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Anand R, Divya D, Mazumdar-Leighton S, Bentur JS, Nair S. Expression Analysis Reveals Differentially Expressed Genes in BPH and WBPH Associated with Resistance in Rice RILs Derived from a Cross between RP2068 and TN1. Int J Mol Sci 2023; 24:13982. [PMID: 37762286 PMCID: PMC10531025 DOI: 10.3390/ijms241813982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 08/31/2023] [Accepted: 09/03/2023] [Indexed: 09/29/2023] Open
Abstract
BPH (brown planthopper) and WBPH (white backed planthopper) are significant rice pests that often co-occur as sympatric species and cause substantial yield loss. Despite their genetic similarities, different host-resistance genes confer resistance against these two hoppers. The defense mechanisms in rice against these pests are complex, and the molecular processes regulating their responses remain largely unknown. This study used specific recombinant inbred lines (RILs) derived from a cross between rice varieties RP2068-18-3-5 (BPH- and WBPH-resistant) and TN1 (BPH- and WBPH-susceptible) to investigate the mechanisms of interaction between these planthoppers and their rice hosts. WBPH and BPH were allowed to feed on specific RILs, and RNA-Seq was carried out on WBPH insects. Transcriptome profiling and qRT-PCR results revealed differential expression of genes involved in detoxification, digestion, transportation, cuticle formation, splicing, and RNA processing. A higher expression of sugar transporters was observed in both hoppers feeding on rice with resistance against either hopper. This is the first comparative analysis of gene expressions in these insects fed on genetically similar hosts but with differential resistance to BPH and WBPH. These results complement our earlier findings on the differential gene expression of the same RILs (BPH- or WBPH-infested) utilized in this study. Moreover, identifying insect genes and pathways responsible for countering host defense would augment our understanding of BPH and WBPH interaction with their rice hosts and enable us to develop lasting strategies to control these significant pests.
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Affiliation(s)
- Rashi Anand
- Plant-Insect Interaction Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India;
- Plant Biotic Interaction Lab, Department of Botany, University of Delhi, Delhi 110007, India;
| | - Dhanasekar Divya
- Agri Biotech Foundation, Rajendranagar, Hyderabad 500030, India; (D.D.); (J.S.B.)
| | | | - Jagadish S. Bentur
- Agri Biotech Foundation, Rajendranagar, Hyderabad 500030, India; (D.D.); (J.S.B.)
| | - Suresh Nair
- Plant-Insect Interaction Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India;
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Sun Z, Liu Y, Xu H, Yan C. Genome-Wide Identification of P450 Genes in Chironomid Propsilocerus akamusi Reveals Candidate Genes Involved in Gut Microbiota-Mediated Detoxification of Chlorpyrifos. INSECTS 2022; 13:insects13090765. [PMID: 36135466 PMCID: PMC9504602 DOI: 10.3390/insects13090765] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/15/2022] [Accepted: 08/20/2022] [Indexed: 06/10/2023]
Abstract
Chironomids commonly dominate macroinvertebrate assemblages in aquatic habitats and these non-biting midges are known for their ability to tolerate contaminants. Studies regarding the interplay between gut microbiota and host detoxification ability is currently a point of interest. Cytochrome P450s (P450s) are critical metabolic enzymes in which a subset is involved in xenobiotic detoxification. In this study, we first conducted an integrated global investigation of P450s based on the whole genomic sequence of Propsilocerus akamusi and retrieved a series of 64 P450 genes which were further classified into 4 clans and 25 families on the basis of phylogenetic relationships. With assistance of RNA-Seq and RT-qPCR validation, the expression profile of screened PaP450s in guts was compared between chlorpyrifos-challenged larvae with deficient gut microbiota (GD) and those with a conventional gut community (CV). An increasing prevalence of chlorpyrifos from sublethal to lethal dosages induced a greater mortality rate of individuals coupled with remarkable downregulation of 14 P450s in GD larval guts when compared to CV ones. Moreover, it turned out that the decreased level of PaCYP3998B1 and PaCYP3987D1 might imply impaired host endogenous detoxification capability potentiated by gut dysbiosis, reflected by a remarkably severe mortality in GD larvae treated with lethal chlorpyrifos. Collectively, our study unveiled candidate P450 genes that might be mediated by gut symbionts in chlorpyrifos-challenged P. akamusi larvae, possibly facilitating further understanding of the detoxified mechanism that chironomids might employ to alleviate poisonousness.
