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Sharma M, Akhter Y, Chatterjee S. A review on remediation of cyanide containing industrial wastes using biological systems with special reference to enzymatic degradation. World J Microbiol Biotechnol 2019; 35:70. [DOI: 10.1007/s11274-019-2643-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 04/08/2019] [Indexed: 11/24/2022]
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Rauwane ME, Odeny DA, Millar I, Rey C, Rees J. The early transcriptome response of cassava (Manihot esculenta Crantz) to mealybug (Phenacoccus manihoti) feeding. PLoS One 2018; 13:e0202541. [PMID: 30133510 PMCID: PMC6105004 DOI: 10.1371/journal.pone.0202541] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 08/06/2018] [Indexed: 11/18/2022] Open
Abstract
The mealybug, Phenacoccus manihoti, is a leading pest of cassava (Manihot esculenta Crantz), damaging this crop globally. Although the biological control of this mealybug using natural predators has been established, resistance breeding remains an important means of control. Understanding plant responses to insect herbivory, by determining and identifying differentially expressed genes (DEGs), is a vital step towards the understanding of molecular mechanisms of defence responses in plants and the development of resistant cultivars by gene editing. Morphological and molecular analysis confirmed the mealybug identity as Phenacoccus manihoti (Matile-Ferrero). The transcriptome response of the green mite resistant cassava genotype AR23.1 was compared to P40/1 with no known resistance at 24 and 72 hours of mealybug infestation compared to non-infested mock. A total of 301 and 206 genes were differentially expressed at 24 and 72 of mealybug infestation for AR23.1 and P40/1 genotypes respectively, using a log2 fold change and P-value ≤ 0.05. Gene ontology functional classification revealed an enrichment of genes in the secondary metabolic process category in AR23.1 in comparison with P40/1, while genes in the regulation of molecular function, cellular component biogenesis and electron carrier categories were more significantly enriched in P40/1 than in AR23.1. Biological pathway analysis, based on KEGG, revealed a significant enrichment of plant-pathogen interaction and plant hormonal signal transduction pathways for a cohort of up-regulated and down-regulated DEGs in both genotypes. Defence-related genes such as 2-oxogluterate, gibberellin oxidase and terpene synthase proteins were only induced in genotype AR23.1 and not in P40/1, and subsequently validated by RT-qPCR. The study revealed a difference in response to mealybug infestation in the two genotypes studied, with AR23.1 showing a higher number of differentially expressed transcripts post mealybug infestation at 24 and 72 hours. Candidate defence-related genes that were overexpressed in the AR23.1 genotype post mealybug infestation will be useful in future functional studies towards the control of mealybugs.
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Affiliation(s)
- Molemi E. Rauwane
- Biotechnology Platform, Agricultural Research Council, Onderstepoort, South Africa
- University of the Witwatersrand, Johannesburg, South Africa
| | | | - Ian Millar
- Biosystematics Division, Plant Protection Research Institute, Agricultural Research Council, Queenswood, Pretoria, South Africa
| | - Chrissie Rey
- University of the Witwatersrand, Johannesburg, South Africa
| | - Jasper Rees
- Biotechnology Platform, Agricultural Research Council, Onderstepoort, South Africa
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Evolution of the Biosynthetic Pathway for Cyanogenic Glucosides in Lepidoptera. J Mol Evol 2018; 86:379-394. [DOI: 10.1007/s00239-018-9854-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 06/27/2018] [Indexed: 10/28/2022]
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4
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Briolat ES, Zagrobelny M, Olsen CE, Blount JD, Stevens M. Sex differences but no evidence of quantitative honesty in the warning signals of six-spot burnet moths (Zygaena filipendulae L.). Evolution 2018; 72:1460-1474. [PMID: 29767461 PMCID: PMC6099377 DOI: 10.1111/evo.13505] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 04/22/2018] [Accepted: 05/05/2018] [Indexed: 11/29/2022]
Abstract
The distinctive black and red wing pattern of six-spot burnet moths (Zygaena filipendulae, L.) is a classic example of aposematism, advertising their potent cyanide-based defences. While such warning signals provide a qualitatively honest signal of unprofitability, the evidence for quantitative honesty, whereby variation in visual traits could provide accurate estimates of individual toxicity, is more equivocal. Combining measures of cyanogenic glucoside content and wing color from the perspective of avian predators, we investigate the relationship between coloration and defences in Z. filipendulae, to test signal honesty both within and across populations. There were no significant relationships between mean cyanogenic glucoside concentration and metrics of wing coloration across populations in males, yet in females higher cyanogenic glucoside levels were associated with smaller and lighter red forewing markings. Trends within populations were similarly inconsistent with quantitative honesty, and persistent differences between the sexes were apparent: larger females, carrying a greater total cyanogenic glucoside load, displayed larger but less conspicuous markings than smaller males, according to several color metrics. The overall high aversiveness of cyanogenic glucosides and fluctuations in color and toxin levels during an individual's lifetime may contribute to these results, highlighting generally important reasons why signal honesty should not always be expected in aposematic species.
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Affiliation(s)
- Emmanuelle Sophie Briolat
- Centre for Ecology and Conservation, College of Life and Environmental SciencesUniversity of ExeterPenrynCornwall TR10 9FEUnited Kingdom
| | - Mika Zagrobelny
- Plant Biochemistry Laboratory and Copenhagen Plant Science CentreDepartment of Plant and Environmental SciencesUniversity of Copenhagen40 Thorvaldsensvej, DK‐1871 Frederiksberg CCopenhagenDenmark
| | - Carl Erik Olsen
- Plant Biochemistry Laboratory and Copenhagen Plant Science CentreDepartment of Plant and Environmental SciencesUniversity of Copenhagen40 Thorvaldsensvej, DK‐1871 Frederiksberg CCopenhagenDenmark
| | - Jonathan D. Blount
- Centre for Ecology and Conservation, College of Life and Environmental SciencesUniversity of ExeterPenrynCornwall TR10 9FEUnited Kingdom
| | - Martin Stevens
- Centre for Ecology and Conservation, College of Life and Environmental SciencesUniversity of ExeterPenrynCornwall TR10 9FEUnited Kingdom
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Abstract
Honeybees (Apis mellifera) pollinate flowers and collect nectar from many important crops. White clover (Trifolium repens) is widely grown as a temperate forage crop, and requires honeybee pollination for seed set. In this study, using a quantitative LC-MS (Liquid Chromatography-Mass Spectrometry) assay, we show that the cyanogenic glucosides linamarin and lotaustralin are present in the leaves, sepals, petals, anthers, and nectar of T. repens. Cyanogenic glucosides are generally thought to be defense compounds, releasing toxic hydrogen cyanide upon degradation. However, increasing evidence indicates that plant secondary metabolites found in nectar may protect pollinators from disease or predators. In a laboratory survival study with chronic feeding of secondary metabolites, we show that honeybees can ingest the cyanogenic glucosides linamarin and amygdalin at naturally occurring concentrations with no ill effects, even though they have enzyme activity towards degradation of cyanogenic glucosides. This suggests that honeybees can ingest and tolerate cyanogenic glucosides from flower nectar. Honeybees retain only a portion of ingested cyanogenic glucosides. Whether they detoxify the rest using rhodanese or deposit them in the hive should be the focus of further research.
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Abstract
Cyanide is generated in larvae of the glucosinolate-specialist Pieris rapae (Lepidoptera:Pieridae) upon ingestion of plant material containing phenylalanine-derived glucosinolates as chemical defenses. As these glucosinolates were widespread within ancient Brassicales, the ability to detoxify cyanide may therefore have been essential for the host plant shift of Pierid species from Fabales to Brassicales species giving rise to the Pierinae subfamily. Previous research identified β-cyanoalanine and thiocyanate as products of cyanide detoxification in P. rapae larvae as well as three cDNAs encoding the β-cyanoalanine synthases PrBSAS1-PrBSAS3. Here, we analyzed a total of eight species of four lepidopteran families to test if their cyanide detoxification capacity correlates with their feeding specialization. We detected β-cyanoalanine synthase activity in gut protein extracts of all six species tested, which included Pierid species with glucosinolate-containing host plants, Pierids with other hosts, and other Lepidoptera with varying food specialization. Rhodanese activity was only scarcely detectable with the highest levels appearing in the two glucosinolate-feeding Pierids. We then amplified by polymerase chain reaction (PCR) 14 cDNAs encoding β-cyanoalanine synthases from seven species. Enzyme characterization and phylogenetic analysis indicated that lepidopterans are generally equipped with one PrBSAS2 homolog with high affinity for cyanide. A second β-cyanoalanine synthase which grouped with PrBSAS3 was restricted to Pierid species, while a third variant (i.e., homologs of PrBSAS1), was only present in members of the Pierinae subfamily. These results are in agreement with the hypothesis that the host shift to Brassicales was associated with the requirement for a specialized cyanide detoxification machinery.
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Pentzold S, Jensen MK, Matthes A, Olsen CE, Petersen BL, Clausen H, Møller BL, Bak S, Zagrobelny M. Spatial separation of the cyanogenic β-glucosidase ZfBGD2 and cyanogenic glucosides in the haemolymph of Zygaena larvae facilitates cyanide release. ROYAL SOCIETY OPEN SCIENCE 2017; 4:170262. [PMID: 28680679 PMCID: PMC5493921 DOI: 10.1098/rsos.170262] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 05/25/2017] [Indexed: 06/01/2023]
Abstract
Low molecular weight compounds are typically used by insects and plants for defence against predators. They are often stored as inactive β-glucosides and kept separate from activating β-glucosidases. When the two components are mixed, the β-glucosides are hydrolysed releasing toxic aglucones. Cyanogenic plants contain cyanogenic glucosides and release hydrogen cyanide due to such a well-characterized two-component system. Some arthropods are also cyanogenic, but comparatively little is known about their system. Here, we identify a specific β-glucosidase (ZfBGD2) involved in cyanogenesis from larvae of Zygaena filipendulae (Lepidoptera, Zygaenidae), and analyse the spatial organization of cyanide release in this specialized insect. High levels of ZfBGD2 mRNA and protein were found in haemocytes by transcriptomic and proteomic profiling. Heterologous expression in insect cells showed that ZfBGD2 hydrolyses linamarin and lotaustralin, the two cyanogenic glucosides present in Z. filipendulae. Linamarin and lotaustralin as well as cyanide release were found exclusively in the haemoplasma. Phylogenetic analyses revealed that ZfBGD2 clusters with other insect β-glucosidases, and correspondingly, the ability to hydrolyse cyanogenic glucosides catalysed by a specific β-glucosidase evolved convergently in insects and plants. The spatial separation of the β-glucosidase ZfBGD2 and its cyanogenic substrates within the haemolymph provides the basis for cyanide release in Z. filipendulae. This spatial separation is similar to the compartmentalization of the two components found in cyanogenic plant species, and illustrates one similarity in cyanide-based defence in these two kingdoms of life.
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Affiliation(s)
- Stefan Pentzold
- Department of Plant and Environmental Sciences and Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
- Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, 07745 Jena, Germany
| | - Mikael Kryger Jensen
- Department of Plant and Environmental Sciences and Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Annemarie Matthes
- Department of Plant and Environmental Sciences and Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Carl Erik Olsen
- Department of Plant and Environmental Sciences and Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Bent Larsen Petersen
- Department of Plant and Environmental Sciences and Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Henrik Clausen
- Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N, Denmark
| | - Birger Lindberg Møller
- Department of Plant and Environmental Sciences and Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Søren Bak
- Department of Plant and Environmental Sciences and Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Mika Zagrobelny
- Department of Plant and Environmental Sciences and Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
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Mannino MC, Rivarola M, Scannapieco AC, González S, Farber M, Cladera JL, Lanzavecchia SB. Transcriptome profiling of Diachasmimorpha longicaudata towards useful molecular tools for population management. BMC Genomics 2016; 17:793. [PMID: 27729028 PMCID: PMC5059965 DOI: 10.1186/s12864-016-2759-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 05/21/2016] [Indexed: 12/05/2022] Open
Abstract
Background Diachasmimorpha longicaudata (Hymenoptera: Braconidae) is a solitary parasitoid of Tephritidae (Diptera) fruit flies of economic importance currently being mass-reared in bio-factories and successfully used worldwide. A peculiar biological aspect of Hymenoptera is its haplo-diploid life cycle, where females (diploid) develop from fertilized eggs and males (haploid) from unfertilized eggs. Diploid males were described in many species and recently evidenced in D. longicaudata by mean of inbreeding studies. Sex determination in this parasitoid is based on the Complementary Sex Determination (CSD) system, with alleles from at least one locus involved in early steps of this pathway. Since limited information is available about genetics of this parasitoid species, a deeper analysis on D. longicaudata’s genomics is required to provide molecular tools for achieving a more cost effective production under artificial rearing conditions. Results We report here the first transcriptome analysis of male-larvae, adult females and adult males of D. longicaudata using 454-pyrosequencing. A total of 469766 reads were analyzed and 8483 high-quality isotigs were assembled. After functional annotation, a total of 51686 unigenes were produced, from which, 7021 isotigs and 20227 singletons had at least one BLAST hit against the NCBI non-redundant protein database. A preliminary comparison of adult female and male evidenced that 98 transcripts showed differential expression profiles, with at least a 10-fold difference. Among the functionally annotated transcripts we detected four sequences potentially involved in sex determination and three homologues to two known genes involved in the sex determination cascade. Finally, a total of 4674SimpleSequence Repeats (SSRs) were in silico identified and characterized. Conclusion The information obtained here will significantly contribute to the development of D. longicaudata functional genomics, genetics and population-based genome studies. Thousands of new microsatellite markers were identified as toolkits for population genetics analysis. The transcriptome characterized here is the starting point to elucidate the molecular bases of the sex determination mechanism in this species. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2759-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- M Constanza Mannino
- Laboratorio de Insectos de Importancia Económica, Instituto de Genética Ewald A. Favret, Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham, Buenos Aires, Argentina. .,Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina.
| | - Máximo Rivarola
- Instituto de Biotecnología, Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
| | - Alejandra C Scannapieco
- Laboratorio de Insectos de Importancia Económica, Instituto de Genética Ewald A. Favret, Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
| | - Sergio González
- Instituto de Biotecnología, Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
| | - Marisa Farber
- Instituto de Biotecnología, Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
| | - Jorge L Cladera
- Laboratorio de Insectos de Importancia Económica, Instituto de Genética Ewald A. Favret, Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham, Buenos Aires, Argentina
| | - Silvia B Lanzavecchia
- Laboratorio de Insectos de Importancia Económica, Instituto de Genética Ewald A. Favret, Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham, Buenos Aires, Argentina
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9
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Salgado AL, Suchan T, Pellissier L, Rasmann S, Ducrest AL, Alvarez N. Differential phenotypic and genetic expression of defence compounds in a plant-herbivore interaction along elevation. ROYAL SOCIETY OPEN SCIENCE 2016; 3:160226. [PMID: 27703688 PMCID: PMC5043307 DOI: 10.1098/rsos.160226] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 08/30/2016] [Indexed: 06/06/2023]
Abstract
Elevation gradients impose large differences in abiotic and biotic conditions over short distances, in turn, likely driving differences in gene expression more than would genetic variation per se, as natural selection and drift are less likely to fix alleles at such a narrow spatial scale. As elevation increases, the pressure exerted on plants by herbivores and on arthropod herbivores by predators decreases, and organisms spanning the elevation gradient are thus expected to show lower levels of defence at high elevation. The alternative hypothesis, based on the optimal defence theory, is that defence allocation should be higher in low-resource habitats such as those at high elevation, due to higher costs associated with tissue replacement. In this study, we analyse variation with elevation in (i) defence compound content in the plant Lotus corniculatus and (ii) gene expression associated with defence against predators in the specific phytophagous moth, Zygaena filipendulae. Both species produce cyanogenic glycosides (CNglcs) such as lotaustralin and linamarin as defence mechanisms, with the moth, in addition, being able to sequester CNglcs from its host plant. Specifically, we tested the assumption that the defence-associated phenotype in plants and the gene expression in the insect herbivore should covary between low- and high-elevation environments. We found that L. corniculatus accumulated more CNglcs at high elevation, a result in agreement with the optimal defence theory. By contrast, we found that the levels of expression in the defence genes of Z. filipendulae larvae were not related to the CNglc content of their host plant. Overall, expression levels were not correlated with elevation either, with the exception of the UGT33A1 gene, which showed a marginally significant trend towards higher expression at high elevation when using a simple statistical framework. These results suggest that the defence phenotype of plants against herbivores, and subsequent herbivore sequestration machineries and de novo production, are based on a complex network of interactions.
