and dipteran pests: Effectors and plant host immune regulators. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2016; 58:350-61. [PMID: 26467026 DOI: 10.1111/jipb.12438] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 10/09/2015] [Indexed: 05/08/2023]
Abstract
Hemipteran and dipteran insects have behavioral, cellular and chemical strategies for evading or coping with the host plant defenses making these insects particularly destructive pests worldwide. A critical component of a host plant's defense to herbivory is innate immunity. Here we review the status of our understanding of the receptors that contribute to perception of hemipteran and dipteran pests and highlight the gaps in our knowledge in these early events in immune signaling. We also highlight recent advances in identification of the effectors that activate pattern-triggered immunity and those involved in effector-triggered immunity.
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Affiliation(s)
- Isgouhi Kaloshian
- Institute of Integrative Genome Biology and Center for Plant Cell Biology, University of California, Riverside, California 92521, USA
- Department of Nematology, University of California, Riverside, California 92521, USA
| | - Linda L Walling
- Institute of Integrative Genome Biology and Center for Plant Cell Biology, University of California, Riverside, California 92521, USA
- Department of Botany and Plant Sciences, University of California, Riverside, California 92521, USA
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Zhao C, Shukle R, Navarro-Escalante L, Chen M, Richards S, Stuart JJ. Avirulence gene mapping in the Hessian fly (Mayetiola destructor) reveals a protein phosphatase 2C effector gene family. JOURNAL OF INSECT PHYSIOLOGY 2016; 84:22-31. [PMID: 26439791 DOI: 10.1016/j.jinsphys.2015.10.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 09/28/2015] [Accepted: 10/01/2015] [Indexed: 05/09/2023]
Abstract
The genetic tractability of the Hessian fly (HF, Mayetiola destructor) provides an opportunity to investigate the mechanisms insects use to induce plant gall formation. Here we demonstrate that capacity using the newly sequenced HF genome by identifying the gene (vH24) that elicits effector-triggered immunity in wheat (Triticum spp.) seedlings carrying HF resistance gene H24. vH24 was mapped within a 230-kb genomic fragment near the telomere of HF chromosome X1. That fragment contains only 21 putative genes. The best candidate vH24 gene in this region encodes a protein containing a secretion signal and a type-2 serine/threonine protein phosphatase (PP2C) domain. This gene has an H24-virulence associated insertion in its promoter that appears to silence transcription of the gene in H24-virulent larvae. Candidate vH24 is a member of a small family of genes that encode secretion signals and PP2C domains. It belongs to the fraction of genes in the HF genome previously predicted to encode effector proteins. Because PP2C proteins are not normally secreted, our results suggest that these are PP2C effectors that HF larvae inject into wheat cells to redirect, or interfere, with wheat signal transduction pathways.
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Affiliation(s)
- Chaoyang Zhao
- Department of Entomology, Purdue University, West Lafayette, IN 47907, United States.
| | - Richard Shukle
- USDA-ARS and Department of Entomology, Purdue University, West Lafayette, IN 47907, United States.
| | | | - Mingshun Chen
- USDA-ARS and Department of Entomology, Kansas State University, Manhattan, KS 66506, United States.
| | - Stephen Richards
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, United States.
| | - Jeffrey J Stuart
- Department of Entomology, Purdue University, West Lafayette, IN 47907, United States.
