Access the full text.
Sign up today, get DeepDyve free for 14 days.
Loading next page...
/lp/springer-journals/comparison-between-a-coffee-single-copy-chromosomal-region-and-Wv8cnkQeG9
References (59)
-
WL Crepet, KC Nixon, MA Gandolfo (2004)
Fossil evidence and phylogeny: the age of major angiosperm clades based on mesofossil and macrofossil evidence from Cretaceous depositsAm J Bot, 91
-
J Cros, M-C Combes, P Trouslot, F Anthony, S Hamon, A Charrier, P Lashermes (1998)
Phylogenetic analysis of chloroplast DNA variation in Coffea LMol Phylogenet Evol, 9
-
HH Yan, J Mudge, DJ Kim, D Larsen, R Denny, RC Shoemaker, DR Cook, ND Young (2004)
Comparative physical mapping reveals features of microsynteny between Glycine max, Medicago truncatula, and Arabidopsis thalianaGenome, 47
-
Gwênlyn Glusman, A. Smit (2009)
Genome Organization -
Chenwei Lin, L. Mueller, J. Carthy, D. Crouzillat, V. Pétiard, S. Tanksley (2005)
Coffee and tomato share common gene repertoires as revealed by deep sequencing of seed and cherry transcriptsTAG. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik, 112
-
G Blanc, A Barakat, R Guyot, R Cooke, M Delseny (2000)
Extensive duplication and reshuffling in the Arabidopsis genomePlant Cell, 12
-
MA Marra, TA Kucaba, NL Dietrich, ED Green, B Brownstein, RK Wilson, KM McDonald, L Hillier, J McPherson, R Waterston (1997)
High throughput fingerprint analysis of large-insert clonesGenome Res, 7
-
P Lashermes, M-C Combes, J Robert, P Trouslot, A D’Hont, F Anthony, A Charrier (1999)
Molecular characterisation and origin of the Coffea arabica L. genomeMol Genet Genomics, 261
-
S Stracke, S Sato, N Sandal, M Koyama, T Kaneko, S Tabata, M Parniske (2004)
Exploitation of colinear relationships between the genomes of Lotus japonicus, Pisum sativum and Arabidopsis thaliana, for positional cloning of a legume symbiosis geneTheor Appl Genet, 108
-
TJ Vision, DG Brown, SD Tanksley (2000)
The origins of genomic duplications in ArabidopsisScience, 290
-
JE Bowers, BA Chapman, J Rong, AH Paterson (2003)
Unravelling angiosperm genome evolution by phylogenetic analysis of`chromosomal duplication eventsNature, 422
-
U Lagercrantz, D Lydiate (1996)
Comparative genome mapping in BrassicaGenetics, 144
-
(1998)
New fossil flower -
S Noir, S Patheyron, MC Combes, P Lashermes, B Bertrand, B Chalhoub (2004)
Construction and characterisation of a BAC library for genome analysis of the allotetraploid coffee species (Coffea arabica L.)Theor Appl Genet, 109
-
Z Kevei, A Seres, A Kereszt, P Kaló, P Kiss, G Tóth, G Endre, B György (2005)
Significant microsynteny with new evolutionary highlights is detected between Arabidopsis and legume model plants despite the lack of macrosyntenyMol Genet Genomics, 274
-
(2002)
COMPARATIVE GENOME MAPPING -
A-M Dodeweerd, CR Hall, EG Bent, SJ Johnson, MW Bevan, I Bancroft (1999)
Identification and analysis of homoeologous segments of the genomes of rice and Arabidopsis thalianaGenome, 42
-
F. Famiani, Niccolò Cultrera, A. Battistelli, V. Casulli, Primo Proietti, Alvaro Standardi, ZHI-HUI Chen, R. Leegood, R. Walker (2005)
Phosphoenolpyruvate carboxykinase and its potential role in the catabolism of organic acids in the flesh of soft fruit during ripening.Journal of experimental botany, 56 421
-
D Grant, P Cregan, RC Shoemaker (2000)
Genome organization in dicots: genome duplication in Arabidopsis and synteny between soybean and ArabidopsisProc Natl Acad Sci USA, 97
-
MA Gandolfo, KC Nixon, WL Crepet (1998)
New fossil flower from the Turonian of New Jersey: Dressiantha bicarpellata gen. et sp. nov. (Capparales)Am J Bot, 85
-
S. Stracke, S. Sato, N. Sandal, M. Koyama, T. Kaneko, S. Tabata, M. Parniske (2004)
Exploitation of colinear relationships between the genomes of Lotus japonicus, Pisum sativum and Arabidopsis thaliana, for positional cloning of a legume symbiosis geneTheoretical and Applied Genetics, 108
-
H-M Ku, T Vision, J Liu, SD Tanksley (2000)
Comparing sequenced segments of the tomato and Arabidopsis genomes: large-scale duplication followed by selective gene loss creates a network of syntenyProc Natl Acad Sci USA, 97
-
AH Paterson (1996)
Towards a unified genetic map of higher plants, transcending the monocot–dicot divergenceNat Genet, 14
-
