Evolutionary Genomics Program

Publicaciones

#	Año	Ficha	Ligas
1	2013	Pérez-Segura, G., Pérez-Oseguera, A. and Cevallos, M.A. (2013). *"The Repac Replication System of the Rhizobium* leguminosarum Prl7 Plasmid is Functional: Implications regarding the Origin and Evolution of repABC Plasmids"*. Plasmid*. 69(1):49-57	PUBMED: #22975386
2	2012	Althabegoiti, M.J., Lozano, L.F., Torres-Tejerizo, G., Ormeño-Orrillo, E., Rogel, M.A., González, V. and Martínez-Romero, E. (2012). *"Genome Sequence Of Rhizobium* Grahamii CCGE502, A Broad-host-range Symbiont With Low Nodulation Competitiveness In Phaseolus vulgaris"*. J Bacteriol. 194*(23):6651-6652	PUBMED: #23144400
3	2012	de la Rosa, J.J.P., Ureostegui, P.V., Martínez, J.A.A., Martínez, C.R., González, V. and Millan, J.V.F. (2012). "Babesia Bigemina: Initial Gene Identification by Expressed Sequence Tags (est) Analysis of the Intraerythrocytic Stage". Rev Mex Cienc Pecu. 3:61-87
4	2012	Fernández-Sandoval, M.T., Huerta-Beristain, G., Trujillo-Martínez, B., Bustos, P., González, V., Bolivar, F., Gosset, G. and Martínez, A. (2012). *"Laboratory Metabolic Evolution Improves Acetate Tolerance And Growth on Acetate of Ethanologenic Escherichia coli* under Non-aerated Conditions in Glucose-mineral Medium"*. Appl Microbiol Biotechnol*. 96(5):1291-1300	PUBMED: #22669633
5	2012	Garza-Ramos, U., Barrios, H., Hernández-Vargas, M.J., Rojas-Moreno, T., Reyna-Flores, F., Tinoco, P., Othon, V., Poirel, L., Nordmann, P., Cattoir, V., Ruíz-Palacios, G., Fernández, J.L., Santamaria, R.I., Bustos, P., Castro, N. and Silva-Sánchez, J. (2012). *"Transfer of Quinolone Resistance Gene qnrA1 to* Escherichia coli through a 50 Kb Conjugative Plasmid Resulting from the Splitting of a 300 Kb Plasmid"*. J Antimicrob Chemoth*. 67(7):1627-1634	PUBMED: #22514263
6	2012	López-Guerrero, M., Ormeño-Orrillo, E., Velázquez, E., Rogel, M.A., Acosta, J.L., González, V., Martínez, J. and Martínez-Romero, E. (2012). *"Rhizobium etli* Taxonomy Revised With Novel Genomic Data and Analyses"*. Syst Appl Microbiol*. 35(6):353-358	PUBMED: #22858268
7	2012	López-Guerrero, M., Ormeño-Orrillo, E., Acosta, J.L., Mendoza-Vargas, A., Rogel, M.A., Ramírez-Romero, M.Á., Rosenblueth, M., Martínez, J. and Martínez-Romero, E. (2012). "Rhizobial Extrachromosomal Replicon Variability, Stability and Expression in Natural Niches". Plasmid. 68(3):149-158	PUBMED: #22813963
8	2012	Mavingui, P., Van, T.V., Wisniewski-Dye, F., Raquin, V., Minard, G., Tran, F.H., Voronin, D., Rouy, Z., Bustos, P., Lozano, L.F., Barbe, V. and González, V. (2012). "Whole-genome Sequence of Wolbachia Strain wAlbB, an Endosymbiont of Tiger Mosquito Vector Aedes Albopictus". J Bacteriol. 194(7):1840-1840	PUBMED: #22408242
9	2012	Tejerizo, G.T., Lozano, L.F., González, V., Bustos, P., Romero, D. and Brom, S. (2012). *"Draft Genome Sequence Of the Bean-nodulating Sinorhizobium fredii* Strain GR64"*. J Bacteriol. 194*(24):6978-6978	PUBMED: #23209231
10	2012	Wisniewski-Dyé, F., Lozano, L.F., Acosta-Cruz, E., Borland, S., Drogue, B., Prigent-Combaret, C., Rouy, Z., Barbe, V., Herrera, A.M., González, V. and Mavingui, P. (2012). *"Genome Sequence Of Azospirillum* brasilense CBG497 and Comparative Analyses Of Azospirillum Core and Accessory Genomes Provide Insight into Niche Adaptation"*. Gene*. 3(4):576-602
11	2011	Acosta, J.L., Eguiarte, L.E., Santamaria, R.I., Bustos, P., Vinuesa, P., Martínez-Romero, E., Dávila, G. and González, V. (2011). *"Genomic Lineages of Rhizobium etli* Revealed by the Extent of Nucleotide Polymorphisms and Low Recombination"*. BMC Evol Biol*. 11	PUBMED: #22004448
12	2011	Cervantes, L., Bustos, P., Girard, L., Santamaria, R.I., Dávila, G., Vinuesa, P., Romero, D. and Brom, S. (2011). *"The Conjugative Plasmid of a Bean-nodulating Sinorhizobium* fredii Strain is Assembled from Sequences of Two Rhizobium Plasmids and the Chromosome of a Sinorhizobium Strain"*. BMC Microbiol*. 11(1):149	PUBMED: #21702991
