Characterization of Liaoning Cashmere Goat Transcriptome: Sequencing, De Novo Assembly, Functional Annotation and Comparative Analysis

PLoS ONE

Volumn 8, Issue 10, 2013, Pages

  Liu, Hongliang ^a   Wang, Tingting ^b   Wang, Jinke ^b   Quan, Fusheng ^a   Zhang, Yong ^a  

^a NORTHWEST A F UNIVERSITY   (China)

^b SOUTHEAST UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTOME;

ANIMAL EXPERIMENT; ANIMAL GENETICS; ANIMAL TISSUE; ARTICLE; CHROMOSOME; COMPARATIVE STUDY; CONTROLLED STUDY; EXPRESSED SEQUENCE TAG; FEMALE; GENE CLUSTER; GENE EXPRESSION; GENE FUNCTION; GENE IDENTIFICATION; GENE MAPPING; GENE SEQUENCE; GENE STRUCTURE; GENETIC ANALYSIS; GENETIC DATABASE; GENETIC IMPROVEMENT; GENETIC LINKAGE; GOAT; LIAONING CASHMERE GOAT; MOLECULAR GENETICS; NONHUMAN; PROTEIN EXPRESSION; SEQUENCE ALIGNMENT; SIMPLE SEQUENCE REPEAT;

ANIMALS; CATTLE; FEMALE; GENE EXPRESSION PROFILING; GENOMICS; GOATS; HUMANS; MICROSATELLITE REPEATS; MOLECULAR SEQUENCE ANNOTATION; SEQUENCE ANALYSIS;

EID: 84885094217     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0077062     Document Type: Article

References (42)