F Wu, LA Mueller, D Crouzillat, V Pétiard, SD Tanksley (2006)
Combining bioinformatics and phylogenetics to identify large sets of single copy, orthologous genes (COS) for comparative, evolutionary and systematic studies: a test case in the Euasterid plant cladeGenetics, 174
-
S Jung, D Main, M Staton, I Cho, T Zhebentyayeva, P Arús, A Abbott (2006)
Synteny conservation between the Prunus genome and both the present and ancestral Arabidopsis genomesBMC Genomics, 7
-
JP Tomkins, Y Yu, H Miller-Smith, DA Frisch, SS Woo, RA Wing (1999)
A bacterial artificial chromosome library for sugarcaneTheor Appl Genet, 99
-
MC Combes, S Andrzejewski, F Anthony, B Bertrand, P Rovelli, G Graziosi, P Lashermes (2000)
Characterization of microsatellite loci in Coffea arabica and related coffee speciesMol Ecol, 9
-
NS Prakash, DV Marques, VMP Varzea, MC Silva, MC Combes, P Lashermes (2004)
Introgression molecular analysis of a leaf rust resistance gene from Coffea liberica into C. arabica LTheor Appl Genet, 109
-
H. Yan, J. Mudge, Dongjin Kim, Dana Larsen, R. Shoemaker, D. Cook, N. Young (2003)
Estimates of conserved microsynteny among the genomes of Glycine max, Medicago truncatula and Arabidopsis thalianaTheoretical and Applied Genetics, 106
-
(1987)
MAP MAKER: an interactive computer -
T. Fulton, R. Hoeven, N. Eannetta, S. Tanksley (2002)
Identification, Analysis, and Utilization of Conserved Ortholog Set Markers for Comparative Genomics in Higher Plants Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.010479.The Plant Cell Online, 14
-
M Lynch, JS Conery (2000)
The evolutionary fate and consequences of duplicate genesScience, 290
-
S Maere, S Bodt, J Raes, T Casneuf, M Montagu, M Kuiper, Y Peer (2005)
Modeling gene and genome duplications in eukaryotesProc Natl Acad Sci USA, 102
-
J-C Herrera, M-C Combes, F Anthony, A Charrier, P Lashermes (2002)
Introgression into the allotetraploid coffee Coffea arabica L.: segregation and recombination of the C. canephora genome in the tetraploid interspecific hybrid C. arabica × C. canephoraTheor Appl Genet, 104
-
K Mayer, G Murphy, R Tarchini, R Wambutt, G Volckaert, T Pohl, A Düsterhöft, W Stiekema, K-D Entian, N Terryn, K Lemcke, D Haase, CR Hall, A-M Dodeweerd, SV Tingey, H-W Mewes, MW Bevan, I Bancroft (2001)
Conservation of microstructure between a sequenced region of the genome of rice and multiple segments of the genome of Arabidopsis thalianaGenome Res, 11
-
HH Yan, J Mudge, DJ Kim, D Larsen, RC Shoemaker, DR Cook, ND Young (2003)
Estimates of conserved microsynteny among the genomes of Glycine max, Medicago truncatula and Arabidopsis thalianaTheor Appl Genet, 106
-
H. Kirk, B. Jeune (1999)
[With the age....].Ugeskrift for laeger, 161 4
-
J Sambrook, EF Fritsch, T Maniatis (1989)
Molecular cloning: a laboratory manual -
(2000)
Analysis of the genome sequence of the flowering plant Arabidopsis thalianaNature, 408
-
D Foster-Hartnett, J Mudge, D Larsen, H Yan, R Denny, S Penuela, ND Young (2002)
Comparative genomic analysis of sequences sampled from a small region on soybean (Glycine max) molecular linkage group GGenome, 45
-
K Wolfe, M Gouy, Y Yang, P Sharp, WH Li (1989)
Date of the monocot dicot divergence estimated from chloroplast DNA sequence dataProc Natl Acad Sci USA, 86
-
M Rossberg, K Theres, A Acarkan, R Herrero, T Schmitt, K Schumacher, G Schmitz, R Schmidt (2001)
Comparative sequence analysis reveals extensive microcolinearity in the lateral suppressor regions of the tomato, Arabidopsis, and capsella genomesPlant Cell, 13
-
MD Ermolaeva, M Wu, JA Eisen, SL Salzberg (2003)
The age of the Arabidopsis thaliana genome duplicationPlant Mol Biol, 51
-
P Lashermes, M-C Combes, NS Prakash, P Trouslot, M Lorieux, A Charrier (2001)
Genetic linkage map of Coffea canephora: effect of segregation distortion and analysis of recombination rate in male and female meiosesGenome, 44
-
BA Chapman, JE Bowers, SR Schulze, AH Paterson (2004)
A comparative phylogenetic approach for dating whole genome duplication eventsBioinformatics, 20
-
T Fulton, R Hoeven, N Eannetta, S Tanksley (2002)
Identification, analysis and utilization of a conserved ortholog set (COS) markers for comparative genomics in higher plantsPlant Cell, 14
-
AH Paterson, JE Bowers, MD Burow, X Draye, CG Elsik, CX Jiang, CS Katsar, TH Lan, YR Lin, R Ming (2000)