13	2011	Cervantes-Rivera, R., Pedraza-López, F., Pérez-Segura, G. and Cevallos, M.A. (2011). *"The Replication Origin of a repABC* Plasmid"*. BMC Microbiol*. 11	PUBMED: #21718544
14	2011	Landeta, C., Dávalos, A., Cevallos, M.A., Geiger, O., Brom, S. and Romero, D. (2011). *"Plasmids With a Chromosome-like Role in Rhizobia". J Bacteriol. 193*(6):1317-1326	PUBMED: #21217003
15	2011	Orduña, P., Cevallos, M.A., De León, S.P., Arvizu, A., Hernández-González, I., Mendoza-Hernández, G. and López-Vidal, Y. (2011). *"Genomic And Proteomic Analyses Of Mycobacterium* Bovis BCG Mexico 1931 Reveal a Diverse Immunogenic Repertoire against Tuberculosis Infection"*. BMC Genomics*. 12	PUBMED: #21981907
16	2011	Reyes, J., Gómez-Romero, L., Ibarra-Soria, X., Palacios-Flores, K., Arriola, L.R., Wences, A., García-Alonso, D., Boege, M., Dávila, G., Flores, M. and Palacios, R. (2011). "Context-dependent Individualization of Nucleotides and Virtual Genomic Hybridization Allow the Precise Location of Human SNPs". P Nat Acad Sci USA. 108(37):15294-15299	PUBMED: #21876154
17	2011	Villaseñor-Toledo, T., Dávalos, A., Lozano, L.F., Romero, D. and García-de los Santos, A. (2011). *"Housekeeping Genes Essential For Pantothenate Biosynthesis Are Plasmid-encoded In Rhizobium* etli and Rhizobium leguminosarum"*. BMC Microbiol*. 11	PUBMED: #21463532
18	2011	Wiesner, M., Calva, E., Fernandez-Mora, M., Cevallos, M.A., Campos, F., Zaidi, M.B. and silva, C. (2011). *"Salmonella* Typhimurium St213 is Associated with Two Types of IncA/c Plasmids Carrying Multiple Resistance Determinants"*. BMC Microbiol*. 11	PUBMED: #21223599
19	2011	Wisniewski-Dye, F., Borziak, K., Khalsa-Moyers, G., Alexandre, G., Sukharnikov, L.O., Wuichet, K., Hurst, G.B., McDonald, W.H., Robertson, J.S., Barbe, V., Calteau, A., Rouy, Z., Mangenot, S., Prigent-Combaret, C., Normand, P., Boyer, M., Siguier, P., Dessaux, Y., Elmerich, C., Condemine, G., Krishnen, G., Kennedy, I., Paterson, A.H., González, V., Mavingui, P. and Zhulin, I.B. (2011). *"Azospirillum* Genomes Reveal Transition Of Bacteria from Aquatic to Terrestrial Environments"*. Plos Genet*. 7(12)	PUBMED: #22216014
20	2010	Cervantes-Rivera, R., Romero-López, C., Berzal-Herranz, A. and Cevallos, M.A. (2010). *"Analysis of the Mechanism of Action of the Antisense RNA that Controls the Replication of the repABC* Plasmid p42d"*. J Bacteriol. 192*(13):3268-3278	PUBMED: #20435728
21	2010	González, V., Acosta, J.L., Santamaria, R.I., Bustos, P., Fernández, J.L., Hernández-González, I., Díaz-Mendez, R., Flores, M., Palacios, R., Mora, J. and Dávila, G. (2010). *"Conserved Symbiotic Plasmid Dna Sequences in the Multireplicon Pangenomic Structure of Rhizobium etli". Appl Environ Microbiol*. 76(5):1604-1614	PUBMED: #20048063
22	2010	Lozano, L.F., Hernández-González, I., Bustos, P., Santamaria, R.I., Souza, V., Young, J.P.W, Dávila, G. and González, V. (2010). *"Evolutionary Dynamics of Insertion Sequences in Relation to the Evolutionary Histories of the Chromosome and Symbiotic Plasmid Genes of Rhizobium etli* Populations"*. Appl Environ Microbiol*. 76(19):6504-6513	PUBMED: #20675442
23	2009	Castillo-Ramírez, S., Vázquez-Castellanos, J.F., González, V. and Cevallos, M.A. (2009). *"Horizontal Gene Transfer And Diverse Functional Constrains within A Common Replication-partitioning System In Alphaproteobacteria: the repABC* Operon"*. BMC Genomics*. 10	PUBMED: #19919719
24	2009	Garza-Ramos, U., Dávila, G., González, V., Alpuche-Aranda, C., López-Collada, V.R., Alcantar-Curiel, D., Newton, O. and Silva-Sánchez, J. (2009). *"The blaSHV-5 Gene Is Encoded in a Compound Transposon Duplicated in Tandem in Enterobacter Cloacae". Clin Microbiol Infec*. 15(9):878-880	PUBMED: #19519856
