Andres Moya

Summary

Affiliation: University of Valencia
Country: Spain

Publications

  1. pmc Metabolic networks of Sodalis glossinidius: a systems biology approach to reductive evolution
    Eugeni Belda
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, Valencia, Spain
    PLoS ONE 7:e30652. 2012
  2. pmc Metatranscriptomic approach to analyze the functional human gut microbiota
    María José Gosalbes
    Unidad Mixta de Investigación en Genómica y Salud Centro Superior Investigación en Salud Pública Generalitat Valenciana Instituto Cavanilles de Biodiversidad y Biología Evolutiva Universitat de València, Valencia, Spain
    PLoS ONE 6:e17447. 2011
  3. pmc Evolutionary convergence and nitrogen metabolism in Blattabacterium strain Bge, primary endosymbiont of the cockroach Blattella germanica
    Maria J López-Sánchez
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, Valencia, Spain
    PLoS Genet 5:e1000721. 2009
  4. pmc Study of the viral and microbial communities associated with Crohn's disease: a metagenomic approach
    Vicente Perez-Brocal
    1 Área de Genómica y Salud, Centro Superior de Investigación en Salud Pública Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana CSISP FISABIO, Valencia, Spain 2 CIBER Epidemiología y Salud Pública CIBERESP, Madrid, Spain 3 Departamento de Genética, Cavanilles Institute on Biodiversity and Evolutionary Biology, University of Valencia, Valencia, Spain
    Clin Transl Gastroenterol 4:e36. 2013
  5. ncbi request reprint Comparison of different assembly and annotation tools on analysis of simulated viral metagenomic communities in the gut
    Jorge F Vázquez-Castellanos
    Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valencia FISABIO Salud Pública, Avenida de Cataluña 21, 46020 Valencia, Spain
    BMC Genomics 15:37. 2014
  6. pmc Large-scale gene discovery in the pea aphid Acyrthosiphon pisum (Hemiptera)
    Beatriz Sabater-Muñoz
    INRA Rennes, UMR INRA Agrocampus BiO3P, BP 35327, F 35653 Le Rheu cedex, France
    Genome Biol 7:R21. 2006
  7. pmc Immunity and other defenses in pea aphids, Acyrthosiphon pisum
    Nicole M Gerardo
    Department of Biology, Emory University, O Wayne Rollins Research Center, 1510 E, Clifton Road NE, Atlanta, GA 30322, USA
    Genome Biol 11:R21. 2010
  8. pmc Analysis of and function predictions for previously conserved hypothetical or putative proteins in Blochmannia floridanus
    Peter Gaudermann
    Dept of Bioinformatics, Biocenter University of Würzburg, 97074 Wurzburg, Germany
    BMC Microbiol 6:1. 2006
  9. pmc Legionella pneumophila pangenome reveals strain-specific virulence factors
    Giuseppe D'Auria
    CIBER en Epidemiología y Salud Pública, Barcelona, Spain
    BMC Genomics 11:181. 2010
  10. pmc Estimating the extent of horizontal gene transfer in metagenomic sequences
    Javier Tamames
    Instituto Cavanilles de Biodiversidad y Biologia Evolutiva, Universidad de Valencia, Poligono la Coma s n, 46980 Paterna Valencia, Spain
    BMC Genomics 9:136. 2008

Detail Information

Publications128 found, 100 shown here

  1. pmc Metabolic networks of Sodalis glossinidius: a systems biology approach to reductive evolution
    Eugeni Belda
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, Valencia, Spain
    PLoS ONE 7:e30652. 2012
    ..In the present study, genome reduction is studied from a systems biology perspective through the reconstruction and functional analysis of genome-scale metabolic networks of S. glossinidius...
  2. pmc Metatranscriptomic approach to analyze the functional human gut microbiota
    María José Gosalbes
    Unidad Mixta de Investigación en Genómica y Salud Centro Superior Investigación en Salud Pública Generalitat Valenciana Instituto Cavanilles de Biodiversidad y Biología Evolutiva Universitat de València, Valencia, Spain
    PLoS ONE 6:e17447. 2011
    ..In this RNA-based survey, we also detected small RNAs, which are important regulatory elements in prokaryotic physiology and pathogenicity...
