메뉴 건너뛰기




Volumn 18, Issue 6, 2006, Pages 1348-1359

Comparative genomics of Brassica oleracea and Arabidopsis thaliana reveal gene loss, fragmentation, and dispersal after polyploidy

Author keywords

[No Author keywords available]

Indexed keywords

DNA SEQUENCES; GENES; GENETIC ENGINEERING; PROTEINS;

EID: 33745467604     PISSN: 10404651     EISSN: None     Source Type: Journal    
DOI: 10.1105/tpc.106.041665     Document Type: Article
Times cited : (337)

References (54)
  • 1
    • 0034649566 scopus 로고    scopus 로고
    • Analysis of the genome of the flowering plant Arabidopsis thaliana
    • Arabidopsis Genome Initiative (2000). Analysis of the genome of the flowering plant Arabidopsis thaliana. Nature 408, 796-815.
    • (2000) Nature , vol.408 , pp. 796-815
  • 2
    • 51249171246 scopus 로고
    • Nuclear DNA content of some important plant species
    • Arumuganthan, K., and Earle, E.D. (1991). Nuclear DNA content of some important plant species. Plant Mol. Biol. Rep. 9, 208-218.
    • (1991) Plant Mol. Biol. Rep. , vol.9 , pp. 208-218
    • Arumuganthan, K.1    Earle, E.D.2
  • 3
    • 0037294791 scopus 로고    scopus 로고
    • Chromosomal mapping of Brassica oleracea based on ESTs from Arabidopsis thaliana: Complexity of the comparative map
    • Babula, D., Kaczmarek, M., Barakat, A., Delseney, M., Quiros, C.F., and Sadowski, J. (2003). Chromosomal mapping of Brassica oleracea based on ESTs from Arabidopsis thaliana: Complexity of the comparative map. Mol. Genet. Genomics 268, 656-665.
    • (2003) Mol. Genet. Genomics , vol.268 , pp. 656-665
    • Babula, D.1    Kaczmarek, M.2    Barakat, A.3    Delseney, M.4    Quiros, C.F.5    Sadowski, J.6
  • 4
    • 0033957834 scopus 로고    scopus 로고
    • The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000
    • Bairoch, A., and Apweiler, R. (2000). The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res. 28, 45-48.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 45-48
    • Bairoch, A.1    Apweiler, R.2
  • 5
    • 0006667895 scopus 로고    scopus 로고
    • Insights into the structural and functional evolution of plant genomes afforded by the nucleotide sequences of chromosomes 2 and 4 of Arabidopsis thaliana
    • Bancroft, I. (2000). Insights into the structural and functional evolution of plant genomes afforded by the nucleotide sequences of chromosomes 2 and 4 of Arabidopsis thaliana. Yeast 17, 1-5.
    • (2000) Yeast , vol.17 , pp. 1-5
    • Bancroft, I.1
  • 6
    • 0035252409 scopus 로고    scopus 로고
    • Duplicate and diverge: The evolution of plant genome microstructure
    • Bancroft, I. (2001). Duplicate and diverge: The evolution of plant genome microstructure. Trends Genet. 17, 89-93.
    • (2001) Trends Genet. , vol.17 , pp. 89-93
    • Bancroft, I.1
  • 8
    • 0033891353 scopus 로고    scopus 로고
    • Extensive duplication and reshuffling in the Arabidopsis genome
    • Blanc, G., Barakat, A., Guyot, R., Cooke, R., and Delseny, M. (2000). Extensive duplication and reshuffling in the Arabidopsis genome. Plant Cell 12, 1093-1101.
    • (2000) Plant Cell , vol.12 , pp. 1093-1101
    • Blanc, G.1    Barakat, A.2    Guyot, R.3    Cooke, R.4    Delseny, M.5
  • 9
    • 3142732892 scopus 로고    scopus 로고
    • Functional divergence of duplicated genes formed by polyploidy during Arabidopsis evolution
    • Blanc, G., and Wolfe, K.H. (2004). Functional divergence of duplicated genes formed by polyploidy during Arabidopsis evolution. Plant Cell 16, 1679-1691.
