De novo transcriptome characterization and development of genomic tools for Scabiosa columbaria L. using next-generation sequencing techniques

Molecular Ecology Resources

Volumn 11, Issue 4, 2011, Pages 662-674

  Angeloni, F ^a   Wagemaker, C A M ^a   Jetten, M S M ^a   Op den Camp, H J M ^a   Janssen Megens, E M ^b   Francoijs, K J ^b   Stunnenberg, H G ^b   Ouborg, N J ^a  

^a RADBOUD UNIVERSITY NIJMEGEN   (Netherlands)

^b RADBOUD UNIVERSITY MEDICAL CENTER   (Netherlands)

Author keywords

Genetic resources; Microsatellites; Next generation sequencing; Scabiosa columbaria; SNPs; Transcriptome characterization

Indexed keywords

ARTICLE; DIPSACACEAE; GENE EXPRESSION PROFILING; GENETICS; GENOMICS; HIGH THROUGHPUT SEQUENCING; METHODOLOGY; PLANT GENOME;

DIPSACACEAE; GENE EXPRESSION PROFILING; GENOME, PLANT; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING;

DIPSACACEAE; SCABIOSA COLUMBARIA;

EID: 79959264079     PISSN: 1755098X     EISSN: 17550998     Source Type: Journal    
DOI: 10.1111/j.1755-0998.2011.02990.x     Document Type: Article

References (69)