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Affiliation(s)
- Ana L. Salgado
- Department of Ecology and Evolution, Biophore building, University of Lausanne, Lausanne, Switzerland
- Metapopulation Research Centre, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Tomasz Suchan
- Department of Ecology and Evolution, Biophore building, University of Lausanne, Lausanne, Switzerland
| | - Loïc Pellissier
- Unit of Ecology and Evolution, Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Sergio Rasmann
- Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Anne-Lyse Ducrest
- Department of Ecology and Evolution, Biophore building, University of Lausanne, Lausanne, Switzerland
| | - Nadir Alvarez
- Department of Ecology and Evolution, Biophore building, University of Lausanne, Lausanne, Switzerland
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Pyrosequencing the Midgut Transcriptome of the Banana Weevil Cosmopolites sordidus (Germar) (Coleoptera: Curculionidae) Reveals Multiple Protease-Like Transcripts. PLoS One 2016; 11:e0151001. [PMID: 26949943 PMCID: PMC4780788 DOI: 10.1371/journal.pone.0151001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 02/21/2016] [Indexed: 11/25/2022] Open
Abstract
The banana weevil Cosmopolites sordidus is an important and serious insect pest in most banana and plantain-growing areas of the world. In spite of the economic importance of this insect pest very little genomic and transcriptomic information exists for this species. In the present study, we characterized the midgut transcriptome of C. sordidus using massive 454-pyrosequencing. We generated over 590,000 sequencing reads that assembled into 30,840 contigs with more than 400 bp, representing a significant expansion of existing sequences available for this insect pest. Among them, 16,427 contigs contained one or more GO terms. In addition, 15,263 contigs were assigned an EC number. In-depth transcriptome analysis identified genes potentially involved in insecticide resistance, peritrophic membrane biosynthesis, immunity-related function and defense against pathogens, and Bacillus thuringiensis toxins binding proteins as well as multiple enzymes involved with protein digestion. This transcriptome will provide a valuable resource for understanding larval physiology and for identifying novel target sites and management approaches for this important insect pest.
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Pentzold S, Zagrobelny M, Khakimov B, Engelsen SB, Clausen H, Petersen BL, Borch J, Møller BL, Bak S. Lepidopteran defence droplets - a composite physical and chemical weapon against potential predators. Sci Rep 2016; 6:22407. [PMID: 26940001 PMCID: PMC4778013 DOI: 10.1038/srep22407] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 02/12/2016] [Indexed: 11/24/2022] Open
Abstract
Insects often release noxious substances for their defence. Larvae of Zygaena filipendulae (Lepidoptera) secrete viscous and cyanogenic glucoside-containing droplets, whose effectiveness was associated with their physical and chemical properties. The droplets glued mandibles and legs of potential predators together and immobilised them. Droplets were characterised by a matrix of an aqueous solution of glycine-rich peptides (H-WG11-NH2) with significant amounts of proteins and glucose. Among the proteins, defensive proteins such as protease inhibitors, proteases and oxidases were abundant. The neurotoxin β-cyanoalanine was also found in the droplets. Despite the presence of cyanogenic glucosides, which release toxic hydrogen cyanide after hydrolysis by a specific β-glucosidase, the only β-glucosidase identified in the droplets (ZfBGD1) was inactive against cyanogenic glucosides. Accordingly, droplets did not release hydrogen cyanide, unless they were mixed with specific β-glucosidases present in the Zygaena haemolymph. Droplets secreted onto the cuticle hardened and formed sharp crystalline-like precipitates that may act as mandible abrasives to chewing predators. Hardening followed water evaporation and formation of antiparallel β-sheets of the peptide oligomers. Consequently, after mild irritation, Zygaena larvae deter predators by viscous and hardening droplets that contain defence proteins and β-cyanoalanine. After severe injury, droplets may mix with exuding haemolymph to release hydrogen cyanide.
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Affiliation(s)
- Stefan Pentzold
- Plant Biochemistry Laboratory and Villum Research Center ‘Plant Plasticity’, Copenhagen Plant Science Center, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Mika Zagrobelny
- Plant Biochemistry Laboratory and Villum Research Center ‘Plant Plasticity’, Copenhagen Plant Science Center, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Bekzod Khakimov
- Spectroscopy and Chemometrics, Department of Food Science, University of Copenhagen, Copenhagen, Denmark
| | - Søren Balling Engelsen
- Spectroscopy and Chemometrics, Department of Food Science, University of Copenhagen, Copenhagen, Denmark
| | - Henrik Clausen
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine , University of Copenhagen, Copenhagen, Denmark
| | - Bent Larsen Petersen
- Plant Glycobiology, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jonas Borch
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Birger Lindberg Møller
- Plant Biochemistry Laboratory and Villum Research Center ‘Plant Plasticity’, Copenhagen Plant Science Center, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
- Carlsberg Laboratory, Copenhagen, Denmark
| | - Søren Bak
- Plant Biochemistry Laboratory and Villum Research Center ‘Plant Plasticity’, Copenhagen Plant Science Center, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
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Patnaik BB, Hwang HJ, Kang SW, Park SY, Wang TH, Park EB, Chung JM, Song DK, Kim C, Kim S, Lee JB, Jeong HC, Park HS, Han YS, Lee YS. Transcriptome Characterization for Non-Model Endangered Lycaenids, Protantigius superans and Spindasis takanosis, Using Illumina HiSeq 2500 Sequencing. Int J Mol Sci 2015; 16:29948-70. [PMID: 26694362 PMCID: PMC4691156 DOI: 10.3390/ijms161226213] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Revised: 11/28/2015] [Accepted: 12/09/2015] [Indexed: 11/22/2022] Open
Abstract
The Lycaenidae butterflies, Protantigius superans and Spindasis takanosis, are endangered insects in Korea known for their symbiotic association with ants. However, necessary genomic and transcriptomics data are lacking in these species, limiting conservation efforts. In this study, the P. superans and S. takanosis transcriptomes were deciphered using Illumina HiSeq 2500 sequencing. The P. superans and S. takanosis transcriptome data included a total of 254,340,693 and 245,110,582 clean reads assembled into 159,074 and 170,449 contigs and 107,950 and 121,140 unigenes, respectively. BLASTX hits (E-value of 1.0 × 10−5) against the known protein databases annotated a total of 46,754 and 51,908 transcripts for P. superans and S. takanosis. Approximately 41.25% and 38.68% of the unigenes for P. superans and S. takanosis found homologous sequences in Protostome DB (PANM-DB). BLAST2GO analysis confirmed 18,611 unigenes representing Gene Ontology (GO) terms and a total of 5259 unigenes assigned to 116 pathways for P. superans. For S. takanosis, a total of 6697 unigenes were assigned to 119 pathways using the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database. Additionally, 382,164 and 390,516 Simple Sequence Repeats (SSRs) were compiled from the unigenes of P. superans and S. takanosis, respectively. This is the first report to record new genes and their utilization for conservation of lycaenid species population and as a reference information for closely related species.
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Affiliation(s)
- Bharat Bhusan Patnaik
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungcheongnam-do 31538, Korea.
- Trident School of Biotech Sciences, Trident Academy of Creative Technology (TACT), Chandaka Industrial Estate, Chandrasekharpur, Bhubaneswar, Odisha 751024, India.
| | - Hee-Ju Hwang
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungcheongnam-do 31538, Korea.
| | - Se Won Kang
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungcheongnam-do 31538, Korea.
| | - So Young Park
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungcheongnam-do 31538, Korea.
| | - Tae Hun Wang
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungcheongnam-do 31538, Korea.
| | - Eun Bi Park
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungcheongnam-do 31538, Korea.
| | - Jong Min Chung
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungcheongnam-do 31538, Korea.
| | - Dae Kwon Song
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungcheongnam-do 31538, Korea.
| | - Changmu Kim
- National Institute of Biological Resources, 42, Hwangyeong-ro, Seo-gu, Incheon 22689, Korea.
| | - Soonok Kim
- National Institute of Biological Resources, 42, Hwangyeong-ro, Seo-gu, Incheon 22689, Korea.
| | - Jae Bong Lee
- Korea Zoonosis Research Institute (KOZRI), Chonbuk National University, 820-120 Hana-ro, Iksan, Jeollabuk-do 54528, Korea.
| | - Heon Cheon Jeong
- Hampyeong County Insect Institute, Hampyeong County Agricultural Technology Center, 90, Hakgyohwasan-gil, Hakgyo-myeon, Hampyeong-gun, Jeollanan-do 57158, Korea.
| | - Hong Seog Park
- Research Institute, GnC BIO Co., LTD. 621-6 Banseok-dong, Yuseong-gu, Daejeon 34069, Korea.
| | - Yeon Soo Han
- College of Agriculture and Life Science, Chonnam National University 77 Yongbong-ro, Buk-gu, Gwangju 61186, Korea.
| | - Yong Seok Lee
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungcheongnam-do 31538, Korea.
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Zhang W, Tian D, Huang X, Xu Y, Mo H, Liu Y, Meng J, Zhang D. Characterization of flower-bud transcriptome and development of genic SSR markers in Asian lotus (Nelumbo nucifera Gaertn.). PLoS One 2014; 9:e112223. [PMID: 25379700 PMCID: PMC4224446 DOI: 10.1371/journal.pone.0112223] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Accepted: 10/10/2014] [Indexed: 01/01/2023] Open
Abstract
Background Asian lotus (Nelumbo nucifera Gaertn.) is the national flower of India, Vietnam, and one of the top ten traditional Chinese flowers. Although lotus is highly valued for its ornamental, economic and cultural uses, genomic information, particularly the expressed sequence based (genic) markers is limited. High-throughput transcriptome sequencing provides large amounts of transcriptome data for promoting gene discovery and development of molecular markers. Results In this study, 68,593 unigenes were assembled from 1.34 million 454 GS-FLX sequence reads of a mixed flower-bud cDNA pool derived from three accessions of N. nucifera. A total of 5,226 SSR loci were identified, and 3,059 primer pairs were designed for marker development. Di-nucleotide repeat motifs were the most abundant type identified with a frequency of 65.2%, followed by tri- (31.7%), tetra- (2.1%), penta- (0.5%) and hexa-nucleotide repeats (0.5%). A total of 575 primer pairs were synthesized, of which 514 (89.4%) yielded PCR amplification products. In eight Nelumbo accessions, 109 markers were polymorphic. They were used to genotype a sample of 44 accessions representing diverse wild and cultivated genotypes of Nelumbo. The number of alleles per locus varied from 2 to 9 alleles and the polymorphism information content values ranged from 0.6 to 0.9. We performed genetic diversity analysis using 109 polymorphic markers. A UPGMA dendrogram was constructed based on Jaccard’s similarity coefficients revealing distinct clusters among the 44 accessions. Conclusions Deep transcriptome sequencing of lotus flower buds developed 3,059 genic SSRs, making a significant addition to the existing SSR markers in lotus. Among them, 109 polymorphic markers were successfully validated in 44 accessions of Nelumbo. This comprehensive set of genic SSR markers developed in our study will facilitate analyses of genetic diversity, construction of linkage maps, gene mapping, and marker-assisted selection breeding for lotus.
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Affiliation(s)
- Weiwei Zhang
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Chenshan Botanical Garden, Shanghai, China
| | - Daike Tian
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Chenshan Botanical Garden, Shanghai, China
- * E-mail:
| | - Xiu Huang
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Chenshan Botanical Garden, Shanghai, China
| | - Yuxian Xu
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Chenshan Botanical Garden, Shanghai, China
- College of life and Environmental Sciences, Shanghai Normal University, Shanghai, China
| | - Haibo Mo
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Chenshan Botanical Garden, Shanghai, China
| | - Yanbo Liu
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Chenshan Botanical Garden, Shanghai, China
- College of Horticulture, Northeast Agricultural University, Harbin, China
| | - Jing Meng
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Chenshan Botanical Garden, Shanghai, China
| | - Dasheng Zhang
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Chenshan Botanical Garden, Shanghai, China
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Fürstenberg-Hägg J, Zagrobelny M, Jørgensen K, Vogel H, Møller BL, Bak S. Chemical defense balanced by sequestration and de novo biosynthesis in a lepidopteran specialist. PLoS One 2014; 9:e108745. [PMID: 25299618 PMCID: PMC4191964 DOI: 10.1371/journal.pone.0108745] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Accepted: 08/25/2014] [Indexed: 11/18/2022] Open
Abstract
The evolution of sequestration (uptake and accumulation) relative to de novo biosynthesis of chemical defense compounds is poorly understood, as is the interplay between these two strategies. The Burnet moth Zygaena filipendulae (Lepidoptera) and its food-plant Lotus corniculatus (Fabaceae) poses an exemplary case study of these questions, as Z. filipendulae belongs to the only insect family known to both de novo biosynthesize and sequester the same defense compounds directly from its food-plant. Z. filipendulae and L. corniculatus both contain the two cyanogenic glucosides linamarin and lotaustralin, which are defense compounds that can be hydrolyzed to liberate toxic hydrogen cyanide. The overall amounts and ratios of linamarin and lotaustralin in Z. filipendulae are tightly regulated, and only to a low extent reflect the ratio in the ingested food-plant. We demonstrate that Z. filipendulae adjusts the de novo biosynthesis of CNglcs by regulation at both the transcriptional and protein level depending on food plant composition. Ultimately this ensures that the larva saves energy and nitrogen while maintaining an effective defense system to fend off predators. By using in situ PCR and immunolocalization, the biosynthetic pathway was resolved to the larval fat body and integument, which infers rapid replenishment of defense compounds following an encounter with a predator. Our study supports the hypothesis that de novo biosynthesis of CNglcs in Z. filipendulae preceded the ability to sequester, and facilitated a food-plant switch to cyanogenic plants, after which sequestration could evolve. Preservation of de novo biosynthesis allows fine-tuning of the amount and composition of CNglcs in Z. filipendulae.
