Tuatara (Sphenodon) genomics: BAC library construction, sequence survey, and application to the DMRT gene family

Journal of Heredity

Volumn 97, Issue 6, 2006, Pages 541-548

  Wang, Zhenshan ^a,d   Miyake, Tsutomu ^b   Edwards, Scott V ^a,c   Amemiya, Chris T ^a,b  

^a UNIVERSITY OF WASHINGTON   (United States)

^b BENAROYA RESEARCH INSTITUTE   (United States)

^c HARVARD UNIVERSITY   (United States)

^d UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; CONTIG; DNA;

AMINO ACID SEQUENCE; ARTICLE; BACTERIAL ARTIFICIAL CHROMOSOME; CONTIG MAPPING; DNA SEQUENCE; DOUBLESEX MALE ABNORMAL 3 RELATED TRANSCRIPTION FACTOR 1 GENE; DOUBLESEX MALE ABNORMAL 3 RELATED TRANSCRIPTION FACTOR 2 GENE; GENE; GENE CONSTRUCT; GENE IDENTIFICATION; GENE INSERTION SEQUENCE; GENE LIBRARY; GENE SEQUENCE; GENETIC CONSERVATION; GENOME ANALYSIS; LONG INTERSPERSED REPEAT; MALE; MOLECULAR CLONING; MOLECULAR PROBE; MULTIGENE FAMILY; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN CONTENT; QUALITY CONTROL; REPTILE; SEQUENCE ANALYSIS; SEX DETERMINATION; SHORT INTERSPERSED REPEAT; SPHENODON PUNCTATUS;

ANIMALS; BAYES THEOREM; CHROMOSOMES, ARTIFICIAL, BACTERIAL; GENE LIBRARY; GENOME; GENOMICS; MALE; MULTIGENE FAMILY; PHYLOGENY; REPTILES; TRANSCRIPTION FACTORS;

BACTERIA (MICROORGANISMS); MAMMALIA; REPTILIA; SPHENODON; SPHENODON PUNCTATUS; VERTEBRATA;

EID: 33845946697     PISSN: 00221503     EISSN: 14657333     Source Type: Journal    
DOI: 10.1093/jhered/esl040     Document Type: Article

References (62)

