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Volumn 15, Issue 2, 2012, Pages 122-130

In silico archeogenomics unveils modern plant genome organisation, regulation and evolution

Author keywords

[No Author keywords available]

Indexed keywords

ARCHEOLOGY; GENETICS; GENOMICS; METHODOLOGY; MOLECULAR EVOLUTION; PLANT GENOME; REVIEW;

EID: 84859893292     PISSN: 13695266     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.pbi.2012.01.001     Document Type: Review
Times cited : (60)

References (53)
  • 1
    • 70450189075 scopus 로고    scopus 로고
    • Improved criteria and comparative genomics tool provide new insights into grass paleogenomics
    • Salse J., Abrouk M., Murat F., Quraishi U.M., Feuillet C. Improved criteria and comparative genomics tool provide new insights into grass paleogenomics. Brief Bioinform 2009, 10:619-630.
    • (2009) Brief Bioinform , vol.10 , pp. 619-630
    • Salse, J.1    Abrouk, M.2    Murat, F.3    Quraishi, U.M.4    Feuillet, C.5
  • 3
    • 79959457523 scopus 로고    scopus 로고
    • Mapping ancestral genomes with massive gene loss: a matrix sandwich problem
    • Gavranović H., Chauve C., Salse J., Tannier E. Mapping ancestral genomes with massive gene loss: a matrix sandwich problem. Bioinformatics 2011, 27:i257-i265.
    • (2011) Bioinformatics , vol.27
    • Gavranović, H.1    Chauve, C.2    Salse, J.3    Tannier, E.4
  • 5
    • 0034649566 scopus 로고    scopus 로고
    • Analysis of the genome sequence of the flowering plant Arabidopsis thaliana
    • Arabidopsis Genome Initiative
    • Arabidopsis Genome Initiative Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 2000, 408:796-815.
    • (2000) Nature , vol.408 , pp. 796-815
  • 14
    • 84859427179 scopus 로고    scopus 로고
    • Translational genomics in legumes allowed placing in silico 5460 unigenes on the pea functional map and identified candidate genes in Pisum sativum L.
    • Bordat A., Savois V., Nicolas M., Salse J., Chauveau A., Bourgeois M., Potier J., Houtin H., Rond C., Murat F., et al. Translational genomics in legumes allowed placing in silico 5460 unigenes on the pea functional map and identified candidate genes in Pisum sativum L. Genes Genomes Genet 2011, 1:93-103.
    • (2011) Genes Genomes Genet , vol.1 , pp. 93-103
    • Bordat, A.1    Savois, V.2    Nicolas, M.3    Salse, J.4    Chauveau, A.5    Bourgeois, M.6    Potier, J.7    Houtin, H.8    Rond, C.9    Murat, F.10
  • 15
    • 84907150192 scopus 로고    scopus 로고
    • The map-based sequence of the rice genome
    • International Rice Genome Sequencing Project
    • International Rice Genome Sequencing Project The map-based sequence of the rice genome. Nature 2005, 436:793-800.
    • (2005) Nature , vol.436 , pp. 793-800
  • 18
    • 76749150030 scopus 로고    scopus 로고
    • Genome sequencing and analysis of the model grass Brachypodium distachyon
    • International Brachypodium Initiative
    • Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature 2010, 463:763-768. International Brachypodium Initiative.
    • (2010) Nature , vol.463 , pp. 763-768
  • 21
    • 79952439365 scopus 로고    scopus 로고
    • Paleogenomics in cereals: modelling of ancestors for modern species improvement
    • Salse J., Feuillet C. Paleogenomics in cereals: modelling of ancestors for modern species improvement. C R Biologies 2011, 334:205-211.
    • (2011) C R Biologies , vol.334 , pp. 205-211
    • Salse, J.1    Feuillet, C.2
  • 23
    • 78649312312 scopus 로고    scopus 로고
    • Ancestral grass karyotype reconstruction unravels new mechanisms of genome shuffling as a source of plant evolution
    • Murat F., Xu J.H., Tannier E., Abrouk M., Guilhot N., Pont C., Messing J., Salse J. Ancestral grass karyotype reconstruction unravels new mechanisms of genome shuffling as a source of plant evolution. Genome Res 2010, 20:1545-1557.
    • (2010) Genome Res , vol.20 , pp. 1545-1557
    • Murat, F.1    Xu, J.H.2    Tannier, E.3    Abrouk, M.4    Guilhot, N.5    Pont, C.6    Messing, J.7    Salse, J.8
  • 24
    • 65249143921 scopus 로고    scopus 로고
    • Plants with double genomes might have had a better chance to survive the Cretaceous-Tertiary extinction event