25	2009	Martínez-Salazar, J.M., Sandoval-Calderón, M., Guo, X.W., Castillo-Ramírez, S., Reyes-González, A., Loza-Correa, M., Rivera, J., Alvarado-Affantranger, X., Sánchez, F, González, V., Dávila, G. and Ramírez-Romero, M.Á. (2009). *"The Rhizobium etli* RpoH1 and RpoH2 Sigma Factors are Involved in Different Stress Responses"*. Microbiology-sgm. 155*:386-397	PUBMED: #19202087
26	2009	Martínez-Salazar, J.M., Salazar, E., Encarnación, S., Ramírez-Romero, M.Á. and Rivera, J. (2009). *"Role Of the Extracytoplasmic Function Sigma Factor RpoE4 in Oxidative and Osmotic Stress Responses in Rhizobium etli". J Bacteriol. 191*(13):4122-4132	PUBMED: #19376852
27	2008	Boyer, M., Haurat, J., Samain, S., Segurens, B., Gavory, F., González, V., Mavingui, P., Rohr, R., Bally, R. and Wisniewski-Dye, F. (2008). *"Bacteriophage Prevalence In the Genus Azospirillum* and Analysis of the First Genome Sequence of an Azospirillum brasilense Integrative Phage"*. Appl Environ Microbiol*. 74(3):861-874	PUBMED: #18065619
28	2008	Castillo-Ramírez, S. and González, V. (2008). "Factors Affecting The Concordance between Orthologous Gene Trees and Species Tree in Bacteria". BMC Evol Biol. 8:300	PUBMED: #18973688
29	2008	Cevallos, M.A., Cervantes-Rivera, R. and Gutierrez-Rios, R.M. (2008). *"The repABC* Plasmid Family"*. Plasmid*. 60(1):19-37	PUBMED: #18433868
30	2008	Crossman, LC., Castillo-Ramírez, S., McAnnula, C., Lozano, L., Vernikos, GS., Acosta, JL., Ghazoui, ZF., Hernández-González, I., Meakin, G., Walker, AW., Hynes, MF., Young, JP., Downie, JA., Romero, D., Johnston, AW., Dávila, G., Parkhill, J. and González, V. (2008). "A Common Genomic Framework for a Diverse Assembly of Plasmids in the Symbiotic Nitrogen Fixing Bacteria". Plos One. 3(7):e2567	PUBMED: #18596979
31	2008	García-de los Santos, A., López, E., Cubillas, C.A., Noel, K.D., Brom, S. and Romero, D. (2008). *"Requirement of a Plasmid-encoded Catalase for Survival of Rhizobium etli* CFN42 in a Polyphenol-rich Environment"*. Appl Environ Microbiol*. 74(8):2398-2403	PUBMED: #18310436
32	2008	Sepúlveda, E., Perez-Mendoza, D., Ramírez-Romero, M.Á., Soto, M.J., López-Lara, I.M., Geiger, O., Sanjuan, J., Brom, S. and Romero, D. (2008). *"Transcriptional Interference And Repression Modulate the Conjugative Ability of the Symbiotic Plasmid of Rhizobium etli". J Bacteriol. 190*(12):4189-4197	PUBMED: #18424522
33	2008	Suárez, R., Wong-Villarreal, A., Ramirez, M., Barraza, A., Orozco, M.D., Cevallos, M.A., Lara-Flores, M., Hernández, G. and Iturriaga, G. (2008). *"Improvement Of Drought Tolerance and Grain Yield in Common Bean by Overexpressing Trehalose-6-phosphate Synthase in Rhizobia". Mol Plant Microbe Interactions*. 21(7):958-966	PUBMED: #18533836
34	2007	Flores, M., Morales, L., Gonzaga-Jáuregui, C., Domínguez-Vidaña, R., Zepeda-Mendoza, C.J., Yáñez, O., Gutierrez-Arcelus, M., Lemus, T., Valle-García, D., Ávila, M.C., Blanco, D., Medina-Ruiz, S., Meza-Sosa, K.F., Ayala, E., García-Alonso, D., Bustos, P., González, V., Girard, L., Tusie-Luna, T., Dávila, G. and Palacios, R. (2007). "Recurrent DNA Inversion Rearrangements in the Human Genome". P Nat Acad Sci USA. 104(15):6099-6106	PUBMED: #17389356
35	2007	Granados-Baeza, M.J., Gómez-Hernández, N., Mora, Y., Delgado, M.J., Romero, D. and Girard, L. (2007). *"Novel Reiterated Fnr-type Proteins Control the Production of the Symbiotic Terminal Oxidase Cbb(3) in Rhizobium etli* CFN42"*. Mol Plant Microbe Interactions*. 20(10):1241-1249	PUBMED: #17918626
36	2007	Guo, X.W., Castillo-Ramírez, S., González, V., Bustos, P., Fernández, J.L., Santamaria, R.I., Arellano, J., Cevallos, M.A. and Dávila, G. (2007). *"Rapid Evolutionary Change of Common Bean (Phaseolus vulgaris* L) Plastome, and the Genomic Diversification of Legume Chloroplasts"*. BMC Genomics*. 8	PUBMED: #17623083
