De novo transcriptomic resources for two sibling species of moths: Ostrinia nubilalis and O. scapulalis

BMC Research Notes

Réjane Streiff²  Denis Bourguet²  Philippe Audiot²  Emmanuelle Beyne¹  Bernhard Gschloessl² 

[1] Present address: Institute of Human Genetics, CNRS, Montpellier, 34396, France;Centre de Biologie pour la Gestion des Populations (CBGP) UMR INRA-IRD-CIRAD-Montpellier SupAgro, Campus International de Baillarguet, Montferrier-sur-Lez Cedex, 34988, France

关键词: Ostrinia scapulalis;    Ostrinia nubilalis;    Sibling species;    Adzuki bean borer;    European corn borer;    Moth;    Tanscriptome;    454 sequencing;    NGS;   

Others  :  1143405
DOI  :  10.1186/1756-0500-6-73

 received in 2012-10-10, accepted in 2013-02-20,  发布年份 2013

【 摘 要 】

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.

【 授权许可】

   
2013 Gschloessl et al; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

【 参考文献 】

• [1]Mutuura A, Monroe E: Taxonomy and distribution of the European corn borer and allied species: genus Ostrinia (lepidoptera: pyralidae). Memoirs of the Entomological Society of America 1970, 71:1-112.
• [2]Frolov AN, Bourguet D, Ponsard S: Reconsidering the taxomony of several Ostrinia species in the light of reproductive isolation: a tale for Ernst Mayr. Biol J Linn Soc 2007, 91(1):49-72.
• [3]Leniaud L, Audiot P, Bourguet D, Frérot B, Genestier G, Lee SF, Malausa T, Le Pallec A-H, Souqual M-C, Ponsard S: Genetic structure of European and Mediterranean maize borer populations on several wild and cultivated host plants. Entomol Exp Appl 2006, 120(1):51-62.
• [4]Malausa T, Dalecky A, Ponsard S, Audiot P, Streiff R, Chaval Y, Bourguet D: Genetic structure and gene flow in french populations of two Ostrinia taxa: host races or sibling species? Mol Ecol 2007, 16(20):4210-4222.
• [5]Midamegbe A, Vitalis R, Malausa T, Delava E, Cros-Arteil S, Streiff R: Scanning the European corn borer (Ostrinia spp.) genome for adaptive divergence between host-affiliated sibling species. Mol Ecol 2011, 20(7):1414-1430.
• [6]Malausa T, Bethenod MT, Bontemps A, Bourguet D, Cornuet JM, Ponsard S: Assortative mating in sympatric host races of the European corn borer. Science 2005, 308(5719):258-260.
• [7]Bethenod MT, Thomas Y, Rousset F, Frérot B, Pélozuelo L, Genestier G, Bourguet D: Genetic isolation between two sympatric host plant races of the European corn borer, Ostrinia nubilalis Hübner. II: assortative mating and host-plant preferences for oviposition. Heredity 2005, 94(2):264-270.
• [8]Pélozuelo L, Meusnier S, Audiot P, Bourguet D, Ponsard S: Assortative mating between European corn borer pheromone races: beyond assortative meeting. PLoS One 2007, 2(6):e555.
• [9]Calcagno V, Thomas Y, Bourguet D: Sympatric host races of the European corn borer: adaptation to host plants and hybrid performance. J Evol Biol 2007, 20(5):1720-1729.
• [10]Malausa T, Pélissié B, Piveteau V, Pelissier C, Bourguet D, Ponsard S: Differences in oviposition behaviour of two sympatric sibling species of the genus Ostrinia. Bull Entomol Res 2008, 98(2):193-201.
• [11]Pélozuelo L, Malosse C, Genestier G, Guenego H, Frérot B: Host-plant specialization in pheromone strains of the European corn borer Ostrinia nubilalis in France. J Chem Ecol 2004, 30(2):335-352.
• [12]Klun JA, Chapman O, Mattes K, Wojtkowski P, Beroza M: Insect sex pheromones: minor amount of opposite geometrical isomer critical to attraction. Science 1973, 181:661-663.
• [13]Kochansky J, Cardé RT, Liebherr J, Roelofs WL: Sex pheromone of the European corn borer, Ostrinia nubilalis (Lepidoptera: Pyralidae), in New York. J Chem Ecol 1975, 1:225-231.
• [14]Cardé RT, Roelofs W, Harrison R, Vawter A, Brussard P: European corn borer: pheromone polymorphism or sibling species? Science 1978, 199:555-556.
• [15]Huang YP, Takanashi T, Hoshizaki S, Tatsuki S, Ishikawa Y: Female sex pheromone polymorphism in Adzuki bean borer, Ostrinia scapulalis, is similar to that in European corn borer. O. nubilalis. Journal of Chemical Ecology 2002, 28(3):533-539.