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Affiliation(s)
- Joel Fürstenberg-Hägg
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Copenhagen, Denmark
- VILLUM Research Center “Plant Plasticity”, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Mika Zagrobelny
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Copenhagen, Denmark
- VILLUM Research Center “Plant Plasticity”, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kirsten Jørgensen
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Copenhagen, Denmark
- VILLUM Research Center “Plant Plasticity”, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Heiko Vogel
- Department of Entomology, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Birger Lindberg Møller
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Copenhagen, Denmark
- VILLUM Research Center “Plant Plasticity”, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Søren Bak
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Copenhagen, Denmark
- VILLUM Research Center “Plant Plasticity”, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
- * E-mail:
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Tang T, Li X, Yang X, Yu X, Wang J, Liu F, Huang D. Transcriptional response of Musca domestica larvae to bacterial infection. PLoS One 2014; 9:e104867. [PMID: 25137050 PMCID: PMC4138075 DOI: 10.1371/journal.pone.0104867] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 07/18/2014] [Indexed: 11/18/2022] Open
Abstract
The house fly Musca domestica, a cosmopolitan dipteran insect, is a significant vector for human and animal bacterial pathogens, but little is known about its immune response to these pathogens. To address this issue, we inoculated the larvae with a mixture of Escherichia coli and Staphylococcus aureus and profiled the transcriptome 6, 24, and 48 h thereafter. Many genes known to controlling innate immunity in insects were induced following infection, including genes encoding pattern recognition proteins (PGRPs), various components of the Toll and IMD signaling pathways and of the proPO-activating and redox systems, and multiple antimicrobial peptides. Interestingly, we also uncovered a large set of novel immune response genes including two broad-spectrum antimicrobial peptides (muscin and domesticin), which might have evolved to adapt to house-fly's unique ecological environments. Finally, genes mediating oxidative phosphorylation were repressed at 48 h post-infection, suggesting disruption of energy homeostasis and mitochondrial function at the late stages of infection. Collectively, our data reveal dynamic changes in gene expression following bacterial infection in the house fly, paving the way for future in-depth analysis of M. domestica's immune system.
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Affiliation(s)
- Ting Tang
- College of Life Sciences, Hebei University, Baoding, China
| | - Xiang Li
- College of Life Sciences, Hebei University, Baoding, China
| | - Xue Yang
- College of Life Sciences, Hebei University, Baoding, China
| | - Xue Yu
- College of Life Sciences, Hebei University, Baoding, China
| | - Jianhui Wang
- Department of Pathology, Yale University, New Haven, Connecticut, United States of America
| | - Fengsong Liu
- College of Life Sciences, Hebei University, Baoding, China
- * E-mail: (FSL); (DWH)
| | - Dawei Huang
- College of Life Sciences, Hebei University, Baoding, China
- Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- * E-mail: (FSL); (DWH)
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16
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Zhu G, Zhong D, Cao J, Zhou H, Li J, Liu Y, Bai L, Xu S, Wang MH, Zhou G, Chang X, Gao Q, Yan G. Transcriptome profiling of pyrethroid resistant and susceptible mosquitoes in the malaria vector, Anopheles sinensis. BMC Genomics 2014; 15:448. [PMID: 24909924 PMCID: PMC4070547 DOI: 10.1186/1471-2164-15-448] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Accepted: 05/28/2014] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Anopheles sinensis is a major malaria vector in China and other Southeast Asian countries, and it is becoming increasingly resistant to the insecticides used for agriculture, net impregnation, and indoor residual spray. Very limited genomic information on this species is available, which has hindered the development of new tools for resistance surveillance and vector control. We used the 454 GS FLX system and generated expressed sequence tag (EST) databases of various life stages of An. sinensis, and we determined the transcriptional differences between deltamethrin resistant and susceptible mosquitoes. RESULTS The 454 GS FLX transcriptome sequencing yielded a total of 624,559 reads (average length of 290 bp) with the pooled An. sinensis mosquitoes across various development stages. The de novo assembly generated 33,411 contigs with average length of 493 bp. A total of 8,057 ESTs were generated with Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation. A total of 2,131 ESTs were differentially expressed between deltamethrin resistant and susceptible mosquitoes collected from the same field site in Jiangsu, China. Among these differentially expressed ESTs, a total of 294 pathways were mapped to the KEGG database, with the predominant ESTs belonging to metabolic pathways. Furthermore, a total of 2,408 microsatellites and 15,496 single nucleotide polymorphisms (SNPs) were identified. CONCLUSIONS The annotated EST and transcriptome databases provide a valuable genomic resource for further genetic studies of this important malaria vector species. The differentially expressed ESTs associated with insecticide resistance identified in this study lay an important foundation for further functional analysis. The identified microsatellite and SNP markers will provide useful tools for future population genetic and comparative genomic analyses of malaria vectors.
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Affiliation(s)
- Guoding Zhu
- />Department of Parasitology, Medical College of Soochow University, Suzhou, 215123 PR China
- />Jiangsu Institute of Parasitic Diseases, Key Laboratory of Parasitic Disease Control and Prevention (Ministry of Health), Jiangsu Provincial Key Laboratory of Parasite Molecular Biology, Wuxi, Jiangsu Province 214064 PR China
- />Program in Public Health, College of Health Sciences, University of California at Irvine, Irvine, CA 92697 USA
| | - Daibin Zhong
- />Program in Public Health, College of Health Sciences, University of California at Irvine, Irvine, CA 92697 USA
| | - Jun Cao
- />Jiangsu Institute of Parasitic Diseases, Key Laboratory of Parasitic Disease Control and Prevention (Ministry of Health), Jiangsu Provincial Key Laboratory of Parasite Molecular Biology, Wuxi, Jiangsu Province 214064 PR China
| | - Huayun Zhou
- />Jiangsu Institute of Parasitic Diseases, Key Laboratory of Parasitic Disease Control and Prevention (Ministry of Health), Jiangsu Provincial Key Laboratory of Parasite Molecular Biology, Wuxi, Jiangsu Province 214064 PR China
| | - Julin Li
- />Jiangsu Institute of Parasitic Diseases, Key Laboratory of Parasitic Disease Control and Prevention (Ministry of Health), Jiangsu Provincial Key Laboratory of Parasite Molecular Biology, Wuxi, Jiangsu Province 214064 PR China
| | - Yaobao Liu
- />Jiangsu Institute of Parasitic Diseases, Key Laboratory of Parasitic Disease Control and Prevention (Ministry of Health), Jiangsu Provincial Key Laboratory of Parasite Molecular Biology, Wuxi, Jiangsu Province 214064 PR China
| | - Liang Bai
- />Jiangsu Institute of Parasitic Diseases, Key Laboratory of Parasitic Disease Control and Prevention (Ministry of Health), Jiangsu Provincial Key Laboratory of Parasite Molecular Biology, Wuxi, Jiangsu Province 214064 PR China
| | - Sui Xu
- />Jiangsu Institute of Parasitic Diseases, Key Laboratory of Parasitic Disease Control and Prevention (Ministry of Health), Jiangsu Provincial Key Laboratory of Parasite Molecular Biology, Wuxi, Jiangsu Province 214064 PR China
| | - Mei-Hui Wang
- />Program in Public Health, College of Health Sciences, University of California at Irvine, Irvine, CA 92697 USA
| | - Guofa Zhou
- />Program in Public Health, College of Health Sciences, University of California at Irvine, Irvine, CA 92697 USA
| | - Xuelian Chang
- />Program in Public Health, College of Health Sciences, University of California at Irvine, Irvine, CA 92697 USA
| | - Qi Gao
- />Department of Parasitology, Medical College of Soochow University, Suzhou, 215123 PR China
- />Jiangsu Institute of Parasitic Diseases, Key Laboratory of Parasitic Disease Control and Prevention (Ministry of Health), Jiangsu Provincial Key Laboratory of Parasite Molecular Biology, Wuxi, Jiangsu Province 214064 PR China
| | - Guiyun Yan
- />Program in Public Health, College of Health Sciences, University of California at Irvine, Irvine, CA 92697 USA
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The de novo transcriptome and its analysis in the worldwide vegetable pest, Delia antiqua (Diptera: Anthomyiidae). G3-GENES GENOMES GENETICS 2014; 4:851-9. [PMID: 24615268 PMCID: PMC4025484 DOI: 10.1534/g3.113.009779] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The onion maggot Delia antiqua is a major insect pest of cultivated vegetables, especially the onion, and a good model to investigate the molecular mechanisms of diapause. To better understand the biology and diapause mechanism of the insect pest species, D. antiqua, the transcriptome was sequenced using Illumina paired-end sequencing technology. Approximately 54 million reads were obtained, trimmed, and assembled into 29,659 unigenes, with an average length of 607 bp and an N50 of 818 bp. Among these unigenes, 21,605 (72.8%) were annotated in the public databases. All unigenes were then compared against Drosophila melanogaster and Anopheles gambiae. Codon usage bias was analyzed and 332 simple sequence repeats (SSRs) were detected in this organism. These data represent the most comprehensive transcriptomic resource currently available for D. antiqua and will facilitate the study of genetics, genomics, diapause, and further pest control of D. antiqua.
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Gschloessl B, Vogel H, Burban C, Heckel D, Streiff R, Kerdelhué C. Comparative analysis of two phenologically divergent populations of the pine processionary moth (Thaumetopoea pityocampa) by de novo transcriptome sequencing. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2014; 46:31-42. [PMID: 24468684 DOI: 10.1016/j.ibmb.2014.01.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Revised: 01/11/2014] [Accepted: 01/13/2014] [Indexed: 06/03/2023]
Abstract
The pine processionary moth Thaumetopoea pityocampa is a Mediterranean lepidopteran defoliator that experiences a rapid range expansion towards higher latitudes and altitudes due to the current climate warming. Its phenology - the time of sexual reproduction - is certainly a key trait for the local adaptation of the processionary moth to climatic conditions. Moreover, an exceptional case of allochronic differentiation was discovered ca. 15 years ago in this species. A population with a shifted phenology (the summer population, SP) co-exists near Leiria, Portugal, with a population following the classical cycle (the winter population, WP). The existence of this population is an outstanding opportunity to decipher the genetic bases of phenology. No genomic resources were so far available for T. pityocampa. We developed a high-throughput sequencing approach to build a first reference transcriptome, and to proceed with comparative analyses of the sympatric SP and WP. We pooled RNA extracted from whole individuals of various developmental stages, and performed a transcriptome characterisation for both populations combining Roche 454-FLX and traditional Sanger data. The obtained sequences were clustered into ca. 12,000 transcripts corresponding to 9265 unigenes. The mean transcript coverage was 21.9 reads per bp. Almost 70% of the de novo assembled transcripts displayed significant similarity to previously published proteins and around 50% of the transcripts contained a full-length coding region. Comparative analyses of the population transcriptomes allowed to investigate genes specifically expressed in one of the studied populations only, and to identify the most divergent homologous SP/WP transcripts. The most divergent pairs of transcripts did not correspond to obvious phenology-related candidate genes, and 43% could not be functionally annotated. This study provides the first comprehensive genome-wide resource for the target species T. pityocampa. Many of the assembled genes are orthologs of published Lepidoptera genes, which allows carrying out gene-specific re-sequencing. Data mining has allowed the identification of SNP loci that will be useful for population genomic approaches and genome-wide scans of population differentiation to identify signatures of selection.
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Affiliation(s)
- Bernhard Gschloessl
- INRA, UMR CBGP (INRA/IRD/CIRAD/Montpellier Supagro), Campus International de Baillarguet, CS30016, F-34988 Montferrier-sur-Lez Cedex, France.
| | - Heiko Vogel
- Max Planck Institute for Chemical Ecology, Department of Entomology, 07745 Jena, Germany
| | - Christian Burban
- INRA, UMR1202 BIOGECO, 69 Route d'Arcachon, F-33612 Cestas Cedex, France
| | - David Heckel
- Max Planck Institute for Chemical Ecology, Department of Entomology, 07745 Jena, Germany
| | - Réjane Streiff
- INRA, UMR CBGP (INRA/IRD/CIRAD/Montpellier Supagro), Campus International de Baillarguet, CS30016, F-34988 Montferrier-sur-Lez Cedex, France
| | - Carole Kerdelhué
- INRA, UMR CBGP (INRA/IRD/CIRAD/Montpellier Supagro), Campus International de Baillarguet, CS30016, F-34988 Montferrier-sur-Lez Cedex, France
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Firmino AAP, Fonseca FCDA, de Macedo LLP, Coelho RR, Antonino de Souza Jr JD, Togawa RC, Silva-Junior OB, Pappas-Jr GJ, da Silva MCM, Engler G, Grossi-de-Sa MF. Transcriptome analysis in cotton boll weevil (Anthonomus grandis) and RNA interference in insect pests. PLoS One 2013; 8:e85079. [PMID: 24386449 PMCID: PMC3874031 DOI: 10.1371/journal.pone.0085079] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 11/22/2013] [Indexed: 12/16/2022] Open
Abstract
Cotton plants are subjected to the attack of several insect pests. In Brazil, the cotton boll weevil, Anthonomus grandis, is the most important cotton pest. The use of insecticidal proteins and gene silencing by interference RNA (RNAi) as techniques for insect control are promising strategies, which has been applied in the last few years. For this insect, there are not much available molecular information on databases. Using 454-pyrosequencing methodology, the transcriptome of all developmental stages of the insect pest, A. grandis, was analyzed. The A. grandis transcriptome analysis resulted in more than 500.000 reads and a data set of high quality 20,841 contigs. After sequence assembly and annotation, around 10,600 contigs had at least one BLAST hit against NCBI non-redundant protein database and 65.7% was similar to Tribolium castaneum sequences. A comparison of A. grandis, Drosophila melanogaster and Bombyx mori protein families’ data showed higher similarity to dipteran than to lepidopteran sequences. Several contigs of genes encoding proteins involved in RNAi mechanism were found. PAZ Domains sequences extracted from the transcriptome showed high similarity and conservation for the most important functional and structural motifs when compared to PAZ Domains from 5 species. Two SID-like contigs were phylogenetically analyzed and grouped with T. castaneum SID-like proteins. No RdRP gene was found. A contig matching chitin synthase 1 was mined from the transcriptome. dsRNA microinjection of a chitin synthase gene to A. grandis female adults resulted in normal oviposition of unviable eggs and malformed alive larvae that were unable to develop in artificial diet. This is the first study that characterizes the transcriptome of the coleopteran, A. grandis. A new and representative transcriptome database for this insect pest is now available. All data support the state of the art of RNAi mechanism in insects.