  3. pmc Evolutionary convergence and nitrogen metabolism in Blattabacterium strain Bge, primary endosymbiont of the cockroach Blattella germanica
    Maria J López-Sánchez
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, Valencia, Spain
    PLoS Genet 5:e1000721. 2009
    ..Here, we explain the metabolic reasons underlying the enigmatic return of cockroaches to the ancestral ammonotelic state...
  4. pmc Study of the viral and microbial communities associated with Crohn's disease: a metagenomic approach
    Vicente Perez-Brocal
    1 Área de Genómica y Salud, Centro Superior de Investigación en Salud Pública Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana CSISP FISABIO, Valencia, Spain 2 CIBER Epidemiología y Salud Pública CIBERESP, Madrid, Spain 3 Departamento de Genética, Cavanilles Institute on Biodiversity and Evolutionary Biology, University of Valencia, Valencia, Spain
    Clin Transl Gastroenterol 4:e36. 2013
    ..This study aimed to analyze and compare the diversity and structure of the viral and microbial communities in fecal samples from a control group of healthy volunteers and from patients affected by Crohn's disease (CD)...
  5. ncbi request reprint Comparison of different assembly and annotation tools on analysis of simulated viral metagenomic communities in the gut
    Jorge F Vázquez-Castellanos
    Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valencia FISABIO Salud Pública, Avenida de Cataluña 21, 46020 Valencia, Spain
    BMC Genomics 15:37. 2014
    ..This study compares the performance of different available assemblers and taxonomic annotation software using simulated viral-metagenomic data...
  6. pmc Large-scale gene discovery in the pea aphid Acyrthosiphon pisum (Hemiptera)
    Beatriz Sabater-Muñoz
    INRA Rennes, UMR INRA Agrocampus BiO3P, BP 35327, F 35653 Le Rheu cedex, France
    Genome Biol 7:R21. 2006
    ..This project is the first to address the genetics of the Hemiptera and of a hemimetabolous insect...
  7. pmc Immunity and other defenses in pea aphids, Acyrthosiphon pisum
    Nicole M Gerardo
    Department of Biology, Emory University, O Wayne Rollins Research Center, 1510 E, Clifton Road NE, Atlanta, GA 30322, USA
    Genome Biol 11:R21. 2010
    ....
  8. pmc Analysis of and function predictions for previously conserved hypothetical or putative proteins in Blochmannia floridanus
    Peter Gaudermann
    Dept of Bioinformatics, Biocenter University of Würzburg, 97074 Wurzburg, Germany
    BMC Microbiol 6:1. 2006
    ..Blochmannia floridanus proteins and metabolites are difficult to study due to its endosymbiontic life style; however, its complete genome sequence became recently available...
  9. pmc Legionella pneumophila pangenome reveals strain-specific virulence factors
    Giuseppe D'Auria
    CIBER en Epidemiología y Salud Pública, Barcelona, Spain
    BMC Genomics 11:181. 2010
    ..The strain "Alcoy 2300/99" is a particularly persistent and recurrent strain that was isolated during one of the most significant outbreaks between the years 1999-2000...
  10. pmc Estimating the extent of horizontal gene transfer in metagenomic sequences
    Javier Tamames
    Instituto Cavanilles de Biodiversidad y Biologia Evolutiva, Universidad de Valencia, Poligono la Coma s n, 46980 Paterna Valencia, Spain
    BMC Genomics 9:136. 2008
    ..However, the methods that have been commonly used for the study of HGT are not suitable for metagenomic samples. Therefore it is important to develop new methods or to adapt existing ones to be used with metagenomic sequences...
  11. pmc Tempo and mode of early gene loss in endosymbiotic bacteria from insects
    F Delmotte
    UMR Santé Végétale INRA ENITAB, INRA BP81, 33883 Villenave d Ornon Cedex, France
    BMC Evol Biol 6:56. 2006
    ..coli (i.e. codon adaptive index, or CAI), and also estimates of evolutionary rates (Ka) between pairs of orthologs either in free-living bacteria or in pairs of symbionts...
  12. pmc Phylogenetic signal and functional categories in Proteobacteria genomes
    Iñaki Comas
    Instituto Cavanilles de Biodiversidad y Biologia Evolutiva, Universidad de Valencia, Apartado Oficial 22085, Valencia E 46071, Spain
    BMC Evol Biol 7:S7. 2007
    ..In this report we have addressed the impact of factors like the universal distribution of the genes, their essentiality or their functional role in the cell on the inference of vertical signal through phylogenomic methods...