37	2007	Guo, X.W., Flores, M., Morales, L., García-Alonso, D., Bustos, P., González, V., Palacios, R. and Dávila, G. (2007). *"Dna Diversification in Two Sinorhizobium* Species"*. J Bacteriol. 189*(17):6474-6476	PUBMED: #17601787
38	2007	Pinero, S., Rivera, J., Romero, D., Cevallos, M.A., Martínez, A., Bolivar, F. and Gosset, G. (2007). *"Tyrosinase From Rhizobium etli* is Involved in Nodulation Efficiency and Symbiosis-associated Stress Resistance"*. J Mol Microbiol Biotechnol*. 13(1-3):35-44	PUBMED: #17693711
39	2006	Aguilar-Diaz, H., Bobes, R.J., Carrero, J.C., Camacho-Carranza, R., Cervantes, C., Cevallos, M.A., Dávila, G., Rodriguez-Dorantes, M., Escobedo, G., Fernández, J.L., Fragoso, G., Gaytan, P., Garciarubio, A., González, V., Gonzalez, L., Jose, M.V., Jimenez, L., Laclette, J.P., Landa, A., Larralde, C., Morales-Montor, J., Morett, E., Ostoa-Saloma, P., Sciutto, E., Santamaria, R.I., Soberon, X., de la Torre, P., Valdes, V. and Yañez, J. (2006). *"The Genome Project of Taenia solium". Parasitol Int*. 55:S127-S130	PUBMED: #16337432
40	2006	Alvarez, R.G., de Mendoza, A.R., Escobedo, D.E., Felix, G.C., Sanchez, I.R., González, V., Dávila, G., Cao, Q., de Jong, P., Fu, Y.X. and Saldana, H.A.B. (2006). "Growth Hormone Locus Expands and Diverges after the Separation of New and Old World Monkeys". Gene. 380(1):38-45	PUBMED: #16872758
41	2006	González, V., Santamaria, R.I., Bustos, P., Hernández-González, I., Medrano-Soto, A., Moreno-Hagelsieb, G., Janga, S.C., Ramírez-Romero, M.Á., Jiménez-Jacinto, V., Collado-Vides, J. and Dávila, G. (2006). *"The Partitioned Rhizobium etli* Genome: Genetic and Metabolic Redundancy in Seven Interacting Replicons"*. P Nat Acad Sci USA. 103*(10):3834-3839	PUBMED: #16505379
42	2006	Hernández-Lucas, I., Ramírez-Trujillo, J.A., Gaitan, M.A., Guo, X.W., Flores, M., Martínez-Romero, E., Perez-Rueda, E. and Mavingui, P. (2006). *"Isolation And Characterization of Functional Insertion Sequences of Rhizobia". FEMS Microbiol Lett. 261*(1):25-31	PUBMED: #16842354
43	2006	Ramírez-Romero, M.Á., Masulis, I., Cevallos, M.A., González, V. and Dávila, G. (2006). *"The Rhizobium etli* Sigma(70) (sigA) Factor Recognizes a Lax Consensus Promoter"*. Nucl Acid Res*. 34(5):1470-1480	PUBMED: #16528104
44	2006	Velasco-Garcia, R., Villalobos-López, M.A., Ramírez-Romero, M.Á., Mujica-Jimenez, C., Iturriaga, G. and Munoz-Clares, R.A. (2006). *"Betaine Aldehyde Dehydrogenase From Pseudomonas Aeruginosa: Cloning, Over-expression in Escherichia coli, and Regulation by Choline and Salt". Arch Microbiol. 185*(1):14-22	PUBMED: #16315011
45	2006	Wang, E.T., Tan, Z.Y., Guo, X.W., Rodriguez-Duran, R., Boll, G. and Martínez-Romero, E. (2006). *"Diverse Endophytic Bacteria Isolated From a Leguminous Tree Conzattia multiflora* Grown in Mexico"*. Arch Microbiol. 186*(4):251-259	PUBMED: #16862424
46	2005	Dávila, S., Pinero, D., Bustos, P., Cevallos, M.A. and Dávila, G. (2005). *"The Mitochondrial Genome Sequence of the Scorpion Centruroides limpidus* (karsch 1879) (chelicerata Arachnida)"*. Gene. 360*(2):92-102	PUBMED: #16183216
47	2005	Flores, M., Morales, L., Ávila, A., González, V., Bustos, P., García-Alonso, D., Mora, Y., Guo, X.W., Collado-Vides, J., Pinero, D., Dávila, G., Mora, J. and Palacios, R. (2005). *"Diversification of DNA Sequences in the Symbiotic Genome of Rhizobium etli". J Bacteriol. 187*(21):7185-7192	PUBMED: #16237002
48	2005	Izquierdo, J., Venkova-Canova, T., Ramírez-Romero, M.Á., Téllez-Sosa, J., Hernández-Lucas, I., Sanjuan, J. and Cevallos, M.A. (2005). "An Antisense RNA Plays a Central Role in the Replication Control of a RepC Plasmid". Plasmid. 54(3):259-277	PUBMED: #16005966
49	2004	Brom, S., Girard, L., Tun-Garrido, C., García-de los Santos, A., Bustos, P., González, V. and Romero, D. (2004). *"Transfer of The Symbiotic Plasmid of Rhizobium etli* CFN42 Requires Cointegration with p42a, Which may be Mediated by Site-Specific Recombination"*. J Bacteriol. 186*(22):7538-7548	PUBMED: #15516565
