Transcriptome analysis of female and male Xiphophorus maculatus Jp 163 A

PLoS ONE

Volumn 6, Issue 4, 2011, Pages

  Zhang, Ziping ^a   Wang, Yilei ^b   Wang, Shuhong ^b   Liu, Jingtao ^a   Warren, Wesley ^c   Mitreva, Makedonka ^c   Walter, Ronald B ^a  

^a Texas State University   (United States)

^b JIMEI UNIVERSITY   (China)

^c WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; DNA LIBRARY; DNA SEQUENCE; FEMALE; FISH; GENE EXPRESSION; GENETIC IDENTIFICATION; MALE; NONHUMAN; PREDICTION; QUANTITATIVE ANALYSIS; REAL TIME POLYMERASE CHAIN REACTION; SEQUENCE HOMOLOGY; SEX DIFFERENCE; TRANSCRIPTOMICS; XIPHOPHORUS MACULATUS; ANIMAL; CYPRINODONTIFORMES; GENE EXPRESSION PROFILING; GENETICS; ISOLATION AND PURIFICATION; METABOLISM; METHODOLOGY; MOLECULAR CLONING; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; REPRODUCIBILITY; SEXUAL DEVELOPMENT;

XIPHOPHORUS; XIPHOPHORUS MACULATUS;

COMPLEMENTARY DNA; FISH PROTEIN; RNA;

ANIMALS; BASE SEQUENCE; CLONING, MOLECULAR; CYPRINODONTIFORMES; DNA, COMPLEMENTARY; FEMALE; FISH PROTEINS; GENE EXPRESSION PROFILING; MALE; POLYMERASE CHAIN REACTION; REPRODUCIBILITY OF RESULTS; RNA; SEQUENCE ANALYSIS, DNA; SEX CHARACTERISTICS;

EID: 79953755781     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0018379     Document Type: Article

References (47)