  13. pmc Identification of the weevil immune genes and their expression in the bacteriome tissue
    Caroline Anselme
    Universite de Lyon, INRA, INSA Lyon, IFR 41, UMR203 BF2I, Biologie Fonctionnelle Insectes et Interactions, F 69621 Villeurbanne, France
    BMC Biol 6:43. 2008
    ....
  14. pmc JANE: efficient mapping of prokaryotic ESTs and variable length sequence reads on related template genomes
    Chunguang Liang
    Department of Bioinformatics, Biocenter, University of Wurzburg, Am Hubland, D 97074 Wurzburg, Germany
    BMC Bioinformatics 10:391. 2009
    ..Use cases include (i) transcriptome studies or (ii) single cell sequencing of bacteria. Without suitable software their further analysis and mapping would have to await finalization of the corresponding genome...
  15. pmc The evolution of RNA viruses: A population genetics view
    A Moya
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva and Departament de Genètica, Universitat de Valencia, Apartat 2085, 46071 Valencia, Spain
    Proc Natl Acad Sci U S A 97:6967-73. 2000
    ..Finally, in an integrative attempt, we discuss pros and cons of the quasispecies theory compared with classic population genetics models for haploid organisms to explain the evolution of RNA viruses...
  16. doi request reprint The evolutionary history of symbiotic associations among bacteria and their animal hosts: a model
    A Moya
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva and Departament de Genètica, Universitat de Valencia, Valencia
    Clin Microbiol Infect 15:11-3. 2009
    ..For this purpose, we propose to sequence the complete genome of SOPE, the primary endosymbiont of the rice weevil...
  17. doi request reprint Toward minimal bacterial cells: evolution vs. design
    Andres Moya
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, Valencia, Spain
    FEMS Microbiol Rev 33:225-35. 2009
    ....
  18. doi request reprint Learning how to live together: genomic insights into prokaryote-animal symbioses
    Andres Moya
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, Apartado de correos 22085 46071 València and CIBER de Epidemiología y Salud Pública, Spain
    Nat Rev Genet 9:218-29. 2008
    ....
  19. ncbi request reprint Comparative molecular evolution of primary (Buchnera) and secondary symbionts of aphids based on two protein-coding genes
    Andres Moya
    Instituto Cavanilles de Biodiversidad y Biología Evolutiva and Departamento de Genética, Universitat de Valencia, P O Box 2085, E 46071 Valencia, Spain
    J Mol Evol 55:127-37. 2002
    ..These results give support to the hypothesis that they are symbionts at different stages of the symbiotic accommodation to the host...
  20. ncbi request reprint The population genetics and evolutionary epidemiology of RNA viruses
    Andres Moya
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, Apartado Postal 22085, 46071 Valencia, Spain
    Nat Rev Microbiol 2:279-88. 2004
  21. ncbi request reprint Hepatitis C virus and the controversial role of the interferon sensitivity determining region in the response to interferon treatment
    Manuela Torres-Puente
    Instituto Cavanilles de Biodiversidad y Biología Evolutiva and Departamento de Genética, Universidad de Valencia, Valencia, Spain
    J Med Virol 80:247-53. 2008
    ..More complex interactions, including the ISDR or not, are likely to exist and govern the HCV response to interferon treatment...
  22. ncbi request reprint Contribution of insertions and deletions to the variability of hepatitis C virus populations
    Manuela Torres-Puente
    Instituto Cavanilles de Biodiversidad y Biología Evolutiva and Departamento de Genética, Universidad de Valencia, Spain
    J Gen Virol 88:2198-203. 2007
    ..Moreover, their frequency distributions between different time samples reflect the quasispecies dynamics of HCV populations. Deletions seem to be subject to negative selection...
  23. ncbi request reprint A small microbial genome: the end of a long symbiotic relationship?
    Vicente Perez-Brocal
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, Apartado Postal 22085, 46071 Valencia, Spain
    Science 314:312-3. 2006
    ..In addition, most retained genes are evolving rapidly. Possibly, B. aphidicola BCc is losing its symbiotic capacity and is being complemented (and might be replaced) by the highly abundant coexisting secondary symbiont...