50	2004	Soberón, N., Venkova-Canova, T., Ramírez-Romero, M.Á., Téllez-Sosa, J. and Cevallos, M.A. (2004). *"Incompatibility And the Partitioning Site of the repABC* Basic Replicon of the Symbiotic Plasmid from Rhizobium etli"*. Plasmid*. 51(3):203-216	PUBMED: #15109827
51	2004	Venkova-Canova, T., Soberón, N., Ramírez-Romero, M.Á. and Cevallos, M.A. (2004). *"Two Discrete Elements Are Required for the Replication of a repABC* Plasmid: an Antisense RNA and a Stem-loop Structure"*. Mol Microbiol*. 54(5):1431-1444	PUBMED: #15554980
52	2003	Desnoues, N., Lin, M., Guo, X.W., Ma, L.Y., Carreno-Lopez, R. and Elmerich, C. (2003). *"Nitrogen Fixation Genetics And Regulation in a Pseudomonas Stutzeri* Strain Associated with Rice"*. Microbiology-sgm. 149*:2251-2262	PUBMED: #12904565
53	2003	González, V., Bustos, P., Ramírez-Romero, M.Á., Medrano-Soto, A., Salgado, H., Hernández-González, I., Hernandez-Celis, J.C., Quintero, V., Moreno-Hagelsieb, G., Girard, L., Rodríguez, O., Flores, M., Cevallos, M.A., Collado-Vides, J., Romero, D. and Dávila, G. (2003). *"The Mosaic Structure of the Symbiotic Plasmid of Rhizobium etli* CFN42 and Its Relation to other Symbiotic Genome Compartments"*. Genome Biol*. 4(6)	PUBMED: #12801410
54	2003	Guo, X.W., Flores, M., Mavingui, P., Fuentes, S.I., Hernández, G., Dávila, G. and Palacios, R. (2003). *"Natural Genomic Design In Sinorhizobium meliloti* Novel Genomic Architectures"*. Genome Res*. 13(8):1810-1817	PUBMED: #12902376
55	2003	Jahn, O.J., Dávila, G., Romero, D. and Noel, K.D. (2003). *"Bacs: an Abundant Bacteroid Protein in Rhizobium etli* Whose Expression Ex Planta Requires nifA"*. Mol Plant Microbe Interactions*. 16(1):65-73	PUBMED: #12580283
56	2003	Tun-Garrido, C., Bustos, P., González, V. and Brom, S. (2003). *"Conjugative Transfer of p42a from Rhizobium etli* CFN42, Which is Required for Mobilization of the Symbiotic Plasmid, is Regulated by Quorum Sensing"*. J Bacteriol. 185*(5):1681-1692	PUBMED: #12591886
57	2002	Cevallos, M.A., Porta, H., Izquierdo, J., Tun-Garrido, C., García-de los Santos, A., Dávila, G. and Brom, S. (2002). *"Rhizobium etli* Cfn42 Contains At Least Three Plasmids of the repABC Family: a Structural and Evolutionary Analysis"*. Plasmid*. 48(2):104-116	PUBMED: #12383728
58	2002	Mavingui, P., Flores, M., Guo, X.W., Dávila, G., Perret, X., Broughton, W.J. and Palacios, R. (2002). *"Dynamics Of Genome Architecture In Rhizobium* sp. Strain NGR234"*. J Bacteriol. 184*(1):171-176	PUBMED: #11741857
59	2002	Quintero, V., Cevallos, M.A. and Dávila, G. (2002). *"A Site-Specific Recombinase (rinq) Is Required to Exert Incompatibility towards the Symbiotic Plasmid of Rhizobium etli". Mol Microbiol*. 46(4):1023-1032	PUBMED: #12421308
60	2002	Téllez-Sosa, J., Soberón, N., Vega-Segura, A., Torres-Marquez, M.E. and Cevallos, M.A. (2002). *"The Rhizobium etli* cyaC Product: Characterization of a Novel Adenylate Cyclase Class"*. J Bacteriol. 184*(13):3560-3568	PUBMED: #12057950
61	2001	Ramírez-Romero, M.Á., Téllez-Sosa, J., Barrios, H., Pérez-Oseguera, A., Rosas, V. and Cevallos, M.A. (2001). *"Repa Negatively Autoregulates the Transcription of the repABC* Operon of the Rhizobium etli Symbiotic Plasmid Basic Replicon"*. Mol Microbiol*. 42(1):195-204	PUBMED: #11679078
62	2000	Flores, M., Mavingui, P., Perret, X., Broughton, W.J., Romero, D., Hernández, G., Dávila, G. and Palacios, R. (2000). *"Prediction, Identification, And Artificial Selection Of DNA Rearrangements in Rhizobium: toward a Natural Genomic Design". P Nat Acad Sci USA*. 97(16):9138-9143	PUBMED: #10922070
63	2000	Ramírez-Romero, M.Á., Soberón, N., Pérez-Oseguera, A., Téllez-Sosa, J. and Cevallos, M.A. (2000). *"Structural Elements Required For Replication and Incompatibility of the Rhizobium etli* Symbiotic Plasmid"*. J Bacteriol. 182*(11):3117-3124	PUBMED: #10809690