    • Fawcett J.A., Maere S., Van de Peer Y. Plants with double genomes might have had a better chance to survive the Cretaceous-Tertiary extinction event. Proc Natl Acad Sci USA 2009, 106:5737-5742.
    • (2009) Proc Natl Acad Sci USA , vol.106 , pp. 5737-5742
    • Fawcett, J.A.1    Maere, S.2    Van de Peer, Y.3
  • 25
    • 76249106402 scopus 로고    scopus 로고
    • Angiosperm genome comparisons reveal early polyploidy in the monocot lineage
    • Tang H., Bowers J.E., Wang X., Paterson A.H. Angiosperm genome comparisons reveal early polyploidy in the monocot lineage. Proc Natl Acad Sci USA 2010, 107:472-477.
    • (2010) Proc Natl Acad Sci USA , vol.107 , pp. 472-477
    • Tang, H.1    Bowers, J.E.2    Wang, X.3    Paterson, A.H.4
  • 27
    • 79953254847 scopus 로고    scopus 로고
    • Journey through the past: 150 million years of plant genome evolution
    • Proost S., Pattyn P., Gerats T., Van de Peer Y. Journey through the past: 150 million years of plant genome evolution. Plant J 2011, 66:58-65.
    • (2011) Plant J , vol.66 , pp. 58-65
    • Proost, S.1    Pattyn, P.2    Gerats, T.3    Van de Peer, Y.4
  • 29
    • 0032478340 scopus 로고    scopus 로고
    • Comparative genetics in grasses
    • Gale M., Devos K.M. Comparative genetics in grasses. Proc Natl Acad Sci USA 1998, 95:1971-1974.
    • (1998) Proc Natl Acad Sci USA , vol.95 , pp. 1971-1974
    • Gale, M.1    Devos, K.M.2
  • 31
  • 35
    • 70349325524 scopus 로고    scopus 로고
    • The evolutionary significance of ancient genome duplications
    • Van de Peer Y., Maere S., Meyer A. The evolutionary significance of ancient genome duplications. Nat Rev Genet 2009, 10:725-732.
    • (2009) Nat Rev Genet , vol.10 , pp. 725-732
    • Van de Peer, Y.1    Maere, S.2    Meyer, A.3
  • 37
    • 77950942128 scopus 로고    scopus 로고
    • Evolutionary consequences of autopolyploidy
    • Parisod C., Holderegger R., Brochmann C. Evolutionary consequences of autopolyploidy. New Phytol 2010, 186:5-17.
    • (2010) New Phytol , vol.186 , pp. 5-17
    • Parisod, C.1    Holderegger, R.2    Brochmann, C.3
  • 38
    • 79956330054 scopus 로고    scopus 로고
    • Interpretation of karyotype evolution should consider chromosome structural constraints
    • Schubert I., Lysak M.A. Interpretation of karyotype evolution should consider chromosome structural constraints. Trends Genet 2011, 27:207-216.
    • (2011) Trends Genet , vol.27 , pp. 207-216
    • Schubert, I.1    Lysak, M.A.2
  • 39
    • 77954741256 scopus 로고    scopus 로고
    • Following tetraploidy in maize, a short deletion mechanism removed genes preferentially from one of the two homologs
    • Woodhouse M.R., Schnable J.C., Pedersen B.S., Lyons E., Lisch D., Subramaniam S., Freeling M. Following tetraploidy in maize, a short deletion mechanism removed genes preferentially from one of the two homologs. PLoS Biol 2010, 8:e1000409.
    • (2010) PLoS Biol , vol.8
    • Woodhouse, M.R.1    Schnable, J.C.2    Pedersen, B.S.3    Lyons, E.4    Lisch, D.5    Subramaniam, S.6    Freeling, M.7
  • 40
    • 79952744855 scopus 로고    scopus 로고
    • Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss
    • Schnable J.C., Springer N.M., Freeling M. Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss. Proc Natl Acad Sci USA 2011, 108:4069-4074.
    • (2011) Proc Natl Acad Sci USA , vol.108 , pp. 4069-4074
    • Schnable, J.C.1    Springer, N.M.2    Freeling, M.3
  • 41
    • 79952301890 scopus 로고    scopus 로고
    • Seventy million years of concerted evolution of a homoeologous chromosome pair, in parallel, in major Poaceae lineages
    • Wang X., Tang H., Paterson A.H. Seventy million years of concerted evolution of a homoeologous chromosome pair, in parallel, in major Poaceae lineages. Plant Cell 2011, 23:27-37.
    • (2011) Plant Cell , vol.23 , pp. 27-37
    • Wang, X.1    Tang, H.2    Paterson, A.H.3
  • 43
    • 82455168160 scopus 로고    scopus 로고
    • RNA-seq in grain unveils fate of neo- and paleopolyploidization events in bread wheat (/Triticum aestivum/L.)
    • Pont C., Murat F., Confolent C., Balzergue S., Salse J. RNA-seq in grain unveils fate of neo- and paleopolyploidization events in bread wheat (/Triticum aestivum/L.). Genome Biol 2011, 12:R119.
    • (2011) Genome Biol , vol.12