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Affiliation(s)
- Alexandre Augusto Pereira Firmino
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, Distrito Federal, Brazil
- Graduate Program in Cellular and Molecular Biology, Center of Biotechnology, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
- * E-mail: (AAPF); (MFGS)
| | - Fernando Campos de Assis Fonseca
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, Distrito Federal, Brazil
- Graduate Program in Biology Molecular, Universidade de Brasília, Brasília, Distrito Federal, Brazil
| | - Leonardo Lima Pepino de Macedo
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, Distrito Federal, Brazil
- Graduate Program in Genomic Sciences and Biotechnology, Universidade Católica de Brasília, Brasília, Distrito Federal, Brazil
| | - Roberta Ramos Coelho
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, Distrito Federal, Brazil
- Graduate Program in Biology Molecular, Universidade de Brasília, Brasília, Distrito Federal, Brazil
| | - José Dijair Antonino de Souza Jr
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, Distrito Federal, Brazil
- Graduate Program in Biology Molecular, Universidade de Brasília, Brasília, Distrito Federal, Brazil
| | | | | | | | | | - Gilbert Engler
- Plateau Microscopique, Institut National de la Recherche Agronomique, Sophia-Antipolis, France
| | - Maria Fatima Grossi-de-Sa
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, Distrito Federal, Brazil
- Graduate Program in Genomic Sciences and Biotechnology, Universidade Católica de Brasília, Brasília, Distrito Federal, Brazil
- * E-mail: (AAPF); (MFGS)
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Wang L, Zhang XW, Pan LL, Liu WF, Wang DP, Zhang GY, Yin YX, Yin A, Jia SG, Yu XG, Sun GY, Hu SN, Al-Mssallem IS, Yu J. A large-scale gene discovery for the red palm weevil Rhynchophorus ferrugineus (Coleoptera: Curculionidae). INSECT SCIENCE 2013; 20:689-702. [PMID: 23955844 DOI: 10.1111/j.1744-7917.2012.01561.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 06/05/2012] [Indexed: 06/02/2023]
Abstract
The red palm weevil (RPW; Rhynchophorus ferrugineus) is a devastating pest of palms, prevalent in the Middle East as well as many other regions of the world. Here, we report a large-scale de novo complementary DNA (cDNA) sequencing effort that acquired ∼5 million reads and assembled them into 26 765 contigs from 12 libraries made from samples of different RPW developmental stages based on the Roche/454 GS FLX platform. We annotated these contigs based on the publically available known insect genes and the Tribolium castaneum genome assembly. We find that over 80% of coding sequences (CDS) from the RPW contigs have high-identity homologs to known proteins with complete CDS. Gene expression analysis shows that the pupa and larval stages have the highest and lowest expression levels, respectively. In addition, we also identified more than 60 000 single nucleotide polymorphisms and 1 200 simple sequence repeat markers. This study provides the first large-scale cDNA dataset for RPW, a much-needed resource for future molecular studies.
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Affiliation(s)
- Lei Wang
- Joint Center for Genomics Research (JCGR), King Abdulaziz City for Science and Technology (KACST) and Chinese Academy of Sciences (CAS), Riyadh, Kingdom of Saudi Arabia; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing; Graduate University of Chinese Academy of Sciences, Beijing, China
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Niu D, Wang L, Sun F, Liu Z, Li J. Development of molecular resources for an intertidal clam, Sinonovacula constricta, using 454 transcriptome sequencing. PLoS One 2013; 8:e67456. [PMID: 23935831 PMCID: PMC3723811 DOI: 10.1371/journal.pone.0067456] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Accepted: 05/17/2013] [Indexed: 12/02/2022] Open
Abstract
Background The razor clam Sinonovacula constricta is a benthic intertidal bivalve species with important commercial value. Despite its economic importance, knowledge of its transcriptome is scarce. Next generation sequencing technologies offer rapid and efficient tools for generating large numbers of sequences, which can be used to characterize the transcriptome, to develop effective molecular markers and to identify genes associated with growth, a key breeding trait. Results Total RNA was isolated from the mantle, gill, liver, siphon, gonad and muscular foot tissues. High-throughput deep sequencing of S. constricta using 454 pyrosequencing technology yielded 859,313 high-quality reads with an average read length of 489 bp. Clustering and assembly of these reads produced 16,323 contigs and 131,346 singletons with average lengths of 1,376 bp and 458 bp, respectively. Based on transcriptome sequencing, 14,615 sequences had significant matches with known genes encoding 147,669 predicted proteins. Subsequently, previously unknown growth-related genes were identified. A total of 13,563 microsatellites (SSRs) and 13,634 high-confidence single nucleotide polymorphism loci (SNPs) were discovered, of which almost half were validated. Conclusion De novo sequencing of the razor clam S. constricta transcriptome on the 454 GS FLX platform generated a large number of ESTs. Candidate growth factors and a large number of SSRs and SNPs were identified. These results will impact genetic studies of S. constricta.
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Affiliation(s)
- Donghong Niu
- Key Laboratory of Freshwater Aquatic Genetic Resources Certificated by Ministry of Agriculture, Shanghai Ocean University, Shanghai, China
- Shanghai Engineering Research Center of Aquaculture, Shanghai, China
| | - Lie Wang
- Key Laboratory of Freshwater Aquatic Genetic Resources Certificated by Ministry of Agriculture, Shanghai Ocean University, Shanghai, China
- Shanghai Engineering Research Center of Aquaculture, Shanghai, China
| | - Fanyue Sun
- Department of Fisheries and Allied Aquacultures, Auburn University, Auburn, Alabama, United States of America
| | - Zhanjiang Liu
- Department of Fisheries and Allied Aquacultures, Auburn University, Auburn, Alabama, United States of America
| | - Jiale Li
- Key Laboratory of Freshwater Aquatic Genetic Resources Certificated by Ministry of Agriculture, Shanghai Ocean University, Shanghai, China
- Shanghai Engineering Research Center of Aquaculture, Shanghai, China
- * E-mail:
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O'Neil ST, Emrich SJ. Assessing De Novo transcriptome assembly metrics for consistency and utility. BMC Genomics 2013. [PMID: 23837739 DOI: 10.1186/1471‐2164‐14‐465] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Transcriptome sequencing and assembly represent a great resource for the study of non-model species, and many metrics have been used to evaluate and compare these assemblies. Unfortunately, it is still unclear which of these metrics accurately reflect assembly quality. RESULTS We simulated sequencing transcripts of Drosophila melanogaster. By assembling these simulated reads using both a "perfect" and a modern transcriptome assembler while varying read length and sequencing depth, we evaluated quality metrics to determine whether they 1) revealed perfect assemblies to be of higher quality, and 2) revealed perfect assemblies to be more complete as data quantity increased.Several commonly used metrics were not consistent with these expectations, including average contig coverage and length, though they became consistent when singletons were included in the analysis. We found several annotation-based metrics to be consistent and informative, including contig reciprocal best hit count and contig unique annotation count. Finally, we evaluated a number of novel metrics such as reverse annotation count, contig collapse factor, and the ortholog hit ratio, discovering that each assess assembly quality in unique ways. CONCLUSIONS Although much attention has been given to transcriptome assembly, little research has focused on determining how best to evaluate assemblies, particularly in light of the variety of options available for read length and sequencing depth. Our results provide an important review of these metrics and give researchers tools to produce the highest quality transcriptome assemblies.
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Affiliation(s)
- Shawn T O'Neil
- Center for Genome Research and Biocomputing, Oregon State University,Corvallis, OR 97333, USA
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O'Neil ST, Emrich SJ. Assessing De Novo transcriptome assembly metrics for consistency and utility. BMC Genomics 2013; 14:465. [PMID: 23837739 PMCID: PMC3733778 DOI: 10.1186/1471-2164-14-465] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Accepted: 06/21/2013] [Indexed: 11/10/2022] Open
Abstract
Background Transcriptome sequencing and assembly represent a great resource for the study of non-model species, and many metrics have been used to evaluate and compare these assemblies. Unfortunately, it is still unclear which of these metrics accurately reflect assembly quality. Results We simulated sequencing transcripts of Drosophila melanogaster. By assembling these simulated reads using both a “perfect” and a modern transcriptome assembler while varying read length and sequencing depth, we evaluated quality metrics to determine whether they 1) revealed perfect assemblies to be of higher quality, and 2) revealed perfect assemblies to be more complete as data quantity increased. Several commonly used metrics were not consistent with these expectations, including average contig coverage and length, though they became consistent when singletons were included in the analysis. We found several annotation-based metrics to be consistent and informative, including contig reciprocal best hit count and contig unique annotation count. Finally, we evaluated a number of novel metrics such as reverse annotation count, contig collapse factor, and the ortholog hit ratio, discovering that each assess assembly quality in unique ways. Conclusions Although much attention has been given to transcriptome assembly, little research has focused on determining how best to evaluate assemblies, particularly in light of the variety of options available for read length and sequencing depth. Our results provide an important review of these metrics and give researchers tools to produce the highest quality transcriptome assemblies.
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Affiliation(s)
- Shawn T O'Neil
- Center for Genome Research and Biocomputing, Oregon State University,Corvallis, OR 97333, USA
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Zou D, Coudron TA, Liu C, Zhang L, Wang M, Chen H. Nutrigenomics in Arma chinensis: transcriptome analysis of Arma chinensis fed on artificial diet and Chinese oak silk moth Antheraea pernyi pupae. PLoS One 2013; 8:e60881. [PMID: 23593338 PMCID: PMC3623872 DOI: 10.1371/journal.pone.0060881] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 03/04/2013] [Indexed: 12/20/2022] Open
Abstract
Background The insect predator, Arma chinensis, is capable of effectively controlling many pests, such as Colorado potato beetle, cotton bollworm, and mirid bugs. Our previous study demonstrated several life history parameters were diminished for A. chinensis reared on an artificial diet compared to a natural food source like the Chinese oak silk moth pupae. The molecular mechanisms underlying the nutritive impact of the artificial diet on A. chinensis health are unclear. So we utilized transcriptome information to better understand the impact of the artificial diet on A. chinensis at the molecular level. Methodology/Principal Findings Illumina HiSeq2000 was used to sequence 4.79 and 4.70 Gb of the transcriptome from pupae-fed and artificial diet-fed A. chinensis libraries, respectively, and a de novo transcriptome assembly was performed (Trinity short read assembler). This resulted in 112,029 and 98,724 contigs, clustered into 54,083 and 54,169 unigenes for pupae-fed and diet-fed A. chinensis, respectively. Unigenes from each sample’s assembly underwent sequence splicing and redundancy removal to acquire non-redundant unigenes. We obtained 55,189 unigenes of A. chinensis, including 12,046 distinct clusters and 43,143 distinct singletons. Unigene sequences were aligned by BLASTx to nr, Swiss-Prot, KEGG and COG (E-value <10−5), and further aligned by BLASTn to nt (E-value <10−5), retrieving proteins of highest sequence similarity with the given unigenes along with their protein functional annotations. Totally, 22,964, 7,898, 18,069, 15,416, 8,066 and 5,341 unigenes were annotated in nr, nt, Swiss-Prot, KEGG, COG and GO, respectively. We compared gene expression variations and found thousands of genes were differentially expressed between pupae-fed and diet-fed A. chinensis. Conclusions/Significance Our study provides abundant genomic data and offers comprehensive sequence information for studying A. chinensis. Additionally, the physiological roles of the differentially expressed genes enable us to predict effects of some dietary ingredients and subsequently propose formulation improvements to artificial diets.
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Affiliation(s)
- Deyu Zou
- Key Laboratory of Integrated Pest Management in Crops, Ministry of Agriculture, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- Sino-American Biological Control Laboratory, USDA-Agricultural Research Service, Beijing, China
| | - Thomas A. Coudron
- Biological Control of Insects Research Laboratory, USDA-Agricultural Research Service, Columbia, Missouri, United States of America
| | - Chenxi Liu
- Key Laboratory of Integrated Pest Management in Crops, Ministry of Agriculture, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- Sino-American Biological Control Laboratory, USDA-Agricultural Research Service, Beijing, China
| | - Lisheng Zhang
- Key Laboratory of Integrated Pest Management in Crops, Ministry of Agriculture, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- Sino-American Biological Control Laboratory, USDA-Agricultural Research Service, Beijing, China
| | - Mengqing Wang
- Key Laboratory of Integrated Pest Management in Crops, Ministry of Agriculture, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- Sino-American Biological Control Laboratory, USDA-Agricultural Research Service, Beijing, China
| | - Hongyin Chen
- Key Laboratory of Integrated Pest Management in Crops, Ministry of Agriculture, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- Sino-American Biological Control Laboratory, USDA-Agricultural Research Service, Beijing, China
- * E-mail:
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Gschloessl B, Beyne E, Audiot P, Bourguet D, Streiff R. De novo transcriptomic resources for two sibling species of moths: Ostrinia nubilalis and O. scapulalis. BMC Res Notes 2013; 6:73. [PMID: 23445568 PMCID: PMC3599821 DOI: 10.1186/1756-0500-6-73] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Accepted: 02/20/2013] [Indexed: 11/10/2022] Open
Abstract
Background This study aimed at enhancing the transcriptomic resources for two sibling species of moths, Ostrinia scapulalis (Adzuki bean borer) and Ostrinia nubilalis (European corn borer), as a foundation for future researches on their divergence history. Previous works on these species had shown that their genetic divergence was low, while they were reproductively isolated in natura and specialized on different host plants. Comparative genomic resources will help facilitate the understanding of the mechanisms involved in this isolation and adaptation to the host plants. Despite their fundamental interest, these species still lack the genomic resources to thoroughly identify candidate genes for functions of interest. We present here a high throughput sequencing and de novo transcriptome assembly for these two sibling species in line with this objective of comparative genomics. Results Based on 322,504 and 307,622 reads of 454 sequencing for O. scapulalis and O. nubilalis respectively, we reconstructed 11,231 and 10,773 transcripts, of which 40% were functionally annotated by BLAST analyzes. We determined the level of completeness of both assemblies as well as the recovery level of published Ostrinia genomic resources. Gene ontology (GO) of common and species-specific de novo transcripts did not reveal GO terms significantly enriched in one or the other species. By applying stringent homology searches on transcripts common to O. scapulalis and O. nubilalis, we identified a set of homologous transcripts, with a mean nucleotide identity value of 98.1%. In this set, the most divergent transcripts revealed candidate genes involved in developmental, sensorial and pathogen defense processes. Conclusions This data greatly increases the genomic resources of Ostrinia species and constitute a solid skeleton for future comparative analyzes of expression or diversity, despite we show that the transcriptomes for both species have not been assembled at full completion. In addition, we provide a set of homologous transcripts together with their annotation as a source of candidate genes for comparative analyzes.
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Affiliation(s)
- Bernhard Gschloessl
- Centre de Biologie pour Gestion des Populations UMR INRA-IRD-CIRAD-Montpellier SupAgro, Campus International de Baillarguet, Montferrier-sur-Lez Cedex 34988, France.