64	1999	Mandon, K., Michel-Reydellet, N., Encarnación, S., Kaminski, P.A., Leija, A., Cevallos, M.A., Elmerich, C. and Mora, J. (1999). *"Poly-beta-hydroxybutyrate Turnover In Azorhizobium caulinodans* is Required for Growth and Affects nifA Expression"*. J Bacteriol. 180*(19):5070-5076	PUBMED: #9748438
65	1999	Wang, E.T., Rogel, M.A., García-de los Santos, A., Martínez, J., Cevallos, M.A. and Martínez-Romero, E. (1999). *"Rhizobium etli* Bv. Mimosae, A Novel Biovar Isolated from Mimosa affinis"*. Int J Syst Bact*. 49:1479-1491	PUBMED: #10555329
66	1998	Flores, M., Mavingui, P., Girard, L., Perret, X., Broughton, W.J., Martínez-Romero, E., Dávila, G. and Palacios, R. (1998). *"Three Replicons Of Rhizobium* Sp. Strain NGR234 Harbor Symbiotic Gene Sequences"*. J Bacteriol. 180*(22):6052-6053	PUBMED: #9811668
67	1997	AguilarGaytan, R., Cerbon, M.A., Cevallos, M.A., Lizano, M. and Huberman, A. (1997). *"Sequence Of a cDNA Encoding the Molt-inhibiting Hormone from the Mexican Crayfish Procambarus bouvieri* (crustacea, Decapoda)"*. Asia-pac J Mol Biol Biotech*. 5(1):51-55
68	1997	Barrera, L.L., Trujillo, M.E., Goodfellow, M., García, F.J., Hernández-Lucas, I., Dávila, G., vanBerkum, P. and Martínez-Romero, E. (1997). *"Biodiversity Of Bradyrhizobia Nodulating Lupinus* spp."*. Int J Syst Bact*. 47(4):1086-1091	PUBMED: #9336911
69	1997	Calderón, J., Olvera, L., Martínez, L.M. and Dávila, G. (1997). *"A Neurospora crassa* Mutant Altered in the Regulation of L-amino Acid Oxidase"*. Microbiology-uk. 143*:1969-1974	PUBMED: #9202472
70	1997	Dunn, M.F., Araíza, G., Cevallos, M.A. and Mora, J. (1997). *"Regulation Of Pyruvate Carboxylase in Rhizobium etli". FEMS Microbiol Lett. 157*(2):301-306	PUBMED: #9435112
71	1997	Ramírez-Romero, M.Á., Bustos, P., Girard, L., Rodríguez, O., Cevallos, M.A. and Dávila, G. (1997). *"Sequence, Localization And Characteristics of the Replicator Region of the Symbiotic Plasmid of Rhizobium etli". Microbiology-uk. 143*:2825-2831	PUBMED: #9274036
72	1996	Cevallos, M.A., Encarnación, S., Leija, A., Mora, Y. and Mora, J. (1996). *"Genetic And Physiological Characterization of a Rhizobium etli* Mutant Strain Unable to Synthesize Poly-beta-hydroxybutyrate"*. J Bacteriol. 178*(6):1646-1654	PUBMED: #8626293
73	1996	De La Vega, F.M., Galindo, J.M., Old, L.G. and Guarneros, G. (1996). *"Microbial Genes Homologous To the Peptidyl-tRNA Hydrolase-encoding Gene of Escherichia coli". Gene. 169*(1):97-100	PUBMED: #8635758
74	1996	Girard, L., Valderrama, B., Palacios, R., Romero, D. and Dávila, G. (1996). *"Transcriptional Activity of the Symbiotic Plasmid of Rhizobium etli* is Affected by Different Environmental Conditions"*. Microbiology-uk. 142*:2847-2856
75	1995	Romero, D., Martínez-Salazar, J.M., Girard, L., Brom, S., Dávila, G., Palacios, R., Flores, M. and Rodríguez, C. (1995). *"Discrete Amplifiable Regions (Amplicons) In The Symbiotic Plasmid of Rhizobium etli* CFN42"*. J Bacteriol. 177*(4):973-980	PUBMED: #7860608
76	1993	Flores, M., Brom, S., Stepkowsky, T., Girard, L., Dávila, G., Romero, D. and Palacios, R. (1993). *"Gene Amplification In Rhizobium* Identification And in vivo Cloning Of Discrete Amplifiable Dna Regions (Amplicons) From Rhizobium leguminosarum Biovar phaseoli"*. P Nat Acad Sci USA*. 90(11):4932-4936	PUBMED: #8506337
77	1992	Brom, S., García-de los Santos, A., Stepkowsky, T., Flores, M., Dávila, G., Romero, D. and Palacios, R. (1992). *"Different Plasmids Of Rhizobium* leguminosarum Bv phaseoli Are Required for Optimal Symbiotic Performance"*. J Bacteriol. 174*(16):5183-5189	PUBMED: #1644746
78	1991	Brom, S., García-de los Santos, A., Girard, L., Dávila, G., Palacios, R. and Romero, D. (1991). *"High-frequency Rearrangements In Rhizobium* leguminosarum Bv. phaseoli Plasmids"*. J Bacteriol. 173*(3):1344-1346	PUBMED: #1991727
