메뉴 건너뛰기




Volumn 67, Issue 2, 2008, Pages 222-232

Evolutionary aspects of functional and pseudogene members of the phytochrome gene family in Scots pine

Author keywords

Gene family evolution; Phytochrome; Pseudogenes; Scots pine

Indexed keywords

PHYTOCHROME;

EID: 50249129581     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-008-9135-z     Document Type: Article
Times cited : (14)

References (47)
  • 1
    • 26944477031 scopus 로고    scopus 로고
    • Evolution of genome size in conifers
    • Ahuja MR, Neale DB (2005) Evolution of genome size in conifers. Silvae Genetica 54:126-137
    • (2005) Silvae Genetica , vol.54 , pp. 126-137
    • Ahuja, M.R.1    Neale, D.B.2
  • 2
    • 0031303812 scopus 로고    scopus 로고
    • Distinguishing the effects of mutational biases and natural selection on DNA sequence variation
    • Akashi H (1997) Distinguishing the effects of mutational biases and natural selection on DNA sequence variation. Genetics 147:1989-1991
    • (1997) Genetics , vol.147 , pp. 1989-1991
    • Akashi, H.1
  • 3
    • 0028220048 scopus 로고    scopus 로고
    • Synonymous codon usage in Drosophila melanogaster: Natural selection and translational accuracy
    • Akashi H (1999) Synonymous codon usage in Drosophila melanogaster: natural selection and translational accuracy. Genetics 136:927-935
    • (1999) Genetics , vol.136 , pp. 927-935
    • Akashi, H.1
  • 4
    • 0031202659 scopus 로고    scopus 로고
    • A deletion in the PHYD gene of the Arabidosis Wassilewskija ecotype defines a role for phytochrome D in far red/red light sensing
    • Aukerman MJ, Hirschfeld M, Wester L, Clack T, Amasino RM, Sharrock RA (1997) A deletion in the PHYD gene of the Arabidosis Wassilewskija ecotype defines a role for phytochrome D in far red/red light sensing. Plant Cell 9:1317-1326
    • (1997) Plant Cell , vol.9 , pp. 1317-1326
    • Aukerman, M.J.1    Hirschfeld, M.2    Wester, L.3    Clack, T.4    Amasino, R.M.5    Sharrock, R.A.6
  • 5
    • 0346155809 scopus 로고    scopus 로고
    • Pseudogenes: Are they "junk" or functional DNA?
    • Balakirev ES, Ayala FJ (2003) Pseudogenes: are they "junk" or functional DNA? Annu Rev Genet 37:123-151
    • (2003) Annu Rev Genet , vol.37 , pp. 123-151
    • Balakirev, E.S.1    Ayala, F.J.2
  • 6
    • 0038204408 scopus 로고    scopus 로고
    • Phylogeny for the faint of heart: A tutorial
    • Baldauf SL (2003) Phylogeny for the faint of heart: a tutorial. Trends Genet 19:345-351
    • (2003) Trends Genet , vol.19 , pp. 345-351
    • Baldauf, S.L.1
  • 7
    • 0027305597 scopus 로고
    • The effect of deleterious mutations on neutral molecular variation
    • Charlesworth B, Morgan MT, Charlesworth D (1993) The effect of deleterious mutations on neutral molecular variation. Genetics 134:1289-1303
    • (1993) Genetics , vol.134 , pp. 1289-1303
    • Charlesworth, B.1    Morgan, M.T.2    Charlesworth, D.3
  • 8
    • 0036149896 scopus 로고    scopus 로고
    • Low nucleotide diversity at the pal1 locus in the widely distributed Pinus sylvestris
    • Dvornyk V, Sirviö A, Mikkonen M, Savolainen O (2002) Low nucleotide diversity at the pal1 locus in the widely distributed Pinus sylvestris. Mol Biol Evol 19:179-188
    • (2002) Mol Biol Evol , vol.19 , pp. 179-188
    • Dvornyk, V.1    Sirviö, A.2    Mikkonen, M.3    Savolainen, O.4
  • 9
    • 0026681074 scopus 로고
