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Gene expression modularity reveals footprints of polygenic adaptation in Theobroma cacao.

Hämälä T, Guiltinan MJ, Marden JH, Maximova S, dePamphilis C, Tiffin P.

Mol Biol Evol. 2019 Sep 10. pii: msz206. doi: 10.1093/molbev/msz206. [Epub ahead of print]


Resistant and susceptible cacao genotypes exhibit defense gene polymorphism and unique early responses to Phytophthora megakarya inoculation.

Pokou DN, Fister AS, Winters N, Tahi M, Klotioloma C, Sebastian A, Marden JH, Maximova SN, Guiltinan MJ.

Plant Mol Biol. 2019 Mar;99(4-5):499-516. doi: 10.1007/s11103-019-00832-y. Epub 2019 Feb 9.


Glucocorticoid receptor-regulated TcLEC2 expression triggers somatic embryogenesis in Theobroma cacao leaf tissue.

Fister AS, Landherr L, Perryman M, Zhang Y, Guiltinan MJ, Maximova SN.

PLoS One. 2018 Nov 26;13(11):e0207666. doi: 10.1371/journal.pone.0207666. eCollection 2018.


Transcriptomic analyses of cacao cell suspensions in light and dark provide target genes for controlled flavonoid production.

Gallego AM, Rojas LF, Parra O, Rodriguez HA, Mazo Rivas JC, Urrea AI, Atehortúa L, Fister AS, Guiltinan MJ, Maximova SN, Pabón-Mora N.

Sci Rep. 2018 Sep 11;8(1):13575. doi: 10.1038/s41598-018-31965-7.


Transient Expression of CRISPR/Cas9 Machinery Targeting TcNPR3 Enhances Defense Response in Theobroma cacao.

Fister AS, Landherr L, Maximova SN, Guiltinan MJ.

Front Plant Sci. 2018 Mar 2;9:268. doi: 10.3389/fpls.2018.00268. eCollection 2018.


Phytophthora megakarya and P. palmivora, closely related causal agents of cacao black pod rot, underwent increases in genome sizes and gene numbers by different mechanisms.

Ali SS, Shao J, Lary DJ, Kronmiller B, Shen D, Strem MD, Amoako-Attah I, Akrofi AY, Begoude BA, Ten Hoopen GM, Coulibaly K, Kebe BI, Melnick RL, Guiltinan MJ, Tyler BM, Meinhardt LW, Bailey BA.

Genome Biol Evol. 2017 Feb 10. doi: 10.1093/gbe/evx021. [Epub ahead of print] No abstract available.


Erratum to: Theobroma cacao L. pathogenesis-related gene tandem array members show diverse expression dynamics in response to pathogen colonization.

Fister AS, Mejia LC, Zhang Y, Herre EA, Maximova SN, Guiltinan MJ.

BMC Genomics. 2016 Sep 7;17(1):715. No abstract available.


Theobroma cacao L. pathogenesis-related gene tandem array members show diverse expression dynamics in response to pathogen colonization.

Fister AS, Mejia LC, Zhang Y, Herre EA, Maximova SN, Guiltinan MJ.

BMC Genomics. 2016 May 17;17:363. doi: 10.1186/s12864-016-2693-3. Erratum in: BMC Genomics. 2016 Sep 7;17(1):715.


Protocol: transient expression system for functional genomics in the tropical tree Theobroma cacao L.

Fister AS, Shi Z, Zhang Y, Helliwell EE, Maximova SN, Guiltinan MJ.

Plant Methods. 2016 Mar 11;12:19. doi: 10.1186/s13007-016-0119-5. eCollection 2016.


Enhanced resistance in Theobroma cacao against oomycete and fungal pathogens by secretion of phosphatidylinositol-3-phosphate-binding proteins.

Helliwell EE, Vega-Arreguín J, Shi Z, Bailey B, Xiao S, Maximova SN, Tyler BM, Guiltinan MJ.

Plant Biotechnol J. 2016 Mar;14(3):875-86. doi: 10.1111/pbi.12436. Epub 2015 Jul 27.


Two Theobroma cacao genotypes with contrasting pathogen tolerance show aberrant transcriptional and ROS responses after salicylic acid treatment.

