A comparison of next generation sequencing technologies for transcriptome assembly and utility for RNA-Seq in a non-model bird

PLoS ONE

Volumn 9, Issue 10, 2014, Pages

  Finseth, Findley R ^a,b   Harrison, Richard G ^a  

^a Department of Obstetrics Gynecology   (United States)

^b UNIVERSITY OF MONTANA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CONTIG; TRANSCRIPTOME;

ANIMAL TISSUE; ARTICLE; COMPARATIVE STUDY; CONTIG MAPPING; CONTROLLED STUDY; COTURNIX JAPONICA; DE NOVO TRANSCRIPTOME ASSEMBLY; FRAMESHIFT MUTATION; GENE EXPRESSION; GENETIC TRANSCRIPTION; GENITAL SYSTEM; INDEL MUTATION; MALE; NEXT GENERATION SEQUENCING; NONHUMAN; RNA ANALYSIS; RNA SEQUENCE; RNA SYNTHESIS; TRANSCRIPTOMICS; ANIMAL; BIOLOGY; BIRD; GENETICS; GENOMICS; HIGH THROUGHPUT SEQUENCING; PROCEDURES; REPRODUCIBILITY; SEQUENCE ANALYSIS;

ANIMALS; BIRDS; COMPUTATIONAL BIOLOGY; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; REPRODUCIBILITY OF RESULTS; SEQUENCE ANALYSIS, RNA; TRANSCRIPTOME;

EID: 84921846989     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0108550     Document Type: Article

References (69)

