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Items: 1 to 50 of 53

1.

Development and evaluation of a genome-wide Coffee 8.5K SNP array and its application for high-density genetic mapping and for investigating the origin of Coffea arabica L.

Merot-L'anthoene V, Tournebize R, Darracq O, Rattina V, Lepelley M, Bellanger L, Tranchant-Dubreuil C, Coulée M, Pégard M, Metairon S, Fournier C, Stoffelen P, Janssens SB, Kiwuka C, Musoli P, Sumirat U, Legnaté H, Kambale JL, Ferreira da Costa Neto J, Revel C, de Kochko A, Descombes P, Crouzillat D, Poncet V.

Plant Biotechnol J. 2018 Dec 24. doi: 10.1111/pbi.13066. [Epub ahead of print]

2.

Structure and Distribution of Centromeric Retrotransposons at Diploid and Allotetraploid Coffea Centromeric and Pericentromeric Regions.

de Castro Nunes R, Orozco-Arias S, Crouzillat D, Mueller LA, Strickler SR, Descombes P, Fournier C, Moine D, de Kochko A, Yuyama PM, Vanzela ALL, Guyot R.

Front Plant Sci. 2018 Feb 15;9:175. doi: 10.3389/fpls.2018.00175. eCollection 2018.

3.

Two disjunct Pleistocene populations and anisotropic postglacial expansion shaped the current genetic structure of the relict plant Amborella trichopoda.

Tournebize R, Manel S, Vigouroux Y, Munoz F, de Kochko A, Poncet V.

PLoS One. 2017 Aug 18;12(8):e0183412. doi: 10.1371/journal.pone.0183412. eCollection 2017.

4.

Distribution of Divo in Coffea genomes, a poorly described family of angiosperm LTR-Retrotransposons.

Dupeyron M, de Souza RF, Hamon P, de Kochko A, Crouzillat D, Couturon E, Domingues DS, Guyot R.

Mol Genet Genomics. 2017 Aug;292(4):741-754. doi: 10.1007/s00438-017-1308-2. Epub 2017 Mar 17.

PMID:
28314936
5.

Genotyping-by-sequencing provides the first well-resolved phylogeny for coffee (Coffea) and insights into the evolution of caffeine content in its species: GBS coffee phylogeny and the evolution of caffeine content.

Hamon P, Grover CE, Davis AP, Rakotomalala JJ, Raharimalala NE, Albert VA, Sreenath HL, Stoffelen P, Mitchell SE, Couturon E, Hamon S, de Kochko A, Crouzillat D, Rigoreau M, Sumirat U, Akaffou S, Guyot R.

Mol Phylogenet Evol. 2017 Apr;109:351-361. doi: 10.1016/j.ympev.2017.02.009. Epub 2017 Feb 16.

PMID:
28212875
6.

Partial sequencing reveals the transposable element composition of Coffea genomes and provides evidence for distinct evolutionary stories.

Guyot R, Darré T, Dupeyron M, de Kochko A, Hamon S, Couturon E, Crouzillat D, Rigoreau M, Rakotomalala JJ, Raharimalala NE, Akaffou SD, Hamon P.

Mol Genet Genomics. 2016 Oct;291(5):1979-90. doi: 10.1007/s00438-016-1235-7. Epub 2016 Jul 28.

PMID:
27469896
7.

Shift in precipitation regime promotes interspecific hybridization of introduced Coffea species.

Gomez C, Despinoy M, Hamon S, Hamon P, Salmon D, Akaffou DS, Legnate H, de Kochko A, Mangeas M, Poncet V.

Ecol Evol. 2016 Apr 8;6(10):3240-55. doi: 10.1002/ece3.2055. eCollection 2016 May.

8.

The Amborella vacuolar processing enzyme family.

Poncet V, Scutt C, Tournebize R, Villegente M, Cueff G, Rajjou L, Balliau T, Zivy M, Fogliani B, Job C, de Kochko A, Sarramegna-Burtet V, Job D.

Front Plant Sci. 2015 Aug 21;6:618. doi: 10.3389/fpls.2015.00618. eCollection 2015.

9.