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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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Zhao C, Escalante L, Chen H, Benatti T, Qu J, Chellapilla S, Waterhouse R, Wheeler D, Andersson M, Bao R, Batterton M, Behura S, Blankenburg K, Caragea D, Carolan J, Coyle M, El-Bouhssini M, Francisco L, Friedrich M, Gill N, Grace T, Grimmelikhuijzen C, Han Y, Hauser F, Herndon N, Holder M, Ioannidis P, Jackson L, Javaid M, Jhangiani S, Johnson A, Kalra D, Korchina V, Kovar C, Lara F, Lee S, Liu X, Löfstedt C, Mata R, Mathew T, Muzny D, Nagar S, Nazareth L, Okwuonu G, Ongeri F, Perales L, Peterson B, Pu LL, Robertson H, Schemerhorn B, Scherer S, Shreve J, Simmons D, Subramanyam S, Thornton R, Xue K, Weissenberger G, Williams C, Worley K, Zhu D, Zhu Y, Harris M, Shukle R, Werren J, Zdobnov E, Chen MS, Brown S, Stuart J, Richards S. A Massive Expansion of Effector Genes Underlies Gall-Formation in the Wheat Pest Mayetiola destructor. Curr Biol 2015; 25:613-20. [DOI: 10.1016/j.cub.2014.12.057] [Citation(s) in RCA: 130] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 12/07/2014] [Accepted: 12/23/2014] [Indexed: 01/27/2023]
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Harris MO, Friesen TL, Xu SS, Chen MS, Giron D, Stuart JJ. Pivoting from Arabidopsis to wheat to understand how agricultural plants integrate responses to biotic stress. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:513-531. [PMID: 25504642 DOI: 10.1093/jxb/eru465] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
In this review, we argue for a research initiative on wheat's responses to biotic stress. One goal is to begin a conversation between the disparate communities of plant pathology and entomology. Another is to understand how responses to a variety of agents of biotic stress are integrated in an important crop. We propose gene-for-gene interactions as the focus of the research initiative. On the parasite's side is an Avirulence (Avr) gene that encodes one of the many effector proteins the parasite applies to the plant to assist with colonization. On the plant's side is a Resistance (R) gene that mediates a surveillance system that detects the Avr protein directly or indirectly and triggers effector-triggered plant immunity. Even though arthropods are responsible for a significant proportion of plant biotic stress, they have not been integrated into important models of plant immunity that come from plant pathology. A roadblock has been the absence of molecular evidence for arthropod Avr effectors. Thirty years after this evidence was discovered in a plant pathogen, there is now evidence for arthropods with the cloning of the Hessian fly's vH13 Avr gene. After reviewing the two models of plant immunity, we discuss how arthropods could be incorporated. We end by showing features that make wheat an interesting system for plant immunity, including 479 resistance genes known from agriculture that target viruses, bacteria, fungi, nematodes, insects, and mites. It is not likely that humans will be subsisting on Arabidopsis in the year 2050. It is time to start understanding how agricultural plants integrate responses to biotic stress.
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Affiliation(s)
- M O Harris
- Department of Entomology, North Dakota State University, Fargo, ND 58105, USA
| | - T L Friesen
- USDA-ARS, Cereal Crops Research Unit, Fargo, ND USA
| | - S S Xu
- USDA-ARS, Cereal Crops Research Unit, Fargo, ND USA
| | - M S Chen
- USDA-ARS, Hard Winter Wheat Genetics Research Unit, Kansas State University, Manhattan, KS, USA
| | - D Giron
- Institut de Recherche sur la Biologie de l'Insecte UMR 7261 CNRS/Université François-Rabelais de Tours, Tours, France
| | - J J Stuart
- Department of Entomology, Purdue University, West Lafayette, IN, USA
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9
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Avirulence effector discovery in a plant galling and plant parasitic arthropod, the Hessian fly (Mayetiola destructor). PLoS One 2014; 9:e100958. [PMID: 24964065 PMCID: PMC4071006 DOI: 10.1371/journal.pone.0100958] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Accepted: 06/02/2014] [Indexed: 12/29/2022] Open
Abstract
Highly specialized obligate plant-parasites exist within several groups of arthropods (insects and mites). Many of these are important pests, but the molecular basis of their parasitism and its evolution are poorly understood. One hypothesis is that plant parasitic arthropods use effector proteins to defeat basal plant immunity and modulate plant growth. Because avirulence (Avr) gene discovery is a reliable method of effector identification, we tested this hypothesis using high-resolution molecular genetic mapping of an Avr gene (vH13) in the Hessian fly (HF, Mayetiola destructor), an important gall midge pest of wheat (Triticum spp.). Chromosome walking resolved the position of vH13, and revealed alleles that determine whether HF larvae are virulent (survive) or avirulent (die) on wheat seedlings carrying the wheat H13 resistance gene. Association mapping found three independent insertions in vH13 that appear to be responsible for H13-virulence in field populations. We observed vH13 transcription in H13-avirulent larvae and the salivary glands of H13-avirulent larvae, but not in H13-virulent larvae. RNA-interference-knockdown of vH13 transcripts allowed some H13-avirulent larvae to escape H13-directed resistance. vH13 is the first Avr gene identified in an arthropod. It encodes a small modular protein with no sequence similarities to other proteins in GenBank. These data clearly support the hypothesis that an effector-based strategy has evolved in multiple lineages of plant parasites, including arthropods.