    • Analysis of molecular variance inferred from metric distances among DNA haplotypes: Application to human mitochondria DNA restriction data
    • Excoffier L, Smouse PE, Quattro JM (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondria DNA restriction data. Genetics 131:479-491
    • (1992) Genetics , vol.131 , pp. 479-491
    • Excoffier, L.1    Smouse, P.E.2    Quattro, J.M.3
  • 10
    • 0038788126 scopus 로고    scopus 로고
    • Nucleotide diversity at two phytochrome loci along a latitudinal cline in Pinus sylvestris
    • García-Gil MR, Mikkonen M, Savolainen O (2003) Nucleotide diversity at two phytochrome loci along a latitudinal cline in Pinus sylvestris. Mol Ecol 12:1195-1206
    • (2003) Mol Ecol , vol.12 , pp. 1195-1206
    • García-Gil, M.R.1    Mikkonen, M.2    Savolainen, O.3
  • 11
    • 0035543129 scopus 로고    scopus 로고
    • Variation in the nrDNA ITS of Pinus cembroides: Implications for molecular systematics studies of pine species complexes
    • Gernandt DS, Liston A, Pineiro D (2001) Variation in the nrDNA ITS of Pinus cembroides: implications for molecular systematics studies of pine species complexes. Mol Phylogenet Evol 21:449-467
    • (2001) Mol Phylogenet Evol , vol.21 , pp. 449-467
    • Gernandt, D.S.1    Liston, A.2    Pineiro, D.3
  • 12
    • 0024234855 scopus 로고
    • CLUSTAL: A package for performing multiple sequence alignment on a microcomputer
    • Higgins DG, Sharp PM (1988) CLUSTAL: a package for performing multiple sequence alignment on a microcomputer. Gene 73:237-244
    • (1988) Gene , vol.73 , pp. 237-244
    • Higgins, D.G.1    Sharp, P.M.2
  • 13
    • 0034849408 scopus 로고    scopus 로고
    • MRBAYES: Bayesian inference of phylogenetic trees
    • Huelsenbeck JP, Ronquist F (2001) MRBAYES: bayesian inference of phylogenetic trees. Bioinformatics 17:754-755
    • (2001) Bioinformatics , vol.17 , pp. 754-755
    • Huelsenbeck, J.P.1    Ronquist, F.2
  • 16
    • 0030773907 scopus 로고    scopus 로고
    • Complex gene families in pine genomes
    • Kinlaw CS, Neale DB (1997) Complex gene families in pine genomes. Trends Plant Sci 2:356-359
    • (1997) Trends Plant Sci , vol.2 , pp. 356-359
    • Kinlaw, C.S.1    Neale, D.B.2
  • 17
    • 0032033629 scopus 로고
    • Molecular evolution of cdc2 pseudogenes in spruce (Picea)
    • Kvarnheden A, Albert VA, Engström P (1995) Molecular evolution of cdc2 pseudogenes in spruce (Picea). Plant Mol Biol 36:767-774
    • (1995) Plant Mol Biol , vol.36 , pp. 767-774
    • Kvarnheden, A.1    Albert, V.A.2    Engström, P.3
  • 18
    • 0003421005 scopus 로고    scopus 로고
    • Sinauer Associates Sunderland, MA
    • Li WH (1997) Molecular evolution. Sinauer Associates, Sunderland, MA
    • (1997) Molecular Evolution
    • Li, W.H.1
  • 19
    • 0019726330 scopus 로고
    • Pseudogenes as a paradigm of neutral evolution
    • Li WH, Gojobori T, Mei M (1981) Pseudogenes as a paradigm of neutral evolution. Nature 292:237-239
    • (1981) Nature , vol.292 , pp. 237-239
    • Li, W.H.1    Gojobori, T.2    Mei, M.3
  • 20
    • 0034634395 scopus 로고    scopus 로고
    • The evolutionary fate and consequences of duplicate genes
    • Lynch M, Conery JS (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
  • 21
    • 0033615479 scopus 로고    scopus 로고
    • The root of angiosperm phylogeny inferred from duplicate phytochrome genes
    • Mathews S, Donoghue MJ (1999) The root of angiosperm phylogeny inferred from duplicate phytochrome genes. Science 286:947-950