1. Zarkower D, (2001) Establishing sexual dimorphism: conservation amidst diversity? Nat Rev Genet 2: 175-185.
2. Walter RB, Hazlewood L, Kazianis S, (2006) The Xiphophorus Genetic Stock Center Manual; Kallman K, Schartl M, eds. San Marcos Texas State University Press pp. 1-129.
3. Kazianis S, Morizot DC, Vielkind JR, Woolcock B, Wigler M, et al. (2005) Sex-determination in platyfishes and swordtails; Uribe MC, Grier HJ, eds. Mexico New Life Publications pp. 381-400.
4. Kallman KD, (1983) The sex determining mechanism of the poeciliid fish, Xiphophorus montezumae, and the genetic control of the sexual maturation process and adult size. Copeia 1983 pp. 755-769.
5. Kallman KD, (1984) A new look at sex determination in poeciliid fishes; Turner BJ, eds. New York Plenum Publishing pp. 95-171.
6. Volff JN, Schartl M, (2001) Variability of genetic sex determination in poeciliid fishes. Genetica 111: 101-110.
7. Schartl M, (2004) A comparative view on sex determination in medaka. Mech Dev 121: 639-645.
8. Volff JN, Nanda I, Schmid M, Schartl M, (2007) Governing sex determination in fish: regulatory putsches and ephemeral dictators. Sex Dev 1: 85-99.
9. Meyer A, Lydeard C, (1993) The evolution of copulatory organs, internal fertilization, placentae and viviparity in killifishes (Cyprinodontiformes) inferred from a DNA phylogeny of the tyrosine kinase gene X-src. Proc Biol Sci 254: 153-162.
10. Holland CM, Saidi SA, Evans AL, Sharkey AM, Latimer JA, et al. (2004) Transcriptome analysis of endometrial cancer identifies peroxisome proliferator-activated receptors as potential therapeutic targets. Mol Cancer Ther 3: 993-1001.
11. Liang P, Pardee AB, (1992) Differential Display of eukaryotic messenger RNA by means. Science 257: 967-971.
12. McClelland M, Mathieu-Daude F, Welsh J, (1995) RNA fingerprinting and differential display using arbitrarily primed PCR. Trends Genet 11: 242-246.
13. Diatchenko L, Lau YF, Campbell AP, Chenchik A, Moqadam F, et al. (1996) Suppression subtractive hybridization: a method for generating differentially regulated or tissue-specific cDNA probes and libraries. Proc Natl Acad Sci U S A 93: 6025-6030.
14. Breyne P, Dreesen R, Cannoot B, Rombaut D, Vandepoele K, et al. (2003) Quantitative cDNA-AFLP analysis for genome-wide expression studies. Mol Genet Genomics 269: 173-179.
15. Macgregor PF, SqUire JA, (2002) Application of microarrays to the analysis of gene expression in cancer. Clin Chem 48: 1170-1177.
16. Nef S, Schaad O, Stallings NR, Cederroth CR, Pitetti JL, et al. (2005) Gene expression during sex determination reveals a robust female genetic program at the onset of ovarian development. Dev Biol 287: 361-377.
17. Debouck C, (1995) Differential display or differential dismay? Curr Opin Biotechnol 6: 597-600.
18. Shendure J, Ji H, (2008) Next-generation DNA sequencing. Nat Biotechnol 26: 1135-1145.
19. Rothberg JM, Leamon JH, (2008) The development and impact of 454 sequencing. Nat Biotechnol 26: 1117-1124.
20. Walter RB, Kazianis S, (2001) Xiphophorus interspecies hybrids as genetic models of induced neoplasia. ILAR JOURNAL 42: 299-321.
21. Zhulidov PA, Bogdanova EA, Shcheglov AS, Vagner LL, Khaspekov GL, et al. (2004) Simple cDNA normalization using kamchatka crab duplex specific nuclease. Nucleic Acids Res 32: e37.
22. Chenchik A, Zhu YY, Diatchenko L, Li R, Hill J, et al. (1998) Generation and use of high-quality cDNA from small amounts of total RNA by SMART PCR. Gene cloning and analysis by RT-PCR pp. 305-319.
23. Gotz S, García-Gómez JM, Terol J, Williams TD, Nagaraj SH, et al. (2008) High-throughput functional annotation and data mining with the Blast 2 GO suite. Nucleic Acids Res 36: 3420.
24. Lord PW, Stevens RD, Brass A, Goble CA, (2003) Investigating semantic similarity measures across the Gene Ontology: the relationship between sequence and annotation. Bioinformatics 19: 1275.
25. Parra G, Bradnam K, Korf I, (2007) CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes. Bioinformatics 23: 1061-1067.
26. Audic S, Claverie JM, (1997) The significance of digital gene expression profiles. Genome Res 7: 986-996.
27. Zhang Z, Wang Y, Jiang Y, Lin P, Jia X, et al. (2007) Ribosomal protein L24 is differentially expressed in ovary and testis of the marine shrimp Marsupenaeus japonicus. Comp Biochem Physiol B Biochem Mol Biol 147: 466-474.
28. Boswell MG, Wells MC, Kirk LM, Ju Z, Zhang Z, et al. (2009) Comparison of gene expression responses to hypoxia in viviparous (Xiphophorus) and oviparous (Oryzias) fishes using a medaka microarray. Comp Biochem Physiol C Toxicol Pharmacol 149: 258-265.
29. Aparicio S, Chapman J, Stupka E, Putnam N, Chia J, et al. (2002) Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science 297: 1301.
30. McPherson JD, Marra M, Hillier LD, Waterston RH, Chinwalla A, et al. (2001) A physical map of the human genome. Nature 409: 934-941.
31. Abbott A, (2005) Competition boosts bid to find human genes. Nature 435: 134.
32. Chen TT, (1983) Identification and characterization of estrogen-responsive gene products in the liver of rainbow trout. Can J Biochem Cell Biol 61: 802-810.
33. Bidwell CA, Carlson DM, (1995) Characterization of vitellogenin from white sturgeon, Acipenser transmontanus. J Mol Evol 41: 104-112.
34. Mouchel N, Trichet V, Youssef Naimi B, Le Pennec JP, Wolff J, (1997) Structure of a fish (Oncorhynchus mykiss) vitellogenin gene and its evolutionary implication. Gene 197: 147-152.
35. Wang H, Yan T, Tan JTT, Gong Z, (2000) A zebrafish vitellogenin gene (vg3) encodes a novel vitellogenin without a phosvitin domain and may represent a primitive vertebrate vitellogenin gene. Gene 256: 303-310.
36. Trichet V, Buisine N, Mouchel N, Moran P, Pendas AM, et al. (2000) Genomic analysis of the vitellogenin locus in rainbow trout (Oncorhynchus mykiss) reveals a complex history of gene amplification and retroposon activity. Mol Gen Genet 263: 828-837.
37. Miracle A, Ankley G, Lattier D, (2006) Expression of two vitellogenin genes (vg1 and vg3) in fathead minnow (Pimephales promelas) liver in response to exposure to steroidal estrogens and androgens. Ecotoxicol Environ Saf 63: 337-342.
38. Sawaguchi S, Kagawa H, Ohkubo N, Hiramatsu N, Sullivan CV, et al. (2006) Molecular characterization of three forms of vitellogenin and their yolk protein products during oocyte growth and maturation in red seabream (Pagrus major), a marine teleost spawning pelagic eggs. Mol Reprod Dev 73: 719-736.
39. Brawand D, Wahli W, Kaessmann H, (2008) Loss of egg yolk genes in mammals and the origin of lactation and placentation. PLoS Biol 6: e63.
40. Chiriva-Internati M, Gagliano N, Donetti E, Costa F, Grizzi F, et al. (2009) Sperm protein 17 is expressed in the sperm fibrous sheath. J Transl Med 7: 61.
41. Shetty J, Wolkowicz MJ, Digilio LC, Klotz KL, Jayes FL, et al. (2003) SAMP14, a novel, acrosomal membrane-associated, glycosylphosphatidylinositol-anchored member of the Ly-6/urokinase-type plasminogen activator receptor superfamily with a role in sperm-egg interaction. J Biol Chem 278: 30506-30515.
42. Deng X, He Y, Martin-Deleon PA, (2000) Mouse Spam1 (PH-20): evidence for its expression in the epididymis and for a new category of spermatogenic-expressed genes. J Androl 21: 822-832.
43. Richardson RT, Bencic DC, O'Rand MG, (2001) Comparison of mouse and human NASP genes and expression in human transformed and tumor cell lines. Gene 274: 67-75.
44. Sinclair AH, Berta P, Palmer MS, Hawkins JR, Griffiths BL, et al. (1990) A gene from the human sex-determining region encodes a protein with homology to a conserved DNA-binding motif. Nature 346: 240-244.
45. Stevanovlc M, Lovell-Badge R, Collignon J, (1993) SOX3 is an X-linked gene related to SRY. Hum Mol Genet 2: 2013-2018.
46. Foster JW, Graves JA, (1994) An SRY-related sequence on the marsupial X chromosome: implications for the evolution of the mammalian testis-determining gene. Proc Natl Acad Sci U S A 91: 1927-1931.
47. King V, Goodfellow PN, Wilkerson AJ, Johnson WE, O'Brien SJ, et al. (2007) Evolution of the male-determining gene SRY within the cat family Felidae. Genetics 175: 1855-1867.