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Pauchet Y, Saski CA, Feltus FA, Luyten I, Quesneville H, Heckel DG. Studying the organization of genes encoding plant cell wall degrading enzymes in Chrysomela tremula provides insights into a leaf beetle genome. INSECT MOLECULAR BIOLOGY 2014; 23:286-300. [PMID: 24456018 DOI: 10.1111/imb.12081] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The ability of herbivorous beetles from the superfamilies Chrysomeloidea and Curculionoidea to degrade plant cell wall polysaccharides has only recently begun to be appreciated. The presence of plant cell wall degrading enzymes (PCWDEs) in the beetle's digestive tract makes this degradation possible. Sequences encoding these beetle-derived PCWDEs were originally identified from transcriptomes and strikingly resemble those of saprophytic and phytopathogenic microorganisms, raising questions about their origin; e.g. are they insect- or microorganism-derived? To demonstrate unambiguously that the genes encoding PCWDEs found in beetle transcriptomes are indeed of insect origin, we generated a bacterial artificial chromosome library from the genome of the leaf beetle Chrysomela tremula, containing 18 432 clones with an average size of 143 kb. After hybridizing this library with probes derived from 12 C. tremula PCWDE-encoding genes and sequencing the positive clones, we demonstrated that the latter genes are encoded by the insect's genome and are surrounded by genes possessing orthologues in the genome of Tribolium castaneum as well as in three other beetle genomes. Our analyses showed that although the level of overall synteny between C. tremula and T. castaneum seems high, the degree of microsynteny between both species is relatively low, in contrast to the more closely related Colorado potato beetle.
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Affiliation(s)
- Y Pauchet
- Entomology, Max Planck Institute for Chemical Ecology, Jena, Germany
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Abstract
Bacterial artificial chromosome (BAC) physical maps embedding a large number of BAC end sequences (BESs) were generated for Oryza sativa ssp. indica varieties Minghui 63 (MH63) and Zhenshan 97 (ZS97) and were compared with the genome sequences of O. sativa spp. japonica cv. Nipponbare and O. sativa ssp. indica cv. 93-11. The comparisons exhibited substantial diversities in terms of large structural variations and small substitutions and indels. Genome-wide BAC-sized and contig-sized structural variations were detected, and the shared variations were analyzed. In the expansion regions of the Nipponbare reference sequence, in comparison to the MH63 and ZS97 physical maps, as well as to the previously constructed 93-11 physical map, the amounts and types of the repeat contents, and the outputs of gene ontology analysis, were significantly different from those of the whole genome. Using the physical maps of four wild Oryza species from OMAP (http://www.omap.org) as a control, we detected many conserved and divergent regions related to the evolution process of O. sativa. Between the BESs of MH63 and ZS97 and the two reference sequences, a total of 1532 polymorphic simple sequence repeats (SSRs), 71,383 SNPs, 1767 multiple nucleotide polymorphisms, 6340 insertions, and 9137 deletions were identified. This study provides independent whole-genome resources for intra- and intersubspecies comparisons and functional genomics studies in O. sativa. Both the comparative physical maps and the GBrowse, which integrated the QTL and molecular markers from GRAMENE (http://www.gramene.org) with our physical maps and analysis results, are open to the public through our Web site (http://gresource.hzau.edu.cn/resource/resource.html).