    • (2004) Plant Cell , vol.16 , pp. 1679-1691
    • Blanc, G.1    Wolfe, K.H.2
  • 10
    • 0037468758 scopus 로고    scopus 로고
    • Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events
    • Bowers, J.E., Chapman, B.A., Rong, J., and Paterson, A.H. (2003). Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature 422, 433-438.
    • (2003) Nature , vol.422 , pp. 433-438
    • Bowers, J.E.1    Chapman, B.A.2    Rong, J.3    Paterson, A.H.4
  • 11
    • 0031586003 scopus 로고    scopus 로고
    • Prediction of complete gene structures in human genomic DNA
    • Burge, C., and Karlin, S. (1997). Prediction of complete gene structures in human genomic DNA. J. Mol. Biol. 268, 78-94.
    • (1997) J. Mol. Biol. , vol.268 , pp. 78-94
    • Burge, C.1    Karlin, S.2
  • 12
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: Multiple sequence alignment with high accuracy and high throughput
    • Edgar, R.C. (2004). MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792-1797.
    • (2004) Nucleic Acids Res. , vol.32 , pp. 1792-1797
    • Edgar, R.C.1
  • 13
    • 0000122573 scopus 로고
    • PHYLIP-Phylogeny Inference Package (version 3.2)
    • Felsenstein, J. (1989). PHYLIP-Phylogeny Inference Package (version 3.2). Cladistics 5, 164-166.
    • (1989) Cladistics , vol.5 , pp. 164-166
    • Felsenstein, J.1
  • 14
    • 5144221911 scopus 로고    scopus 로고
    • Comparative analysis of a Brassica BAC clone containing several major aliphatic glucosinolate genes with its corresponding Arabidopsis sequence
    • Gao, M.Q., Li, G.Y., Yang, B., McCombie, W.R., and Quiros, C.F. (2004). Comparative analysis of a Brassica BAC clone containing several major aliphatic glucosinolate genes with its corresponding Arabidopsis sequence. Genome 47, 666-679.
    • (2004) Genome , vol.47 , pp. 666-679
    • Gao, M.Q.1    Li, G.Y.2    Yang, B.3    McCombie, W.R.4    Quiros, C.F.5
  • 15
    • 0029791403 scopus 로고    scopus 로고
    • Splice site prediction in Arabidopsis thaliana pre-mRNA by combining local and global sequence information
    • Hebsgaard, S.M., Korning, P.G., Tolstrup, N., Engelbrecht, J., Rouze, P., and Brunak, S. (1996). Splice site prediction in Arabidopsis thaliana pre-mRNA by combining local and global sequence information. Nucleic Acids Res. 24, 3439-3452.
    • (1996) Nucleic Acids Res. , vol.24 , pp. 3439-3452
    • Hebsgaard, S.M.1    Korning, P.G.2    Tolstrup, N.3    Engelbrecht, J.4    Rouze, P.5    Brunak, S.6
  • 16
    • 0031573382 scopus 로고    scopus 로고
    • A tool for analyzing and annotating genomic sequences
    • Huang, X., Adams, M.D., Zhou, H., and Kerlavage, A.R. (1997). A tool for analyzing and annotating genomic sequences. Genomics 46, 37-45.
    • (1997) Genomics , vol.46 , pp. 37-45
    • Huang, X.1    Adams, M.D.2    Zhou, H.3    Kerlavage, A.R.4
  • 17
    • 84907150192 scopus 로고    scopus 로고
    • The map-based sequence of the rice genome
    • International Rice Genome Sequencing Project (2005). The map-based sequence of the rice genome. Nature 436, 793-800.
    • (2005) Nature , vol.436 , pp. 793-800
  • 18
    • 4944239027 scopus 로고    scopus 로고
    • Pack-MULE transposable elements mediate gene evolution in plants
    • Jiang, N., Bao, Z., Zhang, X., Eddy, S.R., and Wessler, S.R. (2004). Pack-MULE transposable elements mediate gene evolution in plants. Nature 431, 569-573.
