메뉴 건너뛰기




Volumn 19, Issue 3, 2009, Pages 470-480

Detecting heterozygosity in shotgun genome assemblies: Lessons from obligately outcrossing nematodes

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA;

EID: 61849109937     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.081851.108     Document Type: Article
Times cited : (76)

References (42)
  • 1
    • 0036021412 scopus 로고    scopus 로고
    • Haldane's rule by sexual transformation in Caenorhabditis
    • Baird, S.E. 2002. Haldane's rule by sexual transformation in Caenorhabditis. Genetics 161: 1349-1353.
    • (2002) Genetics , vol.161 , pp. 1349-1353
    • Baird, S.E.1
  • 3
    • 0016063911 scopus 로고
    • The genetics of Caenorhabditis elegans
    • Brenner, S. 1974. The genetics of Caenorhabditis elegans. Genetics 77: 71-94.
    • (1974) Genetics , vol.77 , pp. 71-94
    • Brenner, S.1
  • 4
    • 0032509302 scopus 로고    scopus 로고
    • The C. elegans Sequencing Consortium. 1998. Genome sequence of the nematode C. elegans: A platform for investigating biology. Science 282:2012-2018.
    • The C. elegans Sequencing Consortium. 1998. Genome sequence of the nematode C. elegans: A platform for investigating biology. Science 282:2012-2018.
  • 5
    • 0038305577 scopus 로고    scopus 로고
    • Selection at linked sites in the partial selfer Caenorhabditis elegans
    • Cutter, A.D. and Payseur, B.A. 2003. Selection at linked sites in the partial selfer Caenorhabditis elegans. Mol. Biol. Evol. 20: 665-673.
    • (2003) Mol. Biol. Evol , vol.20 , pp. 665-673
    • Cutter, A.D.1    Payseur, B.A.2
  • 6
    • 33750033346 scopus 로고    scopus 로고
    • High nucleotide polymorphism and rapid decay of linkage disequilibrium in wild populations of Caenorhabditis remanei
    • Cutter, A.D., Baird, S.E., and Charlesworth, D. 2006. High nucleotide polymorphism and rapid decay of linkage disequilibrium in wild populations of Caenorhabditis remanei. Genetics 174: 901-913.
    • (2006) Genetics , vol.174 , pp. 901-913
    • Cutter, A.D.1    Baird, S.E.2    Charlesworth, D.3
  • 7
    • 34249794852 scopus 로고    scopus 로고
    • Inbreeding and outbreeding depression in Caenorhabditis nematodes
    • Dolgin, E.S., Charlesworth, B., Baird, S.E., and Cutter, A.D. 2007. Inbreeding and outbreeding depression in Caenorhabditis nematodes. Evolution 61: 1339-1352.
    • (2007) Evolution , vol.61 , pp. 1339-1352
    • Dolgin, E.S.1    Charlesworth, B.2    Baird, S.E.3    Cutter, A.D.4
  • 8
    • 47149117454 scopus 로고    scopus 로고
    • Drosophila 12 Genome Consortium. 2007. Evolution of genes and genomes on the Drosophila phylogeny. Nature 450: 203-218.
    • Drosophila 12 Genome Consortium. 2007. Evolution of genes and genomes on the Drosophila phylogeny. Nature 450: 203-218.
  • 9
    • 84979186790 scopus 로고
    • Population studies of a lethal mutant in Drosophila melanogaster. I. Behavior in populations with discrete generations
    • Frydenberg, O. 1963. Population studies of a lethal mutant in Drosophila melanogaster. I. Behavior in populations with discrete generations. Hereditas 50: 89-116.
    • (1963) Hereditas , vol.50 , pp. 89-116
    • Frydenberg, O.1
  • 11
    • 0036263181 scopus 로고    scopus 로고
    • Levels of DNA polymorphism vary with mating system in the nematode genus Caenorhabditis
    • Graustein, A., Gaspar, J.M., Walters, J.R., and Palopoli, M.F. 2002. Levels of DNA polymorphism vary with mating system in the nematode genus Caenorhabditis. Genetics 161: 99-107.
    • (2002) Genetics , vol.161 , pp. 99-107
    • Graustein, A.1    Gaspar, J.M.2    Walters, J.R.3    Palopoli, M.F.4
  • 12
    • 0036187351 scopus 로고    scopus 로고
    • Extent of gene duplication in the genomes of Drosophila, nematode, and yeast
    • Gu, Z., Cavalcanti, A., Chen, F.C., Bouman, P., and Li, W.H. 2002. Extent of gene duplication in the genomes of Drosophila, nematode, and yeast. Mol. Biol. Evol. 19: 256-262.
    • (2002) Mol. Biol. Evol , vol.19 , pp. 256-262
    • Gu, Z.1    Cavalcanti, A.2    Chen, F.C.3    Bouman, P.4    Li, W.H.5
  • 13
    • 17044384124 scopus 로고    scopus 로고