1. Amaral AJ, Megens HJ, Kerstens HHD et al. (2009) Application of massive parallel sequencing to whole genome SNP discovery in the porcine genome. BMC Genomics, 10, 374.
2. Andersson S, Waldmann P (2002) Inbreeding depression in a rare plant: Scabiosa canescens (Dipsacaceae). Hereditas, 136, 207-211.
3. Aury JM, Cruaud C, Barbe V et al. (2008) High quality draft sequences for prokaryotic genomes using a mix of new sequencing technologies. BMC Genomics, 9, 603.
4. Avise JC (2010) Perspective: conservation genetics enters the genomic era. Conservation genetics, 11, 665-669.
5. Bai X, Zhang W, Orantes L, Jun T-H, Mittapalli O et al. (2010) Combining Next-Generation Sequencing Strategies for Rapid Molecular Resource Development from an Invasive Aphid Species, Aphis glycines. PLoS ONE, 5, e11370. DOI:.
6. Beaumont MA (2005) Adaptation and speciation: what can FST tell us? Trends in Ecology & Evolution, 20, 435-440.
7. Bevan M, Walsh S (2005) The Arabidopsis genome: a foundation for plant research. Genome Research, 15, 1632-1642.
8. Boeckmann B, Bairoch A, Apweiler R et al. (2003) The SWISS-PROT protein knowledgebase and its supplement TrEMBL. Nucleic Acids Research, 31, 365-370.
9. Bouck A, Vision T (2008) The molecular ecologist's guide to expressed sequence tags. Molecular Ecology, 16, 907-928.
10. Buggs RJA, Chamala S, Wu W et al. (2010) Characterization of duplicate gene evolution in the recent natural allopolyploid Tragopogon miscellus by next-generation sequencing and Sequenom iPLEX MassARRAY genotyping. Molecular Ecology, 19, 132-146.
11. Castoe TA et al. (2010) Rapid identification of thousands of copperhead snake (Agkistrodon contortrix) microsatellite loci from modest amounts of 454 shotgun genome sequence. Molecular Ecology Resources, 10, 341-347.
12. Chapman EJ, Estelle M (2009) Mechanism of auxin-regulated gene expression in plants. Annual Review of Genetics, 43, 265-285.
13. Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, Robles M (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics, 21, 3674-3676.
14. Deschamps S, Campbell MA (2010) Utilization of next-generation sequencing platforms in plant genomics and genetic variant discovery. Molecular Breeding, 25, 553-570.
15. Diguistini S, Liao NY, Platt D et al. (2009) De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data. Genome Biology, 10, R94.
16. Emrich SJ, Barbazuk WB, Li L, Schnable PS (2007) Gene discovery and annotation using LCM-454 transcriptome sequencing. Genome Research, 17, 69-73.
17. Ewing B, Green P (1998) Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Research, 8, 186-194.
18. Ewing B, Hillier L, Wendl MC, Green P (1998) Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Research, 8, 175-185.
19. Feder ME, Mitchell-Olds TM (2003) Evolutionary and ecological functional genomics. Nature reviews genetics, 4, 651-657.
20. Garcia-Reyero N, Griffitt RJ, Liu L et al. (2008) Construction of a robust microarray from a non-model species largemouth bass, Micropterus salmoides (Lacèpede), using pyrosequencing technology. Journal of Fish Biology, 72, 2354-2376.
21. Hale MC, McCormick CR, Jackson JR, DeWoody JA (2009) Next-generation pyrosequencing of gonad transcriptomes in the polyploidy lake sturgeon (Acipenser fulvescens): the relative merits of normalization and rarefaction in gene discovery. BMC Genomics, 10, 203.
22. Kofler R, Schlötterer C, Lelley T (2007) SciRoKo: a new tool for whole genome microsatellite search and investigation. Bioinformatics, 23, 1683-1685.
23. Kohn MH, Murphy WJ, Ostrander EA, Wayne RK (2006) Genomics and conservation genetics. Trends in Ecology and Evolution, 21, 629-637.
24. Kreps JA, Wu Y, Chang H-S, Zhu T, Wang X, Harper JF (2002) Transcriptome changes for Arabidopsis in response to salt, osmotic, and cold stress. Plant Physiology, 130, 2129-2141.
25. Kristensen TN, Pedersen KS, Vermeulen CJ, Loeschcke V (2010) Research on inbreeding in the 'omics' era. Trends in Ecology and Evolution, 25, 44-52.
26. Kristiansson E, Asker N, Forlin L, Larsson DGJ (2009) Characterization of the Zoarces viviparus liver transcriptome using massively parallel pyrosequencing. BMC Genomics, 10, 345.
27. Li R et al. (2009) The sequence and de novo assembly of the giant panda genome. Nature, 463, 311-317.
28. Lomax J (2005) Get ready to GO! A biologist's guide to the Gene Ontology. Briefing in Bioinformatics, 6, 298-304.
29. Luikart G, England PR, Tallmon D, Jordan S, Taberlet P (2003) The power and promise of population genomics: from genotyping to genome typing. Nature Reviews Genetics, 4, 981-994.
30. Margulies M et al. (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature, 437, 376-380.
31. Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y (2008) RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Research, 18, 1509-1517.
32. Meglécz E, Costedoat C, Dubut V et al. (2010) QDD: a user-friendly program to select microsatellite markers and design primers from large sequencing projects. Bioinformatics, 26, 403-404.
33. Metzker ML (2010) Sequencing technologies-the next generation. Nature reviews, 11, 31-46.
34. Meyer E, Aglyamova GV, Wang S et al. (2009) Sequencing and de novo analysis of a coral larval transcriptome using 454 GLFlx. BMC Genomics, 10, 219.
35. Miller JR, Koren S, Sutton G (2010) Assembly algorithm for next-generation sequencing data. Genomics, 95, 315-327.
36. Morozova O, Marra MA (2008) Applications of next-generation sequencing technologies in functional genomics. Genomics, 92, 255-264.