    • (2004) Nature , vol.431 , pp. 569-573
    • Jiang, N.1    Bao, Z.2    Zhang, X.3    Eddy, S.R.4    Wessler, S.R.5
  • 19
    • 0033804889 scopus 로고    scopus 로고
    • Comparative evolutionary analysis of chalcone synthase and alcohol dehydrogenase loci in Arabidopsis, Arabis, and related genera (Brassicaceae)
    • Koch, M.A., Haubold, B., and Mitchell-Olds, T. (2000). Comparative evolutionary analysis of chalcone synthase and alcohol dehydrogenase loci in Arabidopsis, Arabis, and related genera (Brassicaceae). Mol. Biol. Evol. 17, 1483-1498.
    • (2000) Mol. Biol. Evol. , vol.17 , pp. 1483-1498
    • Koch, M.A.1    Haubold, B.2    Mitchell-Olds, T.3
  • 20
    • 0034255126 scopus 로고    scopus 로고
    • Comparing sequenced segments of the tomato and Arabidopsis genomes: Large-scale duplication followed by selective gene loss creates a network of synteny
    • Ku, H.-M., Vision, T., Liu, J., and Tanksley, S.D. (2000). Comparing sequenced segments of the tomato and Arabidopsis genomes: Large-scale duplication followed by selective gene loss creates a network of synteny. Proc. Natl. Acad. Sci. USA 97, 9121-9126.
    • (2000) Proc. Natl. Acad. Sci. USA , vol.97 , pp. 9121-9126
    • Ku, H.-M.1    Vision, T.2    Liu, J.3    Tanksley, S.D.4
  • 21
    • 3242810318 scopus 로고    scopus 로고
    • MEGA3: Integrated software for molecular evolutionary genetics analysis and sequence alignment
    • Kumar, S., Tamura, K., and Nei, M. (2004). MEGA3: Integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief. Bioinform. 5, 150-163.
    • (2004) Brief. Bioinform. , vol.5 , pp. 150-163
    • Kumar, S.1    Tamura, K.2    Nei, M.3
  • 22
    • 0031771373 scopus 로고    scopus 로고
    • Comparative mapping between Arabidopsis thaliana and Brassica nigra indicates that Brassica genomes have evolved through extensive genome replication accompanied by chromosome fusions and frequent rearrangements
    • Lagercrantz, U. (1998). Comparative mapping between Arabidopsis thaliana and Brassica nigra indicates that Brassica genomes have evolved through extensive genome replication accompanied by chromosome fusions and frequent rearrangements. Genetics 150, 1217-1228.
    • (1998) Genetics , vol.150 , pp. 1217-1228
    • Lagercrantz, U.1
  • 23
    • 0030454609 scopus 로고    scopus 로고
    • Comparative genome mapping in Brassica
    • Lagercrantz, U., and Lydiate, D. (1996). Comparative genome mapping in Brassica. Genetics 144, 1903-1910.
    • (1996) Genetics , vol.144 , pp. 1903-1910
    • Lagercrantz, U.1    Lydiate, D.2
  • 24
    • 21144454436 scopus 로고    scopus 로고
    • Gene movement by Helitron transposons contributes to the haplotype variability of maize
    • Lai, J., Li, Y., Messing, J., and Dooner, H.K. (2005). Gene movement by Helitron transposons contributes to the haplotype variability of maize. Proc. Natl. Acad. Sci. USA 102, 9068-9073.
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , pp. 9068-9073
    • Lai, J.1    Li, Y.2    Messing, J.3    Dooner, H.K.4
  • 27
    • 0030854739 scopus 로고    scopus 로고
    • tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence
    • Lowe, T.M., and Eddy, S.R. (1997). tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25, 955-964.
    • (1997) Nucleic Acids Res. , vol.25 , pp. 955-964
    • Lowe, T.M.1    Eddy, S.R.2
  • 28
    • 0032519353 scopus 로고    scopus 로고
    • GeneMark.hmm: New solutions for gene finding
    • Lukashin, A.V., and Borodovsky, M. (1998). GeneMark.hmm: New solutions for gene finding. Nucleic Acids Res. 26, 1107-1115.