  24. ncbi request reprint Combined therapy of interferon plus ribavirin promotes multiple adaptive solutions in hepatitis C virus
    José M Cuevas
    Departamento de Genetica, Instituto Cavanilles de Biodiversidad y Biologia Evolutiva, Universidad de Valencia, Valencia, Spain
    J Med Virol 81:650-6. 2009
    ....
  25. pmc Genetic variability of hepatitis C virus before and after combined therapy of interferon plus ribavirin
    José Manuel Cuevas
    Instituto Cavanilles de Biodiversidad y Biología Evolutiva and Departamento de Genética, Universidad de Valencia, Valencia, Spain
    PLoS ONE 3:e3058. 2008
    ....
  26. pmc Evidence of recombination in intrapatient populations of hepatitis C virus
    Vicente Sentandreu
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València València, Spain
    PLoS ONE 3:e3239. 2008
    ..From these results we conclude that recombination should be considered as a potentially relevant mechanism generating genetic variation in HCV and with important implications for the treatment of this infection...
  27. ncbi request reprint Effect of antiviral treatment and host susceptibility on positive selection in hepatitis C virus (HCV)
    Nuria Jiménez-Hernández
    Instituto Cavanilles de Biodiversidad y Biologia Evolutiva, Universitat de Valencia, Spain
    Virus Res 131:224-32. 2008
    ..We conclude that the host's genetic factors play an important role in whether the disease is contained or becomes chronic...
  28. ncbi request reprint The role of positive selection in hepatitis C virus
    José M Cuevas
    Instituto Cavanilles de Biodiversidad y Biología Evolutiva and Departamento de Genética, Universidad de Valencia, Valencia, Spain
    Infect Genet Evol 9:860-6. 2009
    ..In this sense, the particular systemic response from each patient could play an essential role in determining the outcome of the antiviral treatment...
  29. pmc Serratia symbiotica from the aphid Cinara cedri: a missing link from facultative to obligate insect endosymbiont
    Araceli Lamelas
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, Valencia, Spain
    PLoS Genet 7:e1002357. 2011
    ..aphidicola BCc or taken over by S. symbiotica. In addition, there are several cases of metabolic complementation giving functional stability to the whole consortium and evolutionary preservation of the actors involved...
  30. ncbi request reprint Using evolutionary tools to refine the new hypervariable region 3 within the envelope 2 protein of hepatitis C virus
    Manuela Torres-Puente
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Departament de Genetica, Universitat de Valencia, Valencia, Spain
    Infect Genet Evol 8:74-82. 2008
    ..Moreover, for the recently described HVR3, our results suggest that its location could be restricted to residues 434-450, instead of the originally postulated 431-466...
  31. pmc Evolutionary trajectories of beta-lactamase CTX-M-1 cluster enzymes: predicting antibiotic resistance
    Angela Novais
    Hospital Universitario Ramon y Cajal, IMSALUD, Madrid, Spain
    PLoS Pathog 6:e1000735. 2010
    ....
  32. pmc Gut microbiota disturbance during antibiotic therapy: a multi-omic approach
    Ana Elena Pérez-Cobas
    Unidad Mixta de Investigación en Genómica y Salud del Centro Superior de Investigación en Salud Pública CSISP e Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universitat de Valencia, Valencia, Spain
    Gut 62:1591-601. 2013
    ..Accordingly, we conducted the first comparative omic investigation of gut microbial communities in faecal samples taken at multiple time points from an individual subjected to β-lactam therapy...
  33. ncbi request reprint Massive presence of insertion sequences in the genome of SOPE, the primary endosymbiont of the rice weevil Sitophilus oryzae
    Rosario Gil
    Cavanilles Institute of Biodiversity and Evolutionary Biology, Department of Genetics, University of Valencia, Valencia, Spain
    Int Microbiol 11:41-8. 2008
    ....
  34. ncbi request reprint Gene expression levels influence amino acid usage and evolutionary rates in endosymbiotic bacteria
    Jörg Schaber
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, A C 22085, 46071 Valencia, Spain
    Gene 352:109-17. 2005
    ....
  35. ncbi request reprint Comparative analysis of two genomic regions among four strains of Buchnera aphidicola, primary endosymbiont of aphids
    Vicente Perez-Brocal
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, Apartado de Correos 22085, 46071 Valencia, Spain
    Gene 345:73-80. 2005
    ..aphidicola strains. However, when only conserved genes and intergenic regions of the four B. aphidicola strains are compared, the G+C reduction is higher in the fpr-trxA region...