    • (1999) Science , vol.286 , pp. 947-950
    • Mathews, S.1    Donoghue, M.J.2
  • 22
    • 0026428610 scopus 로고
    • Adaptive evolution of the "adh" locus in "drosophila"
    • McDonald JH, Kreitman M (1991) Adaptive evolution of the "Adh" locus in "Drosophila". Nature 351:652-654
    • (1991) Nature , vol.351 , pp. 652-654
    • McDonald, J.H.1    Kreitman, M.2
  • 23
    • 33646375934 scopus 로고    scopus 로고
    • The causes of protein evolutionary rate variation
    • Mclnerney JO (2006) The causes of protein evolutionary rate variation. Trends Ecol Evol 21:230-232
    • (2006) Trends Ecol Evol , vol.21 , pp. 230-232
    • McLnerney, J.O.1
  • 25
    • 0000211211 scopus 로고
    • Mesozoic conifers
    • Miller CN (1977) Mesozoic conifers. Bot Rev 43:217-280
    • (1977) Bot Rev , vol.43 , pp. 217-280
    • Miller, C.N.1
  • 26
    • 0032412237 scopus 로고    scopus 로고
    • Nuclear DNA amounts in gymnosperms
    • Suppl A
    • Murray BG (1998) Nuclear DNA amounts in gymnosperms. Ann Bot 82 (Suppl A):3-15
    • (1998) Ann Bot , vol.82 , pp. 3-15
    • Murray, B.G.1
  • 27
    • 0034131527 scopus 로고    scopus 로고
    • Light an indicator of time and place
    • Neff MM, Fankhauser C, Chory J (2000) Light an indicator of time and place. Genes Dev 14:257-271
    • (2000) Genes Dev , vol.14 , pp. 257-271
    • Neff, M.M.1    Fankhauser, C.2    Chory, J.3
  • 30
    • 0034809334 scopus 로고    scopus 로고
    • Statistical tests of selective neutrality in the age of genomics
    • Nielsen R (2001) Statistical tests of selective neutrality in the age of genomics. Heredity 86:641-647
    • (2001) Heredity , vol.86 , pp. 641-647
    • Nielsen, R.1
  • 31
    • 0033573925 scopus 로고    scopus 로고
    • Patterns of nucleotide substitution in Drosophila and mammalian genomes
    • Petrov DA, Hartl DL (1999) Patterns of nucleotide substitution in Drosophila and mammalian genomes. Proc Natl Acad Sci USA 96:1475-1479
    • (1999) Proc Natl Acad Sci USA , vol.96 , pp. 1475-1479
    • Petrov, D.A.1    Hartl, D.L.2
  • 32
    • 0029856377 scopus 로고    scopus 로고
    • High intrinsic rate of DNA loss in Drosophila
    • Petrov DA, Lozovskaya ER, Hartl DL (1996) High intrinsic rate of DNA loss in Drosophila. Nature 384:346-349
    • (1996) Nature , vol.384 , pp. 346-349
    • Petrov, D.A.1    Lozovskaya, E.R.2    Hartl, D.L.3
  • 34
    • 34547828004 scopus 로고    scopus 로고
    • Genetic quality of individuals impacts population dynamics
    • Reed DH, Nicholas AC, Stratton GE (2007) Genetic quality of individuals impacts population dynamics. Anim Conserv 10:275-283
    • (2007) Anim Conserv , vol.10 , pp. 275-283
    • Reed, D.H.1    Nicholas, A.C.2    Stratton, G.E.3
  • 35
    • 0036664974 scopus 로고    scopus 로고
    • Molecular characterization and evolution of the cytosolic class II 17.0 kDa small heat-shock protein gene family from Picea abies (L.)
    • Schubert R, Manteuffel R, Eich J, Häger KP (2002) Molecular characterization and evolution of the cytosolic class II 17.0 kDa small heat-shock protein gene family from Picea abies (L.). Plant Sci 163:1-12
    • (2002) Plant Sci , vol.163 , pp. 1-12
    • Schubert, R.1    Manteuffel, R.2    Eich, J.3    Häger, K.P.4
  • 36
    • 0032143143 scopus 로고    scopus 로고
    • Loblolly pine (Pinus taeda L) contains multiple expressed genes encoding light-dependent NADPH:protochlorophyllide oxidoreductase (POR)