    • (1998) Nucleic Acids Res. , vol.26 , pp. 1107-1115
    • Lukashin, A.V.1    Borodovsky, M.2
  • 29
    • 0038192129 scopus 로고    scopus 로고
    • Comparison of a Brassica oleracea genetic map with the genome of Arabidopsis thaliana
    • Lukens, L., Zou, F., Lydiate, D., Parkin, I., and Osborn, T. (2003). Comparison of a Brassica oleracea genetic map with the genome of Arabidopsis thaliana. Genetics 164, 359-372.
    • (2003) Genetics , vol.164 , pp. 359-372
    • Lukens, L.1    Zou, F.2    Lydiate, D.3    Parkin, I.4    Osborn, T.5
  • 31
    • 17844379449 scopus 로고    scopus 로고
    • Chromosome triplication found across the tribe Brassiceae
    • Lysak, M.A., Koch, M.A., Pecinka, A., and Schubert, I. (2005). Chromosome triplication found across the tribe Brassiceae. Genome Res. 15, 516-525.
    • (2005) Genome Res. , vol.15 , pp. 516-525
    • Lysak, M.A.1    Koch, M.A.2    Pecinka, A.3    Schubert, I.4
  • 33
    • 0034917750 scopus 로고    scopus 로고
    • Conservation of microstructure between a sequenced region of the genome of rice and multiple segments of the genome of Arabidopsis thaliana
    • Mayer, K., et al. (2001). Conservation of microstructure between a sequenced region of the genome of rice and multiple segments of the genome of Arabidopsis thaliana. Genome Res. 11, 1167-1174.
    • (2001) Genome Res. , vol.11 , pp. 1167-1174
    • Mayer, K.1
  • 34
    • 0032415864 scopus 로고    scopus 로고
    • Clusters of resistance genes in plants evolve by divergent selection and a birth-and-death process
    • Michelmore, R.W., and Meyers, B.C. (1998). Clusters of resistance genes in plants evolve by divergent selection and a birth-and-death process. Genome Res. 8, 1113-1130.
    • (1998) Genome Res. , vol.8 , pp. 1113-1130
    • Michelmore, R.W.1    Meyers, B.C.2
  • 36
    • 0033230488 scopus 로고    scopus 로고
    • Pronounced intraspecific haplotype divergence at the RPP5 complex disease resistance locus of Arabidopsis
    • Moel, L., Moores, T.L., van der Biezen, E.A., Parniske, M., Daniels, M.J., Parker, J.E., and Jones, J.D.G. (1999). Pronounced intraspecific haplotype divergence at the RPP5 complex disease resistance locus of Arabidopsis. Plant Cell 11, 2099-2111.
    • (1999) Plant Cell , vol.11 , pp. 2099-2111
    • Moel, L.1    Moores, T.L.2    Van Der Biezen, E.A.3    Parniske, M.4    Daniels, M.J.5    Parker, J.E.6    Jones, J.D.G.7
  • 37
    • 0033893554 scopus 로고    scopus 로고
    • Comparative physical mapping of segments of the genome of Brassica oleracea var alboglabra that are homoeologous to sequenced regions of the chromosomes 4 and 5 of Arabidopsis thaliana
    • 0'Neill, C.M., and Bancroft, I. (2000). Comparative physical mapping of segments of the genome of Brassica oleracea var alboglabra that are homoeologous to sequenced regions of the chromosomes 4 and 5 of Arabidopsis thaliana. Plant J. 23, 233-243.
    • (2000) Plant J. , vol.23 , pp. 233-243
    • O'Neill, C.M.1    Bancroft, I.2
  • 38
    • 28644448226 scopus 로고    scopus 로고
    • Physical mapping and microsynteny of Brassica rapa ssp. pekinensis genome corresponding to a 222 kb gene-rich region of Arabidopsis chromosome 4 and partially duplicated on chromosome 5
    • Park, J.Y., et al. (2005). Physical mapping and microsynteny of Brassica rapa ssp. pekinensis genome corresponding to a 222 kb gene-rich region of Arabidopsis chromosome 4 and partially duplicated on chromosome 5. Mol. Genet. Genomics 274, 579-588.