  36. pmc Molecular epidemiology of a hepatitis C virus outbreak in a hemodialysis unit
    Maria Alma Bracho
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, Valencia, Spain
    J Clin Microbiol 43:2750-5. 2005
    ..The direction of the transmissions was further corroborated by different measures of genetic variability within and among samples...
  37. ncbi request reprint Analysis of the overdispersed clock in the short-term evolution of hepatitis C virus: Using the E1/E2 gene sequences to infer infection dates in a single source outbreak
    Borys Wrobel
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, Valencia, Spain
    Mol Biol Evol 23:1242-53. 2006
    ..Consequently, despite the distortion introduced by positive selection on evolutionary rates, it is possible to obtain quite accurate estimates of infection dates, a result of especial relevance for molecular epidemiology studies...
  38. pmc The frontier between cell and organelle: genome analysis of Candidatus Carsonella ruddii
    Javier Tamames
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, Apartado Postal 22085, 46071 Valencia, Spain
    BMC Evol Biol 7:181. 2007
    ..This genome consists of a circular chromosome of 159,662 bp and has been proposed as the smallest bacterial endosymbiont genome known to date...
  39. ncbi request reprint Genome rearrangement distances and gene order phylogeny in gamma-Proteobacteria
    Eugeni Belda
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva and Departament de Genètica, Universitat de Valencia, Valencia, Spain
    Mol Biol Evol 22:1456-67. 2005
    ....
  40. pmc Evolution of the secondary symbiont "Candidatus serratia symbiotica" in aphid species of the subfamily lachninae
    Araceli Lamelas
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, Apartado de Correos 22085, 46071 Valencia, Spain
    Appl Environ Microbiol 74:4236-40. 2008
    ..Phylogenetic and morphological analyses within the subfamily Lachninae indicate two different "Ca. Serratia symbiotica" lineages and support the longtime coevolution of both symbionts in C. cedri...
  41. pmc Molecular evolution in court: analysis of a large hepatitis C virus outbreak from an evolving source
    Fernando Gonzalez-Candelas
    Joint Research Unit Genómica y Salud CSISP FISABIO, Instituto Cavanilles Universidad de Valencia, Paterna, Valencia, Spain
    BMC Biol 11:76. 2013
    ..Here, we present the results of such an analysis that contributed to the conviction of an anesthetist as being responsible for the infection of 275 of his patients with hepatitis C virus...
  42. pmc The genome sequence of Blochmannia floridanus: comparative analysis of reduced genomes
    Rosario Gil
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, Apartat Oficial 2085, 46071 Valencia, Spain
    Proc Natl Acad Sci U S A 100:9388-93. 2003
    ..Comparative analysis of the five known genomes from insect endosymbiotic bacteria reveals they share only 313 genes, a number that may be close to the minimum gene set necessary to sustain endosymbiotic life...
  43. ncbi request reprint Natural selection and the organ-specific differentiation of HIV-1 V3 hypervariable region
    Rafael Sanjuan
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva and Departament de Genètica, Universitat de Valencia, 46071 Valencia, Spain
    Evolution 58:1185-94. 2004
    ..In contrast, positive selection does not seem to be the mechanism responsible for the evolution of patient-specific sequences...
  44. pmc Molecular epidemiology and evolution in an outbreak of fulminant hepatitis B virus
    Maria Alma Bracho
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, Apartado 22085, 46071 Valencia, Spain
    J Clin Microbiol 44:1288-94. 2006
    ....
  45. ncbi request reprint From phylogenetics to phylogenomics: the evolutionary relationships of insect endosymbiotic gamma-Proteobacteria as a test case
    Iñaki Comas
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, Valencia, Spain
    Syst Biol 56:1-16. 2007
    ..Nevertheless, other phylogenomic methods such as supertree approaches were useful in revealing alternative phylogenetic signals and should be included in comprehensive phylogenomic studies...
  46. ncbi request reprint Instability of the faecal microbiota in diarrhoea-predominant irritable bowel syndrome
    Ana Durbán
    Joint Research Unit on Genomics and Health Centro Superior de Investigación en Salud Pública CSISP Instituto Cavanilles de Biodiversidad y Biología Evolutiva ICBiBE, Universitat de Valencia, Valencia, Spain
    FEMS Microbiol Ecol 86:581-9. 2013
    ..Further research is needed to assess whether these changes are a consequence of the abnormal gut function in acute diarrhoeic episodes and the potential usefulness of tackling them. ..
