Population-level transcriptome sequencing of nonmodel organisms Erynnis propertius and Papilio zelicaon

BMC Genomics

Volumn 11, Issue 1, 2010, Pages

  O'Neil, Shawn T ^a   Dzurisin, Jason D K ^b   Carmichael, Rory D ^a   Lobo, Neil F ^b   Emrich, Scott J ^a   Hellmann, Jessica J ^b  

^a University of Notre Dame   (United States)

^b UNIVERSITY OF NOTRE DAME   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

INSECT PROTEIN; TRANSCRIPTOME;

ARTICLE; BIOTECHNOLOGY; CLIMATE CHANGE; CONTROLLED STUDY; DEVELOPMENTAL STAGE; ERYNNIS PROPERTIUS; EXPRESSED SEQUENCE TAG; GENETIC TRANSCRIPTION; GENETIC VARIABILITY; INSECT GENETICS; INSECT GENOME; LEPIDOPTERA; NONHUMAN; NUCLEOTIDE SEQUENCE; ORTHOLOGY; PAPILIO ZELICAON; POPULATION GENETICS; PROTEIN ASSEMBLY; RNA SEQUENCE; SILKWORM; SINGLE NUCLEOTIDE POLYMORPHISM; STRESS; ANIMAL; CLUSTER ANALYSIS; DNA SEQUENCE; FEMALE; GENE; GENE EXPRESSION PROFILING; GENETICS; MALE; METHODOLOGY;

BOMBYX MORI; ERYNNIS; HESPERIIDAE; LEPIDOPTERA; MYRRHIS ODORATA; PAPILIO ZELICAON; PAPILIONIDAE;

ANIMALS; BOMBYX; CLUSTER ANALYSIS; FEMALE; GENE EXPRESSION PROFILING; GENES, INSECT; LEPIDOPTERA; MALE; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA;

EID: 77952183473     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-11-310     Document Type: Article

References (63)

