The plover neurotranscriptome assembly: Transcriptomic analysis in an ecological model species without a reference genome

Molecular Ecology Resources

Volumn 13, Issue 4, 2013, Pages 696-705

  Moghadam, Hooman K ^a   Harrison, Peter W ^b   Zachar, Gergely ^c   Székely, Tamás ^d   Mank, Judith E ^b  

^a INSTITUTE OF OCEANOGRAPHY   (Greece)

^b UNIVERSITY COLLEGE LONDON   (United Kingdom)

^c SEMMELWEIS UNIVERSITY   (Hungary)

^d University of Bath   (United Kingdom)

Author keywords

Behavioural transcriptomics; De novo transcriptome assembly; Neurogenomics; Sex biased gene expression; SNP discovery

Indexed keywords

ANIMAL; ARTICLE; CHARADRIIFORMES; DIENCEPHALON; FEMALE; GENE EXPRESSION PROFILING; GENETICS; MALE; METHODOLOGY; PHYSIOLOGY; SEXUAL BEHAVIOR; TELENCEPHALON;

ANIMALS; CHARADRIIFORMES; DIENCEPHALON; FEMALE; GENE EXPRESSION PROFILING; MALE; SEXUAL BEHAVIOR, ANIMAL; TELENCEPHALON;

AVES; CHARADRIUS ALEXANDRINUS;

EID: 84879410650     PISSN: 1755098X     EISSN: 17550998     Source Type: Journal    
DOI: 10.1111/1755-0998.12096     Document Type: Article

References (62)