79	1991	Girard, L., Flores, M., Brom, S., Romero, D., Palacios, R. and Dávila, G. (1991). *"Structural Complexity Of The Symbiotic Plasmid Of Rhizobium* leguminosarum bv phaseoli"*. J Bacteriol. 173*(8):2411-2419	PUBMED: #2013564
80	1991	Martínez-Salazar, J.M., Romero, D., Girard, L. and Dávila, G. (1991). *"Molecular Cloning and Characterization of the recA* Gene of Rhizobium phaseoli and Construction of recA Mutants"*. J Bacteriol. 173*(10):3035-3040	PUBMED: #2022610
81	1991	Romero, D., Brom, S., Martínez-Salazar, J.M., Girard, L., Palacios, R. and Dávila, G. (1991). *"Amplification And Deletion of A nod-nif* Region in the Symbiotic Plasmid of Rhizobium phaseoli"*. J Bacteriol. 173*(8):2435-2441	PUBMED: #2013567
82	1990	Lara-Ochoa, F. and Bustos, P. (1990). "A Model for Aggregation-dispersion Dynamics of a Population". Biosystems. 24(3):215-222	PUBMED: #2127375
83	1990	Lara-Ochoa, F. and Bustos, P. (1990). "Density Dependent Diffusional Model of an Infective Population". Biosystems. 24(3):223-238	PUBMED: #2073542
84	1989	Cevallos, M.A., Vázquez, M., Dávalos, A., Espín Ocampo, E.G., Sepúlveda, J. and Quinto, C. (1989). *"Characterization Of Rhizobium* phaseoli Sym Plasmid Regions Involved In Nodule Morphogenesis and Host-range Specificity"*. Mol Microbiol*. 3(7):879-889	PUBMED: #2552255
85	1988	Brom, S., Martínez-Romero, E., Dávila, G. and Palacios, R. (1988). *"Narrow-and Broad-host-range Symbiotic Plasmids Of Rhizobium* spp. Strains that Nodulate Phaseolus vulgaris"*. Appl Environ Microbiol*. 54(5):1280-1283	PUBMED: #16347637
86	1988	Flores, M., González, V., Pardo, M.A., Leija, A., Martínez-Romero, E., Romero, D., Piñero, D., Dávila, G. and Palacios, R. (1988). *"Genomic Instability In Rhizobium* phaseoli"*. J Bacteriol. 170*(3):1191-1196	PUBMED: #3343217
87	1988	Martínez-Romero, E., Flores, M., Brom, S., Romero, D., Dávila, G. and Palacios, R. (1988). *"Rhizobium* phaseoli: A Molecular Genetics View"*. Plant Soil. 108*(1):179-184
88	1988	Romero, D., Singleton, P., Segovia, L., Morett, E., Bohlool, B.B., Palacios, R. and Dávila, G. (1988). *"Effect Of Naturally Occurring Nif Reiterations on Symbiotic Effectiveness in Rhizobium* phaseoli"*. Appl Environ Microbiol*. 54(3):848-850	PUBMED: #16347593
89	1987	Flores, M., González, V., Brom, S., Martínez-Romero, E., Piñero, D., Romero, D., Dávila, G. and Palacios, R. (1987). *"Reiterated Dna Sequences In Rhizobium* and Agrobacterium spp."*. J Bacteriol. 169*(12):5782-5788	PUBMED: #3450286
90	1986	Romero, D. and Dávila, G. (1986). *"Genetic And Biochemical Identification of the Glutamate Synthase Structural Gene in Neurospora crassa". J Bacteriol. 167*(3):1043-1047	PUBMED: #2943726
91	1985	González, A., Dávila, G. and Calva, E. (1985). *"Cloning Of A DNA Sequence that Complements Glutamine Auxotrophy in saccharomyces* cerevisiae"*. Gene*. 36(1-2):123-129	PUBMED: #2866146
92	1985	Martínez-Romero, E., Pardo, M.A., Cevallos, M.A. and Palacios, R. (1985). *"Reiteration of Nitrogen Fixation Gene Sequences and Specificity of Rhizobium* in Nodulation and Nitrogen Fixation in Phaseolus vulgaris"*. J. Gen. Microbiol.. 131*(JUL):1779-1786
93	1985	Quinto, C., de la Vega, H., Flores, M., Leemans, J., Cevallos, M.A., Pardo, M.A., Azpiroz, R., Girard, L., Calva, E. and Palacios, R. (1985). *"Nitrogenase Reductase: A Functional Multigene Family In Rhizobium* phaseoli"*. P Nat Acad Sci USA*. 82(4):1170-1174	PUBMED: #16593543
94	1984	Noel, K.D., Sánchez, A., Fernández, L., Leemans, J. and Cevallos, M.A. (1984). *"Rhizobium* phaseoli Symbiotic Mutants With Transposon Tn5 Insertions"*. J Bacteriol. 158*(1):148-155	PUBMED: #6325385
95	1983	Dávila, G., Brom, S., Mora, Y., Palacios, R. and Mora, J. (1983). *"Genetic and Biochemical Characterization of Glutamine Synthetase from Neurospora crassa* Glutamine Auxotrophs and their Revertants"*. J Bacteriol. 156*(3):993-1000	PUBMED: #6139363