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Wang X, Liu Q, Wang H, Luo CX, Wang G, Luo M. A BAC based physical map and genome survey of the rice false smut fungus Villosiclava virens. BMC Genomics 2013; 14:883. [PMID: 24341590 PMCID: PMC3878662 DOI: 10.1186/1471-2164-14-883] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2013] [Accepted: 12/04/2013] [Indexed: 01/08/2023] Open
Abstract
Background Rice false smut caused by Villosiclava virens is a devastating fungal disease that spreads in major rice-growing regions throughout the world. However, the genomic information for this fungal pathogen is limited and the pathogenic mechanism of this disease is still not clear. To facilitate genetic, molecular and genomic studies of this fungal pathogen, we constructed the first BAC-based physical map and performed the first genome survey for this species. Results High molecular weight genomic DNA was isolated from young mycelia of the Villosiclava virens strain UV-8b and a high-quality, large-insert and deep-coverage Bacterial Artificial Chromosome (BAC) library was constructed with the restriction enzyme HindIII. The BAC library consisted of 5,760 clones, which covers 22.7-fold of the UV-8b genome, with an average insert size of 140 kb and an empty clone rate of lower than 1%. BAC fingerprinting generated successful fingerprints for 2,290 BAC clones. Using the fingerprints, a whole genome-wide BAC physical map was constructed that contained 194 contigs (2,035 clones) spanning 51.2 Mb in physical length. Bidirectional-end sequencing of 4,512 BAC clones generated 6,560 high quality BAC end sequences (BESs), with a total length of 3,030,658 bp, representing 8.54% of the genome sequence. Analysis of the BESs revealed general genome information, including 51.52% GC content, 22.51% repetitive sequences, 376.12/Mb simple sequence repeat (SSR) density and approximately 36.01% coding regions. Sequence comparisons to other available fungal genome sequences through BESs showed high similarities to Metarhizium anisopliae, Trichoderma reesei, Nectria haematococca and Cordyceps militaris, which were generally in agreement with the 18S rRNA gene analysis results. Conclusion This study provides the first BAC-based physical map and genome information for the important rice fungal pathogen Villosiclava virens. The BAC clones, physical map and genome information will serve as fundamental resources to accelerate the genetic, molecular and genomic studies of this pathogen, including positional cloning, comparative genomic analysis and whole genome sequencing. The BAC library and physical map have been opened to researchers as public genomic resources (http://gresource.hzau.edu.cn/resource/resource.html).
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Affiliation(s)
| | | | | | | | | | - Meizhong Luo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, PR China.
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Stuart JJ, Chen MS, Shukle R, Harris MO. Gall midges (Hessian flies) as plant pathogens. ANNUAL REVIEW OF PHYTOPATHOLOGY 2012; 50:339-57. [PMID: 22656645 DOI: 10.1146/annurev-phyto-072910-095255] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Gall midges constitute an important group of plant-parasitic insects. The Hessian fly (HF; Mayetiola destructor), the most investigated gall midge, was the first insect hypothesized to have a gene-for-gene interaction with its host plant, wheat (Triticum spp.). Recent investigations support that hypothesis. The minute larval mandibles appear to act in a manner that is analogous to nematode stylets and the haustoria of filamentous plant pathogens. Putative effector proteins are encoded by hundreds of genes and expressed in the HF larval salivary gland. Cultivar-specific resistance (R) genes mediate a highly localized plant reaction that prevents the survival of avirulent HF larvae. Fine-scale mapping of HF avirulence (Avr) genes provides further evidence of effector-triggered immunity (ETI) against HF in wheat. Taken together, these discoveries suggest that the HF, and other gall midges, may be considered biotrophic, or hemibiotrophic, plant pathogens, and they demonstrate the potential that the wheat-HF interaction has in the study of insect-induced plant gall formation.
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Affiliation(s)
- Jeff J Stuart
- Department of Entomology, Purdue University, West Lafayette, Indiana 47907-2089, USA.
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Lin H, Xia P, A Wing R, Zhang Q, Luo M. Dynamic intra-japonica subspecies variation and resource application. MOLECULAR PLANT 2012; 5:218-30. [PMID: 21984334 DOI: 10.1093/mp/ssr085] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
We constructed a physical map of O. sativa ssp. japonica cv. ZH11 and compared it and its random sample sequences with the Nipponbare RefSeq derived from the same subspecies. This comparison showed that the two japonica genomes were highly syntenic but revealed substantial differences in terms of structural variations, rates of substitutions and indels, and transposable element content. For example, contractions/expansions as large as 450 kb and repeat sequences that were present in high copy numbers only in ZH11 were detected. In tri-alignment regions using the indica variety 93-11 sequence as an outgroup, we found that: (1) the substitution rates of the two japonica-indica inter-subspecies comparison combinations were close but almost a magnitude higher than the substitution rate between the japonica rice varieties ZH11 and Nipponbare; (2) of the substitutions found between ZH11 and Nipponbare, 47.2% occurred in ZH11 and 52.6% in Nipponbare; (3) of the indels found between ZH11 and Nipponbare, the indels that occurred in ZH11 were 15.8 times of those in Nipponbare. Of the indels that occurred in ZH11, 75.67% were insertions and 24.33% deletions. Of the indels that occurred in Nipponbare, 48.23% were insertions and 51.77% were deletions. The ZH11 comparative map covered four Nipponbare physical gaps, detected assembly errors in the Nipponbare sequence, and was integrated with the FSTs of a large ZH11 T-DNA insertion mutant library. ZH11 BAC clones can be browsed, searched, and obtained at our website, http://GResource.hzau.edu.cn.