1. Ellegren H (2008) Sequencing goes 454 and takes large-scale genomics into the wild. Mol Ecol 17: 1629-1631. doi:10.1111/j.1365-294X.2008.03699.x.
2. Wheat CW (2010) Rapidly developing functional genomics in ecological model systems via 454 transcriptome sequencing. Genetica 138: 433-451. doi:10.1007/s10709-008-9326-y.
3. Ekblom R, Galindo J (2010) Applications of next generation sequencing in molecular ecology of non-model organisms. Heredity 107: 1-15. doi:10.1038/hdy.2010.152.
4. Hudson ME (2008) Sequencing breakthroughs for genomic ecology and evolutionary biology. Mol Ecol Resour 8: 3-17. doi:10.1111/j.1471-8286.2007.02019.x.
5. Wang Z, Gerstein M, Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10: 57-63. doi:10.1038/nrg2484.
6. Wolf JBW (2013) Principles of transcriptome analysis and gene expression quantification: an RNA-seq tutorial. Mol Ecol Resour 13: 559-572. doi:10.1111/1755-0998.12109.
7. Vera JC, Wheat CW, Fescemyer HW, Frilander MJ, Crawford DL, et al. (2008) Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing. Mol Ecol 17: 1636-1647. doi:10.1111/j.1365-294X.2008.03666.x.
8. Reading BJ, Chapman RW, Schaff JE, Scholl EH, Opperman CH, et al. (2012) An ovary transcriptome for all maturational stages of the striped bass (Morone saxatilis), a highly advanced perciform fish. BMC Res Notes 5: 111. doi:10.1186/1756-0500-5-111.
9. Schwartz TS, Tae H, Yang Y, Mockaitis K, Van Hemert JL, et al. (2010) A garter snake transcriptome: pyrosequencing, de novo assembly, and sex-specific differences. BMC Genomics 11: 694. doi:10.1186/1471-2164-11-694.
10. Meyer E, Aglyamova GV, Wang S, Buchanan-Carter J, Abrego D, et al. (2009) Sequencing and de novo analysis of a coral larval transcriptome using 454 GSFlx. BMC Genomics 10: 219. doi:10.1186/1471-2164-10-219.
11. Ekblom R, Farrell LL, Lank DB, Burke T (2012) Gene expression divergence and nucleotide differentiation between males of different color morphs and mating strategies in the ruff. Ecol and Evol 2: 2485-2505. doi:10.1002/ece3.370.
12. Tarazona S, Garcia-Alcalde F, Dopazo J, Ferrer A, Conesa A (2011) Differential expression in RNA-seq: A matter of depth. Genome Res 21: 2213-2223. doi:10.1101/gr.124321.111.
13. Wang Y, Ghaffari N, Johnson CD, Braga-Neto UM, Wang H, et al. (2011) Evaluation of the coverage and depth of transcriptome by RNA-Seq in chickens. BMC Bioinformatics 12: S5. doi:10.1186/1471-2105-12-S10-S5.
14. Su CL, Chao YT, Alex Chang YC, Chen WC, Chen CY, et al. (2011) De novo assembly of expressed transcripts and global analysis of the Phalaenopsis aphrodite transcriptome. Plant Cell Phy 52: 1501-1514. doi:10.1093/pcp/pcr097.
15. Jensen JK, Schultink A, Keegstra K, Wilkerson CG, Pauly M (2012) RNA-Seq analysis of developing nasturtium seeds (Tropaeolum majus): identification and characterization of an additional galactosyltransferase involved in xyloglucan biosynthesis. Molecular Plant 5: 984-992. doi:10.1093/mp/sss032.
16. Feldmeyer B, Wheat CW, Krezdorn N, Rotter B, Pfenninger M (2011) Short read Illumina data for the de novo assembly of a non-model snail species transcriptome (Radix balthica, Basommatophora, Pulmonata), and a comparison of assembler performance. BMC Genomics 12: 317. doi:10.1186/1471-2164-12-317.
17. Crawford JE, Guelbeogo WM, Sanou A, Traoré A, Vernick KD, et al. (2010) De novo transcriptome sequencing in Anopheles funestus using Illumina RNA-Seq technology. PLoS ONE 5: e14202. doi:10.1371/journal.pone.0014202.g005.
18. Van Belleghem SM, Roelofs D, Van Houdt J, Hendrickx F (2012) De novo transcriptome assembly and SNP discovery in the wing polymorphic salt marsh beetle Pogonus chalceus (Coleoptera, Carabidae). PLoS ONE 7: e42605. doi:10.1371/journal.pone.0042605.t004.
19. Chen S, Yang P, Jiang F, Wei Y, Ma Z, et al. (2010) De novo analysis of transcriptome dynamics in the migratory locust during the development of phase traits. PLoS ONE 5: e15633. doi:10.1371/journal.pone.0015633.t002.
20. Xia Z, Xu H, Zhai J, Li D, Luo H, et al. (2011) RNA-Seq analysis and de novo transcriptome assembly of Hevea brasiliensis. Plant Mol Biol 77: 299-308. doi:10.1007/s11103-011-9811-z.
21. Etebari K, Palfreyman RW, Schlipalius D, Nielsen LK, Glatz RV, et al. (2011) Deep sequencing-based transcriptome analysis of Plutella xylostella larvae parasitized by Diadegma semiclausum. BMC Genomics 12: 446. doi:10.1186/1471-2164-12-446.