1. AlRashidi M, Kosztolányi A, Shobrak M, Kupper C, Székely T (2011) Parental cooperation in an extreme hot environment: natural behaviour and experimental evidence. Animal Behaviour, 82, 235-243.
2. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. Journal of Molecular Biology, 215, 403-410.
3. Anders S, Huber W (2010) Differential expression analysis for sequence count data. Genome Biology, 11, R106.
4. Ashburner M, Ball CA, Blake JA et al. (2000) Gene ontology: tool for the unification of biology The Gene Ontology Consortium. Nature Genetics, 25, 25-29.
5. Bauer S, Grossmann S, Vingron M, Robinson PN (2008) Ontologizer 2.0-a multifunctional tool for GO term enrichment analysis and data exploration. Bioinformatics, 24, 1650-1651.
6. Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society: Series B (Statistical Methodology), 57, 289-300.
7. Benson G (1999) Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Research, 27, 573-580.
8. Conesa A, Gotz S (2008) Blast2GO: a comprehensive suite for functional analysis in plant genomics. International Journal of Plant Genomics, 2008, 619832.
9. Cozzoli DK, Goulding SP, Zhang PW et al. (2009) Binge drinking upregulates accumbens mGluR5-Homer2-PI3K signaling: functional implications for alcoholism. Journal of Neuroscience, 29, 8655-8668.
10. Cuthbert PC, Stanford LE, Coba MP et al. (2007) Synapse-associated protein 102/dlgh3 couples the NMDA receptor to specific plasticity pathways and learning strategies. Journal of Neuroscience, 27, 2673-2682.
11. Dalloul RA, Long JA, Zimin AV et al. (2010) Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis. PLoS Biology, 8, e1000475.
12. Donaldson ZR, Young LJ (2008) Oxytocin, vasopressin, and the neurogenetics of sociality. Science, 322, 900-904.
13. Ekblom R, Galindo J (2011) Applications of next generation sequencing in molecular ecology of non-model organisms. Heredity, 107, 1-15.
14. Ellegren H (2010) Evolutionary stasis: the stable chromosomes of birds. Trends in Ecology and Evolution, 25, 283-291.
15. Ellegren H, Hultin-Rosenberg L, Brunstrom B et al. (2007) Faced with inequality: chicken do not have a general dosage compensation of sex-linked genes. BMC Biology, 5, 40.
16. Fraga RM, Amat JA (1996) Breeding biology of a Kentish Plover (Charadrius alexandrinus) population in an inland saline lake. Ardeola, 43, 69-85.
17. Fraser BA, Weadick CJ, Janowitz I, Rodd FH, Hughes KA (2011) Sequencing and characterization of the guppy (Poecilia reticulata) transcriptome. BMC Genomics, 12, 202.
18. Fridolfsson AK, Cheng H, Copeland NG et al. (1998) Evolution of the avian sex chromosomes from an ancestral pair of autosomes. Proceedings of the National Academy of Sciences USA, 95, 8147-8152.
19. Gao Z, Luo W, Liu H et al. (2012) Transcriptome analysis and SSR/SNP markers information of the blunt snout bream (Megalobrama amblycephala). PLoS ONE, 7, e42637.
20. Glickstein M (2007) What does the cerebellum really do? Current Biology, 17, R824-R827.
21. Grabherr MG, Haas BJ, Yassour M et al. (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature Biotechnology, 29, 644-652.
22. Harrison PW, Mank JE, Wedell N (2012) Incomplete sex chromosome dosage compensation in the Indian meal moth, Plodia interpunctella, based on de novo transcriptome assembly. Genome Biology and Evolution, 4, 1118-1126.
23. Hashimoto R, Hashimoto H, Shintani N et al. (2007) Pituitary adenylate cyclase-activating polypeptide is associated with schizophrenia. Molecular Psychiatry, 12, 1026-1032.
24. Hillier LW, Miller W, Birney E et al. (2004) Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature, 432, 695-716.
25. Hohenlohe PA, Bassham S, Etter PD, et al. (2010) Population genomics of parallel adaptation in threespine stickleback using sequenced RAD tags. PLoS Genetics, 6, e1000862.
26. de Hoon MJ, Imoto S, Nolan J, Miyano S (2004) Open source clustering software. Bioinformatics, 20, 1453-1454.
27. Itoh Y, Melamed E, Yang X et al. (2007) Dosage compensation is less effective in birds than in mammals. Journal of Biology, 6, 2.
28. Kosztolányi A, Barta Z, Kupper C, Székely T (2011) Persistence of an extreme male-biased adult sex ratio in a natural population of polyandrous bird. Journal of Evolutionary Biology, 24, 1842-1846.
29. Kunstner A, Wolf JBW, Backstrom N et al. (2011) Comparative genomics based on massive parallel transcriptome sequencing reveals patterns of substitution and selection across 10 bird species. Molecular Ecology, 20, 2871.
30. Li B, Dewey CN (2011) RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics, 12, 323.
31. Li W, Godzik A (2006) Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics, 22, 1658-1659.
32. Lim MM, Young LJ (2006) Neuropeptidergic regulation of affiliative behavior and social bonding in animals. Hormones and Behavior, 50, 506-517.
33. Lohse M, Bolger AM, Nagel A et al. (2012) RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics. Nucleic Acids Research, 40, W622-W627.
34. Mank JE, Ellegren H (2009) All dosage compensation is local: gene-by-gene regulation of sex-biased expression on the chicken Z chromosome. Heredity, 102, 312-320.
35. Martin JA, Wang Z (2011) Next-generation transcriptome assembly. Nature Review. Genetics, 12, 671-682.
36. Melamed E, Arnold AP (2007) Regional differences in dosage compensation on the chicken Z chromosome. Genome Biology, 8, R202.
37. Miller MR, Dunham JP, Amores A, Cresko WA, Johnson EA (2007) Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers. Genome Research, 17, 240-248.
38. Moghadam HK, Pointer MA, Wright AE, Berlin S, Mank JE (2012) W chromosome expression responds to female-specific selection. Proceedings of the National Academy of Sciences USA, 190, 8207-8211.
39. Nanda I, Schlegelmilch K, Haaf T, Schartl M, Schmid M (2008) Synteny conservation of the Z chromosome in 14 avian species (11 families) supports a role for Z dosage in avian sex determination. Cytogenetic and Genome Research, 122, 150-156.
40. Pinhasov A, Mandel S, Torchinsky A et al. (2003) Activity-dependent neuroprotective protein: a novel gene essential for brain formation. Brain Research Developmental Brain Research, 144, 83-90.
41. Robinson GE, Fernald RD, Clayton DF (2008) Genes and social behavior. Science, 322, 896-900.
42. Rokas A, Abbot P (2009) Harnessing genomics for evolutionary insights. Trends in Ecology and Evolution, 24, 192-200.
43. Saldanha AJ (2004) Java Treeview-extensible visualization of microarray data. Bioinformatics, 20, 3246-3248.
44. Santure AW, Gratten J, Mossman JA, Sheldon BC, Slate J (2011) Characterisation of the transcriptome of a wild great tit Parus major population by next generation sequencing. BMC Genomics, 12, 283.
45. Schmieder R, Edwards R (2011) Quality control and preprocessing of metagenomic datasets. Bioinformatics, 27, 863-864.
46. Stapley J, Reger J, Feulner PGD et al. (2010) Adaptation genomics: the next generation. Trends in Ecology and Evolution, 25, 705-712.
47. Strick PL, Dum RP, Fiez JA (2009) Cerebellum and nonmotor function. The Annual Review of Neuroscience, 32, 413-434.
48. Suzuki R, Shimodaira H (2006) Pvclust: an R package for assessing the uncertainty in hierarchical clustering. Bioinformatics, 22, 1540-1542.
49. Székely T, Cuthill IC (2000) Trade-off between mating opportunities and parental care: brood desertion by female Kentish plovers. Proceedings of the Royal Society B, 267, 2087-2092.
50. Székely T, Lessells CM (1993) Mate change by Kentish Plovers Charadrius alexandrinus. Ornis Scandinavica, 24, 317-322.
51. Székely T, Kosztolányi A, Kupper C, Thomas GH (2007) Sexual conflict over parental care: a case study of shorebirds. Journal of Ornithology, 148, S211-S217.
52. Teranishi M, Shimada Y, Hori T et al. (2001) Transcripts of the MHM region on the chicken Z chromosome accumulate as non-coding RNA in the nucleus of female cells adjacent to the DMRT1 locus. Chromosome Research, 9, 147-165.
53. Thiel T, Michalek W, Varshney RK, Graner A (2003) Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theoretical and Applied Genetics, 106, 411-422.
54. Tran AH, Uwano T, Kimura T et al. (2008) Dopamine D1 receptor modulates hippocampal representation plasticity to spatial novelty. Journal of Neuroscience, 28, 13390-13400.
55. Vijay N, Poelstra JW, Kunstner A, Wolf JB (2012) Challenges and strategies in transcriptome assembly and differential gene expression quantification A comprehensive in silico assessment of RNA-seq experiments. Molecular Ecology, 22, 620-634.
56. Warren WC, Clayton DF, Ellegren H et al. (2010) The genome of a songbird. Nature, 464, 757-762.
57. Weeber EJ, Levy M, Sampson MJ et al. (2002) The role of mitochondrial porins and the permeability transition pore in learning and synaptic plasticity. Journal of Biological Chemistry, 277, 18891-18897.
58. Wolf J, Bryk J (2011) General lack of global dosage compensation in ZZ/ZW systems? Broadening the perspective with RNA-seq. BMC Genomics, 12, 91.
59. Wong GK, Liu B, Wang J et al. (2004) A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms. Nature, 432, 717-722.
60. Wright AE, Moghadam HK, Mank JE (2012) Trade-off between selection for dosage compensation and masculinization on the avian Z chromosome. Genetics, 192, 1434-1445.
61. Young LJ, Winslow JT, Wang Z et al. (1997) Gene targeting approaches to neuroendocrinology: oxytocin, maternal behavior, and affiliation. Hormones and Behavior, 31, 221-231.
62. Zhao QY, Wang Y, Kong YM et al. (2011) Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study. BMC Bioinformatics, 12, S2. doi: 10.1186/1471-2105-12-S14-S2.