    • Pont, C.1    Murat, F.2    Confolent, C.3    Balzergue, S.4    Salse, J.5
  • 45
    • 79959858471 scopus 로고    scopus 로고
    • Two-phase resolution of polyploidy in the Arabidopsis metabolic network gives rise to relative and absolute dosage constraints
    • Bekaert M., Edger P.P., Pires J.C., Conant G.C. Two-phase resolution of polyploidy in the Arabidopsis metabolic network gives rise to relative and absolute dosage constraints. Plant Cell 2011, 23:1719-1728.
    • (2011) Plant Cell , vol.23 , pp. 1719-1728
    • Bekaert, M.1    Edger, P.P.2    Pires, J.C.3    Conant, G.C.4
  • 46
    • 79955597646 scopus 로고    scopus 로고
    • Divergent evolutionary fates of major photosynthetic gene networks following gene and whole genome duplications
    • Coate J.E., Doyle J.J. Divergent evolutionary fates of major photosynthetic gene networks following gene and whole genome duplications. Plant Signal Behav 2011, 6:594-597.
    • (2011) Plant Signal Behav , vol.6 , pp. 594-597
    • Coate, J.E.1    Doyle, J.J.2
  • 47
    • 33745617700 scopus 로고    scopus 로고
    • Following tetraploidy in an Arabidopsis ancestor, genes were removed preferentially from one homeolog leaving clusters enriched in dose-sensitive genes
    • Thomas B.C., Pedersen B., Freeling M. Following tetraploidy in an Arabidopsis ancestor, genes were removed preferentially from one homeolog leaving clusters enriched in dose-sensitive genes. Genome Res 2006, 16:934-946.
    • (2006) Genome Res , vol.16 , pp. 934-946
    • Thomas, B.C.1    Pedersen, B.2    Freeling, M.3
  • 48
    • 77952302158 scopus 로고    scopus 로고
    • The collapse of gene complement following whole genome duplication
    • Sankoff D., Zheng C., Zhu Q. The collapse of gene complement following whole genome duplication. BMC Genomics 2010, 11:313.
    • (2010) BMC Genomics , vol.11 , pp. 313
    • Sankoff, D.1    Zheng, C.2    Zhu, Q.3
  • 49
    • 33750173564 scopus 로고    scopus 로고
    • Many gene and domain families have convergent fates following independent whole-genome duplication events in Arabidopsis, Oryza, Saccharomyces and Tetraodon
    • Paterson A.H., Chapman B.A., Kissinger J.C., Bowers J.E., Feltus F.A., Estill J.C. Many gene and domain families have convergent fates following independent whole-genome duplication events in Arabidopsis, Oryza, Saccharomyces and Tetraodon. Trends Genet 2006, 22:597-602.
    • (2006) Trends Genet , vol.22 , pp. 597-602
    • Paterson, A.H.1    Chapman, B.A.2    Kissinger, J.C.3    Bowers, J.E.4    Feltus, F.A.5    Estill, J.C.6
  • 50
    • 78650334271 scopus 로고    scopus 로고
    • Homoeolog-specific retention and use in allotetraploid Arabidopsis suecica depends on parent of origin and network partners
    • Chang P.L., Dilkes B.P., McMahon M., Comai L., Nuzhdin S.V. Homoeolog-specific retention and use in allotetraploid Arabidopsis suecica depends on parent of origin and network partners. Genome Biol 2010, 11:R125.
    • (2010) Genome Biol , vol.11
    • Chang, P.L.1    Dilkes, B.P.2    McMahon, M.3    Comai, L.4    Nuzhdin, S.V.5
  • 51
    • 0038157152 scopus 로고    scopus 로고
    • Dosage sensitivity and the evolution of gene families in yeast
    • Papp B., Pál C., Hurst L.D. Dosage sensitivity and the evolution of gene families in yeast. Nature 2003, 424:194-197.
    • (2003) Nature , vol.424 , pp. 194-197
    • Papp, B.1    Pál, C.2    Hurst, L.D.3
  • 52
    • 33745004593 scopus 로고    scopus 로고
    • History, protohistory and prehistory of the Arabidopsis thaliana chromosome complement
    • Henry Y., Bedhomme M., Blanc G. History, protohistory and prehistory of the Arabidopsis thaliana chromosome complement. Trends Plant Sci 2006, 11:267-273.
    • (2006) Trends Plant Sci , vol.11 , pp. 267-273
    • Henry, Y.1    Bedhomme, M.2    Blanc, G.3
  • 53
    • 77950949952 scopus 로고    scopus 로고
    • The gene balance hypothesis: implications for gene regulation, quantitative traits and evolution
    • Birchler J.A., Veitia R.A. The gene balance hypothesis: implications for gene regulation, quantitative traits and evolution. New Phytol 2010, 186:54-62.
    • (2010) New Phytol , vol.186 , pp. 54-62
    • Birchler, J.A.1    Veitia, R.A.2


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