  47. pmc Reductive genome evolution in Buchnera aphidicola
    Roeland C H J van Ham
    Centro de Astrobiologia, Instituto Nacional de Técnica Aeroespacial Consejo Superior de Investigaciones Científicas, Carretera de Ajalvir kilómetro 4, 28850 Torrejon de Ardoz, Madrid, Spain
    Proc Natl Acad Sci U S A 100:581-6. 2003
    ..These and other degenerative genomic features are discussed in light of compensatory processes and theoretical predictions on the long-term evolutionary fate of symbionts like Buchnera...
  48. ncbi request reprint A new subtype of hepatitis C virus genotype 1: complete genome and phylogenetic relationships of an Equatorial Guinea isolate
    Maria Alma Bracho
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, 46070 València, Spain
    J Gen Virol 87:1697-702. 2006
    ..Genetic divergence of the coding region of this new sequence with respect to the recognized subtypes of HCV-1 ranged from 20 to 22%. It is proposed that this isolate is a representative of a new, distinct variant of HCV subtype 1...
  49. pmc Extreme genome reduction in Buchnera spp.: toward the minimal genome needed for symbiotic life
    Rosario Gil
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, Apartat Oficial 2085, 46071 Valencia, Spain
    Proc Natl Acad Sci U S A 99:4454-8. 2002
    ..Our findings strongly suggest that the Buchnera genome is still experiencing a reductive process toward a minimum set of genes necessary for its symbiotic lifestyle...
  50. ncbi request reprint Endosymbiotic bacteria: groEL buffers against deleterious mutations
    Mario A Fares
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva and Departament de Genètica, Universitat de Valencia, PO Box 22085, 46071 Valencia, Spain
    Nature 417:398. 2002
  51. pmc Coexistence of Wolbachia with Buchnera aphidicola and a secondary symbiont in the aphid Cinara cedri
    Laura Gomez-Valero
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, Valencia, Spain
    J Bacteriol 186:6626-33. 2004
    ..cedri harbors the B. aphidicola strain with the smallest bacterial genome and that the S symbionts infect all Cinara spp. analyzed so far, suggest the possibility of bacterial replacement in these species...
  52. pmc Epistasis and the adaptability of an RNA virus
    Rafael Sanjuan
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva and Departament de Genètica, Universitat de Valencia, 46071 Valencia, Spain
    Genetics 170:1001-8. 2005
    ..Finally, for genotypes carrying two deleterious mutations, we found evidence of a negative correlation between the epistastic effect and the rate of compensatory evolution...
  53. pmc Comparative genomics of Serratia spp.: two paths towards endosymbiotic life
    Alejandro Manzano-Marín
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, Valencia, Spain
    PLoS ONE 7:e47274. 2012
    ..All these findings provide important evidence for the existence of at least two distinctive S. symbiotica lineages that are characterized by different rearrangements, gene content, genome size and branch lengths...
  54. pmc Genome economization in the endosymbiont of the wood roach Cryptocercus punctulatus due to drastic loss of amino acid synthesis capabilities
    Alexander Neef
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, Spain
    Genome Biol Evol 3:1437-48. 2011
    ....
  55. ncbi request reprint Unequal distribution of RT-PCR artifacts along the E1-E2 region of Hepatitis C virus
    Pilar Domingo-Calap
    Instituto Cavanilles de Biodiversidad y Biologia Evolutiva, Universitat de Valencia, Spain
    J Virol Methods 161:136-40. 2009
    ..The data suggest that the RNA sequence context or secondary structure can determine the fidelity of in vitro transcription or reverse transcription. Potentially, these factors might also modify the fidelity of the viral polymerase...
  56. doi request reprint Blattabacteria, the endosymbionts of cockroaches, have small genome sizes and high genome copy numbers
    María José López-Sánchez
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, Apartado Postal 2085, 46071 Valencia, Spain
    Environ Microbiol 10:3417-22. 2008
    ..Values between 10.2 and 18.3 and between 323 and 353 were found for the symbionts of P. americana and B. orientalis respectively. Polyploidy in intracellular bacteria may play a significant role in the genome reduction process...