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Zhu JY, Yang P, Zhang Z, Wu GX, Yang B. Transcriptomic immune response of Tenebrio molitor pupae to parasitization by Scleroderma guani. PLoS One 2013; 8:e54411. [PMID: 23342153 PMCID: PMC3544796 DOI: 10.1371/journal.pone.0054411] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Accepted: 12/13/2012] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Host and parasitoid interaction is one of the most fascinating relationships of insects, which is currently receiving an increasing interest. Understanding the mechanisms evolved by the parasitoids to evade or suppress the host immune system is important for dissecting this interaction, while it was still poorly known. In order to gain insight into the immune response of Tenebrio molitor to parasitization by Scleroderma guani, the transcriptome of T. molitor pupae was sequenced with focus on immune-related gene, and the non-parasitized and parasitized T. molitor pupae were analyzed by digital gene expression (DGE) analysis with special emphasis on parasitoid-induced immune-related genes using Illumina sequencing. METHODOLOGY/PRINCIPAL FINDINGS In a single run, 264,698 raw reads were obtained. De novo assembly generated 71,514 unigenes with mean length of 424 bp. Of those unigenes, 37,373 (52.26%) showed similarity to the known proteins in the NCBI nr database. Via analysis of the transcriptome data in depth, 430 unigenes related to immunity were identified. DGE analysis revealed that parasitization by S. guani had considerable impacts on the transcriptome profile of T. molitor pupae, as indicated by the significant up- or down-regulation of 3,431 parasitism-responsive transcripts. The expression of a total of 74 unigenes involved in immune response of T. molitor was significantly altered after parasitization. CONCLUSIONS/SIGNIFICANCE obtained T. molitor transcriptome, in addition to establishing a fundamental resource for further research on functional genomics, has allowed the discovery of a large group of immune genes that might provide a meaningful framework to better understand the immune response in this species and other beetles. The DGE profiling data provides comprehensive T. molitor immune gene expression information at the transcriptional level following parasitization, and sheds valuable light on the molecular understanding of the host-parasitoid interaction.
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Affiliation(s)
- Jia-Ying Zhu
- Key Laboratory of Forest Disaster Warning and Control of Yunnan Province, Southwest Forestry University, Kunming, China.
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Riesgo A, Andrade SCS, Sharma PP, Novo M, Pérez-Porro AR, Vahtera V, González VL, Kawauchi GY, Giribet G. Comparative description of ten transcriptomes of newly sequenced invertebrates and efficiency estimation of genomic sampling in non-model taxa. Front Zool 2012; 9:33. [PMID: 23190771 PMCID: PMC3538665 DOI: 10.1186/1742-9994-9-33] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Accepted: 11/08/2012] [Indexed: 12/28/2022] Open
Abstract
UNLABELLED INTRODUCTION Traditionally, genomic or transcriptomic data have been restricted to a few model or emerging model organisms, and to a handful of species of medical and/or environmental importance. Next-generation sequencing techniques have the capability of yielding massive amounts of gene sequence data for virtually any species at a modest cost. Here we provide a comparative analysis of de novo assembled transcriptomic data for ten non-model species of previously understudied animal taxa. RESULTS cDNA libraries of ten species belonging to five animal phyla (2 Annelida [including Sipuncula], 2 Arthropoda, 2 Mollusca, 2 Nemertea, and 2 Porifera) were sequenced in different batches with an Illumina Genome Analyzer II (read length 100 or 150 bp), rendering between ca. 25 and 52 million reads per species. Read thinning, trimming, and de novo assembly were performed under different parameters to optimize output. Between 67,423 and 207,559 contigs were obtained across the ten species, post-optimization. Of those, 9,069 to 25,681 contigs retrieved blast hits against the NCBI non-redundant database, and approximately 50% of these were assigned with Gene Ontology terms, covering all major categories, and with similar percentages in all species. Local blasts against our datasets, using selected genes from major signaling pathways and housekeeping genes, revealed high efficiency in gene recovery compared to available genomes of closely related species. Intriguingly, our transcriptomic datasets detected multiple paralogues in all phyla and in nearly all gene pathways, including housekeeping genes that are traditionally used in phylogenetic applications for their purported single-copy nature. CONCLUSIONS We generated the first study of comparative transcriptomics across multiple animal phyla (comparing two species per phylum in most cases), established the first Illumina-based transcriptomic datasets for sponge, nemertean, and sipunculan species, and generated a tractable catalogue of annotated genes (or gene fragments) and protein families for ten newly sequenced non-model organisms, some of commercial importance (i.e., Octopus vulgaris). These comprehensive sets of genes can be readily used for phylogenetic analysis, gene expression profiling, developmental analysis, and can also be a powerful resource for gene discovery. The characterization of the transcriptomes of such a diverse array of animal species permitted the comparison of sequencing depth, functional annotation, and efficiency of genomic sampling using the same pipelines, which proved to be similar for all considered species. In addition, the datasets revealed their potential as a resource for paralogue detection, a recurrent concern in various aspects of biological inquiry, including phylogenetics, molecular evolution, development, and cellular biochemistry.
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Affiliation(s)
- Ana Riesgo
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
- Centro de Estudios Avanzados de Blanes, CSIC, c/ Accés a la Cala St. Francesc 14, Blanes, Girona, 17300, Spain
| | - Sónia C S Andrade
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
| | - Prashant P Sharma
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
| | - Marta Novo
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
- Current address: Cardiff School of Biosciences, Cardiff University, BIOSI 1, Museum Avenue, Cardiff, CF10 3TL, UK
| | - Alicia R Pérez-Porro
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
- Centro de Estudios Avanzados de Blanes, CSIC, c/ Accés a la Cala St. Francesc 14, Blanes, Girona, 17300, Spain
| | - Varpu Vahtera
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
- Current address: Finnish Museum of Natural History, Zoology Unit, Pohjoinen Rautatiekatu 13, 00014 University of Helsinki, Helsinki, Finland
| | - Vanessa L González
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
| | - Gisele Y Kawauchi
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
| | - Gonzalo Giribet
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
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Analysis of genes expression of Spodoptera exigua larvae upon AcMNPV infection. PLoS One 2012; 7:e42462. [PMID: 22860129 PMCID: PMC3409162 DOI: 10.1371/journal.pone.0042462] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Accepted: 07/09/2012] [Indexed: 02/07/2023] Open
Abstract
Background The impact of Autographa californica multicapsid nucleopolyhedrovirus (AcMNPV) infection on host gene expression in Spodoptera exigua 4th instar larvae was investigated through the use of 454 sequencing-based RNA-seq of cDNA libraries developed from insects challenged with active AcMNPV or heat-inactivated AcMNPV. Methodology/Principal Findings By comparing the two cDNA libraries, we show that 201 host genes are significantly up-regulated and 234 genes are significantly down-regulated by active AcMNPV infection. Down-regulated host genes included genes encoding antimicrobial peptides, namely three gloverin isoforms and an attacin, indicating that the viral infection actively repressed the expression of a portion of the host immune gene repertoire. Another interesting group of down-regulated host genes included genes encoding two juvenile hormone binding proteins and a hexamerin, all of which are involved in juvenile hormone regulation. The expression of these genes was enhanced by the topical application of Juvenile Hormone III (JHIII) in the insects challenged with heat-inactivated AcMNPV. However, infection with the active virus strongly suppresses the expression of these three genes, regardless of the absence or presence of JHIII. Conclusions/Significance Using RNA-seq, we have identified groups of immune-regulated and juvenile hormone-regulated genes that are suppressed by infection with active AcMNPV. This information and further studies on the regulation of host gene expression by AcMNPV will provide the tools needed to enhance the utility of the virus as an effective protein expression system and as an insecticide.
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Li D, Deng Z, Qin B, Liu X, Men Z. De novo assembly and characterization of bark transcriptome using Illumina sequencing and development of EST-SSR markers in rubber tree (Hevea brasiliensis Muell. Arg.). BMC Genomics 2012; 13:192. [PMID: 22607098 PMCID: PMC3431226 DOI: 10.1186/1471-2164-13-192] [Citation(s) in RCA: 204] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Accepted: 05/03/2012] [Indexed: 01/14/2023] Open
Abstract
Background In rubber tree, bark is one of important agricultural and biological organs. However, the molecular mechanism involved in the bark formation and development in rubber tree remains largely unknown, which is at least partially due to lack of bark transcriptomic and genomic information. Therefore, it is necessary to carried out high-throughput transcriptome sequencing of rubber tree bark to generate enormous transcript sequences for the functional characterization and molecular marker development. Results In this study, more than 30 million sequencing reads were generated using Illumina paired-end sequencing technology. In total, 22,756 unigenes with an average length of 485 bp were obtained with de novo assembly. The similarity search indicated that 16,520 and 12,558 unigenes showed significant similarities to known proteins from NCBI non-redundant and Swissprot protein databases, respectively. Among these annotated unigenes, 6,867 and 5,559 unigenes were separately assigned to Gene Ontology (GO) and Clusters of Orthologous Group (COG). When 22,756 unigenes searched against the Kyoto Encyclopedia of Genes and Genomes Pathway (KEGG) database, 12,097 unigenes were assigned to 5 main categories including 123 KEGG pathways. Among the main KEGG categories, metabolism was the biggest category (9,043, 74.75%), suggesting the active metabolic processes in rubber tree bark. In addition, a total of 39,257 EST-SSRs were identified from 22,756 unigenes, and the characterizations of EST-SSRs were further analyzed in rubber tree. 110 potential marker sites were randomly selected to validate the assembly quality and develop EST-SSR markers. Among 13 Hevea germplasms, PCR success rate and polymorphism rate of 110 markers were separately 96.36% and 55.45% in this study. Conclusion By assembling and analyzing de novo transcriptome sequencing data, we reported the comprehensive functional characterization of rubber tree bark. This research generated a substantial fraction of rubber tree transcriptome sequences, which were very useful resources for gene annotation and discovery, molecular markers development, genome assembly and annotation, and microarrays development in rubber tree. The EST-SSR markers identified and developed in this study will facilitate marker-assisted selection breeding in rubber tree. Moreover, this study also supported that transcriptome analysis based on Illumina paired-end sequencing is a powerful tool for transcriptome characterization and molecular marker development in non-model species, especially those with large and complex genomes.
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Affiliation(s)
- Dejun Li
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, Hainan, China.
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Nguyen Q, Palfreyman RW, Chan LCL, Reid S, Nielsen LK. Transcriptome sequencing of and microarray development for a Helicoverpa zea cell line to investigate in vitro insect cell-baculovirus interactions. PLoS One 2012; 7:e36324. [PMID: 22629315 PMCID: PMC3356360 DOI: 10.1371/journal.pone.0036324] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2012] [Accepted: 03/30/2012] [Indexed: 11/18/2022] Open
Abstract
The Heliothine insect complex contains some of the most destructive pests of agricultural crops worldwide, including the closely related Helicoverpa zea and H. armigera. Biological control using baculoviruses is practiced at a moderate level worldwide. In order to enable more wide spread use, a better understanding of cell-virus interactions is required. While many baculoviruses have been sequenced, none of the Heliothine insect genomes have been available. In this study, we sequenced, assembled and functionally annotated 29,586 transcripts from cultured H. zea cells using Illumina 100 bps and paired-end transcriptome sequencing (RNA-seq). The transcript sequences had high assembly coverage (64.5 times). 23,401 sequences had putative protein functions, and over 13,000 sequences had high similarities to available sequences in other insect species. The sequence database was estimated to cover at least 85% of all H. zea genes. The sequences were used to construct a microarray, which was evaluated on the infection of H. zea cells with H. Armigera single-capsid nucleopolyhedrovirus (HearNPV). The analysis revealed that up-regulation of apoptosis genes is the main cellular response in the early infection phase (18 hours post infection), while genes linked to four major immunological signalling pathways (Toll, IMD, Jak-STAT and JNK) were down-regulated. Only small changes (generally downwards) were observed for central carbon metabolism. The transcriptome and microarray platform developed in this study represent a greatly expanded resource base for H. zea insect- HearNPV interaction studies, in which key cellular pathways such as those for metabolism, immune response, transcription and replication have been identified. This resource will be used to develop better cell culture-based virus production processes, and more generally to investigate the molecular basis of host range and susceptibility, virus infectivity and virulence, and the ecology and evolution of baculoviruses.
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Affiliation(s)
- Quan Nguyen
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Queensland, Australia
| | - Robin W. Palfreyman
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Queensland, Australia
| | - Leslie C. L. Chan
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Queensland, Australia
| | - Steven Reid
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Queensland, Australia
- * E-mail:
| | - Lars K. Nielsen
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Queensland, Australia
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Pyrosequencing the Bemisia tabaci transcriptome reveals a highly diverse bacterial community and a robust system for insecticide resistance. PLoS One 2012; 7:e35181. [PMID: 22558125 PMCID: PMC3340392 DOI: 10.1371/journal.pone.0035181] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Accepted: 03/08/2012] [Indexed: 11/19/2022] Open
Abstract
Background Bemisia tabaci (Gennadius) is a phloem-feeding insect poised to become one of the major insect pests in open field and greenhouse production systems throughout the world. The high level of resistance to insecticides is a main factor that hinders continued use of insecticides for suppression of B. tabaci. Despite its prevalence, little is known about B. tabaci at the genome level. To fill this gap, an invasive B. tabaci B biotype was subjected to pyrosequencing-based transcriptome analysis to identify genes and gene networks putatively involved in various physiological and toxicological processes. Methodology and Principal Findings Using Roche 454 pyrosequencing, 857,205 reads containing approximately 340 megabases were obtained from the B. tabaci transcriptome. De novo assembly generated 178,669 unigenes including 30,980 from insects, 17,881 from bacteria, and 129,808 from the nohit. A total of 50,835 (28.45%) unigenes showed similarity to the non-redundant database in GenBank with a cut-off E-value of 10–5. Among them, 40,611 unigenes were assigned to one or more GO terms and 6,917 unigenes were assigned to 288 known pathways. De novo metatranscriptome analysis revealed highly diverse bacterial symbionts in B. tabaci, and demonstrated the host-symbiont cooperation in amino acid production. In-depth transcriptome analysis indentified putative molecular markers, and genes potentially involved in insecticide resistance and nutrient digestion. The utility of this transcriptome was validated by a thiamethoxam resistance study, in which annotated cytochrome P450 genes were significantly overexpressed in the resistant B. tabaci in comparison to its susceptible counterparts. Conclusions This transcriptome/metatranscriptome analysis sheds light on the molecular understanding of symbiosis and insecticide resistance in an agriculturally important phloem-feeding insect pest, and lays the foundation for future functional genomics research of the B. tabaci complex. Moreover, current pyrosequencing effort greatly enriched the existing whitefly EST database, and makes RNAseq a viable option for future genomic analysis.