22. Birzele F, Schaub J, Rust W, Clemens C, Baum P, et al. (2010) Into the unknown: expression profiling without genome sequence information in CHO by next generation sequencing. Nucleic Acids Res 38: 3999-4010. doi:10.1093/nar/gkq116.
23. Moghadam HK, Harrison PW, Zachar G, Székely T, Mank JE (2013) The plover neurotranscriptome assembly: transcriptomic analysis in an ecological model species without a reference genome. Mol Ecol Resour 13: 696-705. doi:10.1111/1755-0998.12096.
24. Hornett EA, Wheat CW (2012) Quantitative RNA-Seq analysis in non-model species: assessing transcriptome assemblies as a scaffold and the utility of evolutionary divergent genomic reference species. BMC Genomics 13: 361. doi:10.1186/1471-2164-13-361.
25. Cahais V, Gayral P, Tsagkogeorga G, Melo-Ferreira J, Ballenghien M, et al. (2012) Reference-free transcriptome assembly in non-model animals from next-generation sequencing data. Mol Ecol Resour 12: 834-845. doi:10.1111/j.1755-0998.2012.03148.x.
26. Wall PK, Leebens-Mack J, Chanderbali AS, Barakat A, Wolcott E, et al. (2009) Comparison of next generation sequencing technologies for transcriptome characterization. BMC Genomics 10: 347. doi:10.1186/1471-2164-10-347.
27. Klemm R, Knight CE, Stein S (1973) Gross and microscopic morphology of glandula-proctodealis (foam gland) of Coturnix c. japonica (aves). J Morphol 141: 171-184.
28. Seiwert C, Adkins-Regan E (1998) The foam production system of the male Japanese quail: Characterization of structure and function. Brain Behav Evol 52: 61-80.
29. Coil WH, Wetherbee DK (1959) Observations on the cloacal gland of the Eurasian quail Coturnix coturnix. Ohio J Sci 59: 268-270.
30. Fujihara N (1992) Accessory reproductive fluids and organs in male domestic birds. Worlds Poult Sci J 48: 39-56.
31. Finseth FR, Iacovelli SR, Harrison RG, Adkins-Regan EK (2013) A nonsemen copulatory fluid influences the outcome of sperm competition in Japanese quail. J Evol Biol 26: 1875-1889. doi:10.1111/jeb.12189.
32. Cheng KM, McIntyre RF, Hickman AR (1989) Proctodeal gland foam enhances competitive fertilization in domestic Japanese quail. Auk 106: 286-291.
33. Adkins-Regan E (1999) Foam produced by male Coturnix quail: What is its function? Auk 116: 184-193.
34. Singh RP, Sastry KVH, Pandey NK, Singh KB, Malecki IA, et al. (2012) The role of the male cloacal gland in reproductive success in Japanese quail (Coturnix japonica). Reprod Fertil Dev 24: 405. doi:10.1071/RD11057.
35. Cheng KM, Hickman AR, Nichols CR (1989) Role of the proctodeal gland foam of male Japanese quail in natural copulations. Auk 106: 279-285.
36. Singh RP, H Sastry von K, Shit N, Pandey NK, Singh KB, et al. (2011) Cloacal gland foam enhances motility and disaggregation of spermatozoa in Japanese quail (Coturnix japonica). Theriogenology 75: 563-569. doi:10.1016/j.theriogenology.2010.09.028.
37. Milano I, Babbucci M, Panitz F, Ogden R, Nielsen RO, et al. (2011) Novel tools for conservation genomics: comparing two high-throughput approaches for SNP discovery in the transcriptome of the European hake. PLoS ONE 6: e28008. doi:10.1371/journal.pone.0028008.t007.
38. Gilles A, Meglécz E, Pech N, Ferreira S, Malausa T, et al. (2011) Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing. BMC Genomics 12: 245. doi:10.1186/1471-2164-12-245.
39. Kumar S, Blaxter ML (2010) Comparing de novo assemblers for 454 transcriptome data. BMC Genomics 11: 571. doi:10.1186/1471-2164-11-571.
40. Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, et al. (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 29: 644-652. doi:10.1038/nbt.1883.
41. Zheng Y, Zhao L, Gao J, Fei Z (2011) iAssembler: a package for de novo assembly of Roche-454/Sanger transcriptome sequences. BMC Bioinformatics 12: 453. doi:10.1186/1471-2105-12-453.
42. Rawat A, Elasri MO, Gust KA, George G, Pham D, et al. (2012) CAPRG: Sequence assembling pipeline for next generation sequencing of non-model organisms. PLoS ONE 7: e30370. doi:10.1371/journal.pone.0030370.g007.
43. Singhal S (2013) De novotranscriptomic analyses for non-model organisms: an evaluation of methods across a multi-species data set. Mol Ecol Resour 13: 403-416. doi:10.1111/1755-0998.12077.