    • (2005) Mol. Genet. Genomics , vol.274 , pp. 579-588
    • Park, J.Y.1
  • 39
    • 31544442199 scopus 로고    scopus 로고
    • Segmental structure of the Brassica napus genome based on comparative analysis with Arabidopsis thaliana
    • Parkin, I.A.P., Gulden, S.M., Sharpe, A.G., Lukens, L., Trick, M., Osborn, T.C., and Lydiate, D.J. (2005). Segmental structure of the Brassica napus genome based on comparative analysis with Arabidopsis thaliana. Genetics 171, 765-781.
    • (2005) Genetics , vol.171 , pp. 765-781
    • Parkin, I.A.P.1    Gulden, S.M.2    Sharpe, A.G.3    Lukens, L.4    Trick, M.5    Osborn, T.C.6    Lydiate, D.J.7
  • 40
    • 0029186820 scopus 로고
    • Identification of the A and C genomes of amphidiploid Brassica napus (oilseed rape)
    • Parkin, I.A.P., Sharpe, A.G., Keith, D.J., and Lydiate, D.J. (1995). Identification of the A and C genomes of amphidiploid Brassica napus (oilseed rape). Genome 38, 1122-1131.
    • (1995) Genome , vol.38 , pp. 1122-1131
    • Parkin, I.A.P.1    Sharpe, A.G.2    Keith, D.J.3    Lydiate, D.J.4
  • 41
    • 0037572292 scopus 로고    scopus 로고
    • Patterns of genome duplication within the Brassica napus genome
    • Parkin, I.A.P., Sharpe, A.G., and Lydiate, D.J. (2003). Patterns of genome duplication within the Brassica napus genome. Genome 46, 291-303.
    • (2003) Genome , vol.46 , pp. 291-303
    • Parkin, I.A.P.1    Sharpe, A.G.2    Lydiate, D.J.3
  • 42
    • 0035282695 scopus 로고    scopus 로고
    • GeneSplicer. A new computational method for splice site prediction
    • Pertea, M., Lin, X., and Salzberg, S.L. (2001). GeneSplicer. A new computational method for splice site prediction. Nucleic Acids Res. 29, 1185-1190.
    • (2001) Nucleic Acids Res. , vol.29 , pp. 1185-1190
    • Pertea, M.1    Lin, X.2    Salzberg, S.L.3
  • 43
    • 0033965855 scopus 로고    scopus 로고
    • The TIGR gene indices: Reconstruction and representation of expressed gene sequences
    • Quackenbush, J., Liang, F., Holt, I., Pertea, G., and Upton, J. (2000). The TIGR gene indices: Reconstruction and representation of expressed gene sequences. Nucleic Acids Res. 28, 141-145.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 141-145
    • Quackenbush, J.1    Liang, F.2    Holt, I.3    Pertea, G.4    Upton, J.5
  • 44
    • 0035100479 scopus 로고    scopus 로고
    • Arabidopsis and Brassica comparative genomics: Sequence, structure and gene content in the ABI -Rps2-Ck chromosomal segment and related regions
    • Quiros, C.F., Grellet, F., Sadowski, J., Suzuki, T., Li, G., and Wroblewski, T. (2001). Arabidopsis and Brassica comparative genomics: Sequence, structure and gene content in the ABI -Rps2-Ck chromosomal segment and related regions. Genetics 157, 1321-1330.
    • (2001) Genetics , vol.157 , pp. 1321-1330
    • Quiros, C.F.1    Grellet, F.2    Sadowski, J.3    Suzuki, T.4    Li, G.5    Wroblewski, T.6
  • 47
    • 0035060915 scopus 로고    scopus 로고
    • Comparative structural genomics in the Brassicaceae family
    • Schmidt, R., Acarkan, A., and Boivin, K. (2001). Comparative structural genomics in the Brassicaceae family. Plant Physiol. Biochem. 39, 253-262.