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Miao Z, Cao X, Jiang H. Digestion-related proteins in the tobacco hornworm, Manduca sexta. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2020; 126:103457. [PMID: 32860882 PMCID: PMC7554134 DOI: 10.1016/j.ibmb.2020.103457] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 07/26/2020] [Accepted: 08/19/2020] [Indexed: 06/11/2023]
Abstract
Food digestion is vital for the survival and prosperity of insects. Research on insect digestive enzymes yields knowledge of their structure and function, and potential targets of antifeedants to control agricultural pests. While such enzymes from pest species are more relevant for inhibitor screening, a systematic analysis of their counterparts in a model insect has broader impacts. In this context, we identified a set of 122 digestive enzyme genes from the genome of Manduca sexta, a lepidopteran model related to some major agricultural pests. These genes encode hydrolases of proteins (85), lipids (20), carbohydrates (16), and nucleic acids (1). Gut serine proteases (62) and their noncatalytic homologs (11) in the S1A subfamily are encoded by abundant transcripts whose levels correlate well with larval feeding stages. Aminopeptidases (10), carboxypeptidases (10), and other proteases (3) also participate in dietary protein digestion. A large group of 11 lipases as well as 9 esterases are probably responsible for digesting lipids in diets. The repertoire of carbohydrate hydrolases (16) is relatively small, including two amylases, three maltases, two sucrases, two α-glucosidases, and others. Lysozymes, peptidoglycan amidases, and β-1,3-glucanase may hydrolyze peptidoglycans and glucans to harvest energy and defend the host from microbes on plant leaves. One alkaline nuclease is associated with larval feeding, which is likely responsible for hydrolyzing denatured DNA and RNA undergoing autolysis at a high pH of midgut. Proteomic analysis of the ectoperitrophic fluid from feeding larvae validated at least 131 or 89% of the digestive enzymes and their homologs. In summary, this study provides for the first time a holistic view of the digestion-related proteins in a lepidopteran model insect and clues for comparative research in lepidopteran pests and beyond.
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Affiliation(s)
- Zelong Miao
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Xiaolong Cao
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Haobo Jiang
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK, 74078, USA.
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Cheng X, Garcés-Carrera S, Whitworth RJ, Fellers JP, Park Y, Chen MS. A Horizontal Gene Transfer Led to the Acquisition of a Fructan Metabolic Pathway in a Gall Midge. ACTA ACUST UNITED AC 2020; 4:e1900275. [PMID: 32293157 DOI: 10.1002/adbi.201900275] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 01/30/2020] [Indexed: 01/19/2023]
Abstract
Animals are thought to use only glucose polymers (glycogen) as energy reserve, whereas both glucose (starch) and fructose polymers (fructans) are used by microbes and plants. Here, it is reported that the gall midge Mayetiola destructor, and likely other herbivorous animal species, gained the ability to utilize dietary fructans directly as storage polysaccharides by a single horizontal gene transfer (HGT) of bacterial levanase/inulinase gene followed by gene expansion and differentiation. Multiple genes encoding levanases/inulinases have their origin in a single HGT event from a bacterium and they show high expression levels and enzymatic activities in different tissues of the gall midge, including nondigestive fat bodies and eggs, both of which contained significant amounts of fructans. This study provides evidence that animals can also use fructans as energy reserve by incorporating bacterial genes in their genomes.