Fister AS, O'Neil ST, Shi Z, Zhang Y, Tyler BM, Guiltinan MJ, Maximova SN.

J Exp Bot. 2015 Oct;66(20):6245-58. doi: 10.1093/jxb/erv334. Epub 2015 Jul 10.


Tc-MYBPA an Arabidopsis TT2-like transcription factor and functions in the regulation of proanthocyanidin synthesis in Theobroma cacao.

Liu Y, Shi Z, Maximova SN, Payne MJ, Guiltinan MJ.

BMC Plant Biol. 2015 Jun 25;15:160. doi: 10.1186/s12870-015-0529-y.


Enhanced somatic embryogenesis in Theobroma cacao using the homologous BABY BOOM transcription factor.

Florez SL, Erwin RL, Maximova SN, Guiltinan MJ, Curtis WR.

BMC Plant Biol. 2015 May 16;15:121. doi: 10.1186/s12870-015-0479-4.


Characterization of a stearoyl-acyl carrier protein desaturase gene family from chocolate tree, Theobroma cacao L.

Zhang Y, Maximova SN, Guiltinan MJ.

Front Plant Sci. 2015 Apr 14;6:239. doi: 10.3389/fpls.2015.00239. eCollection 2015.


Proteome analysis during pod, zygotic and somatic embryo maturation of Theobroma cacao.

Niemenak N, Kaiser E, Maximova SN, Laremore T, Guiltinan MJ.

J Plant Physiol. 2015 May 15;180:49-60. doi: 10.1016/j.jplph.2015.02.011. Epub 2015 Apr 1.


Pervasive effects of a dominant foliar endophytic fungus on host genetic and phenotypic expression in a tropical tree.

Mejía LC, Herre EA, Sparks JP, Winter K, García MN, Van Bael SA, Stitt J, Shi Z, Zhang Y, Guiltinan MJ, Maximova SN.

Front Microbiol. 2014 Sep 12;5:479. doi: 10.3389/fmicb.2014.00479. eCollection 2014.


Genome-wide analysis reveals divergent patterns of gene expression during zygotic and somatic embryo maturation of Theobroma cacao L., the chocolate tree.

Maximova SN, Florez S, Shen X, Niemenak N, Zhang Y, Curtis W, Guiltinan MJ.

BMC Plant Biol. 2014 Jul 16;14:185. doi: 10.1186/1471-2229-14-185.


Application of glycerol as a foliar spray activates the defence response and enhances disease resistance of Theobroma cacao.

Zhang Y, Smith P, Maximova SN, Guiltinan MJ.

Mol Plant Pathol. 2015 Jan;16(1):27-37. doi: 10.1111/mpp.12158. Epub 2014 Jul 9.


The Theobroma cacao B3 domain transcription factor TcLEC2 plays a duel role in control of embryo development and maturation.

Zhang Y, Clemens A, Maximova SN, Guiltinan MJ.

BMC Plant Biol. 2014 Apr 24;14:106. doi: 10.1186/1471-2229-14-106.


Genome and secretome analysis of the hemibiotrophic fungal pathogen, Moniliophthora roreri, which causes frosty pod rot disease of cacao: mechanisms of the biotrophic and necrotrophic phases.

Meinhardt LW, Costa GG, Thomazella DP, Teixeira PJ, Carazzolle MF, Schuster SC, Carlson JE, Guiltinan MJ, Mieczkowski P, Farmer A, Ramaraj T, Crozier J, Davis RE, Shao J, Melnick RL, Pereira GA, Bailey BA.

BMC Genomics. 2014 Feb 27;15:164. doi: 10.1186/1471-2164-15-164.


TcNPR3 from Theobroma cacao functions as a repressor of the pathogen defense response.

Shi Z, Zhang Y, Maximova SN, Guiltinan MJ.

BMC Plant Biol. 2013 Dec 6;13:204. doi: 10.1186/1471-2229-13-204.


Proanthocyanidin synthesis in Theobroma cacao: genes encoding anthocyanidin synthase, anthocyanidin reductase, and leucoanthocyanidin reductase.

Liu Y, Shi Z, Maximova S, Payne MJ, Guiltinan MJ.

BMC Plant Biol. 2013 Dec 5;13:202. doi: 10.1186/1471-2229-13-202.