1. Jin M, Wang L, Li S, Xing MX, Zhang X, (2011) Characterization and expression analysis of KAP7. 1, KAP8. 2 gene in Liaoning new-breeding cashmere goat hair follicle. Mol Biol Rep 38: 3023-3028. doi:10.1007/s11033-010-9968-6. PubMed: 20151326.
2. Bai WL, Yin RH, Jiang WQ, Luo GB, Yin RL, et al. (2012) Molecular Characterization of Prolactin cDNA and Its Expression Pattern in Skin Tissue of Liaoning Cashmere Goat. Biochem Genet, 50: 1-8. PubMed: 22580795.
3. Jin M, Guo C-L, Hu J-H, Gao W-B, Wang W, (2006) Correlation analysis of economic traits in Liaoning new breed of cashmere goats using microsatellite DNA markers. Acta Genet Sin 33: 230-235. doi:10.1016/S0379-4172(06)60045-0. PubMed: 16553211.
4. Guo D, Han D, Wang C-y, Zheng X, Gao Y, et al. (2010) Genetic Diversity of Seven Microsatellite Markers in Liaoning Cashmere Goat. China Animal Husbandry Veterinary Med 12: 030.
5. Blanca J, Cañizares J, Roig C, Ziarsolo P, Nuez F, et al. (2011) Transcriptome characterization and high throughput SSRs and SNPs discovery in Cucurbita pepo (Cucurbitaceae). BMC Genomics 12: 104. doi:10.1186/1471-2164-12-104. PubMed: 21310031.
6. Hornshøj H, Bendixen E, Conley LN, Andersen PK, Hedegaard J, et al. (2009) Transcriptomic and proteomic profiling of two porcine tissues using high-throughput technologies. BMC Genomics 10: 30. doi:10.1186/1471-2164-10-S3-S30. PubMed: 19152685.
7. Torres TT, Metta M, Ottenwälder B, Schlötterer C, (2008) Gene expression profiling by massively parallel sequencing. Genome Res 18: 172-177. PubMed: 18032722.
8. Barbazuk WB, Emrich SJ, Chen HD, Li L, Schnable PS, (2007) SNP discovery via 454 transcriptome sequencing. Plant J 51: 910-918. doi:10.1111/j.1365-313X.2007.03193.x. PubMed: 17662031.
9. Cheung F, Win J, Lang JM, Hamilton J, Vuong H, et al. (2008) Analysis of the Pythium ultimum transcriptome using Sanger and Pyrosequencing approaches. BMC Genomics 9: 542. doi:10.1186/1471-2164-9-542. PubMed: 19014603.
10. Garg R, Patel RK, Tyagi AK, Jain M, (2011) De novo assembly of chickpea transcriptome using short reads for gene discovery and marker identification. DNA Res 18: 53-63. doi:10.1093/dnares/dsq028. PubMed: 21217129.
11. Zhou Y, Gao F, Liu R, Feng J, Li H, (2012) De novo sequencing and analysis of root transcriptome using 454 pyrosequencing to discover putative genes associated with drought tolerance in Ammopiptanthus mongolicus. BMC Genomics 13: 266. doi:10.1186/1471-2164-13-266. PubMed: 22721448.
12. Wang B, Ekblom R, Castoe TA, Jones EP, Kozma R, et al. (2012) Transcriptome sequencing of black grouse (Tetrao tetrix) for immune gene discovery and microsatellite development. Open Biol 2: 120054. doi:10.1098/rsob.120054. PubMed: 22724064.
13. Ma K, Qiu G, Feng J, Li J, (2012) Transcriptome Analysis of the Oriental River Prawn, Macrobrachium nipponense Using 454 Pyrosequencing for Discovery of Genes and Markers. PLOS ONE 7: e39727. doi:10.1371/journal.pone.0039727. PubMed: 22745820.
14. Huh JW, Kim YH, Park SJ, Kim DS, Lee SR, et al. (2012) Large-scale transcriptome sequencing and gene analyses in the crab-eating macaque (macaca fascicularis) for biomedical research. BMC Genomics 13: 163. doi:10.1186/1471-2164-13-163. PubMed: 22554259.
15. Xia JH, He XP, Bai ZY, Lin G, Yue GH, (2011) Analysis of the Asian seabass transcriptome based on expressed sequence tags. DNA Res 18: 513-522. doi:10.1093/dnares/dsr036. PubMed: 22086997.
16. Clark MS, Thorne MA, Toullec JY, Meng Y, Guan Le L, et al. (2011) Antarctic krill 454 pyrosequencing reveals chaperone and stress transcriptome. PLOS ONE 6: e15919. doi:10.1371/journal.pone.0015919. PubMed: 21253607.
17. Bai X, Mamidala P, Rajarapu SP, Jones SC, Mittapalli O, (2011) Transcriptomics of the bed bug (Cimex lectularius). PLOS ONE 6: e16336. doi:10.1371/journal.pone.0016336. PubMed: 21283830.
18. Salem M, Rexroad CE 3rd, Wang J, Thorgaard GH, Yao J, (2010) Characterization of the rainbow trout transcriptome using Sanger and 454-pyrosequencing approaches. BMC Genomics 11: 564. doi:10.1186/1471-2164-11-564. PubMed: 20942956.
19. Gao Z, Luo W, Liu H, Zeng C, Liu X, et al. (2012) Transcriptome Analysis and SSR/SNP Markers Information of the Blunt Snout Bream (Megalobrama amblycephala). PLOS ONE 7: e42637. doi:10.1371/journal.pone.0042637. PubMed: 22880060.
20. Pereiro P, Balseiro P, Romero A, Dios S, Forn-Cuni G, et al. (2012) High-throughput sequence analysis of turbot (Scophthalmus maximus) transcriptome using 454-pyrosequencing for the discovery of antiviral immune genes. PLOS ONE 7: e35369. doi:10.1371/journal.pone.0035369. PubMed: 22629298.