Large distribution and high sequence identity of a Copia-type retrotransposon in angiosperm families.

Dias ES, Hatt C, Hamon S, Hamon P, Rigoreau M, Crouzillat D, Carareto CM, de Kochko A, Guyot R.

Plant Mol Biol. 2015 Sep;89(1-2):83-97. doi: 10.1007/s11103-015-0352-8. Epub 2015 Aug 6.

PMID:
26245353
10.

Active transposable elements recover species boundaries and geographic structure in Madagascan coffee species.

Roncal J, Guyot R, Hamon P, Crouzillat D, Rigoreau M, Konan ON, Rakotomalala JJ, Nowak MD, Davis AP, de Kochko A.

Mol Genet Genomics. 2016 Feb;291(1):155-68. doi: 10.1007/s00438-015-1098-3. Epub 2015 Aug 1.

PMID:
26231981
11.

The coffee genome provides insight into the convergent evolution of caffeine biosynthesis.

Denoeud F, Carretero-Paulet L, Dereeper A, Droc G, Guyot R, Pietrella M, Zheng C, Alberti A, Anthony F, Aprea G, Aury JM, Bento P, Bernard M, Bocs S, Campa C, Cenci A, Combes MC, Crouzillat D, Da Silva C, Daddiego L, De Bellis F, Dussert S, Garsmeur O, Gayraud T, Guignon V, Jahn K, Jamilloux V, Joët T, Labadie K, Lan T, Leclercq J, Lepelley M, Leroy T, Li LT, Librado P, Lopez L, Muñoz A, Noel B, Pallavicini A, Perrotta G, Poncet V, Pot D, Priyono, Rigoreau M, Rouard M, Rozas J, Tranchant-Dubreuil C, VanBuren R, Zhang Q, Andrade AC, Argout X, Bertrand B, de Kochko A, Graziosi G, Henry RJ, Jayarama, Ming R, Nagai C, Rounsley S, Sankoff D, Giuliano G, Albert VA, Wincker P, Lashermes P.

Science. 2014 Sep 5;345(6201):1181-4. doi: 10.1126/science.1255274. Epub 2014 Sep 4.

12.

Phylogeography and niche modelling of the relict plant Amborella trichopoda (Amborellaceae) reveal multiple Pleistocene refugia in New Caledonia.

Poncet V, Munoz F, Munzinger J, Pillon Y, Gomez C, Couderc M, Tranchant-Dubreuil C, Hamon S, de Kochko A.

Mol Ecol. 2013 Dec;22(24):6163-78. doi: 10.1111/mec.12554. Epub 2013 Nov 11.

PMID:
24118476
13.

BAC-end sequences analysis provides first insights into coffee (Coffea canephora P.) genome composition and evolution.

Dereeper A, Guyot R, Tranchant-Dubreuil C, Anthony F, Argout X, de Bellis F, Combes MC, Gavory F, de Kochko A, Kudrna D, Leroy T, Poulain J, Rondeau M, Song X, Wing R, Lashermes P.

Plant Mol Biol. 2013 Oct;83(3):177-89. doi: 10.1007/s11103-013-0077-5. Epub 2013 May 25.

PMID:
23708951
14.

Genetic structure and diversity of coffee (Coffea) across Africa and the Indian Ocean islands revealed using microsatellites.

Razafinarivo NJ, Guyot R, Davis AP, Couturon E, Hamon S, Crouzillat D, Rigoreau M, Dubreuil-Tranchant C, Poncet V, De Kochko A, Rakotomalala JJ, Hamon P.

Ann Bot. 2013 Feb;111(2):229-48. doi: 10.1093/aob/mcs283. Epub 2012 Dec 28.

15.

Microsatellite markers for Amborella (Amborellaceae), a monotypic genus endemic to New Caledonia.

Poncet V, Couderc M, Tranchant-Dubreuil C, Gomez C, Hamon P, Hamon S, Pillon Y, Munzinger J, de Kochko A.

Am J Bot. 2012 Oct;99(10):e411-4. doi: 10.3732/ajb.1200131. Epub 2012 Oct 1.

16.