Comparative genomics of plant chromosomesPlant Cell, 12
-
J Salse, B Piegu, R Cooke, M Delseny (2002)
Synteny between Arabidopsis thaliana and rice at the genome level: a tool to identify conservation in the ongoing rice genome sequencing projectNucleic Acids Res, 30
-
ES Lander, P Green, J Abrahamson, A Bralow, MJ Daly, SE Loincoln, L Newburg (1987)
MAP MAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populationsGenomics, 1
-
C Simillion, K Vandepoele, MCE Montagu, M Zabeau, Y Peer (2002)
The hidden duplication past of Arabidopsis thalianaProc Natl Acad Sci USA, 99
-
L Savard, P Li, SH Strauss, MW Chase, M Michaud, J Bousquet (1994)
Chloroplast and nuclear gene sequences indicate late Pennsylvanian time for the last common ancestor of extant seed plantsProc Natl Acad Sci USA, 91
-
C Agwanda, P Lashermes, P Trouslot, MC Combes, A Charrier (1997)
Identification of RAPD markers for resistance to Coffee Berry Disease, Colletotrichum kahawae, in Arabica coffeeEuphytica, 97
-
G Blanc, K Hokamp, KH Wolfe (2003)
A recent polyploidy superimposed on older large-scale duplications in the Arabidopsis genomeGenome Res, 13
-
C Lin, LA Mueller, J McCarthy, D Crouzillat, V Pétiard, SD Tanksley (2005)
Coffee and tomato share common gene repertoires as revealed by deep sequencing of seed and cherry transcriptsTheor Appl Genet, 5
-
A. Paterson, T. Lan, K. Reischmann, Charlene Chang, Yann-rong Lin, Sin-Chieh Liu, M. Burow, S. Kowalski, C. Katsar, T. Delmonte, K. Feldmann, K. Schertz, J. Wendel (1997)
Erratum: Toward a unified genetic map of higher plants, transcending the monocot–dicot divergenceNature Genetics, 15
-
S Moore, P Payton, M Wright, S Tanksley, J Giovannoni (2005)
Utilization of tomato microarrays for comparative gene expression analysis in the SolanaceaeJ Exp Bot, 56
-
Lai-Jiu Lin, M. Yang, Q. Ansari, G. Kassay (2005)
Existence results for Stampacchia and Minty type implicit variational inequalities with multivalued mapsNonlinear Analysis-theory Methods & Applications, 61
-
NS Prakash, MC Combes, N Somanna, P Lashermes (2002)
AFLP analysis of introgression in coffee cultivars (Coffea arabica L.) derived from a natural interspecific hybridEuphytica, 124
-
KM Devos, MD Gale (2000)
Genome relationships: the grass model in current researchPlant Cell, 12
- Publisher
- Springer Journals
- Copyright
- Copyright © 2007 by Springer Science+Business Media B.V.
- Subject
- Life Sciences; Plant Pathology; Biochemistry, general; Plant Sciences
- ISSN
- 0167-4412
- eISSN
- 1573-5028
- DOI
- 10.1007/s11103-007-9191-6
- pmid
- 17551672
- Publisher site
- See Article on Publisher Site
Abstract
The Arabidopsis thaliana genome sequence provides a catalogue of reference genes that can be used for comparative analysis of other species thereby facilitating map-based cloning in economically important crops. We made use of a coffee bacterial artificial chromosome (BAC) contig linked to the SH3 leaf rust resistance gene to assess microsynteny between coffee (Coffea arabica L.) and Arabidopsis. Microsynteny was revealed and the matching counterparts to C. arabica contigs were seen to be scattered throughout four different syntenic segments of Arabidopsis on chromosomes (Ath) I, III, IV and V. Coffee BAC filter hybridizations were performed using coffee putative conserved orthologous sequences to Arabidopsis predicted genes located on the different Arabidopsis syntenic regions. The coffee BAC contig related to the SH3 region was successfully consolidated and later on validated by fingerprinting. Furthermore, the anchoring markers appeared in same order on the coffee BAC contigs and in all Arabidopsis segments with the exception of a single inversion on AtIII and AtIV Arabidopsis segments. However, the SH3 coffee region appears to be closer to the ancestral genome segment (before the divergence of Arabidopsis and coffee) than any of the duplicated counterparts in the present-day Arabidopsis genome. The genome duplication events at the origin of its Arabidopsis counterparts occurred most probably after the separation (i.e. 94 million years ago) of Euasterid (Coffee) and Eurosid (Arabidopsis).
Journal
Plant Molecular Biology – Springer Journals
Published: Jun 6, 2007