  57. pmc Environmental distribution of prokaryotic taxa
    Javier Tamames
    Unidad Mixta de Investigación en Genómica y Salud, Centro Superior de Investigación en Salud Pública CSISP y Universidad de Valencia Instituto Cavanilles de Biodiversidad y Biología Evolutiva, 46020 Valencia, Spain
    BMC Microbiol 10:85. 2010
    ..We also assessed the most significant environmental factors shaping the environmental distribution of taxa...
  58. pmc Evolution of the leucine gene cluster in Buchnera aphidicola: insights from chromosomal versions of the cluster
    Beatriz Sabater-Muñoz
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, 46071 Valencia, Spain
    J Bacteriol 186:2646-54. 2004
    ..These findings do not support a chromosomal origin for the leucine genes in the ancestral B. aphidicola and do support a back transfer evolutionary scenario from a plasmid to the main chromosome...
  59. ncbi request reprint Selection on coding regions determined Hox7 genes evolution
    Mario Ali Fares
    Departamento de Genetica, Univesidad de Valencia, Valencia, Spain
    Mol Biol Evol 20:2104-12. 2003
    ..Our results show that both positive and negative selection on coding regions are influencing Hox7 genes evolution...
  60. pmc Molecular basis of adaptive convergence in experimental populations of RNA viruses
    José M Cuevas
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva and Departament de Genètica, Universitat de Valencia, Spain
    Genetics 162:533-42. 2002
    ..Keeping in mind statistical uncertainties, these estimates suggest that along with several beneficial mutations of major effect, many other mutations got fixed as part of a group of epistatic mutations...
  61. pmc Comparative genomics of Blattabacterium cuenoti: the frozen legacy of an ancient endosymbiont genome
    Rafael Patiño-Navarrete
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, Valencia, Spain
    Genome Biol Evol 5:351-61. 2013
    ....
  62. ncbi request reprint Molecular systematics of aphids (Homoptera: Aphididae): new insights from the long-wavelength opsin gene
    Benjamín Ortiz-Rivas
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, Apartado de Correos 22085, 46071 Valencia, Spain
    Mol Phylogenet Evol 30:24-37. 2004
    ..Moreover, our data also suggest a basal position of Lachninae which has implications on current discussions about the ancestrality of conifer-feeding in modern aphids...
  63. pmc Network dynamics of eukaryotic LTR retroelements beyond phylogenetic trees
    Carlos Llorens
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva ICBiBE, Universitat de Valencia, Paterna, Valencia, Spain
    Biol Direct 4:41. 2009
    ..Phylogenetic analyses usually show that these split into multiple distinct lineages but what is yet to be understood is how deep evolution occurred in this system...
  64. pmc The striking case of tryptophan provision in the cedar aphid Cinara cedri
    María José Gosalbes
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, Apartado de Correos 2085, 46071 Valencia, Spain
    J Bacteriol 190:6026-9. 2008
    ..The remaining genes for the pathway (trpDCBA) are located on the chromosome of the secondary endosymbiont "Candidatus Serratia symbiotica." Thus, we propose that a symbiotic consortium is necessary to provide tryptophan...
  65. pmc The active human gut microbiota differs from the total microbiota
    Francesc Peris-Bondia
    Joint Unit of Research in Genomics and Health, Centre for Public Health Research CSISP Cavanilles Institute for Biodiversity and Evolutionary Biology University of Valencia, Valencia, Spain
    PLoS ONE 6:e22448. 2011
    ..Moreover, a huge number of families appeared as part of the active fraction when cell sorting was applied, indicating reads that are simply statistically hidden by the total reads...
  66. ncbi request reprint Mapping natural polymorphisms of hepatitis C virus NS3/4A protease and antiviral resistance to inhibitors in worldwide isolates
    F Xavier López-Labrador
    Public Health Department, Generalitat Valenciana, Institut Cavanilles de Biodiversitat i Biologia Evolutiva ICBiBE, E 46071 Valencia, Spain
    Antivir Ther 13:481-94. 2008
    ..Here, we aimed to determine both the natural variability and presence of resistance or compensatory mutations to new protease inhibitors (PI) in NS3/4A proteases from worldwide HCV isolates...
  67. doi request reprint High diversity of the viral community from an Antarctic lake
    Alberto López-Bueno
    Centro de Biologia Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas CSIC Universidad Autónoma de Madrid, Madrid, Spain
    Science 326:858-61. 2009
    ....