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Affiliation(s)
- Xiaoyan Cheng
- Department of Entomology, Kansas State University, 123 Waters Hall, Manhattan, KS, 66506, USA
| | | | - Robert Jeff Whitworth
- Department of Entomology, Kansas State University, 123 Waters Hall, Manhattan, KS, 66506, USA
| | - John P Fellers
- Hard Winter Wheat Genetics Research Unit, Center for Grain and Animal Health Research Center, USDA-ARS, 4008 Throckmorton, Manhattan, KS, 66506, USA
| | - Yoonseong Park
- Department of Entomology, Kansas State University, 123 Waters Hall, Manhattan, KS, 66506, USA
| | - Ming-Shun Chen
- Department of Entomology, Kansas State University, 123 Waters Hall, Manhattan, KS, 66506, USA
- Hard Winter Wheat Genetics Research Unit, Center for Grain and Animal Health Research Center, USDA-ARS, 4008 Throckmorton, Manhattan, KS, 66506, USA
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Oppert B, Perkin L, Martynov AG, Elpidina EN. Cross-species comparison of the gut: Differential gene expression sheds light on biological differences in closely related tenebrionids. JOURNAL OF INSECT PHYSIOLOGY 2018; 106:114-124. [PMID: 28359776 DOI: 10.1016/j.jinsphys.2017.03.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 03/24/2017] [Accepted: 03/24/2017] [Indexed: 06/07/2023]
Abstract
The gut is one of the primary interfaces between an insect and its environment. Understanding gene expression profiles in the insect gut can provide insight into interactions with the environment as well as identify potential control methods for pests. We compared the expression profiles of transcripts from the gut of larval stages of two coleopteran insects, Tenebrio molitor and Tribolium castaneum. These tenebrionids have different life cycles, varying in the duration and number of larval instars. T. castaneum has a sequenced genome and has been a model for coleopterans, and we recently obtained a draft genome for T. molitor. We assembled gut transcriptome reads from each insect to their respective genomes and filtered mapped reads to RPKM>1, yielding 11,521 and 17,871 genes in the T. castaneum and T. molitor datasets, respectively. There were identical GO terms in each dataset, and enrichment analyses also identified shared GO terms. From these datasets, we compiled an ortholog list of 6907 genes; 45% of the total assembled reads from T. castaneum were found in the top 25 orthologs, but only 27% of assembled reads were found in the top 25 T. molitor orthologs. There were 2281 genes unique to T. castaneum, and 2088 predicted genes unique to T. molitor, although improvements to the T. molitor genome will likely reduce these numbers as more orthologs are identified. We highlight a few unique genes in T. castaneum or T. molitor that may relate to distinct biological functions. A large number of putative genes expressed in the larval gut with uncharacterized functions (36 and 68% from T. castaneum and T. molitor, respectively) support the need for further research. These data are the first step in building a comprehensive understanding of the physiology of the gut in tenebrionid insects, illustrating commonalities and differences that may be related to speciation and environmental adaptation.
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Affiliation(s)
- Brenda Oppert
- USDA Agricultural Research Service, Center for Grain and Animal Health Research, Manhattan, KS 66502, USA.
| | - Lindsey Perkin
- USDA Agricultural Research Service, Center for Grain and Animal Health Research, Manhattan, KS 66502, USA
| | - Alexander G Martynov
- Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow 143026, Russia
| | - Elena N Elpidina
- A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119991, Russia
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Oates CN, Denby KJ, Myburg AA, Slippers B, Naidoo S. Insect Gallers and Their Plant Hosts: From Omics Data to Systems Biology. Int J Mol Sci 2016; 17:E1891. [PMID: 27869732 PMCID: PMC5133890 DOI: 10.3390/ijms17111891] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Revised: 10/28/2016] [Accepted: 11/04/2016] [Indexed: 12/30/2022] Open
Abstract
Gall-inducing insects are capable of exerting a high level of control over their hosts' cellular machinery to the extent that the plant's development, metabolism, chemistry, and physiology are all altered in favour of the insect. Many gallers are devastating pests in global agriculture and the limited understanding of their relationship with their hosts prevents the development of robust management strategies. Omics technologies are proving to be important tools in elucidating the mechanisms involved in the interaction as they facilitate analysis of plant hosts and insect effectors for which little or no prior knowledge exists. In this review, we examine the mechanisms behind insect gall development using evidence from omics-level approaches. The secretion of effector proteins and induced phytohormonal imbalances are highlighted as likely mechanisms involved in gall development. However, understanding how these components function within the system is far from complete and a number of questions need to be answered before this information can be used in the development of strategies to engineer or breed plants with enhanced resistance.
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Affiliation(s)
- Caryn N Oates
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Private Bag x20, Pretoria 0028, South Africa.
| | - Katherine J Denby
- Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK.
| | - Alexander A Myburg
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Private Bag x20, Pretoria 0028, South Africa.
| | - Bernard Slippers
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Private Bag x20, Pretoria 0028, South Africa.
| | - Sanushka Naidoo
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Private Bag x20, Pretoria 0028, South Africa.
