Genome-wide transcriptome analysis between Small-tail Han sheep and the Surabaya fur sheep using high-throughput RNA sequencing

Reproduction

Volumn 145, Issue 6, 2013, Pages 587-596

  Miao, Xiangyang ^a   Luo, Qingmiao ^a  

^a INSTITUTE OF PLANT PROTECTION   (China)

Author keywords

[No Author keywords available]

Indexed keywords

CONTIG; RNA;

ARTICLE; FERTILITY; GENE; GENE EXPRESSION; HIGH THROUGHPUT SEQUENCING; NONHUMAN; PRIORITY JOURNAL; REAL TIME POLYMERASE CHAIN REACTION; REPRODUCTION; RNA SEQUENCE; SHEEP;

ANIMALS; ANIMALS, INBRED STRAINS; CHINA; COMPUTATIONAL BIOLOGY; FEMALE; FERTILITY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE ONTOLOGY; GENOME-WIDE ASSOCIATION STUDY; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; OVARY; REAL-TIME POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, MESSENGER; SEQUENCE ANALYSIS, RNA; SHEEP, DOMESTIC; SPECIES SPECIFICITY; TRANSCRIPTOME;

EID: 84878000741     PISSN: 14701626     EISSN: 17417899     Source Type: Journal    
DOI: 10.1530/REP-12-0507     Document Type: Article

References (28)