1. Altschul S, Madden T, Schaffer A, Zhang J, Zhang Z, Miller W, Lipman D. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search program. Nucleic Acids Res. 25:3389-3402.
2. Amemiya CT, Amores A, Ota T, Mueller GD, Postlethwait JH, Litman GW. 2001. Generation of a P1 artificial chromosome library of the Southern pufferfish. Gene. 272:283-289.
3. Amemiya CT, Ota T, Litman GW. 1996. Construction of P1 artificial chromosome (PAC) libraries from lower vertebrates. In: Lai E, Birren B, editors. Analysis of nonmammalian genomes. San Diego (CA): Academic Press. p. 223-256.
4. Axelsson E, Webster MT, Smith NG, Burt DW, Ellegren H. 2005. Comparison of the chicken and turkey genomes reveals a higher rate of nucleotide divergence on microchromosomes than macrochromosomes. Genome Res. 15:120-125.
5. Belle EM, Duret L, Galtier N, Eyre-Walker A. 2004. The decline of isochores in mammals: an assessment of the GC content variation along the mammalian phylogeny. J Mol Evol. 58:653-660.
6. Brunner B, Hornung U, Shan Z, Nanda I, Kondo M, Zend-Ajusch E, Haaf T, Roper HH, Shima A, Schmid M, Kalscheuer VM, Schartl M. 2001. Genomic organization and expression of the double-sex-related gene cluster in vertebrates and detection of putative regulatory regions for DMRT1. Genomics. 77:8-17.
7. Cai L, Taylor JF, Wing RA, Gallagher DS, Woo SS, Davis SK. 1995. Construction and characterization of a bovine bacterial artificial chromosome library. Genomics. 29:413-425.
8. Clarke L, Carbon J. 1976. A colony bank containing synthetic ColE1 hybrid plasmids representative of the entire E. coli genome. Cell. 9:91-99.
9. Consortium ICG. 2004. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature. 432:695-716.
10. Couzin J. 2002. NSF's ark draws alligators, algae, and wasps. Science. 297:1638-1639.
11. Cree A, Daugherty CH, Hay JM. 1995. Reproduction of a rare New Zealand reptile, the tuatara Sphenodon punctatus, on rat-free and rat-inhabited islands. Conserv Biol. 9:373-383.
12. Cree A, Thompson MB, Daugherty CH. 1995. Tuatara sex determination. Nature. 375:543.
13. Daugherty CH, Cree A, Hay JM, Thompson MB. 1990. Neglected taxonomy and continuing extinctions of tuatara (Sphenodon). Nature. 347:177-179.
14. Daugherty CH, Towns DR, Cree A, Hay JM. 1992. The roles of legal protection versus intervention in conserving the New Zealand tuatara, Sphenodon. Dev Landsc Manage Urban Plann. 7:247-259.
15. Fjell CD, Bosdet I, Schein JE, Jones SJ, Marra MA. 2003. Internet Contig Explorer (iCE) - a tool for visualizing clone fingerprint maps. Genome Res. 13:1244-1249.
16. Gans C. 1983. Is Sphenodon punctatus a maladapted relict? In: Rhodin AGJ, Miyata K, editors. Advances in herpetology and evolutionary biology. Cambridge (MA): Museum of Comparative Zoology, Harvard University. p. 613-620.
17. Gaze P. 2001. Tuatara recovery plan 2001-2011. Wellington (New Zealand): New Zealand Department of Conservation. (Threatened species recovery plan series no. 47).
18. Groombridge B. 1982. The IUCN amphibia-reptilia red data book. Part 1. Testudines Crocodylia Rhynchocephalia. Gland (Switzerland): World Conservation Union.
19. Haag E, Doty A. 2005. Sex determination across evolution: connecting the dots. PLoS Biol. 3:e21.
20. Hedges SB, Poling LL. 1999. A molecular phylogeny of reptiles. Science. 283:998-1001.
21. Hillier LW, Miller W, Birney E, Warren W, Hardison RC, Ponting CP, et al. 2004. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature. 432:695-716.
22. Hong YS, Hogan JR, Wang X, Sarkar A, Sim C, Loftus BJ, Ren C, Huff ER, Carlile JL, Black K, Zhang HB, Gardner MJ, Collins FH. 2003. Construction of a BAC library and generation of BAC end sequence-tagged connectors for genome sequencing of the African malaria mosquito Anopheles gambiae. Mol Genet Genomics. 268:720-728.
23. Huang X, Cheng H, Guo Y, Liu L, Gui J, Zhou R. 2002. A conserved family of doublesex-related genes from fishes. J Exp Zool. 294:63-67.
24. Huelsenbeck JP, Ronquist F. 2001. MrBayes: Bayesian inference of phylogeny. Bioinformatics. 17:754-755.
25. Hughes S, Zelus D, Mouchiroud D. 1999. Warm-blooded isochore structure in Nile crocodile and turtle. Mol Biol Evol. 16:1521-1527.
26. Ioannou PA, Amemiya CT, Garnes J, Kroisel PM, Shizuya H, Chen C, Batzer MA, de Jong PJ. 1994. A new bacteriophage P1-derived vector for the propagation of large human DNA fragments. Nat Genet. 6:84-89.
27. Jones DT, Taylor WR, Thornton JR. 1992. The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci. 8:275-282.
28. Kadi F, Mouchiroud D, Sabeur G, Bernardi G. 1993. The compositional patterns of the avian genomes and their evolutionary implications. J Mol Evol. 37:544-551.
29. Kajikawa M, Ohshima K, Okada N. 1997. Determination of the entire sequence of turtle CR1: the first open reading frame of the turtle CR1 element encodes a protein with a novel zinc finger motif. Mol Biol Evol. 14:1206-1217.
30. Kimura M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol. 16:111-120.
31. Kuraku S, Ishijima J, Nishida-Umehara C, Agata K, Kuratani S, Matsuda Y. 2006. cDNA-based gene mapping and GC3 profiling in the soft-shelled turtle suggest a chromosomal size-dependent GC bias shared by sauropsids. Chromosome Res. 14:187-202.