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Martinez M, Santamaria ME, Diaz-Mendoza M, Arnaiz A, Carrillo L, Ortego F, Diaz I. Phytocystatins: Defense Proteins against Phytophagous Insects and Acari. Int J Mol Sci 2016; 17:E1747. [PMID: 27775606 PMCID: PMC5085774 DOI: 10.3390/ijms17101747] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 10/11/2016] [Accepted: 10/12/2016] [Indexed: 01/31/2023] Open
Abstract
This review deals with phytocystatins, focussing on their potential role as defence proteins against phytophagous arthropods. Information about the evolutionary, molecular and biochemical features and inhibitory properties of phytocystatins are presented. Cystatin ability to inhibit heterologous cysteine protease activities is commented on as well as some approaches of tailoring cystatin specificity to enhance their defence function towards pests. A general landscape on the digestive proteases of phytophagous insects and acari and the remarkable plasticity of their digestive physiology after feeding on cystatins are highlighted. Biotechnological approaches to produce recombinant cystatins to be added to artificial diets or to be sprayed as insecticide-acaricide compounds and the of use cystatins as transgenes are discussed. Multiple examples and applications are included to end with some conclusions and future perspectives.
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Affiliation(s)
- Manuel Martinez
- Centro de Biotecnologia y Genomica de Plantas, Universidad Politecnica de Madrid (UPM), Instituto Nacional de Investigacion y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo, Pozuelo de Alarcon, Madrid 28223, Spain.
| | - Maria Estrella Santamaria
- Centro de Biotecnologia y Genomica de Plantas, Universidad Politecnica de Madrid (UPM), Instituto Nacional de Investigacion y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo, Pozuelo de Alarcon, Madrid 28223, Spain.
| | - Mercedes Diaz-Mendoza
- Centro de Biotecnologia y Genomica de Plantas, Universidad Politecnica de Madrid (UPM), Instituto Nacional de Investigacion y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo, Pozuelo de Alarcon, Madrid 28223, Spain.
| | - Ana Arnaiz
- Centro de Biotecnologia y Genomica de Plantas, Universidad Politecnica de Madrid (UPM), Instituto Nacional de Investigacion y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo, Pozuelo de Alarcon, Madrid 28223, Spain.
| | - Laura Carrillo
- Centro de Biotecnologia y Genomica de Plantas, Universidad Politecnica de Madrid (UPM), Instituto Nacional de Investigacion y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo, Pozuelo de Alarcon, Madrid 28223, Spain.
| | - Felix Ortego
- Departamento de Biologia Medioambiental, Centro de Investigaciones Biologicas, CSIC, Ramiro de Maeztu, 9, Madrid 28040, Spain.
| | - Isabel Diaz
- Centro de Biotecnologia y Genomica de Plantas, Universidad Politecnica de Madrid (UPM), Instituto Nacional de Investigacion y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo, Pozuelo de Alarcon, Madrid 28223, Spain.
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Thorpe P, Cock PJA, Bos J. Comparative transcriptomics and proteomics of three different aphid species identifies core and diverse effector sets. BMC Genomics 2016; 17:172. [PMID: 26935069 PMCID: PMC4776380 DOI: 10.1186/s12864-016-2496-6] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 02/17/2016] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Aphids are phloem-feeding insects that cause significant economic losses to agriculture worldwide. While feeding and probing these insects deliver molecules, called effectors, inside their host to enable infestation. The identification and characterization of these effectors from different species that vary in their host range is an important step in understanding the infestation success of aphids and aphid host range variation. This study employs a multi-disciplinary approach based on transcriptome sequencing and proteomics to identify and compare effector candidates from the broad host range aphid Myzus persicae (green peach aphid) (genotypes O, J and F), and narrow host range aphids Myzus cerasi (black cherry aphid) and Rhopalosiphum padi (bird-cherry oat aphid). RESULTS Using a combination of aphid transcriptome sequencing on libraries derived from head versus body tissues as well as saliva proteomics we were able to predict candidate effectors repertoires from the different aphid species and genotypes. Among the identified conserved or core effector sets, we identified a significant number of previously identified aphid candidate effectors indicating these proteins may be involved in general infestation strategies. Moreover, we identified aphid candidate effector sequences that were specific to one species, which are interesting candidates for further validation and characterization with regards to species-specific functions during infestation. We assessed our candidate effector repertoires for evidence of positive selection, and identified 49 candidates with DN/DS ratios >1. We noted higher rates of DN/DS ratios in predicted aphid effectors than non-effectors. Whether this reflects positive selection due to co-evolution with host plants, or increased neofunctionalization upon gene duplication remains to be investigated. CONCLUSION Our work provides a comprehensive overview of the candidate effector repertoires from three different aphid species with varying host ranges. Comparative analyses revealed candidate effectors that are most likely are involved in general aspects of infestation, whereas others, that are highly divergent, may be involved in specific processes important for certain aphid species. Insights into the overlap and differences in aphid effector repertoires are important in understanding how different species successfully infest different ranges of plant species.