1. Al-Shahrour F, Diaz-Uriarte R & Dopazo J 2004 FatiGO: a web tool for finding significant associations of gene ontology terms with groups of genes. Bioinformatics 20 578-580. (doi:10.1093/bioinformatics/btg455)
2. Anders S & Huber W 2010 Differential expression analysis for sequence count data. Genome Biology 11 R106. (doi:10.1186/gb-2010-11-10-r106)
3. Blumer JB, Lord K, Saunders TL, Pacchioni A, Black C, Lazartigues E, Varner KJ, Gettys TW & Lanier SM 2008 Activator of G protein signaling 3 null mice: I. Unexpected alterations in metabolic and cardiovascular function. Endocrinology 149 3842-3849. (doi:10.1210/en.2008-0050)
4. Bongiorni S, Chillemi G, Prosperini G, Bueno S, Valentini A & Pariset L 2009 A tool for sheep product quality: custom microarrays from public databases. Nutrients 1 235-250. (doi:10.3390/nu1020235)
5. Bonnet A, Bevilacqua C, Benne F, Bodin L, Cotinot C, Liaubet L, Sancristobal M, Sarry J, Terenina E, Martin P et al. 2011 Transcriptome profiling of sheep granulosa cells and oocytes during early follicular development obtained by laser capture microdissection. BMC Genomics 12 417-431. (doi:10.1186/1471-2164-12-417)
6. Canty-Laird E, Carré GA, Mandon-Pépin B, Kadler KE & Fabre S 2010 First evidence of bone morphogenetic protein 1 expression and activity in sheep ovarian follicles. Biology of Reproduction 83 138-146. (doi:10.1095/biolreprod.109.082115)
7. Feary ES, Juengel JL, Smith P, French MC, O'Connell AR, Lawrence SB, Galloway SM, Davis GH & McNatty KP 2007 Patterns of expression of messenger RNAs encoding GDF9, BMP15, TGFBR1, BMPR1B, and BMPR2 during follicular development and characterization of ovarian follicular populations in ewes carrying the Woodlands FecX2W mutation. Biology of Reproduction 77 990-998. (doi:10.1095/biolreprod.107.062752)
8. Gibbons JG, Janson EM, Hittinger CT, Johnston M, Abbot P & Rokas A 2009 Benchmarking next-generation transcriptome sequencing for functional and evolutionary genomics. Molecular Biology and Evolution 26 2731-2744. (doi:10.1093/molbev/msp188)
9. Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q et al. 2011 Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature Biotechnology 29 644-652. (doi:10.1038/nbt.1883)
10. Knight PG & Glister C 2006 TGF- b superfamily members and ovarian follicle development. Reproduction 132 191-206. (doi:10.1530/rep.1.01074)
11. 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. (doi:10.1093/bioinformatics/btl158)
12. Li R, Fan W, Tian G, Zhu H, He L, Cai J, Huang Q, Cai Q, Li B, Bai Y et al. 2009 The sequence and de novo assembly of the giant panda genome. Nature 463 311-317. (doi:10.1038/nature08696)
13. Livak KJ & Schmittgen TD 2001 Analysis of relative gene expression data using real-time quantitative PCR and the 2KDDCt method. Methods 25 402-408. (doi:10.1006/meth.2001.1262)
14. Mardis ER 2008 The impact of next-generation sequencing technology on genetics. Trends inGenetics 24 133-141. (doi:10.1016/j.tig.2007.12.007)
15. Mortazavi A, Williams BA, McCue K, Schaeffer L & Wold B 2008 Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature Methods 5 621-628. (doi:10.1038/nmeth.1226)
16. Mosimann C, Hausmann G & Basler K 2009 b -Catenin hits chromatin: regulation of Wnt target gene activation. Nature Reviews. Molecular Cell Biology 10 276-286. (doi:10.1038/nrm2654)
17. Otsuka F, McTavish KJ & Shimasaki S 2011 Integral role of GDF-9 and BMP-15 in ovarian function. Molecular Reproduction and Development 78 9-21. (doi:10.1002/mrd.21265)
18. Paradis F, Novak S, Murdoch GK, Dyck MK, DixonWT & Foxcroft GR 2009 Temporal regulation of BMP2, BMP6, BMP15, GDF9, BMPR1A, BMPR1B, BMPR2 and TGFBR1 mRNA expression in the oocyte, granulosa and theca cells of developing preovulatory follicles in the pig. Reproduction 138 115-129. (doi:10.1530/REP-08-0538)
19. Paulini F & Melo EO 2011 The role of oocyte-secreted factors GDF9 and BMP15 in follicular development and oogenesis. Reproduction in Domestic Animals 46 354-361. (doi:10.1111/j.1439-0531.2010.01739.x)
20. Peñagaricano F, Zorrilla P, Naya H, Robello C & Urioste JI 2012 Gene expression analysis identifies new candidate genes associated with the development of black skin spots in Corriedale sheep. Journal of Applied Genetics 53 99-106. (doi:10.1007/s13353-011-0066-9)
21. Quintero-Elisea JA, Macias-Cruz U, Alvarez-Valenzuela FD, Correa-Calderon A, Gonzalez-Reyna A, Lucero-Magaña FA, Soto-Navarro SA & Avendaño-Reyes L 2011 The effects of time and dose of pregnant mare serum gonadotropin (PMSG) on reproductive efficiency in hair sheep ewes. Tropical Animal Health and Production 43 1567-1573. (doi:10.1007/s11250-011-9843-z)
22. Raabe T & Rapp UR 2002 KSR - a regulator and scaffold protein of the MAPK pathway. Science's STKE 136 28. (doi:10.1126/stke.2002.136.pe28)
23. Shimasaki S, Zachow RJ, Li D, Kim H, Iemura S, Ueno N, Sampath K, Chang RJ & Erickson GF 1999 A functional bone morphogenetic protein system in the ovary. PNAS 96 7282-7287. (doi:10.1073/pnas.96.13.7282)
24. Smedley D, Haider S, Ballester B, Holland R, London D, Thorisson G & Kasprzyk A 2009 BioMart-biological queries made easy. BMC Genomics 10 22. (doi:10.1186/1471-2164-10-22)
25. Sugiura K, Su YQ, Li Q, Wigglesworth K, Matzuk MM & Eppig JJ 2010 Estrogen promotes the development of mouse cumulus cells in coordination with oocyte-derived GDF9 and BMP15. Molecular Endocrinology 24 2303-2314. (doi:10.1210/me.2010-0260)
26. Wathes DC, Clempson AM & Pollott GE 2012 Associations between lipid metabolism and fertility in the dairy cow. Reproduction, Fertility, and Development 25 48-61. (doi:10.1071/RD12272)
27. Wolf JB, Bayer T, Haubold B, Schilhabel M, Rosenstiel P & Tautz D 2010 Nucleotide divergence vs. gene expression differentiation: comparative transcriptome sequencing in natural isolates from the carrion crow and its hybrid zone with the hooded crow. Molecular Ecology 19 (Suppl 1) 162-175. (doi:10.1111/j.1365-294X.2009.04471.x)
28. Yee WK, Sutton KL & Dowling DK 2013 In vivo male fertility is affected by naturally occurring mitochondrial haplotypes. Current Biology 3 R55-R56. (doi:10.1016/j.cub.2012.12.002)