21. Blanca J, Cañizares J, Roig C, Ziarsolo P, Nuez F, et al. (2011) Transcriptome characterization and high throughput SSRs and SNPs discovery in Cucurbita pepo (Cucurbitaceae). BMC Genomics 12: 104. doi:10.1186/1471-2164-12-104. PubMed: 21310031.
22. Bai X, Rivera-Vega L, Mamidala P, Bonello P, Herms DA, et al. (2011) Transcriptomic signatures of ash (Fraxinus spp.) phloem. PLOS ONE 6: e16368. doi:10.1371/journal.pone.0016368. PubMed: 21283712.
23. Torales SL, Rivarola M, Pomponio MF, Fernández P, Acuña CV, et al. (2012) Transcriptome survey of Patagonian southern beech Nothofagus nervosa (= N. alpina): assembly, annotation and molecular marker discovery. BMC Genomics 13: 291. doi:10.1186/1471-2164-13-291. PubMed: 22747958.
24. Tanase K, Nishitani C, Hirakawa H, Isobe S, Tabata S, et al. (2012) Transcriptome analysis of carnation (Dianthus caryophyllus L.) based on next-generation sequencing technology. BMC Genomics 13: 292. doi:10.1186/1471-2164-13-292. PubMed: 22747974.
25. Schmid J, Müller-Hagen D, Bekel T, Funk L, Stahl U, et al. (2010) Transcriptome sequencing and comparative transcriptome analysis of the scleroglucan producer Sclerotium rolfsii. BMC Genomics 11: 329. doi:10.1186/1471-2164-11-329. PubMed: 20504312.
26. Sato S, Feltus FA, Iyer P, Tien M, (2009) The first genome-level transcriptome of the wood-degrading fungus Phanerochaete chrysosporium grown on red oak. Curr Genet 55: 273-286. doi:10.1007/s00294-009-0243-0. PubMed: 19396602.
27. Poroyko V, White JR, Wang M, Donovan S, Alverdy J, et al. (2010) Gut microbial gene expression in mother-fed and formula-fed piglets. PLOS ONE 5: e12459. doi:10.1371/journal.pone.0012459. PubMed: 20805981.
28. Zhou X, Ren L, Meng Q, Li Y, Yu Y, et al. (2010) The next-generation sequencing technology and application. Proteins Cell 1: 520-536. doi:10.1007/s13238-010-0065-3. PubMed: 21204006.
29. Metzker ML, (2009) Sequencing technologies-the next generation. Nat Rev Genet 11: 31-46. PubMed: 19997069.
30. 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. PubMed: 18266620.
31. 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. PubMed: 19435504.
32. 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. doi:10.1186/1471-2164-11-180. PubMed: 20233449.
33. Nyberg KG, Conte MA, Kostyun JL, Forde A, Bely AE, (2012) Transcriptome characterization via 454 pyrosequencing of the annelid Pristina leidyi, an emerging model for studying the evolution of regeneration. BMC Genomics 13: 287. doi:10.1186/1471-2164-13-287. PubMed: 22747785.
34. Peterson MP, Whittaker DJ, Ambreth S, Sureshchandra S, Buechlein A, et al. (2012) De novo transcriptome sequencing in a songbird, the dark-eyed junco (Junco hyemalis): genomic tools for an ecological model system. BMC Genomics 13: 305. doi:10.1186/1471-2164-13-305. PubMed: 22776250.
35. Rice P, Longden I, Bleasby A, (2000) EMBOSS: the European molecular biology open software suite. Trends Genet 16: 276-277. doi:10.1016/S0168-9525(00)02024-2. PubMed: 10827456.
36. Chen Z, Xue C, Zhu S, Zhou F, Liu G, et al. (2005) GoPipe: streamlined gene ontology annotation for batch anonymous sequences with statistics. Prog Biochem Biophys 32: 187-191.
37. Dong Y, Xie M, Jiang Y, Xiao N, Du X, et al. (2012) Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus). Nat Biotechnol 31: 135-141. doi:10.1038/nbt.2478. PubMed: 23263233.
38. Zhang L, Yuan D, Yu S, Li Z, Cao Y, et al. (2004) Preference of simple sequence repeats in coding and non-coding regions of Arabidopsis thaliana. Bioinformatics 20: 1081-1086. doi:10.1093/bioinformatics/bth043. PubMed: 14764542.
39. Xu T, Guo X, Wang H, Hao F, Du X, et al. (2013) Differential gene expression analysis between anagen and telogen of Capra hircus skin based on the de novo assembled transcriptome sequence. Gene 520: 30-38. doi:10.1016/j.gene.2013.01.068. PubMed: 23466980.
40. Lagercrantz U, Ellegren H, Andersson L, (1993) The abundance of various polymorphic microsatellite motifs differs between plants and vertebrates. Nucleic Acids Res 21: 1111-1115. doi:10.1093/nar/21.5.1111. PubMed: 8464696.
41. He M, Wang Y, Hua W, Zhang Y, Wang Z, (2012) De Novo Sequencing of Hypericum perforatum Transcriptome to Identify Potential Genes Involved in the Biosynthesis of Active Metabolites. PLOS ONE 7: e42081. doi:10.1371/journal.pone.0042081. PubMed: 22860059.
42. Rozen S, Skaletsky H, (2000) Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 132: 365-386. PubMed: 10547847.