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Ahn SJ, Vogel H, Heckel DG. Comparative analysis of the UDP-glycosyltransferase multigene family in insects. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2012; 42:133-147. [PMID: 22155036 DOI: 10.1016/j.ibmb.2011.11.006] [Citation(s) in RCA: 155] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Revised: 11/26/2011] [Accepted: 11/28/2011] [Indexed: 05/31/2023]
Abstract
UDP-glycosyltransferases (UGT) catalyze the conjugation of a range of diverse small lipophilic compounds with sugars to produce glycosides, playing an important role in the detoxification of xenobiotics and in the regulation of endobiotics in insects. Recent progress in genome sequencing has enabled an assessment of the extent of the UGT multigene family in insects. Here we report over 310 putative UGT genes identified from genomic databases of eight different insect species together with a transcript database from the lepidopteran Helicoverpa armigera. Phylogenetic analysis of the insect UGTs showed Order-specific gene diversification and inter-species conservation of this multigene family. Only one family (UGT50) is found in all insect species surveyed (except the pea aphid) and may be homologous to mammalian UGT8. Three families (UGT31, UGT32, and UGT305) related to Lepidopteran UGTs are unique to baculoviruses. A lepidopteran sub-tree constructed with 40 H. armigera UGTs and 44 Bombyx mori UGTs revealed that lineage-specific expansions of some families in both species appear to be driven by diversification in the N-terminal substrate binding domain, increasing the range of compounds that could be detoxified or regulated by glycosylation. By comparison of the deduced protein sequences, several important domains were predicted, including the N-terminal signal peptide, UGT signature motif, and C-terminal transmembrane domain. Furthermore, several conserved residues putatively involved in sugar donor binding and catalytic mechanism were also identified by comparison with human UGTs. Many UGTs were expressed in fat body, midgut, and Malpighian tubules, consistent with functions in detoxification, and some were expressed in antennae, suggesting a role in pheromone deactivation. Transcript variants derived from alternative splicing, exon skipping, or intron retention produced additional UGT diversity. These findings from this comparative study of two lepidopteran UGTs as well as other insects reveal a diversity comparable to this gene family in vertebrates, plants and fungi and show the magnitude of the task ahead, to determine biochemical function and physiological relevance of each UGT enzyme.
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Affiliation(s)
- Seung-Joon Ahn
- Department of Entomology, Max Planck Institute for Chemical Ecology, Jena 07745, Germany
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Rhee JS, Won EJ, Kim RO, Choi BS, Choi IY, Park GS, Shin KH, Lee YM, Lee JS. The polychaete, Perinereis nuntia ESTs and its use to uncover potential biomarker genes for molecular ecotoxicological studies. ENVIRONMENTAL RESEARCH 2012; 112:48-57. [PMID: 22018924 DOI: 10.1016/j.envres.2011.09.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2011] [Revised: 09/17/2011] [Accepted: 09/21/2011] [Indexed: 05/31/2023]
Abstract
The polychaete, Perinereis nuntia, has been used as an indicator species to assess the environmental condition of benthic communities in coastal marine environments. Recently, high-throughput sequencing technology has been proven to be a useful method for analyzing expressed sequence tags (ESTs) in non-model species. Thus, we have obtained extensive cDNA information by the pyrosequencing method, to utilize the polychaete species as a test organism for sediment quality monitoring studies. From the total RNA of P. nuntia, cDNA was reversely synthesized and randomly sequenced using a GS-FLX sequencer. In the assembly stage 1, 40,379 transcripts (13,666 contigs and 26,713 singletons) were acquired and showed 47% hitting rate compared with the GenBank non-redundant (NR) amino acid sequence database using BLASTX. After the stage-2 assembly, 21,657 transcripts were identified and showed 28% hitting rate. Finally, we obtained 6 064 unigenes that corresponded to the GenBank NR amino acid sequence database using BLASTX. Of the transcripts obtained in this species, we found a number of stress- and cell defense-related genes (e.g. heat shock protein family, antioxidant-related genes, cytochrome P450 genes) that are potentially useful for sediment monitoring at the molecular level, indicating that the pyrosequencing method is an effective approach to uncover gene families of potential biomarker genes simultaneously, and thus make transcriptomic studies possible. To confirm the usefulness of those potential biomarker genes, we analyzed the comparative profiling of P. nuntia mRNA transcripts between the samples collected from the polychaete aquaculture farm and the southern coast field of South Korea. In this paper, we summarize the expressed cDNA information of P. nuntia and discussed its potential use in environmental genomics and ecotoxicological studies for uncovering the potential molecular mechanisms of environmental stresses and chemical toxicity to the indicator species, P. nuntia in marine sediments.
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Affiliation(s)
- Jae-Sung Rhee
- Department of Molecular and Environmental Bioscience, Graduate School, Hanyang University, Seoul 133-791, South Korea
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Poelchau MF, Reynolds JA, Denlinger DL, Elsik CG, Armbruster PA. A de novo transcriptome of the Asian tiger mosquito, Aedes albopictus, to identify candidate transcripts for diapause preparation. BMC Genomics 2011; 12:619. [PMID: 22185595 PMCID: PMC3258294 DOI: 10.1186/1471-2164-12-619] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2011] [Accepted: 12/20/2011] [Indexed: 12/12/2022] Open
Abstract
Background Many temperate insects survive the harsh conditions of winter by undergoing photoperiodic diapause, a pre-programmed developmental arrest initiated by short day lengths. Despite the well-established ecological significance of photoperiodic diapause, the molecular basis of this crucial adaptation remains largely unresolved. The Asian tiger mosquito, Aedes albopictus (Skuse), represents an outstanding emerging model to investigate the molecular basis of photoperiodic diapause in a well-defined ecological and evolutionary context. Ae. albopictus is a medically significant vector and is currently considered the most invasive mosquito in the world. Traits related to diapause appear to be important factors contributing to the rapid spread of this mosquito. To generate novel sequence information for this species, as well as to discover transcripts involved in diapause preparation, we sequenced the transcriptome of Ae. albopictus oocytes destined to become diapausing or non-diapausing pharate larvae. Results 454 GS-FLX transcriptome sequencing yielded >1.1 million quality-filtered reads, which we assembled into 69,474 contigs (N50 = 1,009 bp). Our contig filtering approach, where we took advantage of strong sequence similarity to the fully sequenced genome of Aedes aegypti, as well as other reference organisms, resulted in 11,561 high-quality, conservative ESTs. Differential expression estimates based on normalized read counts revealed 57 genes with higher expression, and 257 with lower expression under diapause-inducing conditions. Analysis of expression by qPCR for 47 of these genes indicated a high correlation of expression levels between 454 sequence data and qPCR, but congruence of statistically significant differential expression was low. Seven genes identified as differentially expressed based on qPCR have putative functions that are consistent with the insect diapause syndrome; three genes have unknown function and represent novel candidates for the transcriptional basis of diapause. Conclusions Our transcriptome database provides a rich resource for the comparative genomics and functional genetics of Ae. albopictus, an invasive and medically important mosquito. Additionally, the identification of differentially expressed transcripts related to diapause enriches the limited knowledge base for the molecular basis of insect diapause, in particular for the preparatory stage. Finally, our analysis illustrates a useful approach that draws from a closely related reference genome to generate high-confidence ESTs in a non-model organism.
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Affiliation(s)
- Monica F Poelchau
- Department of Biology, Georgetown University, 37th and O Streets NW, Washington, DC, USA.
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Sui C, Zhang J, Wei J, Chen S, Li Y, Xu J, Jin Y, Xie C, Gao Z, Chen H, Yang C, Zhang Z, Xu Y. Transcriptome analysis of Bupleurum chinense focusing on genes involved in the biosynthesis of saikosaponins. BMC Genomics 2011; 12:539. [PMID: 22047182 PMCID: PMC3219613 DOI: 10.1186/1471-2164-12-539] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2011] [Accepted: 11/02/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Bupleurum chinense DC. is a widely used traditional Chinese medicinal plant. Saikosaponins are the major bioactive constituents of B. chinense, but relatively little is known about saikosaponin biosynthesis. The 454 pyrosequencing technology provides a promising opportunity for finding novel genes that participate in plant metabolism. Consequently, this technology may help to identify the candidate genes involved in the saikosaponin biosynthetic pathway. RESULTS One-quarter of the 454 pyrosequencing runs produced a total of 195, 088 high-quality reads, with an average read length of 356 bases (NCBI SRA accession SRA039388). A de novo assembly generated 24, 037 unique sequences (22, 748 contigs and 1, 289 singletons), 12, 649 (52.6%) of which were annotated against three public protein databases using a basic local alignment search tool (E-value ≤1e-10). All unique sequences were compared with NCBI expressed sequence tags (ESTs) (237) and encoding sequences (44) from the Bupleurum genus, and with a Sanger-sequenced EST dataset (3, 111). The 23, 173 (96.4%) unique sequences obtained in the present study represent novel Bupleurum genes. The ESTs of genes related to saikosaponin biosynthesis were found to encode known enzymes that catalyze the formation of the saikosaponin backbone; 246 cytochrome P450 (P450s) and 102 glycosyltransferases (GTs) unique sequences were also found in the 454 dataset. Full length cDNAs of 7 P450s and 7 uridine diphosphate GTs (UGTs) were verified by reverse transcriptase polymerase chain reaction or by cloning using 5' and/or 3' rapid amplification of cDNA ends. Two P450s and three UGTs were identified as the most likely candidates involved in saikosaponin biosynthesis. This finding was based on the coordinate up-regulation of their expression with β-AS in methyl jasmonate-treated adventitious roots and on their similar expression patterns with β-AS in various B. chinense tissues. CONCLUSIONS A collection of high-quality ESTs for B. chinense obtained by 454 pyrosequencing is provided here for the first time. These data should aid further research on the functional genomics of B. chinense and other Bupleurum species. The candidate genes for enzymes involved in saikosaponin biosynthesis, especially the P450s and UGTs, that were revealed provide a substantial foundation for follow-up research on the metabolism and regulation of the saikosaponins.
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Affiliation(s)
- Chun Sui
- Institute of Medicinal Plant Development (IMPLAD), Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151, Malianwa North Road, Haidian District, Beijing 100193, China
| | - Jie Zhang
- Institute of Medicinal Plant Development (IMPLAD), Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151, Malianwa North Road, Haidian District, Beijing 100193, China
| | - Jianhe Wei
- Institute of Medicinal Plant Development (IMPLAD), Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151, Malianwa North Road, Haidian District, Beijing 100193, China
| | - Shilin Chen
- Institute of Medicinal Plant Development (IMPLAD), Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151, Malianwa North Road, Haidian District, Beijing 100193, China
| | - Ying Li
- Institute of Medicinal Plant Development (IMPLAD), Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151, Malianwa North Road, Haidian District, Beijing 100193, China
| | - Jiesen Xu
- Institute of Medicinal Plant Development (IMPLAD), Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151, Malianwa North Road, Haidian District, Beijing 100193, China
| | - Yue Jin
- Institute of Medicinal Plant Development (IMPLAD), Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151, Malianwa North Road, Haidian District, Beijing 100193, China
| | - Caixiang Xie
- Institute of Medicinal Plant Development (IMPLAD), Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151, Malianwa North Road, Haidian District, Beijing 100193, China
| | - Zhihui Gao
- Institute of Medicinal Plant Development (IMPLAD), Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151, Malianwa North Road, Haidian District, Beijing 100193, China
| | - Hongjiang Chen
- Institute of Medicinal Plant Development (IMPLAD), Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151, Malianwa North Road, Haidian District, Beijing 100193, China
| | - Chengmin Yang
- Institute of Medicinal Plant Development (IMPLAD), Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151, Malianwa North Road, Haidian District, Beijing 100193, China
| | - Zheng Zhang
- Institute of Medicinal Plant Development (IMPLAD), Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151, Malianwa North Road, Haidian District, Beijing 100193, China
| | - Yanhong Xu
- Institute of Medicinal Plant Development (IMPLAD), Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151, Malianwa North Road, Haidian District, Beijing 100193, China
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Haseneyer G, Schmutzer T, Seidel M, Zhou R, Mascher M, Schön CC, Taudien S, Scholz U, Stein N, Mayer KFX, Bauer E. From RNA-seq to large-scale genotyping - genomics resources for rye (Secale cereale L.). BMC PLANT BIOLOGY 2011; 11:131. [PMID: 21951788 PMCID: PMC3191334 DOI: 10.1186/1471-2229-11-131] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2011] [Accepted: 09/28/2011] [Indexed: 05/18/2023]
Abstract
BACKGROUND The improvement of agricultural crops with regard to yield, resistance and environmental adaptation is a perpetual challenge for both breeding and research. Exploration of the genetic potential and implementation of genome-based breeding strategies for efficient rye (Secale cereale L.) cultivar improvement have been hampered by the lack of genome sequence information. To overcome this limitation we sequenced the transcriptomes of five winter rye inbred lines using Roche/454 GS FLX technology. RESULTS More than 2.5 million reads were assembled into 115,400 contigs representing a comprehensive rye expressed sequence tag (EST) resource. From sequence comparisons 5,234 single nucleotide polymorphisms (SNPs) were identified to develop the Rye5K high-throughput SNP genotyping array. Performance of the Rye5K SNP array was investigated by genotyping 59 rye inbred lines including the five lines used for sequencing, and five barley, three wheat, and two triticale accessions. A balanced distribution of allele frequencies ranging from 0.1 to 0.9 was observed. Residual heterozygosity of the rye inbred lines varied from 4.0 to 20.4% with higher average heterozygosity in the pollen compared to the seed parent pool. CONCLUSIONS The established sequence and molecular marker resources will improve and promote genetic and genomic research as well as genome-based breeding in rye.
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Affiliation(s)
- Grit Haseneyer
- Plant Breeding, Technische Universität München, Centre of Life and Food Sciences Weihenstephan, 85354 Freising, Germany
| | - Thomas Schmutzer
- Bioinformatics and Information Technology, Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), D-06466 Gatersleben, Germany
| | - Michael Seidel
- MIPS/IBIS, Institute for Bioinformatics and Systems Biology, Helmholtz Centre Munich, German Research Centre for Environmental Health (GmbH), 85764 Neuherberg, Germany
| | - Ruonan Zhou
- Genome Diversity, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Gatersleben, Germany
| | - Martin Mascher
- Bioinformatics and Information Technology, Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), D-06466 Gatersleben, Germany
| | - Chris-Carolin Schön
- Plant Breeding, Technische Universität München, Centre of Life and Food Sciences Weihenstephan, 85354 Freising, Germany
| | - Stefan Taudien
- Genome Analysis, Leibniz Institute for Age Research, Fritz-Lipmann-Institute (FLI), 07745 Jena, Germany
| | - Uwe Scholz
- Bioinformatics and Information Technology, Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), D-06466 Gatersleben, Germany
| | - Nils Stein
- Genome Diversity, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Gatersleben, Germany
| | - Klaus FX Mayer
- MIPS/IBIS, Institute for Bioinformatics and Systems Biology, Helmholtz Centre Munich, German Research Centre for Environmental Health (GmbH), 85764 Neuherberg, Germany
| | - Eva Bauer
- Plant Breeding, Technische Universität München, Centre of Life and Food Sciences Weihenstephan, 85354 Freising, Germany
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Zagrobelny M, Møller BL. Cyanogenic glucosides in the biological warfare between plants and insects: the Burnet moth-Birdsfoot trefoil model system. PHYTOCHEMISTRY 2011; 72:1585-1592. [PMID: 21429539 DOI: 10.1016/j.phytochem.2011.02.023] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2010] [Revised: 02/01/2011] [Accepted: 02/22/2011] [Indexed: 05/30/2023]
Abstract
Cyanogenic glucosides are important components of plant defense against generalist herbivores due to their bitter taste and the release of toxic hydrogen cyanide upon tissue disruption. Some specialized herbivores, especially insects, preferentially feed on cyanogenic plants. Such herbivores have acquired the ability to metabolize cyanogenic glucosides or to sequester them for use in their own predator defense. Burnet moths (Zygaena) sequester the cyanogenic glucosides linamarin and lotaustralin from their food plants (Fabaceae) and, in parallel, are able to carry out de novo synthesis of the very same compounds. The ratio and content of cyanogenic glucosides is tightly regulated in the different stages of the Zygaena filipendulae lifecycle and the compounds play several important roles in addition to defense. The transfer of a nuptial gift of cyanogenic glucosides during mating of Zygaena has been demonstrated as well as the possible involvement of hydrogen cyanide in male assessment and nitrogen metabolism. As the capacity to de novo synthesize cyanogenic glucosides was developed independently in plants and insects, the great similarities of the pathways between the two kingdoms indicate that cyanogenic glucosides are produced according to a universal route providing recruitment of the enzymes required. Pyrosequencing of Z. filipendulae larvae de novo synthesizing cyanogenic glucosides served to provide a set of good candidate genes, and demonstrated that the genes encoding the pathway in plants and Z. filipendulae are not closely related phylogenetically. Identification of insect genes involved in the biosynthesis and turn-over of cyanogenic glucosides will provide new insights into biological warfare as a determinant of co-evolution between plants and insects.