44. Vijay N, Poelstra JW, Künstner A, Wolf JBW (2013) Challenges and strategies in transcriptome assembly and differential gene expression quantification. A comprehensive in silico assessment of RNA-seq experiments. Mol Ecol 22: 620-634. doi:10.1111/mec.12014.
45. O'Neil ST, Emrich SJ (2013) Assessing De Novo transcriptome assembly metrics for consistency and utility. BMC Genomics 14: 465. doi:10.1186/1471-2164-14-465.
46. Kayang BB, Fillon V, Inoue-Murayama M, Miwa M, Leroux S, et al. (2006) Integrated maps in quail (Coturnix japonica) confirm the high degree of synteny conservation with chicken (Gallus gallus) despite 35 million years of divergence. BMC Genomics 7: 101. doi:10.1186/1471-2164-7-101.
47. Sasazaki S, Hinenoya T, Lin B, Fujiwara A, Mannen H (2006) A comparative map of macrochromosomes between chicken and Japanese quail based on orthologous genes. Anim Genet 37: 316-320.
48. Sasazaki S, Hinenoya T, Fujima D, Kikuchi S, Fujiwara A, et al. (2006) Mapping of expressed sequence tag markers with a cDNA-amplified fragment length polymorphism method in Japanese quail (Coturnix japonica). Animal Sci J 77: 42-46.
49. Schumacher M, Balthazart J (1983) The effects of testosterone and its metabolites on sexual-behavior and morphology in male and female Japanese quail. Physiol Behav 30: 335-339.
50. Adkins E (1977) Effects of diverse androgens on sexual-behavior and morphology of castrated male quail. Horm Behav 8: 201-207.
51. Rumble SM, Lacroute P, Dalca AV, Fiume M, Sidow A, et al. (2009) SHRiMP: Accurate Mapping of Short Color-space Reads. PLoS Comput Biol 5: e1000386. doi:10.1371/journal.pcbi.1000386.t004.
52. Wickham H (2009) ggplot2: elegant graphics for data analysis. New York: Springer Publishing Company, Incorporated.
53. Kasprzyk A (2011) BioMart: driving a paradigm change in biological data management. Database (Oxford) 2011: bar049. doi:10.1093/database/bar049.
54. Min XJ, Butler G, Storms R, Tsang A (2005) OrfPredictor: predicting protein-coding regions in EST-derived sequences. Nucleic Acids Res 33: W677-W680. doi:10.1093/nar/gki394.
55. Koonin EV (2005) Orthologs, paralogs, and evolutionary genomics. Annual Rev Genet 39: 309-338. doi:10.1146/annurev.genet.39.073003.114725.
56. Bork P, Koonin EV (1998) Predicting functions from protein sequences - where are the bottlenecks? Nat Genet 18: 313-318. doi:10.1038/ng0498-313.
57. Tatusov RL (1997) A genomic perspective on protein families. Science 278: 631-637. doi:10.1126/science.278.5338.631.
58. Chen H, Boutros PC (2011) VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R. BMC Bioinformatics 12: 35. doi:10.1186/1471-2105-12-35.
59. Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754-1760. doi:10.1093/bioinformatics/btp324.
60. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, et al. (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics 25: 2078-2079. doi:10.1093/bioinformatics/btp352.
61. Xu L (2006) Average gene length is highly conserved in prokaryotes and eukaryotes and diverges only between the two kingdoms. Mol Biol Evol 23: 1107-1108. doi:10.1093/molbev/msk019.
62. O'Neil ST, Dzurisin JD, Carmichael RD, Lobo NF, Emrich SJ, et al. (2010) Population-level transcriptome sequencing of nonmodel organisms Erynnis propertius and Papilio zelicaon. BMC Genomics 11: 310. doi:10.1186/1471-2164-11-310.
63. Treangen TJ, Salzberg SL (2012) Repetitive DNA and next-generation sequencing: computational challenges and solutions. Nat Rev Genet 13: 36-46. doi:10.1038/nrg3117.
64. Fang Z, Cui X (2011) Design and validation issues in RNA-seq experiments. Brief Bioinform 12: 280-287. doi:10.1093/bib/bbr004.
65. Desjardins P, Morais R (1991) Nucleotide sequence and evolution of coding and noncoding regions of a quail mitochondrial genome. J Mol Evol 32: 153-161.
66. Toung JM, Morley M, Li M, Cheung VG (2011) RNA-sequence analysis of human B-cells. Genome Res 21: 991-998. doi:10.1101/gr.116335.110.
67. Glenn TC (2011) Field guide to next-generation sequencers. Mol Ecol Resour 11: 759-769.
68. Loman NJ, Constantinidou C, Chan JZM, Halachev M, Sergeant M, et al. (2012) High-throughput bacterial genome sequencing: an embarassment of choice, a world of opportunity. Nat Rev Microbiol 10: 598-606.
69. Quail MA, Smith M, Coupland P, Otto TD, Harris SR, et al. (2012) A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers. BMC Genomics 13: 341.