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Affiliation(s)
- Haiyan Lin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
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Behura SK, Shukle RH, Stuart JJ. Assessment of structural variation and molecular mapping of insertion sites of Desmar-like elements in the Hessian fly genome. INSECT MOLECULAR BIOLOGY 2010; 19:707-715. [PMID: 20636348 DOI: 10.1111/j.1365-2583.2010.01028.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The Hessian fly (Mayetiola destructor) is an agriculturally important pest of wheat. A mariner element (Desmar1) has been previously identified in the Hessian fly genome. Using Desmar1 as a probe, we isolated individual copies of Desmar-like elements from the Hessian fly genome cloned in bacterial artificial chromosomes (BACs) and studied their structural variability and flanking DNA sequences. The partial Desmar-like copies are relatively more abundant (∼64%) than full length copies (∼36%) in the Hessian fly genome. Most of the full length copies are consistently flanked by an EcoRI restriction site that occurs 32 bp from one end and 66 bp from the other end of the mariner. Using an amplified fragment length polymorphism-PCR (AFLP-PCR) based method, we identified segregating polymorphisms associated with Desmar elements in a F₂ mapping population. We were able to use the segregation data to localize the chromosomal position of three Desmar elements by linkage analysis. As paternal chromosomes are eliminated in the Hessian fly during early embryogenesis, two-thirds of the AFLPs were expected to be polymorphic in the mapping population and this was observed for AFLPs anchored to full length Desmar copies but not to the partial copies. Thus, our data indicate that dead and partial Desmar-like copies are probably associated with less polymorphic regions and may represent mariner graveyards in the Hessian fly genome.
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Affiliation(s)
- S K Behura
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA.
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Construction and characterisation of a BAC library made from field specimens of the onchocerciasis vector Simulium squamosum (Diptera: Simuliidae). Genomics 2010; 96:251-7. [PMID: 20603211 DOI: 10.1016/j.ygeno.2010.06.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2010] [Revised: 06/25/2010] [Accepted: 06/28/2010] [Indexed: 12/21/2022]
Abstract
A Bacterial Artificial Chromosome (BAC) library was made from wild-caught Simulium squamosum, which is an important vector of human onchocerciasis. The library is composed of 12,288 BACs, with an average insert size of 128 kb, and is expected to contain ~1.54 GB of cloned DNA. Random BAC-end sequencing generated over 95 kb of DNA sequence data from which putative S. squamosum gene sequences and novel repetitive DNA families were identified, including DNA transposons, retrotransposons and simple sequence repeats (SSRs). The sequence survey also provided evidence of DNA of microbial origin, and dissection of sample blackflies indicated that some of those used to prepare the library were likely to be parasitized by the mermithid Isomermis lairdi. Hybridisations with a set of three independent blackfly single-copy genes and two Wolbachia genes suggest that the library provides around 13-fold coverage of the S. squamosum genome and about 12-fold coverage of its Wolbachia endosymbiont.
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Benatti TR, Valicente FH, Aggarwal R, Zhao C, Walling JG, Chen MS, Cambron SE, Schemerhorn BJ, Stuart JJ. A neo-sex chromosome that drives postzygotic sex determination in the hessian fly (Mayetiola destructor). Genetics 2010; 184:769-77. [PMID: 20026681 PMCID: PMC2845344 DOI: 10.1534/genetics.109.108589] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2009] [Accepted: 12/11/2009] [Indexed: 11/18/2022] Open
Abstract
Two nonoverlapping autosomal inversions defined unusual neo-sex chromosomes in the Hessian fly (Mayetiola destructor). Like other neo-sex chromosomes, these were normally heterozygous, present only in one sex, and suppressed recombination around a sex-determining master switch. Their unusual properties originated from the anomalous Hessian fly sex determination system in which postzygotic chromosome elimination is used to establish the sex-determining karyotypes. This system permitted the evolution of a master switch (Chromosome maintenance, Cm) that acts maternally. All of the offspring of females that carry Cm-associated neo-sex chromosomes attain a female-determining somatic karyotype and develop as females. Thus, the chromosomes act as maternal effect neo-W's, or W-prime (W') chromosomes, where ZW' females mate with ZZ males to engender female-producing (ZW') and male-producing (ZZ) females in equal numbers. Genetic mapping and physical mapping identified the inversions. Their distribution was determined in nine populations. Experimental matings established the association of the inversions with Cm and measured their recombination suppression. The inversions are the functional equivalent of the sciarid X-prime chromosomes. We speculate that W' chromosomes exist in a variety of species that produce unisexual broods.