37. Namroud MC, Beaulieu J, Juge N, Laroche J, Bousquet J (2008) Scanning the genome for gene SNPs involved in adaptive population differentiation in white spruce. Molecular Ecology, 17, 3599-3613.
38. Novaes ED, Drost R, Farmerie WG et al. (2008) High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome. BMC Genomics, 9, 312.
39. Nowrousian M, Stajich JE, Chu M, Engh I, Espagne E et al. (2010) De novo Assembly of a 40 Mb eukaryotic genome from short sequence reads: Sordaria macrospora, a model organism for fungal morphogenesis. PLoS Genetics, 6, e1000891. doi:.
40. Ossowski S, Schneeberger K, Clark RM et al. (2008) Sequencing of natural strains of Arabidopsis thaliana with short reads. Genome Research, 18, 2024-2033.
41. Ouborg NJ, Vriezen WH (2007) An ecologist's guide to ecogenomics. Journal of Ecology, 95, 8-16.
42. Ouborg NJ, Angeloni F, Vergeer P (2010a) An essay on the necessity and feasibility of conservation genomics. Conservation genetics, 11, 643-653.
43. Ouborg NJ, Pertoldi C, Loeschcke V, Bijlsma R, Hedrick PW (2010b) Conservation genetics in transition to conservation genomics. Trends in genetics, 26, 177-187.
44. Paige NK (2010) The functional genomics of inbreeding depression: a new approach to an old problem. BioScience, 60, 267-277.
45. Parchman TL, Geist KS, Grahnen JA, Benkman CW, Buerkle CA (2010) Transcriptome sequencing in an ecologically important tree species: assembly, annotation, and marker discovery. BMC genomics, 11, 180.
46. Picó FX, Ouborg NJ, van Groenendael JM (2004) Evaluation of the extent of among-family variation in inbreeding depression in the perennial herb Scabiosa columbaria (Dipsacaceae). American Journal of Botany, 91, 1183-1189.
47. Pluess AR, Stöcklin J (2004) Genetic diversity and fitness in Scabiosa columbaria in the Swiss Jura in relation to population size. Conservation Genetics, 5, 145-156.
48. Primmer CR (2009) From conservation genetics to conservation genomics. Annals of the New York Academy of Science, 1162, 357-368.
49. Quinn NL, Levenkova N, Chow W et al. (2008) Assessing the feasibility of GS FLX Pyrosequencing for sequencing the Atlantic salmon genome. BMC Genomics, 9, 404.
50. Reinhardt JA, Baltrus DA, Nishimura MT, Jeck WR, Jones CD, Dangl JL (2009) De novo assembly using low-coverage short read sequence data from the rice pathogen Pseudomonas syringae pv. oryzae. Genome Research, 19, 294-305.
51. Reisch C, Poschlod P (2009) Land use affects flowering time: seasonal and genetic differentiation in the grassland plant Scabiosa columbaria. Evolutionary ecology, 23, 753-764.
52. Rusk N (2009) Cheap third-generation sequencing. Nature Methods, 6, 244-245.
53. Schatz MC, Delcher AL, Saltzberg SL (2010) Assembly of large genomes using second generation sequencing. Genome research, in press. DOI:.
54. Shendure J, Ji H (2008) Next-generation DNA sequencing. Nature biotechnology, 26, 1135-1145.
55. Stinchcombe JR, Hoekstra HE (2008) Combining population genomics and quantitative genetics: finding the genes underlying ecologically important traits. Heredity, 100, 158-170.
56. Strausberg RL, Levy S, Rogers YH (2008) Emerging DNA sequencing technologies for human genomic medicine. Drug Discovery Today, 13, 569-577.
57. Swarbreck D, Wilks C, Lamesch P et al. (2008) The Arabidopsis Information Resource (TAIR): gene structure and function annotation. Nucleic Acids Research, 36, 1009-1014.
58. Szittya G, Moxon S, Santos DM et al. (2008) High-throughput sequencing of Medicago truncatula short RNAs identifies eight new miRNA families. BMC Genomics, 9, 593.
59. Van Straalen NM, Roelofs D (2006) An Introduction to Ecological Genomics. Oxford University Press, Oxford, UK.
60. Van Treuren R, Bijlsma R, Van Delden W, Ouborg NJ (1991) The significance of genetic erosion in the process of extinction. 1. Genetic differentiation in Salvia pratensis and Scabiosa columbaria in relation to population size. Heredity, 66, 181-189.
61. Van Treuren R, Bijlsma R, Ouborg NJ, van Delden W (1993) The significance of genetic erosion in the process of extinction. IV. Inbreeding depression and heterosis effects caused by selfing and outcrossing Scabiosa columbaria. Evolution, 47, 1669-1680.
62. Vera JC, Wheat CW, Fescemyer HW et al. (2008) Rapid transcriptome characterization for a non model organism using 454 pyrosequencing. Molecular Ecology, 17, 1636-1647.
63. Waldmann P (2002) Fluctuating asymmetry in Scabiosa canescens and Scabiosa columbaria. Association with genetic variation and population size. International Journal of Plant Science, 163, 329-334.
64. Waldmann P, Andersson S (2000) Comparison of genetic (co)variance matrices within and between Scabiosa canescens and S. columbaria. Journal of evolutionary Biology, 13, 826-835.
65. Wall PK, Leebens-Mack J, Chanderbali AS et al. (2009) Comparison of next generation sequencing technologies for transcriptome characterization. BMC Genomics, 10, 347.
66. Wheat CW (2010) Rapidly developing functional genomics in ecological model systems via 454 transcriptome sequencing. Genetica, 138, 433-451.
67. Yamamoto T, Nagasaki H, Ji Y et al. (2010) Fine definition of the pedigree haplotypes of closely related rice cultivars by means of genome-wide discovery of singlenucleotide polymorphisms. BMC Genomics, 11, 267.
68. Zeng S, Xiao G, Guo J et al. (2010) Development of a EST dataset and characterization of EST-SSRs in a traditional Chinese medicinal plant, Epimedium sagittattum (Sieb. Et Zucc.) Maxim. BMC genomics, 11, 94.
69. Zhang G, Guo G, Hu X et al. (2010) Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome. Genome Research, 20, 646-654.