    • (2001) Plant Physiol. Biochem. , vol.39 , pp. 253-262
    • Schmidt, R.1    Acarkan, A.2    Boivin, K.3
  • 48
    • 0029162810 scopus 로고
    • Rapid genome change in synthetic polyploids of Brassica and its implications for polyploid evolution
    • Song, K., Lu, P., Tang, K., and Osborn, T.C. (1995). Rapid genome change in synthetic polyploids of Brassica and its implications for polyploid evolution. Proc. Natl. Acad. Sci. USA 92, 7719-7723.
    • (1995) Proc. Natl. Acad. Sci. USA , vol.92 , pp. 7719-7723
    • Song, K.1    Lu, P.2    Tang, K.3    Osborn, T.C.4
  • 49
    • 0038744597 scopus 로고    scopus 로고
    • Structure, sequence and phylogeny of the members of the Ck1 gene family in Brassica oleracea and Arabidopsis thaliana (Brassicaceae)
    • Suzuki, T., Grellet, F., Potter, D., Li, G., and Quiros, C.F. (2003). Structure, sequence and phylogeny of the members of the Ck1 gene family in Brassica oleracea and Arabidopsis thaliana (Brassicaceae). Plant Sci. 164, 735-742.
    • (2003) Plant Sci. , vol.164 , pp. 735-742
    • Suzuki, T.1    Grellet, F.2    Potter, D.3    Li, G.4    Quiros, C.F.5
  • 50
    • 0002427832 scopus 로고
    • Molecular systematics of Brassica and allied genera(subtribe Brassicinae, Brassiceae) - Chloroplast genome and cytodeme congruence
    • Warwick, S.I., and Black, L.D. (1991). Molecular systematics of Brassica and allied genera(subtribe Brassicinae, Brassiceae)-Chloroplast genome and cytodeme congruence. Theor. Appl. Genet. 82, 81-92.
    • (1991) Theor. Appl. Genet. , vol.82 , pp. 81-92
    • Warwick, S.I.1    Black, L.D.2
  • 51
    • 0030730886 scopus 로고    scopus 로고
    • Molecular phytogenies from theory to application in Brassica and allies (tribe Brassiceae, Brassicaceae)
    • Warwick, S.I., and Black, L.D. (1997). Molecular phytogenies from theory to application in Brassica and allies (tribe Brassiceae, Brassicaceae). Opera Bot. 132, 159-168.
    • (1997) Opera Bot. , vol.132 , pp. 159-168
    • Warwick, S.I.1    Black, L.D.2
  • 52
    • 0033974956 scopus 로고    scopus 로고
    • Genome evolution in polyploids
    • Wendel, J.F. (2000). Genome evolution in polyploids. Plant Mol. Biol. 42, 225-249.
    • (2000) Plant Mol. Biol. , vol.42 , pp. 225-249
    • Wendel, J.F.1
  • 53
    • 0024712231 scopus 로고
    • Date of the monocot-dicot divergence estimated from the chloroplast DNA sequence data
    • Wolfe, K.H., Gouy, M., Yang, Y.W., Sharp, P.M., and Li, W.H. (1989). Date of the monocot-dicot divergence estimated from the chloroplast DNA sequence data. Proc. Natl. Acad. Sci. USA 86, 6201-6205.
    • (1989) Proc. Natl. Acad. Sci. USA , vol.86 , pp. 6201-6205
    • Wolfe, K.H.1    Gouy, M.2    Yang, Y.W.3    Sharp, P.M.4    Li, W.H.5
  • 54
    • 0032954807 scopus 로고    scopus 로고
    • Rates of nucleotide substitution in angiosperm mitochondrial DNA sequences and dates of divergence between Brassica and other angiosperm lineages
    • Yang, Y.W., Lai, K.W., Tai, P.Y., and Li, W.H. (1999). Rates of nucleotide substitution in angiosperm mitochondrial DNA sequences and dates of divergence between Brassica and other angiosperm lineages. J. Mol. Evol. 48, 597-604.
    • (1999) J. Mol. Evol. , vol.48 , pp. 597-604
    • Yang, Y.W.1    Lai, K.W.2    Tai, P.Y.3    Li, W.H.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.