    • Skinner JS, Timko MP (1998). Loblolly pine (Pinus taeda L) contains multiple expressed genes encoding light-dependent NADPH:protochlorophyllide oxidoreductase (POR). Plant Cell Physiol 39:795-806
    • (1998) Plant Cell Physiol , vol.39 , pp. 795-806
    • Skinner, J.S.1    Timko, M.P.2
  • 37
    • 0032849322 scopus 로고    scopus 로고
    • A method for detecting positive selection at single amino acid sites
    • Suzuki Y, Gojobori T (1999) A method for detecting positive selection at single amino acid sites. Mol Biol Evol 16:1315-1328
    • (1999) Mol Biol Evol , vol.16 , pp. 1315-1328
    • Suzuki, Y.1    Gojobori, T.2
  • 38
    • 0344585286 scopus 로고    scopus 로고
    • Adaptive evolution of genes and gene families
    • Swanson WJ (2003) Adaptive evolution of genes and gene families. Curr Opin Genet Dev 13:617-622
    • (2003) Curr Opin Genet Dev , vol.13 , pp. 617-622
    • Swanson, W.J.1
  • 39
    • 0028043489 scopus 로고
    • Loss of all Ndh genes as determined by sequencing the entire chloroplast genome of the black pine Pinus thumbergii
    • Wakasugi T, Tsudzuki J, Nakashima K, Tsudzuki T, Sugiura M (1994) Loss of all Ndh genes as determined by sequencing the entire chloroplast genome of the black pine Pinus thumbergii. Proc Natl Acad Sci USA 91:9794-9798
    • (1994) Proc Natl Acad Sci USA , vol.91 , pp. 9794-9798
    • Wakasugi, T.1    Tsudzuki, J.2    Nakashima, K.3    Tsudzuki, T.4    Sugiura, M.5
  • 40
    • 0021066331 scopus 로고
    • On the time for gene silencing at duplicated loci
    • Watterson GA (1983) On the time for gene silencing at duplicated loci. Genetics 105:745-766
    • (1983) Genetics , vol.105 , pp. 745-766
    • Watterson, G.A.1
  • 41
    • 4644290626 scopus 로고    scopus 로고
    • Recolonization and radiation in Larix (Pinaceae): Evidence from nuclear ribosomal DNA paralogues
    • Wei XX, Wang XQ (2004) Recolonization and radiation in Larix (Pinaceae): evidence from nuclear ribosomal DNA paralogues. Mol Ecol 13:3115-3123
    • (2004) Mol Ecol , vol.13 , pp. 3115-3123
    • Wei, X.X.1    Wang, X.Q.2
  • 43
    • 0025318864 scopus 로고
    • The "effective number of codons" used in a gene
    • Wright F (1986) The "effective number of codons" used in a gene. Gene 87:23-29
    • (1986) Gene , vol.87 , pp. 23-29
    • Wright, F.1
  • 44
    • 20644465818 scopus 로고    scopus 로고
    • A highly unexpected strong correlation between fixation probability of nonsynonymous mutations and mutation rate
    • Wyckoff GJ, Malcom CM, Vallender EJ, Lahn BT (2005) A highly unexpected strong correlation between fixation probability of nonsynonymous mutations and mutation rate. Trends Genet 21:381-385
    • (2005) Trends Genet , vol.21 , pp. 381-385
    • Wyckoff, G.J.1    Malcom, C.M.2    Vallender, E.J.3    Lahn, B.T.4
  • 45
    • 0029970817 scopus 로고    scopus 로고
    • Maximizing transcription efficiency causes codon usage bias
    • Xia X (1996) Maximizing transcription efficiency causes codon usage bias. Genetics 144:1309-1320
    • (1996) Genetics , vol.144 , pp. 1309-1320
    • Xia, X.1
  • 47
    • 0033639150 scopus 로고    scopus 로고
    • Statistical methods for detecting molecular adaptation
    • Yang Z, Bielawski JP (2000) Statistical methods for detecting molecular adaptation. TREE 15:496-503
    • (2000) TREE , vol.15 , pp. 496-503
    • Yang, Z.1    Bielawski, J.P.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.