    • Intraspecific variation in fem-3 and tra-2, two rapidly coevolving nematode sex-determining genes
    • Haag, E.S. and Ackerman, A.D. 2005. Intraspecific variation in fem-3 and tra-2, two rapidly coevolving nematode sex-determining genes. Gene 349: 35-42.
    • (2005) Gene , vol.349 , pp. 35-42
    • Haag, E.S.1    Ackerman, A.D.2
  • 14
    • 0034013790 scopus 로고    scopus 로고
    • Regulatory elements required for development of Caenorhabditis elegans hermaphrodites are conserved in the tra-2 homologue of C. remanei, a male/female sister species
    • Haag, E.S. and Kimble, J. 2000. Regulatory elements required for development of Caenorhabditis elegans hermaphrodites are conserved in the tra-2 homologue of C. remanei, a male/female sister species. Genetics 155: 105-116.
    • (2000) Genetics , vol.155 , pp. 105-116
    • Haag, E.S.1    Kimble, J.2
  • 15
    • 0036898532 scopus 로고    scopus 로고
    • Rapid coevolution of the nematode sex-determining genes fem-3 and tra-2
    • Haag, E.S., Wang, S., and Kimble, J. 2002. Rapid coevolution of the nematode sex-determining genes fem-3 and tra-2. Curr. Biol. 12: 2035- 2041.
    • (2002) Curr. Biol , vol.12 , pp. 2035-2041
    • Haag, E.S.1    Wang, S.2    Kimble, J.3
  • 17
    • 33645530743 scopus 로고    scopus 로고
    • Genetic flexibility in the convergent evolution of hermaphroditism in Caenorhabditis nematodes
    • Hill, R.C., de Carvalho, C.E., Salogiannis, J., Schlager, B., Pilgrim, D., and Haag, E.S. 2006. Genetic flexibility in the convergent evolution of hermaphroditism in Caenorhabditis nematodes. Dev. Cell 10: 531-538.
    • (2006) Dev. Cell , vol.10 , pp. 531-538
    • Hill, R.C.1    de Carvalho, C.E.2    Salogiannis, J.3    Schlager, B.4    Pilgrim, D.5    Haag, E.S.6
  • 18
    • 34547137683 scopus 로고    scopus 로고
    • Hillier, L.W., Miller, R.D., Baird, S.E., Chinwalla, A., Fulton, L.A., Koboldt, D.C., and Waterston, R.H. 2007. Comparison of C. elegans and C. briggsae genome sequences reveals extensive conservation of chromosome organization and synteny. PLoS Biol. 5: el 67. doi: 10.1371/journal.pbio.0050167.
    • Hillier, L.W., Miller, R.D., Baird, S.E., Chinwalla, A., Fulton, L.A., Koboldt, D.C., and Waterston, R.H. 2007. Comparison of C. elegans and C. briggsae genome sequences reveals extensive conservation of chromosome organization and synteny. PLoS Biol. 5: el 67. doi: 10.1371/journal.pbio.0050167.
  • 20
    • 34347376733 scopus 로고    scopus 로고
    • Diploid genome reconstruction of Ciona intestinalis and comparative analysis with Ciona savignyi
    • Kim, J.H., Waterman, M.S., and Li, L.M. 2007. Diploid genome reconstruction of Ciona intestinalis and comparative analysis with Ciona savignyi. Genome Res. 17: 1101-1110.
    • (2007) Genome Res , vol.17 , pp. 1101-1110
    • Kim, J.H.1    Waterman, M.S.2    Li, L.M.3
  • 21
    • 2942669900 scopus 로고    scopus 로고
    • Caenorhabditis phytogeny predicts convergence of hermaphroditism and extensive intron loss
    • Kiontke, K., Gavin, N.P., Raynes, Y., Roehrig, C., Piano, F., and Fitch, D.H. 2004. Caenorhabditis phytogeny predicts convergence of hermaphroditism and extensive intron loss. Proc. Natl. Acad. Sci. 101: 9003-9008.
    • (2004) Proc. Natl. Acad. Sci , vol.101 , pp. 9003-9008
    • Kiontke, K.1    Gavin, N.P.2    Raynes, Y.3    Roehrig, C.4    Piano, F.5    Fitch, D.H.6
  • 23
    • 0028099294 scopus 로고
    • Cloning by synteny: Identifying C. briggsae homologues of C. elegans genes
    • Kuwabara, P.E. and Shah, S. 1994. Cloning by synteny: Identifying C. briggsae homologues of C. elegans genes. Nucleic Acids Res. 22: 4414-4418.
    • (1994) Nucleic Acids Res , vol.22 , pp. 4414-4418
    • Kuwabara, P.E.1    Shah, S.2
  • 24
    • 0028847817 scopus 로고
    • Genetic adaptation to captivity and inbreeding depression in small laboratory populations of Drosophila melanogaster
    • Latter, B.D. and Mulley, J.C. 1995. Genetic adaptation to captivity and inbreeding depression in small laboratory populations of Drosophila melanogaster. Genetics 139: 255-266.
    • (1995) Genetics , vol.139 , pp. 255-266
    • Latter, B.D.1    Mulley, J.C.2
  • 26