Programa de Genómica Evolutiva

Responsable de Programa: Guillermo Dávila, PhD

Estudiamos la simbiosis de la fijación del nitrógeno utilizando la interacción entre el Rhizobium etli y la planta de frijol común como modelo. El objetivo de nuestra investigación es comprender los procesos evolutivos moleculares que llevan a la simbiosis y contribuir al entendimiento de la diversidad del R. etli y el Phaseolus vulgaris. También estudiamos los mecanismos de réplica entre los plásmidos de Rhizobium, así como el papel que juegan los diferentes factores sigma y los reguladores en la expresión del gen de Rhizobium. Nuestros enfoques consisten en el análisis de las secuencias genómicas de ADN con herramientas de bioinformática, genética y biología molecular, dentro del contexto de la teoría de la evolución. Este programa es pionero en ciencias genómicas en México. El laboratorio produjo la primera secuencia genómica de un organismo, el R.etli, que se ha hecho en nuestro país.

Líneas de investigación actuales:
1. Microevolución de R. etli y diversidad de P. vulgaris.
2. Análisis molecular de sistemas de réplica de R. etli.
3. Caracterización funcional de factores sigma y regulación en Rhizobium.

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Functional characterization of regulatory networks in Rhizobium etli.

The general goal of this research line is to contribute to the understanding of the regulatory networks that control genetic expression in R. etli in response to different external signals during free life and symbiosis. An integrative global regulatory model requires the identification of target genes for a certain transcriptional factor and the characterization of the molecular mechanisms that participate in its expression. Focused in new ORFs identified in the R. etli complete genome sequence, the objectives of my research include:

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Transcriptional Regulation of the Heat Shock Regulon in Rhizobium etli.

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Identification of Promoters in the Rhizobium etli Genome.

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Evolution of Cell Organelles Genomes

In eucaryotic cells there are two important organelles, mitochondria and plastids, which produce the energy and synthesize substances for cell metabolism respectively. These organelles are compartmentalized by two layers of membrane, have multiple copies of its genome, and are inherited in non-Mendelian fashion. It is now accepted that these organelles were originated from ancient endosymbionts of eukaryotic cell. Therefore, the genetic information from organelle genomes can provide an independent view of the phylogeny of their host organisms.

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Evolutionary Coherence among Orthologs of the Order Rhizobiales.

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Evolution of Insertion Sequences in Rhizobium

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Microevolutionary Genomics of Rhizobium etli .

Earlier genetic population studies pointed out that R. etli has high diversity levels as measured by multilocus enzyme electrophoresis. There are also differences in plasmid number and size. Recently, we obtain the complete genome sequence of R. etli CFN42. This strain contains six large plasmids and a circular chromosome that together account for 6, 530, 234 bp. In this context, we want to evaluate the levels of molecular variation among strains of R. etli, to answer the following questions: