Characterization of the transcriptome of an ecologically important avian species, the Vinous-throated Parrotbill Paradoxornis webbianus bulomachus (Paradoxornithidae; Aves)

BMC Genomics

Volumn 13, Issue 1, 2012, Pages

  Chu, Jui Hua ^a   Lin, Rong Chien ^a   Yeh, Chia Fen ^a   Hsu, Yu Cheng ^b   Li, Shou Hsien ^a  

^a NATIONAL TAIWAN NORMAL UNIVERSITY   (Taiwan)

^b NATIONAL DONG HWA UNIVERSITY   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTOME;

ADAPTATION; ANIMAL GENETICS; ANIMAL TISSUE; ARTICLE; BIRD; CLIMATE; CONTROLLED STUDY; ECOLOGICAL GENETICS; GENE MAPPING; GENE SEQUENCE; GENETIC ALGORITHM; GENETIC CONSERVATION; GENETIC HETEROGENEITY; GENETIC TRANSCRIPTION; GENETIC VARIABILITY; HETEROZYGOSITY; MALE; MOLECULAR EVOLUTION; NONHUMAN; PARADOXORNIS WEBBIANUS BULOMACHUS; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; SIMPLE SEQUENCE REPEAT; SINGLE NUCLEOTIDE POLYMORPHISM; SPECIES DISTRIBUTION; TAENIOPYGIA GUTTATA;

ADAPTATION, BIOLOGICAL; ANIMALS; BASE SEQUENCE; BRAIN; GENE EXPRESSION PROFILING; GENETIC MARKERS; GENOME; LIVER; MICROSATELLITE REPEATS; MOLECULAR SEQUENCE DATA; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA; SEQUENCE ANALYSIS, RNA; SONGBIRDS; TRANSCRIPTOME;

AVES; GALLUS GALLUS; PARADOXORNIS WEBBIANUS; TAENIOPYGIA GUTTATA;

EID: 84862179274     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-13-149     Document Type: Article

References (38)

1. Losos JB. Adaptive radiation, ecological opportunity, and evolutionary determinism. Am Nat 2010, 175(6):623-639. 10.1086/652433, 20412015.
2. Rundle HD, Nosil P. Ecological speciation. Ecol Lett 2005, 8(3):336-352.
3. Schluter D, Conte GL. Genetics and ecological speciation. Proc Natl Acad Sci U S A 2009, 106:9955-9962. 10.1073/pnas.0901264106, 2702799, 19528639.
4. Rice AM, Rudh A, Ellegren H, Qvarnstrom A. A guide to the genomics of ecological speciation in natural animal populations. Ecol Lett 2011, 14(1):9-18. 10.1111/j.1461-0248.2010.01546.x, 21070555.
5. Simonson TS, Yang YZ, Huff CD, Yun HX, Qin G, Witherspoon DJ, Bai ZZ, Lorenzo FR, Xing JC, Jorde LB, et al. Genetic evidence for high-altitude adaptation in Tibet. Science 2010, 329(5987):72-75. 10.1126/science.1189406, 20466884.
6. Turner TL, Bourne EC, Von Wettberg EJ, Hu TT, Nuzhdin SV. Population resequencing reveals local adaptation of Arabidopsis lyrata to serpentine soils. Nature Genet 2010, 42(3):260-263. 10.1038/ng.515, 20101244.
7. White BJ, Lawniczak MKN, Cheng CD, Coulibaly MB, Wilson MD, Sagnon N, Costantini C, Simard F, Christophides GK, Besansky NJ. Adaptive divergence between incipient species of Anopheles gambiae increases resistance to Plasmodium. Proc Natl Acad Sci U S A 2011, 108(1):244-249. 10.1073/pnas.1013648108, 3017163, 21173248.
8. Hudson ME. Sequencing breakthroughs for genomic ecology and evolutionary biology. Mol Ecol Resour 2008, 8(1):3-17. 10.1111/j.1471-8286.2007.02019.x, 21585713.
9. Morozova O, Marra MA. Applications of next-generation sequencing technologies in functional genomics. Genomics 2008, 92(5):255-264. 10.1016/j.ygeno.2008.07.001, 18703132.
10. Seeb JE, Pascal CE, Grau ED, Seeb LW, Templin WD, Harkins T, Roberts SB. Transcriptome sequencing and high-resolution melt analysis advance single nucleotide polymorphism discovery in duplicated salmonids. Mol Ecol Resour 2011, 11(2):335-348. 10.1111/j.1755-0998.2010.02936.x, 21429141.
11. Renaut S, Nolte AW, Bernatchez L. Mining transcriptome sequences towards identifying adaptive single nucleotide polymorphisms in lake whitefish species pairs (Coregonus spp. Salmonidae). Mol Ecol 2010, 19:115-131.
12. Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 2009, 10(1):57-63. 10.1038/nrg2484, 2949280, 19015660.
13. Metzker ML. Sequencing technologies - the next generation. Nat Rev Genet 2010, 11(1):31-46. 10.1038/nrg2626, 19997069.
14. Ozsolak F, Milos PM. RNA sequencing: advances, challenges and opportunities. Nat Rev Genet 2011, 12(2):87-98. 10.1038/nrg2934, 3031867, 21191423.
15. Robertson G, Schein J, Chiu R, Corbett R, Field M, Jackman SD, Mungall K, Lee S, Okada HM, Qian JQ, et al. De novo assembly and analysis of RNA-seq data. Nat Meth 2010, 7(11):909-912.
16. Paszkiewicz K, Studholme DJ. De novo assembly of short sequence reads. Brief Bioinform 2010, 11(5):457-472. 10.1093/bib/bbq020, 20724458.
17. Surget-Groba Y, Montoya-Burgos JI. Optimization of de novo transcriptome assembly from next-generation sequencing data. Genome Res 2010, 20(10):1432-1440. 10.1101/gr.103846.109, 2945192, 20693479.
18. Robson C. Family Paradoxornithidae (Parrotbills). Handbook of the birds of the world 2007, Barcelona: Lynx Edicions, Hoyo J, Elliott A, Christie DA.
19. Hachisuka M, Udagawa T. Contributions to the ornithology of Formosa part II. Quarterly J Taiwan Museum 1951, 4:1-180.
20. Korner C. The use of 'altitude' in ecological research. Trends Ecol Evol 2007, 22(11):569-574. 10.1016/j.tree.2007.09.006, 17988759.
21. Hancock AM, Witonsky DB, Gordon AS, Eshel G, Pritchard JK, Coop G, Di Rienzo A. Adaptations to climate in candidate genes for common metabolic disorders. PLoS Genet 2008, 4(2):e32. 10.1371/journal.pgen.0040032, 2242814, 18282109.
22. Ellegren H. Evolutionary stasis: the stable chromosomes of birds. Trends Ecol Evol 2010, 25(5):283-291. 10.1016/j.tree.2009.12.004, 20363047.
23. Warren WC, Clayton DF, Ellegren H, Arnold AP, Hillier LW, Kunstner A, Searle S, White S, Vilella AJ, Fairley S, et al. The genome of a songbird. Nature 2010, 464(7289):757-762. 10.1038/nature08819, 3187626, 20360741.
24. Seeb JE, Carvalho G, Hauser L, Naish K, Roberts S, Seeb LW. Single-nucleotide polymorphism (SNP) discovery and applications of SNP genotyping in nonmodel organisms. Mol Ecol Resour 2011, 11:1-8.
25. Garant D, Kruuk LEB. How to use molecular marker data to measure evolutionary parameters in wild populations. Mol Ecol 2005, 14(7):1843-1859. 10.1111/j.1365-294X.2005.02561.x, 15910310.
26. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, et al. The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 2010, 20(9):1297-1303. 10.1101/gr.107524.110, 2928508, 20644199.
27. Smith CT, Elfstrom CM, Seeb LW, Seeb JE. Use of sequence data from rainbow trout and Atlantic salmon for SNP detection in Pacific salmon. Mol Ecol 2005, 14(13):4193-4203. 10.1111/j.1365-294X.2005.02731.x, 16262869.
28. Faircloth BC. MSATCOMMANDER: detection of microsatellite repeat arrays and automated, locus-specific primer design. Mol Ecol Resour 2008, 8(1):92-94. 10.1111/j.1471-8286.2007.01884.x, 21585724.
29. Yi X, Liang Y, Huerta-Sanchez E, Jin X, Cuo ZXP, Pool JE, Xu X, Jiang H, Vinckenbosch N, Korneliussen TS, et al. Sequencing of 50 human exomes reveals adaptation to high altitude. Science 2010, 329(5987):75-78. 10.1126/science.1190371, 20595611.
30. Alstrom P, Ericson PGP, Olsson U, Sundberg P. Phylogeny and classification of the avian superfamily Sylvioidea. Mol Phylogenet Evol 2006, 38(2):381-397. 10.1016/j.ympev.2005.05.015, 16054402.
31. Penhallurick J, Robson C. The generic taxonomy of parrotbills (Ayes, Timaliidae). Forktail 2009, 25:137-141.
32. Cibois A. Mitochondrial DNA phylogeny of babblers (Timaliidae). Auk 2003, 120(1):35-54.
33. 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. 10.1093/bioinformatics/bti610, 16081474.
34. Gotz S, Garcia-Gomez JM, Terol J, Williams TD, Nagaraj SH, Nueda MJ, Robles M, Talon M, Dopazo J, Conesa A. High-throughput functional annotation and data mining with the Blast2GO suite. Nucleic Acids Res 2008, 36(10):3420-3435. 10.1093/nar/gkn176, 2425479, 18445632.
35. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. Gene Ontology: tool for the unification of biology. Nature Genet 2000, 25(1):25-29. 10.1038/75556, 3037419, 10802651.
36. Wheelan SJ, Marchler-Bauer A, Bryant SH. Domain size distributions can predict domain boundaries. Bioinformatics 2000, 16(7):613-618. 10.1093/bioinformatics/16.7.613, 11038331.
37. Islam SA, Luo JC, Sternberg MJE. Identification and analysis of domains in proteins. Protein Eng 1995, 8(6):513-525. 10.1093/protein/8.6.513, 8532675.
38. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009, 25(14):1754-1760. 10.1093/bioinformatics/btp324, 2705234, 19451168.