• [16]Bourguet D, Bethenod MT, Pasteur N, Viard F: Gene flow in the European corn borer Ostrinia nubilalis: implications for the sustainability of transgenic insecticidal maize. Proceedings of the Royal Society Biological Sciences 2000, 267(1439):117-122.
• [17]Bourguet D, Bethenod MT, Trouvé C, Viard F: Host-plant diversity of the European corn borer Ostrinia nubilalis: what value for sustainable transgenic insecticidal Bt maize? Proceedings of the Royal Society Biological Sciences Series B 2000, 267(1449):1177-1184.
• [18]Martel C, Réjasse A, Rousset F, Bethenod MT, Bourguet D: Host-plant-associated genetic differentiation in Northern French populations of the European corn borer. Heredity 2003, 90(2):141-149.
• [19]Thomas Y, Bethenod MT, Pélozuelo L, Frérot B, Bourguet D: Genetic isolation between two sympatric host-plant races of the European corn borer, Ostrinia nubilalis Hübner. I. sex pheromone, moth emergence timing, and parasitism. Evolution 2003, 57(2):261-273.
• [20]Malausa T, Leniaud L, Martin JF, Audiot P, Bourguet D, Ponsard S, Lee SF, Harrison RG, Dopman E: Molecular differentiation at nuclear loci in French host races of the European corn borer (Ostrinia nubilalis). Genetics 2007, 176(4):2343-2355.
• [21]Frolov AN, Audiot P, Bourguet D, Kononchuk AG, Malysh JM, Ponsard S, Streiff R, Tokarev YS: “From Russia with lobe”: genetic differentiation in trilobed uncus Ostrinia spp. follows food plant, not hairy legs. Heredity 2012, 108(2):147-156.
• [22]Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol 1990, 215(3):403-410.
• [23]Huse SM, Huber JA, Morrison HG, Sogin ML, Welch DM: Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biol 2007, 8:R143. BioMed Central Full Text
• [24]Gilles A, Meglécz E, Pech N, Ferreira S, Malausa T, Martin J-F: Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing. BMC Genomics 2011, 12:245. BioMed Central Full Text
• [25]Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, Robles M: Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 2005, 21(18):3674-3676.
• [26]Gouzy J, Carrere S, Schiex T: FrameDP: sensitive peptide detection on noisy matured sequences. Bioinformatics 2009, 25(5):670-671.
• [27]O'Neil ST, Dzurisin JDK, Carmichael RD, Lobo NF, Emrich SJ, Hellmann JJ: Population-level transcriptome sequencing of nonmodel organisms Erynnis propertius and Papilio zelicaon. BMC Genomics 2010, 11(1):310. BioMed Central Full Text
• [28]Coates BS, Bayles DO, Wanner KW, Robertson HM, Hellmich RL, Sappington TW: The application and performance of single nucleotide polymorphism markers for population genetic analyses of Lepidoptera. Frontiers in genomic assay technology 2011, 2:38.
• [29]Coates BS, Sumerford DV, Hellmich RL, Lewis LC: Mining an Ostrinia nubilalis midgut expressed sequence tag (EST) library for candidate genes and single nucleotide polymorphisms (SNPs). Insect Molecular Biology 2008, 17(6):607-620.
• [30]Wanner KW, Nichols AS, Allen JE, Bunger PL, Garczynski SF, Linn CE, Robertson HM, Luetje CW: Sex pheromone receptor specificity in the European corn borer moth. Ostrinia nubilalis. PLoS ONE 2010, 5(1):e8685.
• [31]Logacheva MD, Kasianov AS, Vinogradov DV, Samigullin TH, Gelfand MS, Makeev VJ, Penin AA: De novo sequencing and characterization of floral transcriptome in two species of buckwheat (Fagopyrum). BMC Genomics 2011, 12(1):30. BioMed Central Full Text
• [32]Kristensen NP, Scoble MJ, Karsholt O: Lepidoptera phylogeny and systematics: the state of inventorying moth and butterfly diversity. Zootaxa 2007, 1668:699-747.
• [33]The International Silkworm G: The genome of a lepidopteran model insect, the silkworm Bombyx mori. Insect Biochemistry and Molecular Biology 2008, 38(12):1036-1045.
• [34]Liberles D, Margam VM, Coates BS, Bayles DO, Hellmich RL, Agunbiade T, Seufferheld MJ, Sun W, Kroemer JA, Ba MN: Transcriptome sequencing and rapid development and application of SNP markers for the legume pod borer Maruca vitrata (Lepidoptera: Crambidae). PLoS ONE 2011, 6(7):e21388.