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Affiliation(s)
- Mika Zagrobelny
- Plant Biochemistry Laboratory, Department of Plant Biology and Biotechnology, University of Copenhagen, 40 Thorvaldsensvej, DK-1871 Frederiksberg C, Copenhagen, Denmark
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Jensen NB, Zagrobelny M, Hjernø K, Olsen CE, Houghton-Larsen J, Borch J, Møller BL, Bak S. Convergent evolution in biosynthesis of cyanogenic defence compounds in plants and insects. Nat Commun 2011; 2:273. [PMID: 21505429 PMCID: PMC4354137 DOI: 10.1038/ncomms1271] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2010] [Accepted: 03/09/2011] [Indexed: 11/17/2022] Open
Abstract
For more than 420 million years, plants, insects and their predators have co-evolved based on a chemical arms race including deployment of refined chemical defence systems by each player. Cyanogenic glucosides are produced by numerous plants and by some specialized insects and serve an important role as defence compounds in these intimate interactions. Burnet moth larvae are able to sequester cyanogenic glucosides from their food plant as well as to carry out de novo biosynthesis. Here we show that three genes (CYP405A2, CYP332A3 and UGT33A1) encode the entire biosynthetic pathway of cyanogenic glucosides in the Burnet moth Zygaena filipendulae. In both plants and insects, convergent evolution has led to two multifunctional P450 enzymes each catalysing unusual reactions and a glucosyl-transferase acting in sequence to catalyse cyanogenic glucoside formation. Thus, plants and insects have independently found a way to package a cyanide time bomb to fend off herbivores and predators. Cyanide-releasing defence systems in plants and animals are important to the evolution of plant–herbivore interactions. The authors identify the enzymes responsible for biosynthesis of cyanogenic glucosides by Six-spot Burnet moth caterpillars, which have evolved independently from the known plant pathway.
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Affiliation(s)
- Niels Bjerg Jensen
- Plant Biochemistry Laboratory, Department of Plant Biology and Biotechnology, University of Copenhagen, 40 Thorvaldsensvej, DK 1871 Frederiksberg C, Copenhagen, Denmark
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Price DP, Nagarajan V, Churbanov A, Houde P, Milligan B, Drake LL, Gustafson JE, Hansen IA. The fat body transcriptomes of the yellow fever mosquito Aedes aegypti, pre- and post- blood meal. PLoS One 2011; 6:e22573. [PMID: 21818341 PMCID: PMC3144915 DOI: 10.1371/journal.pone.0022573] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Accepted: 06/24/2011] [Indexed: 12/01/2022] Open
Abstract
BACKGROUND The fat body is the main organ of intermediary metabolism in insects and the principal source of hemolymph proteins. As part of our ongoing efforts to understand mosquito fat body physiology and to identify novel targets for insect control, we have conducted a transcriptome analysis of the fat body of Aedes aegypti before and in response to blood feeding. RESULTS We created two fat body non-normalized EST libraries, one from mosquito fat bodies non-blood fed (NBF) and another from mosquitoes 24 hrs post-blood meal (PBM). 454 pyrosequencing of the non-normalized libraries resulted in 204,578 useable reads from the NBF sample and 323,474 useable reads from the PBM sample. Alignment of reads to the existing reference Ae. aegypti transcript libraries for analysis of differential expression between NBF and PBM samples revealed 116,912 and 115,051 matches, respectively. De novo assembly of the reads from the NBF sample resulted in 15,456 contigs, and assembly of the reads from the PBM sample resulted in 15,010 contigs. Collectively, 123 novel transcripts were identified within these contigs. Prominently expressed transcripts in the NBF fat body library were represented by transcripts encoding ribosomal proteins. Thirty-five point four percent of all reads in the PBM library were represented by transcripts that encode yolk proteins. The most highly expressed were transcripts encoding members of the cathepsin b, vitellogenin, vitellogenic carboxypeptidase, and vitelline membrane protein families. CONCLUSION The two fat body transcriptomes were considerably different from each other in terms of transcript expression in terms of abundances of transcripts and genes expressed. They reflect the physiological shift of the pre-feeding fat body from a resting state to vitellogenic gene expression after feeding.
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Affiliation(s)
- David P. Price
- The Molecular Biology Program, New Mexico State University, Las Cruces, New Mexico, United States of America
| | - Vijayaraj Nagarajan
- Bioinformatics and Computational Biosciences Branch (BCBB), OCICB/OSMO/OD/NIAID/NIH, Bethesda, Maryland, United States of America
| | - Alexander Churbanov
- Department of Biology, New Mexico State University, Las Cruces, New Mexico, United States of America
- The Roadrunner Sequencing Lab, New Mexico State University, Las Cruces, New Mexico, United States of America
| | - Peter Houde
- Department of Biology, New Mexico State University, Las Cruces, New Mexico, United States of America
- The Roadrunner Sequencing Lab, New Mexico State University, Las Cruces, New Mexico, United States of America
| | - Brook Milligan
- Department of Biology, New Mexico State University, Las Cruces, New Mexico, United States of America
- The Roadrunner Sequencing Lab, New Mexico State University, Las Cruces, New Mexico, United States of America
| | - Lisa L. Drake
- Department of Biology, New Mexico State University, Las Cruces, New Mexico, United States of America
| | - John E. Gustafson
- Department of Biology, New Mexico State University, Las Cruces, New Mexico, United States of America
- The Molecular Biology Program, New Mexico State University, Las Cruces, New Mexico, United States of America
| | - Immo A. Hansen
- Department of Biology, New Mexico State University, Las Cruces, New Mexico, United States of America
- The Institute of Applied Biosciences, New Mexico State University, Las Cruces, New Mexico, United States of America
- The Molecular Biology Program, New Mexico State University, Las Cruces, New Mexico, United States of America
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Hou R, Bao Z, Wang S, Su H, Li Y, Du H, Hu J, Wang S, Hu X. Transcriptome sequencing and de novo analysis for Yesso scallop (Patinopecten yessoensis) using 454 GS FLX. PLoS One 2011; 6:e21560. [PMID: 21720557 PMCID: PMC3123371 DOI: 10.1371/journal.pone.0021560] [Citation(s) in RCA: 192] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2010] [Accepted: 06/03/2011] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Bivalves comprise 30,000 extant species, constituting the second largest group of mollusks. However, limited genetic research has focused on this group of animals so far, which is, in part, due to the lack of genomic resources. The advent of high-throughput sequencing technologies enables generation of genomic resources in a short time and at a minimal cost, and therefore provides a turning point for bivalve research. In the present study, we performed de novo transcriptome sequencing to first produce a comprehensive expressed sequence tag (EST) dataset for the Yesso scallop (Patinopecten yessoensis). RESULTS In a single 454 sequencing run, 805,330 reads were produced and then assembled into 32,590 contigs, with about six-fold sequencing coverage. A total of 25,237 unique protein-coding genes were identified from a variety of developmental stages and adult tissues based on sequence similarities with known proteins. As determined by GO annotation and KEGG pathway mapping, functional annotation of the unigenes recovered diverse biological functions and processes. Transcripts putatively involved in growth, reproduction and stress/immune-response were identified. More than 49,000 single nucleotide polymorphisms (SNPs) and 2,700 simple sequence repeats (SSRs) were also detected. CONCLUSION Our data provide the most comprehensive transcriptomic resource currently available for P. yessoensis. Candidate genes potentially involved in growth, reproduction, and stress/immunity-response were identified, and are worthy of further investigation. A large number of SNPs and SSRs were also identified and ready for marker development. This resource should lay an important foundation for future genetic or genomic studies on this species.
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Affiliation(s)
- Rui Hou
- Key Laboratory of Marine Genetics and Breeding (MGB), Ministry of Education, College of Marine Life Sciences. Ocean University of China, Qingdao, China
| | - Zhenmin Bao
- Key Laboratory of Marine Genetics and Breeding (MGB), Ministry of Education, College of Marine Life Sciences. Ocean University of China, Qingdao, China
| | - Shan Wang
- Key Laboratory of Marine Genetics and Breeding (MGB), Ministry of Education, College of Marine Life Sciences. Ocean University of China, Qingdao, China
| | - Hailin Su
- Key Laboratory of Marine Genetics and Breeding (MGB), Ministry of Education, College of Marine Life Sciences. Ocean University of China, Qingdao, China
| | - Yan Li
- Key Laboratory of Marine Genetics and Breeding (MGB), Ministry of Education, College of Marine Life Sciences. Ocean University of China, Qingdao, China
| | - Huixia Du
- Key Laboratory of Marine Genetics and Breeding (MGB), Ministry of Education, College of Marine Life Sciences. Ocean University of China, Qingdao, China
| | - Jingjie Hu
- Key Laboratory of Marine Genetics and Breeding (MGB), Ministry of Education, College of Marine Life Sciences. Ocean University of China, Qingdao, China
| | - Shi Wang
- Key Laboratory of Marine Genetics and Breeding (MGB), Ministry of Education, College of Marine Life Sciences. Ocean University of China, Qingdao, China
- * E-mail: (SW); (XH)
| | - Xiaoli Hu
- Key Laboratory of Marine Genetics and Breeding (MGB), Ministry of Education, College of Marine Life Sciences. Ocean University of China, Qingdao, China
- * E-mail: (SW); (XH)
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Gregory R, Darby AC, Irving H, Coulibaly MB, Hughes M, Koekemoer LL, Coetzee M, Ranson H, Hemingway J, Hall N, Wondji CS. A de novo expression profiling of Anopheles funestus, malaria vector in Africa, using 454 pyrosequencing. PLoS One 2011; 6:e17418. [PMID: 21364769 PMCID: PMC3045460 DOI: 10.1371/journal.pone.0017418] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2010] [Accepted: 01/25/2011] [Indexed: 11/25/2022] Open
Abstract
Background Anopheles funestus is one of the major malaria vectors in Africa and yet there are few genomic tools available for this species compared to An. gambiae. To start to close this knowledge gap, we sequenced the An. funestus transcriptome using cDNA libraries developed from a pyrethroid resistant laboratory strain and a pyrethroid susceptible field strain from Mali. Results Using a pool of life stages (pupae, larvae, adults: females and males) for each strain, 454 sequencing generated 375,619 reads (average length of 182 bp). De novo assembly generated 18,103 contigs with average length of 253 bp. The average depth of coverage of these contigs was 8.3. In total 20.8% of all reads were novel when compared to reference databases. The sequencing of the field strain generated 204,758 reads compared to 170,861 from the insecticide resistant laboratory strain. The contigs most differentially represented in the resistant strain belong to the P450 gene family and cuticular genes which correlates with previous studies implicating both of these gene families in pyrethroid resistance. qPCR carried out on six contigs indicates that these ESTs could be suitable for gene expression studies such as microarray. 31,000 sites were estimated to contain Single Nucleotide Polymorphisms (SNPs) and analysis of SNPs from 20 contigs suggested that most of these SNPs are likely to be true SNPs. Gene conservation analysis confirmed the close phylogenetic relationship between An. funestus and An. gambiae. Conclusion This study represents a significant advance for the genetics and genomics of An. funestus since it provides an extensive set of both Expressed Sequence Tags (ESTs) and SNPs which can be readily adopted for the design of new genomic tools such as microarray or SNP platforms.
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Affiliation(s)
- Richard Gregory
- University of Liverpool, School of Biological Sciences, Cornwall House, United Kingdom
| | - Alistair C. Darby
- University of Liverpool, School of Biological Sciences, Cornwall House, United Kingdom
| | - Helen Irving
- Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | | | - Margaret Hughes
- University of Liverpool, School of Biological Sciences, Cornwall House, United Kingdom
| | - Lizette L. Koekemoer
- Medical Entomology and Vector Control, Division of Virology and Communicable Disease Surveillance, University of the Witwatersrand and the National Institute for Communicable Diseases (NICD), Sandringham, Johannesburg, South Africa
| | - Maureen Coetzee
- Medical Entomology and Vector Control, Division of Virology and Communicable Disease Surveillance, University of the Witwatersrand and the National Institute for Communicable Diseases (NICD), Sandringham, Johannesburg, South Africa
| | - Hilary Ranson
- Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Janet Hemingway
- Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Neil Hall
- University of Liverpool, School of Biological Sciences, Cornwall House, United Kingdom
| | - Charles S. Wondji
- Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- * E-mail:
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Der JP, Barker MS, Wickett NJ, dePamphilis CW, Wolf PG. De novo characterization of the gametophyte transcriptome in bracken fern, Pteridium aquilinum. BMC Genomics 2011; 12:99. [PMID: 21303537 PMCID: PMC3042945 DOI: 10.1186/1471-2164-12-99] [Citation(s) in RCA: 96] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2010] [Accepted: 02/08/2011] [Indexed: 11/23/2022] Open
Abstract
Background Because of their phylogenetic position and unique characteristics of their biology and life cycle, ferns represent an important lineage for studying the evolution of land plants. Large and complex genomes in ferns combined with the absence of economically important species have been a barrier to the development of genomic resources. However, high throughput sequencing technologies are now being widely applied to non-model species. We leveraged the Roche 454 GS-FLX Titanium pyrosequencing platform in sequencing the gametophyte transcriptome of bracken fern (Pteridium aquilinum) to develop genomic resources for evolutionary studies. Results 681,722 quality and adapter trimmed reads totaling 254 Mbp were assembled de novo into 56,256 unique sequences (i.e. unigenes) with a mean length of 547.2 bp and a total assembly size of 30.8 Mbp with an average read-depth coverage of 7.0×. We estimate that 87% of the complete transcriptome has been sequenced and that all transcripts have been tagged. 61.8% of the unigenes had blastx hits in the NCBI nr protein database, representing 22,596 unique best hits. The longest open reading frame in 52.2% of the unigenes had positive domain matches in InterProScan searches. We assigned 46.2% of the unigenes with a GO functional annotation and 16.0% with an enzyme code annotation. Enzyme codes were used to retrieve and color KEGG pathway maps. A comparative genomics approach revealed a substantial proportion of genes expressed in bracken gametophytes to be shared across the genomes of Arabidopsis, Selaginella and Physcomitrella, and identified a substantial number of potentially novel fern genes. By comparing the list of Arabidopsis genes identified by blast with a list of gametophyte-specific Arabidopsis genes taken from the literature, we identified a set of potentially conserved gametophyte specific genes. We screened unigenes for repetitive sequences to identify 548 potentially-amplifiable simple sequence repeat loci and 689 expressed transposable elements. Conclusions This study is the first comprehensive transcriptome analysis for a fern and represents an important scientific resource for comparative evolutionary and functional genomics studies in land plants. We demonstrate the utility of high-throughput sequencing of a normalized cDNA library for de novo transcriptome characterization and gene discovery in a non-model plant.