Ancestral synteny shared between distantly-related plant species from the asterid (Coffea canephora and Solanum Sp.) and rosid (Vitis vinifera) clades.

Guyot R, Lefebvre-Pautigny F, Tranchant-Dubreuil C, Rigoreau M, Hamon P, Leroy T, Hamon S, Poncet V, Crouzillat D, de Kochko A.

BMC Genomics. 2012 Mar 20;13:103. doi: 10.1186/1471-2164-13-103.

17.

Characterization, high-resolution mapping and differential expression of three homologous PAL genes in Coffea canephora Pierre (Rubiaceae).

Lepelley M, Mahesh V, McCarthy J, Rigoreau M, Crouzillat D, Chabrillange N, de Kochko A, Campa C.

Planta. 2012 Jul;236(1):313-26. doi: 10.1007/s00425-012-1613-2. Epub 2012 Feb 21.

18.

Site-Specific Insertion Polymorphism of the MITE Alex-1 in the Genus Coffea Suggests Interspecific Gene Flow.

Dubreuil-Tranchant C, Guyot R, Guellim A, Duret C, de la Mare M, Razafinarivo N, Poncet V, Hamon S, Hamon P, de Kochko A.

Int J Evol Biol. 2011;2011:358412. doi: 10.4061/2011/358412. Epub 2011 Sep 27.

19.

Two novel Ty1-copia retrotransposons isolated from coffee trees can effectively reveal evolutionary relationships in the Coffea genus (Rubiaceae).

Hamon P, Duroy PO, Dubreuil-Tranchant C, Mafra D'Almeida Costa P, Duret C, Razafinarivo NJ, Couturon E, Hamon S, de Kochko A, Poncet V, Guyot R.

Mol Genet Genomics. 2011 Jun;285(6):447-60. doi: 10.1007/s00438-011-0617-0. Epub 2011 Apr 20.

PMID:
21505885
20.

Micro-collinearity and genome evolution in the vicinity of an ethylene receptor gene of cultivated diploid and allotetraploid coffee species (Coffea).

Yu Q, Guyot R, de Kochko A, Byers A, Navajas-Pérez R, Langston BJ, Dubreuil-Tranchant C, Paterson AH, Poncet V, Nagai C, Ming R.

Plant J. 2011 Jul;67(2):305-17. doi: 10.1111/j.1365-313X.2011.04590.x. Epub 2011 May 12.

21.

The 'PUCE CAFE' Project: the first 15K coffee microarray, a new tool for discovering candidate genes correlated to agronomic and quality traits.

Privat I, Bardil A, Gomez AB, Severac D, Dantec C, Fuentes I, Mueller L, Joët T, Pot D, Foucrier S, Dussert S, Leroy T, Journot L, de Kochko A, Campa C, Combes MC, Lashermes P, Bertrand B.

BMC Genomics. 2011 Jan 5;12:5. doi: 10.1186/1471-2164-12-5.

22.

MoccaDB - an integrative database for functional, comparative and diversity studies in the Rubiaceae family.

Plechakova O, Tranchant-Dubreuil C, Benedet F, Couderc M, Tinaut A, Viader V, De Block P, Hamon P, Campa C, de Kochko A, Hamon S, Poncet V.

BMC Plant Biol. 2009 Sep 29;9:123. doi: 10.1186/1471-2229-9-123.

23.

Physical mapping of rDNA and heterochromatin in chromosomes of 16 Coffea species: a revised view of species differentiation.

Hamon P, Siljak-Yakovlev S, Srisuwan S, Robin O, Poncet V, Hamon S, de Kochko A.

Chromosome Res. 2009;17(3):291-304. doi: 10.1007/s10577-009-9033-2. Epub 2009 Mar 31.

PMID:
19333769
24.

Microcollinearity in an ethylene receptor coding gene region of the Coffea canephora genome is extensively conserved with Vitis vinifera and other distant dicotyledonous sequenced genomes.

Guyot R, de la Mare M, Viader V, Hamon P, Coriton O, Bustamante-Porras J, Poncet V, Campa C, Hamon S, de Kochko A.

BMC Plant Biol. 2009 Feb 25;9:22. doi: 10.1186/1471-2229-9-22.

25.