1. Adams M, Kelley J, Gocayne J, Dubnick M, Polymeropoulos M, Xiao H, Merril C, Wu A, Olde B, Moreno R, Kerlavage A, McCombie W, Venter J. Complementary DNA sequencing: Expressed sequence tags and the human genome project. Science 1991, 252:1651-1656. 10.1126/science.2047873, 2047873.
2. Rudd S. Expressed sequence tags: alternative or complement to whole genome sequences?. Trends in Plant Science 2003, 8(7):321-329. 10.1016/S1360-1385(03)00131-6, 12878016.
3. Barbazuk B, Emrich S, Chen H, Li L, Schnable P. SNP discovery via 454 transcriptome sequencing. The Plant Journal 2007, 51(5):910-918. 10.1111/j.1365-313X.2007.03193.x, 2169515, 17662031.
4. Emrich S, Barbazuk W, Li L, Schnable P. Gene discovery and annotation using LCM-454 transcriptome sequencing. Genome Res 2007, 17:69-73. 10.1101/gr.5145806, 1716268, 17095711.
5. Mao C, Evans C, Jensen R, Sobral B. Identification of new genes in Sinorhizobium meliloti using the Genome Sequencer FLX system. BMC Microbiology 2008, 8:72+. 10.1186/1471-2180-8-72, 2396165, 18454850.
6. Lee A, Hansen KD, Bullard J, Dudoit S, Sherlock G. Novel Low Abundance and Transient RNAs in Yeast Revealed by Tiling Microarrays and Ultra High-Throughput Sequencing Are Not Conserved Across Closely Related Yeast Species. PLoS Genet 2008, 4(12):e1000299+. 10.1371/journal.pgen.1000299, 2601015, 19096707.
7. Khajuria C, Zhu Y, Chen M, Buschman L, Higgins R, Yao J, Creso A, Siegfried B, Muthukrishnan S, Zhu K. Expressed sequence tags from larval gut of the European corn borer (Ostrinia nubilalis): Exploring candidate genes potentially involved in Bacillus thuringiensis toxicity and resistance. BMC Genomics 2009, 10:286+. 10.1186/1471-2164-10-286, 2717985, 19558725.
8. Ohtsu K, Smith M, Emrich S, Borsuk L, Zhou R, Chen T, Zhang X, Timmermans M, Beck J, Buckner B, Janick-Buckner D, Nettleton D, Scanlon M, Schnable P. Global gene expression analysis of the shoot apical meristem of maize (Zea mays L.). The Plant Journal 2007, 52(3):391-404. 10.1111/j.1365-313X.2007.03244.x, 2156186, 17764504.
9. Torres T, Metta M, Ottenwälder BCS. Gene expression profiling by massively parallel sequencing. Genome Research 2008, 18:172-177. 10.1101/gr.6984908, 2134766, 18032722.
10. Hornshøj H, Bendixen E, Conley L, Andersen P, Hedegaard J, Panitz F, Bendixen C. Transcriptomic and proteomic profiling of two porcine tissues using high-throughput technologies. BMC Genomics 2009, 10:30. 10.1186/1471-2164-10-30, 2633351, 19152685.
11. Vera CJ, Wheat C, Fescemyer H, Frilander M, Crawford D, Hanski I, Marden J. Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing. Molecular Ecology 2008, 17(7):1636-1647. 10.1111/j.1365-294X.2008.03666.x, 18266620.
12. Novaes E, Drost D, Farmerie W, Pappas G, Grattapaglia D, Sederoff R, Kirst M. High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome. BMC Genomics 2008, 9. 10.1186/1471-2164-9-312, 2483731, 18590545.
13. Cheung F, Win J, Lang J, Hamilton J, Vuong H, Leach J, Kamoun S, André Lévesque C, Tisserat N, Buell C. Analysis of the Pythium ultimum transcriptome using Sanger and Pyrosequencing approaches. BMC Genomics 2008, 9:542+. 10.1186/1471-2164-9-542, 2612028, 19014603.
14. Meyer E, Aglyamova G, Wang S, Carter J, Abrego D, Colbourne J, Willis B, Matz M. Sequencing and de novo analysis of a coral larval transcriptome using 454 GS-FLX. BMC Genomics 2009, 10:219+. 10.1186/1471-2164-10-219, 2689275, 19435504.
15. Roeding F, Borner J, Kube M, Klages S, Reinhardt R, Burmester T. A 454 sequencing approach for large scale phylogenomic analysis of the common emperor scorpion (Pandinus imperator). Mol Phylogenet Evol 2009, 53(3):826-834. 10.1016/j.ympev.2009.08.014, 19695333.
16. Weber A, Weber K, Carr K, Wilkerson C, Ohlrogge J. Sampling the Arabidopsis transcriptome with massively parallel pyrosequencing. Plant Physiol 2007, 144:32-42. 10.1104/pp.107.096677, 1913805, 17351049.
17. Papanicolaou A, Joron M, McMillan W, Blaxter M, Jiggins C. Genomic tools and cDNA derived markers for butterflies. Molecular Ecology 2005, 14(9):2883-2897. 10.1111/j.1365-294X.2005.02609.x, 16029486.
18. Ozaki K, Utoguchi A, Yamada A, Yoshikawa H. Identification and genomic structure of chemosensory proteins (CSP) and odorant binding proteins (OBP) genes expressed in foreleg tarsi of the swallowtail butterfly Papilio xuthus. Insect Biochem Mol Biol 2008, 38(11):969-976. 10.1016/j.ibmb.2008.07.010, 18771731.