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Affiliation(s)
- Peter Thorpe
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
- Dundee Effector Consortium, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Peter J A Cock
- Information and Computational Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
- Dundee Effector Consortium, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Jorunn Bos
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK.
- Dundee Effector Consortium, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK.
- College of Life Sciences, University of Dundee, Dundee, UK.
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Abstract
Plant protease inhibitors (PIs) are natural plant defense proteins that inhibit proteases of invading insect herbivores. However, their anti-insect efficacy is determined not only by their potency toward a vulnerable insect system but also by the response of the insect to such a challenge. Through the long history of coevolution with their host plants, insects have developed sophisticated mechanisms to circumvent antinutritional effects of dietary challenges. Their response takes the form of changes in gene expression and the protein repertoire in cells lining the alimentary tract, the first line of defense. Research in insect digestive proteases has revealed the crucial roles they play in insect adaptation to plant PIs and has brought about a new appreciation of how phytophagous insects employ this group of molecules in both protein digestion and counterdefense. This review provides researchers in related fields an up-to-date summary of recent advances.
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Nandety RS, Kuo YW, Nouri S, Falk BW. Emerging strategies for RNA interference (RNAi) applications in insects. Bioengineered 2014; 6:8-19. [PMID: 25424593 PMCID: PMC4601220 DOI: 10.4161/21655979.2014.979701] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Revised: 09/29/2014] [Accepted: 10/14/2014] [Indexed: 11/19/2022] Open
Abstract
RNA interference (RNAi) in insects is a gene regulatory process that also plays a vital role in the maintenance and in the regulation of host defenses against invading viruses. Small RNAs determine the specificity of the RNAi through precise recognition of their targets. These small RNAs in insects comprise small interfering RNAs (siRNAs), micro RNAs (miRNAs) and Piwi interacting RNAs (piRNAs) of various lengths. In this review, we have explored different forms of the RNAi inducers that are presently in use, and their applications for an effective and efficient fundamental and practical RNAi research with insects. Further, we reviewed trends in next generation sequencing (NGS) technologies and their importance for insect RNAi, including the identification of novel insect targets as well as insect viruses. Here we also describe a rapidly emerging trend of using plant viruses to deliver the RNAi inducer molecules into insects for an efficient RNAi response.
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Affiliation(s)
| | - Yen-Wen Kuo
- Department of Plant Pathology; University of California; Davis, CA USA
| | - Shahideh Nouri
- Department of Plant Pathology; University of California; Davis, CA USA
| | - Bryce W Falk
- Department of Plant Pathology; University of California; Davis, CA USA
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Sequencing, De Novo assembly and annotation of the Colorado Potato Beetle, Leptinotarsa decemlineata, Transcriptome. PLoS One 2014; 9:e86012. [PMID: 24465841 PMCID: PMC3900453 DOI: 10.1371/journal.pone.0086012] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2012] [Accepted: 12/09/2013] [Indexed: 12/18/2022] Open
Abstract
Background The Colorado potato beetle (Leptinotarsa decemlineata) is a major pest and a serious threat to potato cultivation throughout the northern hemisphere. Despite its high importance for invasion biology, phenology and pest management, little is known about L. decemlineata from a genomic perspective. We subjected European L. decemlineata adult and larval transcriptome samples to 454-FLX massively-parallel DNA sequencing to characterize a basal set of genes from this species. We created a combined assembly of the adult and larval datasets including the publicly available midgut larval Roche 454 reads and provided basic annotation. We were particularly interested in diapause-specific genes and genes involved in pesticide and Bacillus thuringiensis (Bt) resistance. Results Using 454-FLX pyrosequencing, we obtained a total of 898,048 reads which, together with the publicly available 804,056 midgut larval reads, were assembled into 121,912 contigs. We established a repository of genes of interest, with 101 out of the 108 diapause-specific genes described in Drosophila montana; and 621 contigs involved in insecticide resistance, including 221 CYP450, 45 GSTs, 13 catalases, 15 superoxide dismutases, 22 glutathione peroxidases, 194 esterases, 3 ADAM metalloproteases, 10 cadherins and 98 calmodulins. We found 460 putative miRNAs and we predicted a significant number of single nucleotide polymorphisms (29,205) and microsatellite loci (17,284). Conclusions This report of the assembly and annotation of the transcriptome of L. decemlineata offers new insights into diapause-associated and insecticide-resistance-associated genes in this species and provides a foundation for comparative studies with other species of insects. The data will also open new avenues for researchers using L. decemlineata as a model species, and for pest management research. Our results provide the basis for performing future gene expression and functional analysis in L. decemlineata and improve our understanding of the biology of this invasive species at the molecular level.