32. Lee MSY. 2001. Molecules, morphology and the monophyly of diapsid reptiles. Contrib Zool. 70:1-22.
33. Marra MA, Kucaba TA, Dietrich NL, Green ED, Bownstein B, Wilson RK, McDonald KM, Hillier LW, McPherson JD, Waterston RW. 1997. High-throughput fingerprint analysis of large-insert clones. Genome Res. 7:1072-1084.
34. Marshall Graves JA. 2002. The rise and fall of SRY. Trends Genet. 18:259-264.
35. Matsuda M, Nagahama Y, Shinomiya A, Sato T, Matsuda C, Kobayashi T, Morrey CE, Shibata N, Asakawa S, Shimizu N, Hori H, Hamaguchi S, Sakaizumi M. 2002. DMY is a Y-specific DM-domain gene required for male development in the medaka fish. Nature. 417:559-563.
36. Modi WS, Crews D. 2005. Sex chromosome and sex determination in reptiles. Curr Opin genet Dev. 15:660-665.
37. Olmo E. 1981. Evolution of genome size and DNA base composition in reptiles. Genetica. 57:39-50.
38. Osoegawa K, Woon PY, Zhao B, Frengen E, Tateno M, Catanese JJ, de Jong PJ. 1998. An improved approach for construction of bacterial artificial chromosome libraries. Genomics. 52:1-8.
39. Ottolenghi C, Fellous M, Barbieri M, McElreavey K. 2002. Novel paralogy relations among human chromosomes support a link between the phylogeny of doublesex-related genes and evolution of sex determination. Genomics. 79:333-343.
40. Paterson AH. 1996. The DNA revolution. San Diego (CA): Academic Press.
41. Pillai S, Silventoinen V, Kallio K, Senger M, Sobhang S, Tate J, Velankar S, Golovin A, Henrick K, Rice P, Stoehr P, Lopez R. 2005. SOAP-based services provided by the European Bioinformatics Institute. Nucleic Acids Res. 33:W25-W28.
42. Raymond C, Kettlewell J, Hirsch B, Bardwell V, Zarkower D. 1999. Expression of Dmrt1 in the genital ridge of mouse and chicken embryos suggests a role in vertebrate sexual development. Dev Biol. 215:208-220.
43. Rest JS, Ast JC, Austin CC, Waddell PJ, Tibbetts EA, Hay JM, Mindell DP. 2003. Molecular systematics of primary reptilian lineages and the tuatara mitochondrial genome. Mol Phylogenet Evol. 29:289-297.
44. Sarre S, Georges A, Quinn A. 2004. The ends of a continuum: genetic and temperature-dependent sex determination in reptiles. Bioessays. 26:639-645.
45. Shedlock, A. M. 2006. Phylogenomic diversity of CR1 LINE elements in reptiles. Syst Biol. Forthcoming.
46. Smit AFA, Hubley R, Green P. 2004. RepeatMasker Open-3.0.5 [Internet]. Available from: www.repeatmasker.org.
47. Smith CA, McClive P, Western P, Reed K, Sinclair AH. 1999. Conservation of a sex-determining gene. Nature. 402:601-602.
48. Smith CA, Sinclair AH. 2004. Sex determination: insights from the chicken. Bioessays. 26:120-132.
49. Strong SJ, Ohta Y, Litman GW, Amemiya CT. 1997. Marked improvement of PAC and BAC cloning is achieved using electroelution of pulsed-field gel-separated partial digests of genomic DNA. Nucleic Acids Res. 25:3959-3961.
50. Vandergon TL, Reitman M. 1994. Evolution of chicken repeat 1(CR1) elements: evidence for ancient subfamilies and multiple progenitors. Mol Biol Evol. 11:886-898.
51. Veith AM, Froschauer A, Korting C, Nanda I, Hanel R, Schmid M, Schartl M, Volff JN. 2003. Cloning of the dmrt1 gene of Xiphophorus maculates: dmY/dmrt1Y is not the master sex-determining gene in the platyfish. Gene. 317:59-66.
52. Volff JN, Zarkower D, Bardwell VJ, Schartl M. 2003. Evolutionary dynamics of the DM domain gene family in metazoans. J Mol Evol. 57:S241-S249.
53. Waltari E, Edwards SV. 2002. The evolutionary dynamics of intron size, genome size, and physiological correlates in archosaurs. Am Nat. 160:539-552.
54. Western P, Hary JL, Marshall Graves JA, Sinclair AH. 2000. Temperature-dependent sex determination in the American alligator: expression of SF1, WT1 and DAX1 during gonadogenesis. Gene. 241:223-232.
55. Wicker T, Robertson JS, Schulze SR, Feltus FA, Magrini V, Morrison JA, Mardis ER, Wilson RK, Peterson DG, Paterson AH, Ivarie R. 2005. The repetitive landscape of the chicken genome. Genome Res. 15:126-136.
56. Woo SS, Jiang J, Gill BS, Paterson AH, Wing RA. 1994. Construction and characterization of a bacterial artificial chromosome library of Sorghum bicolor. Nucleic Acids Res. 22:4922-4931.
57. Wu XC. 1994. Late Triassic-Early Jurassic sphenodontians from China and the phylogeny of the Sphenodontia. Cambridge (UK): Cambridge University Press.
58. Zardoya R, Meyer A. 1998. Complete mitochondrial genome suggests diapsid affinities of turtles. Proc Natl Acad Sci USA. 95:14226-14231.
59. Zarkower D. 2002. Invertebrates may not be so different after all. Novartis Found Symp. 244:115-126.
60. Zhao S, Shatsman S, Ayodeji B, Geer K, Tsegaye G, Krol M, Gebregeorgis E, Shvartsbeyn A, Russell D, Overton L, Jiang L, Dimitrov G, Tran K, Shetty J, Malek JA, Feldblyum T, Nierman WC, Fraser CM. 2001. Mouse BAC ends quality assessment and sequence analyses. Genome Res. 11:1736-1745.
61. Zhu H, Choi S, Johnston AK, Wing RA, Dean RA. 1997. A large-insert (130 kbp) bacterial artificial chromosome library of the rice blast fungus Magnaporthe grisea: genome analysis, contig assembly, and gene cloning. Fungal Genet Biol. 21:337-347.
62. Zimmer R, Gibbin AMV. 1997. Construction and characterization of a large-fragment chicken bacterial bacterial chromosome library. Genomics. 42:217-226.