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Affiliation(s)
- Thiago R. Benatti
- Department of Entomology, Purdue University, West Lafayette, Indiana 47907-2089, U.S. Department of Agriculture–Agricultural Research Service and Department of Entomology, Kansas State University, Manhattan, Kansas 66506 and U.S. Department of Agriculture–Agricultural Research Service and Department of Entomology, Purdue University, West Lafayette, Indiana 47907-2089
| | - Fernando H. Valicente
- Department of Entomology, Purdue University, West Lafayette, Indiana 47907-2089, U.S. Department of Agriculture–Agricultural Research Service and Department of Entomology, Kansas State University, Manhattan, Kansas 66506 and U.S. Department of Agriculture–Agricultural Research Service and Department of Entomology, Purdue University, West Lafayette, Indiana 47907-2089
| | - Rajat Aggarwal
- Department of Entomology, Purdue University, West Lafayette, Indiana 47907-2089, U.S. Department of Agriculture–Agricultural Research Service and Department of Entomology, Kansas State University, Manhattan, Kansas 66506 and U.S. Department of Agriculture–Agricultural Research Service and Department of Entomology, Purdue University, West Lafayette, Indiana 47907-2089
| | - Chaoyang Zhao
- Department of Entomology, Purdue University, West Lafayette, Indiana 47907-2089, U.S. Department of Agriculture–Agricultural Research Service and Department of Entomology, Kansas State University, Manhattan, Kansas 66506 and U.S. Department of Agriculture–Agricultural Research Service and Department of Entomology, Purdue University, West Lafayette, Indiana 47907-2089
| | - Jason G. Walling
- Department of Entomology, Purdue University, West Lafayette, Indiana 47907-2089, U.S. Department of Agriculture–Agricultural Research Service and Department of Entomology, Kansas State University, Manhattan, Kansas 66506 and U.S. Department of Agriculture–Agricultural Research Service and Department of Entomology, Purdue University, West Lafayette, Indiana 47907-2089
| | - Ming-Shun Chen
- Department of Entomology, Purdue University, West Lafayette, Indiana 47907-2089, U.S. Department of Agriculture–Agricultural Research Service and Department of Entomology, Kansas State University, Manhattan, Kansas 66506 and U.S. Department of Agriculture–Agricultural Research Service and Department of Entomology, Purdue University, West Lafayette, Indiana 47907-2089
| | - Sue E. Cambron
- Department of Entomology, Purdue University, West Lafayette, Indiana 47907-2089, U.S. Department of Agriculture–Agricultural Research Service and Department of Entomology, Kansas State University, Manhattan, Kansas 66506 and U.S. Department of Agriculture–Agricultural Research Service and Department of Entomology, Purdue University, West Lafayette, Indiana 47907-2089
| | - Brandon J. Schemerhorn
- Department of Entomology, Purdue University, West Lafayette, Indiana 47907-2089, U.S. Department of Agriculture–Agricultural Research Service and Department of Entomology, Kansas State University, Manhattan, Kansas 66506 and U.S. Department of Agriculture–Agricultural Research Service and Department of Entomology, Purdue University, West Lafayette, Indiana 47907-2089
| | - Jeffrey J. Stuart
- Department of Entomology, Purdue University, West Lafayette, Indiana 47907-2089, U.S. Department of Agriculture–Agricultural Research Service and Department of Entomology, Kansas State University, Manhattan, Kansas 66506 and U.S. Department of Agriculture–Agricultural Research Service and Department of Entomology, Purdue University, West Lafayette, Indiana 47907-2089
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