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Nandety RS, Kamita SG, Hammock BD, Falk BW. Sequencing and de novo assembly of the transcriptome of the glassy-winged sharpshooter (Homalodisca vitripennis). PLoS One 2013; 8:e81681. [PMID: 24339955 PMCID: PMC3858241 DOI: 10.1371/journal.pone.0081681] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Accepted: 10/15/2013] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND The glassy-winged sharpshooter Homalodisca vitripennis (Hemiptera: Cicadellidae), is a xylem-feeding leafhopper and important vector of the bacterium Xylella fastidiosa; the causal agent of Pierce's disease of grapevines. The functional complexity of the transcriptome of H. vitripennis has not been elucidated thus far. It is a necessary blueprint for an understanding of the development of H. vitripennis and for designing efficient biorational control strategies including those based on RNA interference. RESULTS Here we elucidate and explore the transcriptome of adult H. vitripennis using high-throughput paired end deep sequencing and de novo assembly. A total of 32,803,656 paired-end reads were obtained with an average transcript length of 624 nucleotides. We assembled 32.9 Mb of the transcriptome of H. vitripennis that spanned across 47,265 loci and 52,708 transcripts. Comparison of our non-redundant database showed that 45% of the deduced proteins of H. vitripennis exhibit identity (e-value ≤1(-5)) with known proteins. We assigned Gene Ontology (GO) terms, Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations, and potential Pfam domains to each transcript isoform. In order to gain insight into the molecular basis of key regulatory genes of H. vitripennis, we characterized predicted proteins involved in the metabolism of juvenile hormone, and biogenesis of small RNAs (Dicer and Piwi sequences) from the transcriptomic sequences. Analysis of transposable element sequences of H. vitripennis indicated that the genome is less expanded in comparison to many other insects with approximately 1% of the transcriptome carrying transposable elements. CONCLUSIONS Our data significantly enhance the molecular resources available for future study and control of this economically important hemipteran. This transcriptional information not only provides a more nuanced understanding of the underlying biological and physiological mechanisms that govern H. vitripennis, but may also lead to the identification of novel targets for biorationally designed control strategies.
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Affiliation(s)
- Raja Sekhar Nandety
- Department of Plant Pathology, University of California Davis, Davis, California, United States of America
| | - Shizuo G. Kamita
- Department of Entomology and UC Davis Comprehensive Cancer Research Center, University of California Davis, Davis, California, United States of America
| | - Bruce D. Hammock
- Department of Entomology and UC Davis Comprehensive Cancer Research Center, University of California Davis, Davis, California, United States of America
| | - Bryce W. Falk
- Department of Plant Pathology, University of California Davis, Davis, California, United States of America
- * E-mail:
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Chen H, Zhu YC, Whitworth RJ, Reese JC, Chen MS. Serine and cysteine protease-like genes in the genome of a gall midge and their interactions with host plant genotypes. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2013; 43:701-711. [PMID: 23727407 DOI: 10.1016/j.ibmb.2013.05.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Revised: 05/03/2013] [Accepted: 05/21/2013] [Indexed: 06/02/2023]
Abstract
Proteases play important roles in a wide range of physiological processes in organisms. For plant-feeding insects, digestive proteases are targets for engineering protease inhibitors for pest control. In this study, we identified 105 putative serine- and cysteine-protease genes from the genome of the gall midge Mayetiola destructor (commonly known as Hessian fly), a destructive pest of wheat. Among the genes, 31 encode putative trypsins, 18 encode putative chymotrypsins, seven encode putative cysteine proteases, and the remaining may encode either other proteases or protease homologues. Developmental stage- and tissue-specific expression profiles of the genes encoding putative trypsins, chymotrypsins, and cysteine proteases were determined by quantitative reverse-transcription PCR. Comparative analyses of stage- and tissue-specific expression patterns suggested that several genes are likely to encode digestive proteases in the M. destructor larval gut, including genes encoding putative trypsins MDP3, MDP5, MDP9, MDP24, MDP48, MDP51, MDP57, MDP61, MDP71, and MDP90; genes encoding putative chymotrypsins MDP1, MDP7, MDP8, MDP18, MDP19, and MDP20; and genes encoding putative cysteine proteases MDP95 and MDP104. The expression of some protease genes was affected by plant genotypes. Genes encoding trypsins MDP3, MDP9, and MPD23, chymotrypsins MDP20 and MDP21, and cysteine proteases MDP99 and MDP104 were upregulated in M. destructor larvae feeding in resistant plants, whereas genes encoding trypsins MDP12, MDP24, and MDP33, and chymotrypsins mdp8, mdp15, and mdp16 were downregulated in M. destructor larvae feeding in resistant plants. This study provides a foundation for further comparative studies on proteases in different insects, and further characterization of M. destructor digestive proteases and their interactions with host plants, as well as potential targets for transgenic wheat plants.
