Comparative sequence analyses indicate that Coffea (Asterids) and Vitis (Rosids) derive from the same paleo-hexaploid ancestral genome

Molecular Genetics and Genomics

Volumn 283, Issue 5, 2010, Pages 493-501

  Cenci, Alberto ^a   Combes, Marie Christine ^a   Lashermes, Philippe ^a  

^a INSTITUT DE RECHERCHE POUR LE DÉVELOPPEMENT   (France)

Author keywords

Asterids; Comparative genomics; CoVea; Paleo polyploid; Rosids

Indexed keywords

AMINO ACID SEQUENCE; ARABIDOPSIS; ARTICLE; ASPEN; COFFEE; DIPLOIDY; GENE DUPLICATION; GENE LOSS; GENETIC VARIABILITY; GRAPE; HEXAPLOIDY; NONHUMAN; NUCLEOTIDE SEQUENCE; ORTHOLOGY; PARALOGY; PLANT GENETICS; POLYPLOIDY; PRIORITY JOURNAL; SEQUENCE ANALYSIS; BACTERIAL ARTIFICIAL CHROMOSOME; CLASSIFICATION; COMPARATIVE STUDY; CONTIG MAPPING; DNA SEQUENCE; GENETICS; MOLECULAR EVOLUTION; PALEONTOLOGY; PHYLOGENY; PLANT GENE; PLANT GENOME; SYNTENY;

ARABIDOPSIS THALIANA; ASTERIDS; COFFEA; LYCOPERSICON ESCULENTUM; POPULUS TRICHOCARPA; ROSIDAE; ROSIDS; SOLANUM TUBEROSUM; VITIS; VITIS VINIFERA;

ARABIDOPSIS; CHROMOSOMES, ARTIFICIAL, BACTERIAL; COFFEA; CONTIG MAPPING; EVOLUTION, MOLECULAR; GENE DUPLICATION; GENES, PLANT; GENETIC VARIATION; GENOME, PLANT; PALEONTOLOGY; PHYLOGENY; POLYPLOIDY; POPULUS; SEQUENCE ANALYSIS, DNA; SYNTENY; VITIS;

EID: 77951635682     PISSN: 16174615     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00438-010-0534-7     Document Type: Article

References (23)

1. Blanc G, Wolfe K (2004) Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes. Plant Cell 16:1667-1678. doi:10.1105/tpc.021345
2. Bowers JE, Chapman BA, Rong J, Paterson AH (2003) Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature 422:433-438. doi:10.1038/nature01521
3. Cui L, Wall PK, Leebens-Mack JH, Lindsay BG, Soltis DE, Doyle JJ, Soltis PS, Carlson JE, Arumuganathan K, Barakat A, Albert VA, Ma H, de Pamphilis CW (2006) Widespread genome duplications throughout the history of Xowering plants. Genome Res 16:738-749. doi:10.1101/gr.4825606
4. Gaut BS, Doebley JF (1997) DNA sequence evidence for the segmental allotetraploid origin of maize. Proc Natl Acad Sci USA 94:6809-6814
5. Guyot R, de la Mare M, Viader V, Hamon P, Coriton O, Bustamante-Porras J, Poncet V, Campa C, Hamon S, de Kochko A (2009) Microcollinearity in an ethylene receptor coding gene region of the CoVea canephora genome is extensively conserved with Vitis vinifera and other distant dicotyledonous sequenced genomes. BMC Plant Biol 9:22. doi:10.1186/1471-2229-9-22
6. Helentjaris T, Weber D, Wright S (1988) IdentiWcation of the genomic locations of duplicate nucleotide sequences in maize by analysis of restriction fragment length polymorphisms. Genetics 118:353-363
7. Herrera JC, D'Hont A, Lashermes P (2007) Use of Xuorescence in situ hybridization as a tool for introgression analysis and chromosome identiWcation in coVee (CoVea arabica L.). Genome 50:619-626. doi:10.1139/g07-034
8. International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature 436:793-800. doi:10.1038/nature03895
9. Jaillon O et al (2007) The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449:463-467. doi:10.1038/nature06148
10. Lashermes P, Combes M-C, Robert J, Trouslot P, D'Hont A, Anthony F, Charrier A (1999) Molecular characterisation and origin of the CoVea arabica L. genome. Mol Gen Genet 261:259-266
11. Leroy T, Marraccini P, Dufour M, Montagnon C, Lashermes C, Sabau X, Ferreira LP, Jourdan I, Pot D, Andrade AC, Glaszmann JC, Vieira LGE, PiVanelli P (2005) Construction and characterization of a CoVea canephora BAC library to study the organization of sucrose biosynthesis genes. Theor Appl Genet 111:1032-1041. doi:10.1007/s00122-005-0018-z
12. Lin C, Mueller LA, McCarthy J, Crouzillat D, Pétiard V, Tanksley SD (2005) CoVee and tomato share common gene repertoires as revealed by deep sequencing of seed and cherry transcripts. Theor Appl Genet 112:114-130. doi:10.1007/s00122-005-0112-2
13. Mahé L, Combes M-C, Lashermes P (2007) Comparison between a coVee single copy chromosomal region and Arabidopsis duplicated counterparts evidenced high level synteny between the coVee genome and the ancestral Arabidopsis genome. Plant Mol Biol 64:699-711. doi:10.1007/s11103-007-9191-6
14. Ming R et al (2008) The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature 452:991-996. doi:10.1038/ nature06856
15. Noir S, Patheyron S, Combes M-C, Lashermes P, Chalhoub B (2004) Construction and characterisation of a BAC library for genome analysis of the allotetraploid coVee species (CoVea arabica L.). Theor Appl Genet 109:225-230. doi:10.1007/s00122-004-1604-1
16. Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P, Rajandream MA, Barrell B (2000) Artemis: sequence visualization and annotation. Bioinformatics 16:944-945
17. Smith SA, Donoghue MJ (2008) Rates of molecular evolution are linked to life history in Xowering plants. Science 322:86-89. doi:10.1126/science.1163197
18. Tang H, Bowers JE, Wang X, Ming R, Alam M, Paterson AH (2008a) Synteny and collinearity in plant genomes. Science 320:486-488. doi:10.1126/science. 1153917
19. Tang H, Wang X, Bowers JE, Ming R, Alam M, Paterson AH (2008b) Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps. Genomic Res 18:1944-1954. doi:10.1101/gr.080978.108
20. The Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the Xowering plant Arabidopsis thaliana. Nature 408:796-815. doi:10.1038/35048692
21. Tuskan GA et al (2006) The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313:1596-1604. doi:10.1126/science. 1128691
22. Wendel J (2000) Genome evolution in polyploids. Plant Mol Biol 42:225-249
23. Wu F, Mueller LA, Crouzillat D, Petiard V, Tanksley SD (2006) Combining bioinformatics and phylogenetics to identify large sets of single-copy orthologous genes (COSII) for comparative, evolutionary and systematic studies: a test case in the euasterid plant clade. Genetics 174:1407-1420. doi:10.1534/genetics.106.062455