Metabolic pathways in tropical dicotyledonous albuminous seeds: Coffea arabica as a case study.

Joët T, Laffargue A, Salmona J, Doulbeau S, Descroix F, Bertrand B, de Kochko A, Dussert S.

New Phytol. 2009;182(1):146-62. doi: 10.1111/j.1469-8137.2008.02742.x. Epub 2009 Jan 21.

26.

Effectiveness of the fatty acid and sterol composition of seeds for the chemotaxonomy of Coffea subgenus Coffea.

Dussert S, Laffargue A, de Kochko A, Joët T.

Phytochemistry. 2008 Dec;69(17):2950-60. doi: 10.1016/j.phytochem.2008.09.021. Epub 2008 Nov 6.

PMID:
18995872
27.

Near immunity to rice tungro spherical virus achieved in rice by a replicase-mediated resistance strategy.

Huet H, Mahendra S, Wang J, Sivamani E, Ong CA, Chen L, de Kochko A, Beachy RN, Fauquet C.

Phytopathology. 1999 Nov;89(11):1022-7. doi: 10.1094/PHYTO.1999.89.11.1022.

28.

Development of genomic microsatellite markers in Coffea canephora and their transferability to other coffee species.

Poncet V, Dufour M, Hamon P, Hamon S, de Kochko A, Leroy T.

Genome. 2007 Dec;50(12):1156-61.

PMID:
18059542
29.

Deciphering transcriptional networks that govern Coffea arabica seed development using combined cDNA array and real-time RT-PCR approaches.

Salmona J, Dussert S, Descroix F, de Kochko A, Bertrand B, Joët T.

Plant Mol Biol. 2008 Jan;66(1-2):105-24. Epub 2007 Nov 15.

PMID:
18026845
30.

Development of solid-phase extraction and methylation procedures to analyse free fatty acids in lipid-rich seeds.

Laffargue A, de Kochko A, Dussert S.

Plant Physiol Biochem. 2007 Mar-Apr;45(3-4):250-7. Epub 2007 Jan 30.

PMID:
17360190
31.

Functional characterization of two p-coumaroyl ester 3'-hydroxylase genes from coffee tree: evidence of a candidate for chlorogenic acid biosynthesis.

Mahesh V, Million-Rousseau R, Ullmann P, Chabrillange N, Bustamante J, Mondolot L, Morant M, Noirot M, Hamon S, de Kochko A, Werck-Reichhart D, Campa C.

Plant Mol Biol. 2007 May;64(1-2):145-59. Epub 2007 Feb 27.

PMID:
17333503
32.

Molecular characterization of an ethylene receptor gene (CcETR1) in coffee trees, its relationship with fruit development and caffeine content.

Bustamante-Porras J, Campa C, Poncet V, Noirot M, Leroy T, Hamon S, de Kochko A.

Mol Genet Genomics. 2007 Jun;277(6):701-12. Epub 2007 Feb 21.

PMID:
17318584
33.

SSR mining in coffee tree EST databases: potential use of EST-SSRs as markers for the Coffea genus.

Poncet V, Rondeau M, Tranchant C, Cayrel A, Hamon S, de Kochko A, Hamon P.

Mol Genet Genomics. 2006 Nov;276(5):436-49. Epub 2006 Aug 19.

PMID:
16924545
34.

Evolution in caffeoylquinic acid content and histolocalization during Coffea canephora leaf development.

Mondolot L, La Fisca P, Buatois B, Talansier E, de Kochko A, Campa C.

Ann Bot. 2006 Jul;98(1):33-40. Epub 2006 May 4.

35.

Isolation and genetic mapping of a Coffea canephora phenylalanine ammonia-lyase gene (CcPAL1) and its involvement in the accumulation of caffeoyl quinic acids.

Mahesh V, Rakotomalala JJ, Le Gal L, Vigne H, de Kochko A, Hamon S, Noirot M, Campa C.

Plant Cell Rep. 2006 Sep;25(9):986-92. Epub 2006 Apr 4.

PMID:
16586075
36.

The mechanism of action of alpha-amylase from Lactobacillus fermentum on maltooligosaccharides.