• [35]Margam VM, Coates BS, Bayles DO, Hellmich RL, Agunbiade T, Seufferheld MJ, Sun WL, Kroemer JA, Ba MN, Binso-Dabire CL: Transcriptome sequencing, and rapid development and application of SNP markers for the legume pod borer Maruca vitrata (Lepidoptera: Crambidae). PLoS ONE 2011, 6(7):e21388. Epub 2011 Jul 6
• [36]Vogel H, Altincicek B, Glöckner G, Vilcinskas A: A comprehensive transcriptome and immune-gene repertoire of the lepidopteran model host Galleria mellonella. BMC Genomics 2011, 12(1):308. BioMed Central Full Text
• [37]Zhang S, Gunaratna RT, Zhang X, Najar F, Wang Y, Roe B, Jiang H: Pyrosequencing-based expression profiling and identification of differentially regulated genes from Manduca sexta, a lepidopteran model insect. Insect Biochemistry and Molecular Biology 2011, 41(9):733-746.
• [38]Lassance JM: Journey in the Ostrinia World: from pest to model in chemical ecology. Journal of Chemical Ecology 2010, 36(10):1155-1169.
• [39]Holt RA, Subramanian GM, Halpern A, Sutton GG, Charlab R, Nusskern DR, Wincker P, Clark AG, Ribeiro JMC, Wides R: The genome sequence of the malaria mosquito Anopheles gambiae. Science 2002, 298(5591):129-149.
• [40]Zagrobelny M, Scheibye-Alsing K, Jensen N, Møller B, Gorodkin J, Bak S: 454 pyrosequencing based transcriptome analysis of Zygaena filipendulae with focus on genes involved in biosynthesis of cyanogenic glucosides. BMC Genomics 2009, 10(1):574. BioMed Central Full Text
• [41]Vera JC, Wheat CW, Fescemyer HW, Frilander MJ, Crawford DL, Hanski I, Marden JH: Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing. Molecular Ecology 2008, 17(7):1636-1647.
• [42]Ewen-Campen B, Shaner N, Panfilio KA, Suzuki Y, Roth S, Extavour CG: The maternal and early embryonic transcriptome of the milkweed bug Oncopeltus fasciatus. BMC Genomics 2011, 12(1):61. BioMed Central Full Text
• [43]Dworkin I, Jones CD: Genetic changes accompanying the evolution of host specialization in Drosophila sechellia. Genetics 2008, 181(2):721-736.
• [44]Matsubayashi KW, Ohshima I, Nosil P: Ecological speciation in phytophagous insects. Entomologia Experimentalis et Applicata 2010, 134(1):1-27.
• [45]Meglécz E, Petenian F, Danchin E, Coeur d'acier A, Rasplus JY, Faure E: High similarity between flanking regions of different microsatellites detected within each of two species of Lepidoptera: Parnassius apollo and Euphydryas aurinia. Mol Ecol 2004, 13(6):1693-1700.
• [46]Malausa T, Gilles A, Meglécz E, Blanquart H, Duthoy S, Costedoat C, Dubut V, Pech N, Castagnone-Sereno P, Délye C: High-throughput microsatellite isolation through 454 GS-FLX Titanium pyrosequencing of enriched DNA libraries. Molecular Ecology Resources 2011, 11(4):638-644.
• [47]Dalecky A, Bogdanowicz SM, Dopman EB, Bourguet D, Harrison RG: Two multiplex sets of eight and five microsatellite markers for the European corn borer, Ostrinia nubilalis Hübner (Lepidoptera: Crambidae). Molecular Ecology Notes 2006, 6(3):945-947.
• [48]Kim KS, Coates BS, Hellmich RL, Sumerford DV, Sappington TW: Isolation and characterization of microsatellite loci from the European corn borer, Ostrinia nubilalis (Hübner) (Insecta: Lepidoptera: Crambidae). Molecular Ecology Resources 2008, 8(2):409-411.
• [49]Galindo J, Grahame JW, Butlin RK: An EST-based genome scan using 454 sequencing in the marine snail Littorina saxatilis. Journal of Evolutionary Biology 2010, 23(9):2004-2016.
• [50]Azam S, Thakur V, Ruperao P, Shah T, Balaji J, Amindala B, Farmer AD, Studholme DJ, May GD, Edwards D: Coverage based consensus calling (CBCC) of short sequence reads and comparison of CBCC results to identify SNPs in chickpea (Cicer arietinum, Fabaceae), a crop species without a reference genome. American Journal of Botany 2012, 99(2):186-192.
• [51]Rice P, Longden I, Bleasby A: EMBOSS: The European molecular biology open software suite. Trends in Genetics 2000, 16(6):276-277.