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Affiliation(s)
- Joshua P Der
- Department of Biology and Center for Integrated Biosystems, Utah State University, Logan, UT 84322-5305, USA.
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Bai X, Mamidala P, Rajarapu SP, Jones SC, Mittapalli O. Transcriptomics of the bed bug (Cimex lectularius). PLoS One 2011; 6:e16336. [PMID: 21283830 PMCID: PMC3023805 DOI: 10.1371/journal.pone.0016336] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2010] [Accepted: 12/10/2010] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Bed bugs (Cimex lectularius) are blood-feeding insects poised to become one of the major pests in households throughout the United States. Resistance of C. lectularius to insecticides/pesticides is one factor thought to be involved in its sudden resurgence. Despite its high-impact status, scant knowledge exists at the genomic level for C. lectularius. Hence, we subjected the C. lectularius transcriptome to 454 pyrosequencing in order to identify potential genes involved in pesticide resistance. METHODOLOGY AND PRINCIPAL FINDINGS Using 454 pyrosequencing, we obtained a total of 216,419 reads with 79,596,412 bp, which were assembled into 35,646 expressed sequence tags (3902 contigs and 31744 singletons). Nearly 85.9% of the C. lectularius sequences showed similarity to insect sequences, but 44.8% of the deduced proteins of C. lectularius did not show similarity with sequences in the GenBank non-redundant database. KEGG analysis revealed putative members of several detoxification pathways involved in pesticide resistance. Lamprin domains, Protein Kinase domains, Protein Tyrosine Kinase domains and cytochrome P450 domains were among the top Pfam domains predicted for the C. lectularius sequences. An initial assessment of putative defense genes, including a cytochrome P450 and a glutathione-S-transferase (GST), revealed high transcript levels for the cytochrome P450 (CYP9) in pesticide-exposed versus pesticide-susceptible C. lectularius populations. A significant number of single nucleotide polymorphisms (296) and microsatellite loci (370) were predicted in the C. lectularius sequences. Furthermore, 59 putative sequences of Wolbachia were retrieved from the database. CONCLUSIONS To our knowledge this is the first study to elucidate the genetic makeup of C. lectularius. This pyrosequencing effort provides clues to the identification of potential detoxification genes involved in pesticide resistance of C. lectularius and lays the foundation for future functional genomics studies.
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Affiliation(s)
- Xiaodong Bai
- Department of Entomology, Ohio Agricultural and Research Development Center, The Ohio State University, Wooster, Ohio, United States of America
| | - Praveen Mamidala
- Department of Entomology, Ohio Agricultural and Research Development Center, The Ohio State University, Wooster, Ohio, United States of America
| | - Swapna P. Rajarapu
- Department of Entomology, Ohio Agricultural and Research Development Center, The Ohio State University, Wooster, Ohio, United States of America
| | - Susan C. Jones
- Department of Entomology, The Ohio State University, Columbus, Ohio, United States of America
| | - Omprakash Mittapalli
- Department of Entomology, Ohio Agricultural and Research Development Center, The Ohio State University, Wooster, Ohio, United States of America
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Barreto FS, Moy GW, Burton RS. Interpopulation patterns of divergence and selection across the transcriptome of the copepod Tigriopus californicus. Mol Ecol 2010; 20:560-72. [PMID: 21199025 DOI: 10.1111/j.1365-294x.2010.04963.x] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The accumulation of genetic incompatibilities between isolated populations is thought to lead to the evolution of intrinsic postzygotic isolation. The molecular basis for these mechanisms, however, remains poorly understood. The intertidal copepod Tigriopus californicus provides unique opportunities for addressing mechanistic questions regarding the early stages of speciation; hybrids between highly divergent populations are fertile and viable, but exhibit reduced fitness at the F(2) or later generations. Given the current scarcity of genomic information in taxa at incipient stages of reproductive isolation, we utilize high-throughout 454 pyrosequencing to characterize a substantial fraction of protein-coding regions (the transcriptome) of T. californicus. Our sequencing effort was divided equally between two divergent populations in order to estimate levels of divergence and to reveal patterns of selection across the transcriptome. Assembly of sequences generated over 40,000 putatively unique transcripts (unigenes) for each population, 19,622 of which were orthologous between populations. BLAST searches of public databases determined protein identity and functional features for 15,402 and 12,670 unigenes, respectively. Based on rates of nonsynonymous and synonymous substitutions in 5897 interpopulation orthologs (those >150 bp and with at least 2X coverage), we identified 229 potential targets of positive selection. Many of these genes are predicted to be involved in several metabolic processes, and to function in hydrolase, peptidase and binding activities. The library of T. californicus coding regions, annotated with their predicted functions and level of divergence, will serve as an invaluable resource for elucidating molecular mechanisms underlying the early stages of speciation.
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Affiliation(s)
- Felipe S Barreto
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California-San Diego, La Jolla, CA 92037, USA.
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Wang Z, Fang B, Chen J, Zhang X, Luo Z, Huang L, Chen X, Li Y. De novo assembly and characterization of root transcriptome using Illumina paired-end sequencing and development of cSSR markers in sweet potato (Ipomoea batatas). BMC Genomics 2010; 11:726. [PMID: 21182800 PMCID: PMC3016421 DOI: 10.1186/1471-2164-11-726] [Citation(s) in RCA: 333] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2010] [Accepted: 12/24/2010] [Indexed: 12/31/2022] Open
Abstract
Background The tuberous root of sweetpotato is an important agricultural and biological organ. There are not sufficient transcriptomic and genomic data in public databases for understanding of the molecular mechanism underlying the tuberous root formation and development. Thus, high throughput transcriptome sequencing is needed to generate enormous transcript sequences from sweetpotato root for gene discovery and molecular marker development. Results In this study, more than 59 million sequencing reads were generated using Illumina paired-end sequencing technology. De novo assembly yielded 56,516 unigenes with an average length of 581 bp. Based on sequence similarity search with known proteins, a total of 35,051 (62.02%) genes were identified. Out of these annotated unigenes, 5,046 and 11,983 unigenes were assigned to gene ontology and clusters of orthologous group, respectively. Searching against the Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG) indicated that 17,598 (31.14%) unigenes were mapped to 124 KEGG pathways, and 11,056 were assigned to metabolic pathways, which were well represented by carbohydrate metabolism and biosynthesis of secondary metabolite. In addition, 4,114 cDNA SSRs (cSSRs) were identified as potential molecular markers in our unigenes. One hundred pairs of PCR primers were designed and used for validation of the amplification and assessment of the polymorphism in genomic DNA pools. The result revealed that 92 primer pairs were successfully amplified in initial screening tests. Conclusion This study generated a substantial fraction of sweetpotato transcript sequences, which can be used to discover novel genes associated with tuberous root formation and development and will also make it possible to construct high density microarrays for further characterization of gene expression profiles during these processes. Thousands of cSSR markers identified in the present study can enrich molecular markers and will facilitate marker-assisted selection in sweetpotato breeding. Overall, these sequences and markers will provide valuable resources for the sweetpotato community. Additionally, these results also suggested that transcriptome analysis based on Illumina paired-end sequencing is a powerful tool for gene discovery and molecular marker development for non-model species, especially those with large and complex genome.
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Affiliation(s)
- Zhangying Wang
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 PR China
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Joubert C, Piquemal D, Marie B, Manchon L, Pierrat F, Zanella-Cléon I, Cochennec-Laureau N, Gueguen Y, Montagnani C. Transcriptome and proteome analysis of Pinctada margaritifera calcifying mantle and shell: focus on biomineralization. BMC Genomics 2010; 11:613. [PMID: 21040589 PMCID: PMC3091754 DOI: 10.1186/1471-2164-11-613] [Citation(s) in RCA: 161] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2010] [Accepted: 11/01/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The shell of the pearl-producing bivalve Pinctada margaritifera is composed of an organic cell-free matrix that plays a key role in the dynamic process of biologically-controlled biomineralization. In order to increase genomic resources and identify shell matrix proteins implicated in biomineralization in P. margaritifera, high-throughput Expressed Sequence Tag (EST) pyrosequencing was undertaken on the calcifying mantle, combined with a proteomic analysis of the shell. RESULTS We report the functional analysis of 276 738 sequences, leading to the constitution of an unprecedented catalog of 82 P. margaritifera biomineralization-related mantle protein sequences. Components of the current "chitin-silk fibroin gel-acidic macromolecule" model of biomineralization processes were found, in particular a homolog of a biomineralization protein (Pif-177) recently discovered in P. fucata. Among these sequences, we could show the localization of two other biomineralization protein transcripts, pmarg-aspein and pmarg-pearlin, in two distinct areas of the outer mantle epithelium, suggesting their implication in calcite and aragonite formation. Finally, by combining the EST approach with a proteomic mass spectrometry analysis of proteins isolated from the P. margaritifera shell organic matrix, we demonstrated the presence of 30 sequences containing almost all of the shell proteins that have been previously described from shell matrix protein analyses of the Pinctada genus. The integration of these two methods allowed the global composition of biomineralizing tissue and calcified structures to be examined in tandem for the first time. CONCLUSIONS This EST study made on the calcifying tissue of P. margaritifera is the first description of pyrosequencing on a pearl-producing bivalve species. Our results provide direct evidence that our EST data set covers most of the diversity of the matrix protein of P. margaritifera shell, but also that the mantle transcripts encode proteins present in P. margaritifera shell, hence demonstrating their implication in shell formation. Combining transcriptomic and proteomic approaches is therefore a powerful way to identify proteins involved in biomineralization. Data generated in this study supply the most comprehensive list of biomineralization-related sequences presently available among protostomian species, and represent a major breakthrough in the field of molluskan biomineralization.
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Affiliation(s)
- Caroline Joubert
- Ifremer - Laboratoire de Biotechnologie et de Qualité de Perle, Centre Océanologique du Pacifique - BP 7004, 98719 Taravao, French Polynesia
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Kumar S, Blaxter ML. Comparing de novo assemblers for 454 transcriptome data. BMC Genomics 2010; 11:571. [PMID: 20950480 PMCID: PMC3091720 DOI: 10.1186/1471-2164-11-571] [Citation(s) in RCA: 214] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2010] [Accepted: 10/16/2010] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Roche 454 pyrosequencing has become a method of choice for generating transcriptome data from non-model organisms. Once the tens to hundreds of thousands of short (250-450 base) reads have been produced, it is important to correctly assemble these to estimate the sequence of all the transcripts. Most transcriptome assembly projects use only one program for assembling 454 pyrosequencing reads, but there is no evidence that the programs used to date are optimal. We have carried out a systematic comparison of five assemblers (CAP3, MIRA, Newbler, SeqMan and CLC) to establish best practices for transcriptome assemblies, using a new dataset from the parasitic nematode Litomosoides sigmodontis. RESULTS Although no single assembler performed best on all our criteria, Newbler 2.5 gave longer contigs, better alignments to some reference sequences, and was fast and easy to use. SeqMan assemblies performed best on the criterion of recapitulating known transcripts, and had more novel sequence than the other assemblers, but generated an excess of small, redundant contigs. The remaining assemblers all performed almost as well, with the exception of Newbler 2.3 (the version currently used by most assembly projects), which generated assemblies that had significantly lower total length. As different assemblers use different underlying algorithms to generate contigs, we also explored merging of assemblies and found that the merged datasets not only aligned better to reference sequences than individual assemblies, but were also more consistent in the number and size of contigs. CONCLUSIONS Transcriptome assemblies are smaller than genome assemblies and thus should be more computationally tractable, but are often harder because individual contigs can have highly variable read coverage. Comparing single assemblers, Newbler 2.5 performed best on our trial data set, but other assemblers were closely comparable. Combining differently optimal assemblies from different programs however gave a more credible final product, and this strategy is recommended.
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Affiliation(s)
- Sujai Kumar
- Institute of Evolutionary Biology, University of Edinburgh, West Mains Road, Edinburgh EH9 3JT, UK
| | - Mark L Blaxter
- Institute of Evolutionary Biology, University of Edinburgh, West Mains Road, Edinburgh EH9 3JT, UK
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Sun C, Li Y, Wu Q, Luo H, Sun Y, Song J, Lui EMK, Chen S. De novo sequencing and analysis of the American ginseng root transcriptome using a GS FLX Titanium platform to discover putative genes involved in ginsenoside biosynthesis. BMC Genomics 2010; 11:262. [PMID: 20416102 PMCID: PMC2873478 DOI: 10.1186/1471-2164-11-262] [Citation(s) in RCA: 190] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2009] [Accepted: 04/24/2010] [Indexed: 11/10/2022] Open
Abstract
Background American ginseng (Panax quinquefolius L.) is one of the most widely used herbal remedies in the world. Its major bioactive constituents are the triterpene saponins known as ginsenosides. However, little is known about ginsenoside biosynthesis in American ginseng, especially the late steps of the pathway. Results In this study, a one-quarter 454 sequencing run produced 209,747 high-quality reads with an average sequence length of 427 bases. De novo assembly generated 31,088 unique sequences containing 16,592 contigs and 14,496 singletons. About 93.1% of the high-quality reads were assembled into contigs with an average 8-fold coverage. A total of 21,684 (69.8%) unique sequences were annotated by a BLAST similarity search against four public sequence databases, and 4,097 of the unique sequences were assigned to specific metabolic pathways by the Kyoto Encyclopedia of Genes and Genomes. Based on the bioinformatic analysis described above, we found all of the known enzymes involved in ginsenoside backbone synthesis, starting from acetyl-CoA via the isoprenoid pathway. Additionally, a total of 150 cytochrome P450 (CYP450) and 235 glycosyltransferase unique sequences were found in the 454 cDNA library, some of which encode enzymes responsible for the conversion of the ginsenoside backbone into the various ginsenosides. Finally, one CYP450 and four UDP-glycosyltransferases were selected as the candidates most likely to be involved in ginsenoside biosynthesis through a methyl jasmonate (MeJA) inducibility experiment and tissue-specific expression pattern analysis based on a real-time PCR assay. Conclusions We demonstrated, with the assistance of the MeJA inducibility experiment and tissue-specific expression pattern analysis, that transcriptome analysis based on 454 pyrosequencing is a powerful tool for determining the genes encoding enzymes responsible for the biosynthesis of secondary metabolites in non-model plants. Additionally, the expressed sequence tags (ESTs) and unique sequences from this study provide an important resource for the scientific community that is interested in the molecular genetics and functional genomics of American ginseng.
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Affiliation(s)
- Chao Sun
- Institute of Medicinal Plant Development (IMPLAD), Chinese Academy of Medical Sciences, Haidian District, Beijing, China
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