Talamond P, Noirot M, de Kochko A.

J Chromatogr B Analyt Technol Biomed Life Sci. 2006 Apr 13;834(1-2):42-7. Epub 2006 Mar 13.

PMID:
16531129
37.
38.
39.

Genome size variations in diploid African Coffea species.

Noirot M, Poncet V, Barre P, Hamon P, Hamon S, De Kochko A.

Ann Bot. 2003 Nov;92(5):709-14.

40.

Genetic mapping of a caffeoyl-coenzyme A 3-O-methyltransferase gene in coffee trees. Impact on chlorogenic acid content.

Campa C, Noirot M, Bourgeois M, Pervent M, Ky CL, Chrestin H, Hamon S, de Kochko A.

Theor Appl Genet. 2003 Aug;107(4):751-6. Epub 2003 Jul 12.

PMID:
12861362
41.

Evidence of synergism between African cassava mosaic virus and a new double-recombinant geminivirus infecting cassava in Cameroon.

Fondong VN, Pita JS, Rey ME, de Kochko A, Beachy RN, Fauquet CM.

J Gen Virol. 2000 Jan;81(Pt 1):287-97.

PMID:
10640569
42.

Rice tungro bacilliform virus open reading frame 3 encodes a single 37-kDa coat protein.

Marmey P, Bothner B, Jacquot E, de Kochko A, Ong CA, Yot P, Siuzdak G, Beachy RN, Fauquet CM.

Virology. 1999 Jan 20;253(2):319-26.

43.

Expression and inheritance of multiple transgenes in rice plants.

Chen L, Marmey P, Taylor NJ, Brizard JP, Espinoza C, D'Cruz P, Huet H, Zhang S, de Kochko A, Beachy RN, Fauquet CM.

Nat Biotechnol. 1998 Nov;16(11):1060-4.

PMID:
9831036
44.

Functional organization of the cassava vein mosaic virus (CsVMV) promoter.

Verdaguer B, de Kochko A, Fux CI, Beachy RN, Fauquet C.

Plant Mol Biol. 1998 Aug;37(6):1055-67.

PMID:
9700077
45.

Cassava vein mosaic virus (CsVMV), type species for a new genus of plant double stranded DNA viruses?

de Kochko A, Verdaguer B, Taylor N, Carcamo R, Beachy RN, Fauquet C.

Arch Virol. 1998;143(5):945-62.

PMID:
9645200
46.

Isolation and expression in transgenic tobacco and rice plants, of the cassava vein mosaic virus (CVMV) promoter.

Verdaguer B, de Kochko A, Beachy RN, Fauquet C.

Plant Mol Biol. 1996 Sep;31(6):1129-39.

PMID:
8914529
47.

Partial desiccation of mature embryo-derived calli, a simple treatment that dramatically enhances the regeneration ability of indica rice.

Rancé IM, Tian W, Mathews H, de Kochko A, Beachy RN, Fauquet C.

Plant Cell Rep. 1994 Aug;13(11):647-51. doi: 10.1007/BF00232938.

PMID:
24196246
48.

An improved rice transformation system using the biolistic method.

Li L, Qu R, de Kochko A, Fauquet C, Beachy RN.

Plant Cell Rep. 1993 Mar;12(5):250-5. doi: 10.1007/BF00237129.

PMID:
24197151
49.

Characterization of the genome of rice tungro bacilliform virus: comparison with Commelina yellow mottle virus and caulimoviruses.

Qu R, Bhattacharyya M, Laco GS, de Kochko A, Rao BL, Kaniewska MB, Elmer JS, Rochester DE, Smith CE, Beachy RN.

Virology. 1992 Feb;186(2):798. No abstract available.

PMID:
1733115
50.

Characterization of the genome of rice tungro bacilliform virus: comparison with Commelina yellow mottle virus and caulimoviruses.

Qu RD, Bhattacharyya M, Laco GS, De Kochko A, Rao BL, Kaniewska MB, Elmer JS, Rochester DE, Smith CE, Beachy RN.

Virology. 1991 Nov;185(1):354-64. Erratum in: Virology. 1992 Feb;186(2):798.

PMID:
1926781

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