19. Guppy C, Shepard R. Butterflies of British Columbia 2001, Vancouver: UBC Press.
20. Prior K, Hellmann J. The ecology and life history of Erynnis Propertius, a threatened oak feeding butterfly. Canadian Entomology 2009, 141:161-171.
21. Scott J. The Butterflies of North America: a Natural History and Field Guide 1992, Stanford, California: Stanford University Press.
22. Zakharov E, Hellmann J. Genetic differentiation across a latitudinal gradient in two co-occurring butterfly species: revealing population differences in a context of climate change. Molecular Ecology 2008, 17:189-208. 10.1111/j.1365-294X.2007.03488.x, 17784923.
23. Zakharov E, Lobo N, Nowak C, Hellmann J. Introgression as a likely cause of mtDNA paraphyly in two allopatric skippers (Lepidoptera: Hesperiidae). Heredity 2009, 102:590-599. 10.1038/hdy.2009.26, 19293835.
24. Hellmann J, Pelini S, Prior K, Dzurisin J. The response of two butterfly species to climatic variation at the edge of their range and the implications for poleward range shifts. Oecologia 2008, 157(4):583-592. 10.1007/s00442-008-1112-0, 18648857.
25. Pelini S, Dzurisin J, Prior K, Williams C, Marsicos T, Sinclair B, Hellmann J. Translocation experiments with butterflies reveal limits to enhancement of poleward populations under climate change. Proceedings of the National Academy of Sciences 2009,
26. Zakharov E, Hellmann J. Characterization of 17 polymorphic microsatellite loci in the Anise swallowtail, Papilio zelicaon (Lepidoptera: Papilionidae), and their amplification in related species. Molecular Ecology Notes 2007, 7:144-146.
27. Zakharov E, Hellmann J, Romero-Severson J. Microsatellite loci in the Propertius duskywing, Erynnis propertius (Lepidoptera: Hesperiidae), and related species. Molecular Ecology Notes 2007, 7(2):266-268.
28. Li W, Berenbaum M, Schuler M. Molecular analysis of multiple CYP6B genes from polyphagous Papilio species. Insect Biochemistry and Molecular Biology 2001, 31(10):999-1011. 10.1016/S0965-1748(01)00048-0, 11483436.
29. Li W, Petersen R, Schuler M, Berenbaum M. CYP6B cytochrome P450 monooxygenases from Papilio canadensis and Papilio glaucus: potential contributions of sequence divergence to host plant associations. Insect Molecular Biology 2002, 11(6):543-551. 10.1046/j.1365-2583.2002.00363.x, 12421412.
30. Boggs C, Watt W, Ehrlich P. Butterflies: ecology and evolution taking flight 2003, Chicago, IL: University of Chicago Press.
31. Boggs C. Reproductive strategies of female butterflies: variation in and constraints on fecundity. Ecological Entomology 1986, 11:7-15.
32. Leather S. Size, reproductive potential and fecundity in insects: Things aren't as simple as they seem. Oikos 1988, 51:386-389.
33. Stockhoff B. Starvation resistance of gypsy moth, Lymantria dispar (L.) (Lepidoptera: Lymantriidae): tradeoffs among growth, body size, and survival. Oecologia 1991, 88(3):422-429.
34. Oberhauser K. Fecundity, lifespan and egg mass in butterflies: Effects of male-derived nutrients and female size. Func Ecology 1997, 11:166-175.
35. Hahn D, Denlinger D. Meeting the energetic demands of insect diapause: Nutrient storage and utilization. Journal of Insect Physiology 2007, 53(8):760-773. 10.1016/j.jinsphys.2007.03.018, 17532002.
36. DFCI Gene Indices Software Tools. , http://compbio.dfci.harvard.edu/tgi/software/
37. Huang X, Madan A. CAP3: A DNA sequence assembly program. Genome Research 1999, 9:868-877. 10.1101/gr.9.9.868, 310812, 10508846.
38. Bouck A, Vision T. The molecular ecologist's guide to expressed sequence tags. Molecular Ecology 2007, 16:907-924. 10.1111/j.1365-294X.2006.03195.x, 17305850.
39. Myers E, Sutton G, Delcher A, Dew I, Fasulo D, Flanigan M, Kravitz S, Mobarry C, Reinert K, Remington K, Anson E, Bolanos R, Chou H, Jordan C, Halpern A, Lonardi S, Beasley E, Brandon R, Chen L, Dunn Z, PJ L, Liang Y, Nusskern D, Zhan M, Zhang Q, Zheng X, Rubin G, Adams M, Venter J. A whole-genome assembly of Drosophila. Science 2000, 287(5461):2196-2204. 10.1126/science.287.5461.2196, 10731133.
40. Celera Assembler SFF Standard Operating Procedures. , http://sourceforge.net/apps/mediawiki/wgs-assembler/index.php?title=SFF_ SOP