The salicylic acid receptor NPR3 is a negative regulator of the transcriptional defense response during early flower development in Arabidopsis.

Shi Z, Maximova S, Liu Y, Verica J, Guiltinan MJ.

Mol Plant. 2013 May;6(3):802-16. doi: 10.1093/mp/sss091. Epub 2012 Sep 17.


The mitochondrial genome of Moniliophthora roreri, the frosty pod rot pathogen of cacao.

Costa GG, Cabrera OG, Tiburcio RA, Medrano FJ, Carazzolle MF, Thomazella DP, Schuster SC, Carlson JE, Guiltinan MJ, Bailey BA, Mieczkowski P, Pereira GA, Meinhardt LW.

Fungal Biol. 2012 May;116(5):551-62. doi: 10.1016/j.funbio.2012.01.008. Epub 2012 Feb 15.


Deficiency of maize starch-branching enzyme I results in altered starch fine structure, decreased digestibility and reduced coleoptile growth during germination.

Xia H, Yandeau-Nelson M, Thompson DB, Guiltinan MJ.

BMC Plant Biol. 2011 May 21;11:95. doi: 10.1186/1471-2229-11-95.


Starch-branching enzyme IIa is required for proper diurnal cycling of starch in leaves of maize.

Yandeau-Nelson MD, Laurens L, Shi Z, Xia H, Smith AM, Guiltinan MJ.

Plant Physiol. 2011 Jun;156(2):479-90. doi: 10.1104/pp.111.174094. Epub 2011 Apr 20.


The genome of Theobroma cacao.

Argout X, Salse J, Aury JM, Guiltinan MJ, Droc G, Gouzy J, Allegre M, Chaparro C, Legavre T, Maximova SN, Abrouk M, Murat F, Fouet O, Poulain J, Ruiz M, Roguet Y, Rodier-Goud M, Barbosa-Neto JF, Sabot F, Kudrna D, Ammiraju JS, Schuster SC, Carlson JE, Sallet E, Schiex T, Dievart A, Kramer M, Gelley L, Shi Z, Bérard A, Viot C, Boccara M, Risterucci AM, Guignon V, Sabau X, Axtell MJ, Ma Z, Zhang Y, Brown S, Bourge M, Golser W, Song X, Clement D, Rivallan R, Tahi M, Akaza JM, Pitollat B, Gramacho K, D'Hont A, Brunel D, Infante D, Kebe I, Costet P, Wing R, McCombie WR, Guiderdoni E, Quetier F, Panaud O, Wincker P, Bocs S, Lanaud C.

Nat Genet. 2011 Feb;43(2):101-8. doi: 10.1038/ng.736. Epub 2010 Dec 26.


Functional analysis of the Theobroma cacao NPR1 gene in Arabidopsis.

Shi Z, Maximova SN, Liu Y, Verica J, Guiltinan MJ.

BMC Plant Biol. 2010 Nov 15;10:248. doi: 10.1186/1471-2229-10-248.


Genes acquired by horizontal transfer are potentially involved in the evolution of phytopathogenicity in Moniliophthora perniciosa and Moniliophthora roreri, two of the major pathogens of cacao.

Tiburcio RA, Costa GG, Carazzolle MF, Mondego JM, Schuster SC, Carlson JE, Guiltinan MJ, Bailey BA, Mieczkowski P, Meinhardt LW, Pereira GA.

J Mol Evol. 2010 Jan;70(1):85-97. doi: 10.1007/s00239-009-9311-9. Epub 2009 Dec 23.


A genome survey of Moniliophthora perniciosa gives new insights into Witches' Broom Disease of cacao.

Mondego JM, Carazzolle MF, Costa GG, Formighieri EF, Parizzi LP, Rincones J, Cotomacci C, Carraro DM, Cunha AF, Carrer H, Vidal RO, Estrela RC, García O, Thomazella DP, de Oliveira BV, Pires AB, Rio MC, Araújo MR, de Moraes MH, Castro LA, Gramacho KP, Gonçalves MS, Neto JP, Neto AG, Barbosa LV, Guiltinan MJ, Bailey BA, Meinhardt LW, Cascardo JC, Pereira GA.