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Affiliation(s)
- Hang Chen
- Department of Entomology, Kansas State University, Manhattan, KS 66506, USA
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Strelec I, Šarkanj B, Mrša V, Ugarčić-Hardi Ž. Chemical Composition, Quality Parameters, Exopeptidase and Oxidoreductase Activity Changes During Temporal Development of Wheat Grain Infestation by Sitophilus granarius. J Food Biochem 2013. [DOI: 10.1111/jfbc.12036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- I. Strelec
- Faculty of Food Technology; University of Osijek; Franje Kuhača 20 31000 Osijek Croatia
| | - B. Šarkanj
- Faculty of Food Technology; University of Osijek; Franje Kuhača 20 31000 Osijek Croatia
| | - V. Mrša
- Faculty of Food Technology and Biotechnology; Pierrotti Street 6 10000 Zagreb Croatia
| | - Ž. Ugarčić-Hardi
- Faculty of Food Technology; University of Osijek; Franje Kuhača 20 31000 Osijek Croatia
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Sinha DK, Nagaraju J, Tomar A, Bentur JS, Nair S. Pyrosequencing-based transcriptome analysis of the asian rice gall midge reveals differential response during compatible and incompatible interaction. Int J Mol Sci 2012; 13:13079-103. [PMID: 23202939 PMCID: PMC3497313 DOI: 10.3390/ijms131013079] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Revised: 09/14/2012] [Accepted: 09/27/2012] [Indexed: 01/21/2023] Open
Abstract
The Asian rice gall midge (Orseolia oryzae) is a major pest responsible for immense loss in rice productivity. Currently, very little knowledge exists with regard to this insect at the molecular level. The present study was initiated with the aim of developing molecular resources as well as identifying alterations at the transcriptome level in the gall midge maggots that are in a compatible (SH) or in an incompatible interaction (RH) with their rice host. Roche 454 pyrosequencing strategy was used to develop both transcriptomics and genomics resources that led to the identification of 79,028 and 85,395 EST sequences from gall midge biotype 4 (GMB4) maggots feeding on a susceptible and resistant rice variety, TN1 (SH) and Suraksha (RH), respectively. Comparative transcriptome analysis of the maggots in SH and RH revealed over-representation of transcripts from proteolysis and protein phosphorylation in maggots from RH. In contrast, over-representation of transcripts for translation, regulation of transcription and transcripts involved in electron transport chain were observed in maggots from SH. This investigation, besides unveiling various mechanisms underlying insect-plant interactions, will also lead to a better understanding of strategies adopted by insects in general, and the Asian rice gall midge in particular, to overcome host defense.
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Affiliation(s)
- Deepak Kumar Sinha
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India; E-Mail:
| | - Javaregowda Nagaraju
- Laboratory of Molecular Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad 500001, India; E-Mail:
| | - Archana Tomar
- Laboratory of Molecular Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad 500001, India; E-Mail:
| | | | - Suresh Nair
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India; E-Mail:
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Santamaría ME, Hernández-Crespo P, Ortego F, Grbic V, Grbic M, Diaz I, Martinez M. Cysteine peptidases and their inhibitors in Tetranychus urticae: a comparative genomic approach. BMC Genomics 2012; 13:307. [PMID: 22784002 PMCID: PMC3407033 DOI: 10.1186/1471-2164-13-307] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2012] [Accepted: 07/11/2012] [Indexed: 11/28/2022] Open
Abstract
Background Cysteine peptidases in the two-spotted spider mite Tetranychus urticae are involved in essential physiological processes, including proteolytic digestion. Cystatins and thyropins are inhibitors of cysteine peptidases that modulate their activity, although their function in this species has yet to be investigated. Comparative genomic analyses are powerful tools to obtain advanced knowledge into the presence and evolution of both, peptidases and their inhibitors, and could aid to elucidate issues concerning the function of these proteins. Results We have performed a genomic comparative analysis of cysteine peptidases and their inhibitors in T. urticae and representative species of different arthropod taxonomic groups. The results indicate: i) clade-specific proliferations are common to C1A papain-like peptidases and for the I25B cystatin family of inhibitors, whereas the C1A inhibitors thyropins are evolutionarily more conserved among arthropod clades; ii) an unprecedented extensive expansion for C13 legumain-like peptidases is found in T. urticae; iii) a sequence-structure analysis of the spider mite cystatins suggests that diversification may be related to an expansion of their inhibitory range; and iv) an in silico transcriptomic analysis shows that most cathepsin B and L cysteine peptidases, legumains and several members of the cystatin family are expressed at a higher rate in T. urticae feeding stages than in embryos. Conclusion Comparative genomics has provided valuable insights on the spider mite cysteine peptidases and their inhibitors. Mite-specific proliferations of C1A and C13 peptidase and I25 cystatin families and their over-expression in feeding stages of mites fit with a putative role in mite’s feeding and could have a key role in its broad host feeding range.