    • 0034634395 scopus 로고    scopus 로고
    • The evolutionary fate and consequences of duplicate genes
    • Lynch, M. and Conery, J.S. 2000. The evolutionary fate and consequences of duplicate genes. Science 290: 1151-1155.
    • (2000) Science , vol.290 , pp. 1151-1155
    • Lynch, M.1    Conery, J.S.2
  • 27
    • 1542563409 scopus 로고    scopus 로고
    • Initial sequencing and comparative analysis of the mouse genome
    • Mouse Genome Sequencing Consortium
    • Mouse Genome Sequencing Consortium. 2002. Initial sequencing and comparative analysis of the mouse genome. Nature 420: 520-562.
    • (2002) Nature , vol.420 , pp. 520-562
  • 29
    • 14644429103 scopus 로고    scopus 로고
    • fog-2 and the evolution of self- fertile hermaphroditism in Caenorhabditis
    • doi: 10.1371/journal/pbio.0030006
    • Nayak, S., Goree, J., and Schedl, T. 2005. fog-2 and the evolution of self- fertile hermaphroditism in Caenorhabditis. PLoS Biol. 3: e6. doi: 10.1371/journal/pbio.0030006.
    • (2005) PLoS Biol , vol.3
    • Nayak, S.1    Goree, J.2    Schedl, T.3
  • 31
    • 0032962457 scopus 로고    scopus 로고
    • Twilight zone of protein sequence alignments
    • Rost, B. 1999. Twilight zone of protein sequence alignments. Protein Eng. 12: 85-94.
    • (1999) Protein Eng , vol.12 , pp. 85-94
    • Rost, B.1
  • 32
    • 0028280289 scopus 로고
    • Decline in heterozygosity under full-sib and double first-cousin inbreeding in Drosophila melanogaster
    • Rumball, W., Franklin, I.R., Frankham, R., and Sheldon, B.L. 1994. Decline in heterozygosity under full-sib and double first-cousin inbreeding in Drosophila melanogaster. Genetics 136: 1039-1049.
    • (1994) Genetics , vol.136 , pp. 1039-1049
    • Rumball, W.1    Franklin, I.R.2    Frankham, R.3    Sheldon, B.L.4
  • 34
    • 33750995860 scopus 로고    scopus 로고
    • The genome of the sea urchin Strongylocentrotus purpuratus
    • Sea Urchin Genome Sequencing Consortium
    • Sea Urchin Genome Sequencing Consortium. 2006. The genome of the sea urchin Strongylocentrotus purpuratus. Science 314: 941-952.
    • (2006) Science , vol.314 , pp. 941-952
  • 35
    • 34250206347 scopus 로고    scopus 로고
    • A haplome alignment and reference sequence of the highly polymorphic Ciona savignyi genome
    • doi: 10.1186/gb-2007-8-3-241
    • Small, K.S., Brudno, M., Hill, M.M., and Sidow, A. 2007. A haplome alignment and reference sequence of the highly polymorphic Ciona savignyi genome. Genome Biol. 8: R41. doi: 10.1186/gb-2007-8-3-241.
    • (2007) Genome Biol , vol.8
    • Small, K.S.1    Brudno, M.2    Hill, M.M.3    Sidow, A.4
  • 37
    • 61849153179 scopus 로고    scopus 로고
    • Sternberg, P., Waterston, R., Spieth, J., Eddy, S., and Wilson, R. 2003. Genome sequence of additional Caenorhabditis species: Enhancing the utility of C. elegans as a model organism. [Genome sequencing white paper proposal to NHGRI.] www.genome.gov/Pages/Research/Sequencing/SeqProposals/C- remaneiSEQ.pdf.
    • Sternberg, P., Waterston, R., Spieth, J., Eddy, S., and Wilson, R. 2003. Genome sequence of additional Caenorhabditis species: Enhancing the utility of C. elegans as a model organism. [Genome sequencing white paper proposal to NHGRI.] www.genome.gov/Pages/Research/Sequencing/SeqProposals/C- remaneiSEQ.pdf.
  • 41
    • 0028965146 scopus 로고
    • Sexual isolation in Drosophila melanogaster: A possible case of incipient speciation
    • Wu, C.I., Hollocher, H., Begun, D.J., Aquadro, CF., Xu, Y., and Wu, M.L. 1995. Sexual isolation in Drosophila melanogaster: A possible case of incipient speciation. Proc. Natl. Acad. Sci. 92: 2519-2523.
    • (1995) Proc. Natl. Acad. Sci , vol.92 , pp. 2519-2523
    • Wu, C.I.1    Hollocher, H.2    Begun, D.J.3    Aquadro, C.F.4    Xu, Y.5    Wu, M.L.6
  • 42
    • 0030683599 scopus 로고    scopus 로고
    • PAML: A program package for phylogenetic analysis by maximum likelihood
    • Yang, Z. 1997. PAML: A program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13: 555-556.
    • (1997) Comput. Appl. Biosci , vol.13 , pp. 555-556
    • Yang, Z.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.