BMC Genomics. 2008 Nov 18;9:548. doi: 10.1186/1471-2164-9-548.


Towards the understanding of the cocoa transcriptome: Production and analysis of an exhaustive dataset of ESTs of Theobroma cacao L. generated from various tissues and under various conditions.

Argout X, Fouet O, Wincker P, Gramacho K, Legavre T, Sabau X, Risterucci AM, Da Silva C, Cascardo J, Allegre M, Kuhn D, Verica J, Courtois B, Loor G, Babin R, Sounigo O, Ducamp M, Guiltinan MJ, Ruiz M, Alemanno L, Machado R, Phillips W, Schnell R, Gilmour M, Rosenquist E, Butler D, Maximova S, Lanaud C.

BMC Genomics. 2008 Oct 30;9:512. doi: 10.1186/1471-2164-9-512.


Mutation of the maize sbe1a and ae genes alters morphology and physical behavior of wx-type endosperm starch granules.

Li JH, Guiltinan MJ, Thompson DB.

Carbohydr Res. 2007 Dec 10;342(17):2619-27. Epub 2007 Aug 2.


Over-expression of a cacao class I chitinase gene in Theobroma cacao L. enhances resistance against the pathogen, Colletotrichum gloeosporioides.

Maximova SN, Marelli JP, Young A, Pishak S, Verica JA, Guiltinan MJ.

Planta. 2006 Sep;224(4):740-9. Epub 2005 Dec 16.


Developmental expression of stress response genes in Theobroma cacao leaves and their response to Nep1 treatment and a compatible infection by Phytophthora megakarya.

Bailey BA, Bae H, Strem MD, Antúnez de Mayolo G, Guiltinan MJ, Verica JA, Maximova SN, Bowers JH.

Plant Physiol Biochem. 2005 Jun;43(6):611-22.


Isolation of ESTs from cacao (Theobroma cacao L.) leaves treated with inducers of the defense response.

Verica JA, Maximova SN, Strem MD, Carlson JE, Bailey BA, Guiltinan MJ.

Plant Cell Rep. 2004 Nov;23(6):404-13. Epub 2004 Aug 31.


Phosphatase under-producer mutants have altered phosphorus relations.

Tomscha JL, Trull MC, Deikman J, Lynch JP, Guiltinan MJ.

Plant Physiol. 2004 May;135(1):334-45. Epub 2004 Apr 30.


Stable transformation of Theobroma cacao L. and influence of matrix attachment regions on GFP expression.

Maximova S, Miller C, Antúnez de Mayolo G, Pishak S, Young A, Guiltinan MJ.

Plant Cell Rep. 2003 Jun;21(9):872-83. Epub 2003 Apr 3.


The maize EmBP-1 orthologue differentially regulates opaque2-dependent gene expression in yeast and cultured maize endosperm cells.

Carlini LE, Ketudat M, Parsons RL, Prabhakar S, Schmidt RJ, Guiltinan MJ.

Plant Mol Biol. 1999 Oct;41(3):339-49.


Bipartite determinants of DNA-binding specificity of plant basic leucine zipper proteins.

Niu X, Renshaw-Gegg L, Miller L, Guiltinan MJ.

Plant Mol Biol. 1999 Sep;41(1):1-13.


Molecular cloning and characterization of the Amylose-Extender gene encoding starch branching enzyme IIB in maize.

Kim KN, Fisher DK, Gao M, Guiltinan MJ.

Plant Mol Biol. 1998 Dec;38(6):945-56.


Genomic organization and promoter activity of the maize starch branching enzyme I gene.

Kim KN, Fisher DK, Gao M, Guiltinan MJ.

Gene. 1998 Aug 31;216(2):233-43.


Independent genetic control of maize starch-branching enzymes IIa and IIb. Isolation and characterization of a Sbe2a cDNA.

Gao M, Fisher DK, Kim KN, Shannon JC, Guiltinan MJ.

Plant Physiol. 1997 May;114(1):69-78.


Evolutionary conservation and expression patterns of maize starch branching enzyme I and IIb genes suggests isoform specialization.

Gao M, Fisher DK, Kim KN, Shannon JC, Guiltinan MJ.

Plant Mol Biol. 1996 Mar;30(6):1223-32.


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