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Affiliation(s)
- María Estrella Santamaría
- Department of Biology WSC 339/341, The University of Western Ontario, 1151 Richmond St, London, ON N6A 5B7, Canada
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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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Sinha DK, Bentur JS, Nair S. Compatible interaction with its rice host leads to enhanced expression of the gamma subunit of oligosaccharyl transferase in the Asian rice gall midge, Orseolia oryzae. INSECT MOLECULAR BIOLOGY 2011; 20:567-575. [PMID: 21668550 DOI: 10.1111/j.1365-2583.2011.01085.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The Asian rice gall midge, Orseolia oryzae, is a fast evolving, damaging pest of rice. Understanding the underlying molecular mechanism of interaction between the gall midge and rice will help in devising strategies to control and manage the pest. The present study aims to identify rice-responsive genes in the gall midge that aid pest survival. The abundance of transcripts coding for enzymes related to glycosylation, in a cDNA library prepared from maggots of the rice gall midge feeding on susceptible hosts, indicated their probable involvement in the gall midge-rice interaction. Hence, a full-length transcript for a gamma subunit of the oligosaccharyl transferase gene (OoOST) from the gall midge was cloned and characterized. It has 72% similarity to its orthologue cloned from Aedes aegypti. Tissue-specific analysis of the expression of OoOST revealed an increase (> sevenfold) in the transcripts of the gene in the salivary glands of maggots in susceptible plants when compared with the transcript level in the salivary glands of maggots feeding on resistant hosts. Using quantitative PCR, performed on different developmental stages of the maggots in two susceptible and two resistant hosts, we observed similar expression patterns (i.e. overexpression in the compatible interaction). These results indicate the involvement of OoOST in maggot survival and establishment in the susceptible host. In order to identify polymorphism in the gene, OoOST was cloned from three gall midge biotypes GMB1, GMB4 and GMB4M.
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Affiliation(s)
- D K Sinha
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
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Serine proteases-like genes in the asian rice gall midge show differential expression in compatible and incompatible interactions with rice. Int J Mol Sci 2011; 12:2842-52. [PMID: 21686154 PMCID: PMC3116160 DOI: 10.3390/ijms12052842] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2011] [Revised: 03/21/2011] [Accepted: 04/12/2011] [Indexed: 11/24/2022] Open
Abstract
The Asian rice gall midge, Orseolia oryzae (Wood-Mason), is a serious pest of rice. Investigations into the gall midge-rice interaction will unveil the underlying molecular mechanisms which, in turn, can be used as a tool to assist in developing suitable integrated pest management strategies. The insect gut is known to be involved in various physiological and biological processes including digestion, detoxification and interaction with the host. We have cloned and identified two genes, OoprotI and OoprotII, homologous to serine proteases with the conserved His87, Asp136 and Ser241 residues. OoProtI shared 52.26% identity with mosquito-type trypsin from Hessian fly whereas OoProtII showed 52.49% identity to complement component activated C1s from the Hessian fly. Quantitative real time PCR analysis revealed that both the genes were significantly upregulated in larvae feeding on resistant cultivar than in those feeding on susceptible cultivar. These results provide an opportunity to understand the gut physiology of the insect under compatible or incompatible interactions with the host. Phylogenetic analysis grouped these genes in the clade containing proteases of phytophagous insects away from hematophagous insects.
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