41. Hale M, McCormick C, Jackson J, DeWoody J. Next-generation pyrosequencing of gonad transcriptomes in the polyploid lake sturgeon (Acipenser fulvescens): the relative merits of normalization and rarefaction in gene discovery. BMC Genomics 2009, 10:203. 10.1186/1471-2164-10-203, 2688523, 19402907.
42. Duan J, Li R, Cheng D, Fan W, Zha X, Cheng T, Wu Y, Wang J, Mita K, Xiang Z, Xia Q. SilkDB v2.0: a platform for silkworm (Bombyx mori) genome biology. Nucl Acids Res 2009, gkp801+.
43. Altschul S, Madden T, Schaffer A, Zhang J, Zhang Z, Miller W, Lipman D. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acid Res 1997, 25:3389-3402. 10.1093/nar/25.17.3389, 146917, 9254694.
44. Lottaz C, Iseli C, Jongeneel C, Bucher P. Modeling sequencing errors by combining Hidden Markov models. Bioinformatics 2003, 16:ii103-ii112.
45. Tweedie S, Ashburner M, Falls K, Leyland P, McQuilton P, Marygold S, Millburn G, Osumi-Sutherland D, Schroeder A, Seal R, Zhang H, . The FlyBase Consortium FlyBase: enhancing Drosophila Gene Ontology annotations. Nucleic Acids Research 2009, 37:D555-D559. 10.1093/nar/gkn788, 2686450, 18948289, The FlyBase Consortium.
46. Papanicolaou A, Gebauer-Jung S, Blaxter M, Owen McMillan W, Jiggins C. ButterflyBase: a platform for lepidopteran genomes. Nucleic Acid Research 2008, 36:D582-D587.
47. Jiggins C. personal communication 2009,
48. Wiegmann B, Trautwein M, Kim J, Cassel B, Bertone M, Winterton S, Yeates D. Single-copy nuclear genes resolve the phylogeny of the holometabolous insects. BMC Biology 2009, 7(34):34+. 10.1186/1741-7007-7-34, 2709105, 19552814.
49. Cheng T, Xia Q, Qian J, Liu C, Lin Y, Zha X, Xiang Z. Mining single nucleotide polymorphisms from EST data of silkworm, Bombyx mori, inbred strain Dazao. Insect Biochemistry and Molecular Biology 2004, 34(6):523-530. 10.1016/j.ibmb.2004.02.004, 15147754.
50. Berger J, Suzuki T, Senti KA, Stubbs J, Schaffner G, Dickson BJ. Genetic mapping with SNP markers in Drosophila. Nature Genetics 2001, 29(4):475-481. 10.1038/ng773, 11726933.
51. Denisov G, Walenz B, Halpern AL, Miller J, Axelrod N, Levy S, Sutton G. Consensus generation and variant detection by Celera Assembler. Bioinformatics (Oxford, England) 2008, 24(8):1035-1040. 10.1093/bioinformatics/btn074, 18321888.
52. Watanabe M. Multiple matings increase the fecundity of the yellow swallowtail butterfly, Papilio xuthus L., in summer generations. Journal of Insect Behavior 1988, 1:17-27.
53. Sims S. Aspects of mating frequency and reproductive maturity in Papilio zelicaon. American Midland Naturalist 1979, 102:36-50.
54. Watterson G. On the number of segregating sites in genetical models without recombination. Theoretical Population Biology 1975, 7(2):256-276. 10.1016/0040-5809(75)90020-9, 1145509.
55. Heber S, Alekseyev M, Sze S, Tang H, Pevzer P. Splicing graphs and the EST assembly problem. Bioinformatics 2002, 18:S181-S188.
56. Liang F, Holt I, Pertea G, Karamycheva S, Salzberg S, Quackenbush J. An optimized protocol for analysis of EST sequences. Nucl. Acids Res 2000, 28(18):3657-3665.
57. Bainbridge M, Warren R, Hirst M, Romanuik T, Zeng T, Go A, Delaney A, Griffith M, Hickenbotham M, Magarini V, Mardis E, Sadar M, Siddiqui A, Marra M, Jones S. Analysis of the prostate cancer cell line LNCaP transcriptome using a sequencing-by-synthesis approach. BMC Genomics 2006, 7:246+. 10.1186/1471-2164-7-246, 1592491, 17010196.
58. Berenbaum M. Coumarins and Caterpillars: A Case for Coevolution. Evolution 1983, 37:163-179.
59. Götz S, García-Gómez J, Terol J, Williams T, Nagaraj S, Nueda M, Robles M, Talón M, Dopazo J, Conesa A. High-throughput functional annotation and data mining with the Blast2GO suite. Nucleic acids research 2008, 36(10):3420-3435. 10.1093/nar/gkn176, 2425479, 18445632.
60. Hu Z, Jie B, Reecy J. CateGOrizer: A Web-Based Program to Batch Analyze Gene Ontology Classification Categories. Online Journal of Bioinformatics 2008, 9(2).
61. Long A, Beldade P, Macdonald S. Estimation of population heterozygosity and library construction-induced mutation rate from expresed sequence tag collections. Genetics 2007, 176:711-714. 10.1534/genetics.106.063610, 1893025, 17179075.
62. Huson D, Auch A, Qi J, Schuster S. MEGAN analysis of metagenome data. Genome Research 2007, 17:377-386. 10.1101/gr.5969107, 1800929, 17255551.
63. Cormen T, Leiserson C, Rivest R, Stein C. Introduction to Algorithms 2000, MIT Press, McGraw-Hill Book Company, 2.