  68. ncbi request reprint Variations in two gene sequences of Citrus tristeza virus after host passage
    María A Ayllón
    Instituto Valenciano de Investigaciones Agrarias, Moncada, Valencia, Spain
    Virus Genes 32:119-28. 2006
    ..Our results suggest that aphid transmission and host passage may significantly alter the composition of CTV populations and thus be an important factor in their evolution...
  69. pmc The cost of replication fidelity in an RNA virus
    Victoria Furió
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, P O Box 22085, 46071 Valencia, Spain
    Proc Natl Acad Sci U S A 102:10233-7. 2005
    ..We demonstrate that the observed mutation rate in vesicular stomatitis virus can be explained by a trade-off between replication rate and replication fidelity...
  70. pmc Effect of oligonucleotide primers in determining viral variability within hosts
    Maria Alma Bracho
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, Edifici Instituts, Polígon La Coma s n, Paterna, Spain
    Virol J 1:13. 2004
    ..Although bias in template-to-product ratios has been described before, its relevance in describing viral genetic variability at the intrapatient level has not been fully assessed yet...
  71. pmc The contribution of epistasis to the architecture of fitness in an RNA virus
    Rafael Sanjuan
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, P O Box 22085, 46071 Valencia, Spain
    Proc Natl Acad Sci U S A 101:15376-9. 2004
    ..In this case, all significant interactions were antagonistic. Our results show that the architecture of the fitness depends on complex interactions among genome components...
  72. pmc Mealybugs nested endosymbiosis: going into the 'matryoshka' system in Planococcus citri in depth
    Sergio López-Madrigal
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, Apartado Postal 22085, Valencia 46071, Spain
    BMC Microbiol 13:74. 2013
    ..Usually, both endosymbionts maintain their cellular identity. An exception is the endosymbiosis found in mealybugs of the subfamily Pseudoccinae, such as Planococcus citri, with Moranella endobia located inside Tremblaya princeps...
  73. pmc Blueprint for a minimal photoautotrophic cell: conserved and variable genes in Synechococcus elongatus PCC 7942
    Luis Delaye
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, Valencia, Spain
    BMC Genomics 12:25. 2011
    ..7 Mb) that could be used as targets for deletion. We also looked for conserved genes that might be essential for cell survival...
  74. pmc Validating viral quasispecies with digital organisms: a re-examination of the critical mutation rate
    Iñaki Comas
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, Spain
    BMC Evol Biol 5:5. 2005
    ..These experiments revealed that under high mutation rates populations of less fit organisms previously adapted to such high mutation rates were able to outcompete organisms with higher average fitness but adapted to low mutation rates...
  75. pmc Virulence factor rtx in Legionella pneumophila, evidence suggesting it is a modular multifunctional protein
    Giuseppe D'Auria
    Instituto Cavanilles de Biodiversidad y Biologia Evolutiva, Universitat de Valencia, Spain
    BMC Genomics 9:14. 2008
    ..Its role in escaping the host immune system and cytotoxic activity is well known. Its repeated motives and modularity make Rtx a multifunctional factor in pathogenicity...
  76. doi request reprint Assessing gut microbial diversity from feces and rectal mucosa
    Ana Durbán
    Centro Superior de Investigación en Salud Pública CSISP, Avenida de Cataluña 21, 46020, Valencia, Spain
    Microb Ecol 61:123-33. 2011
    ..We do not expect clinicians to stop using feces for research, but we think it is important to caution them on their potential lack of representativeness with respect to the bacterial biofilm on the rectal mucosa...
  77. pmc New clues about the evolutionary history of metabolic losses in bacterial endosymbionts, provided by the genome of Buchnera aphidicola from the aphid Cinara tujafilina
    Araceli Lamelas
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, Apartado de Correos 2085, 46071 Valencia, Spain
    Appl Environ Microbiol 77:4446-54. 2011
    ..Although stochastic gene loss plays a role in the genome reduction process, it is also clear that metabolism, as a functional constraint, is also a powerful evolutionary force in insect endosymbionts...
  78. doi request reprint Genomics of intracellular symbionts in insects
    María José Gosalbes
    Unidad Mixta de Investigación en Genómica y Salud Centro Superior de Investigación en Salud Pública CSISP, Institut Cavanilles de Biodiversitat i Biologia Evolutiva Universitat de València, Apartado Postal 22085, 46071 Valencia, Spain
    Int J Med Microbiol 300:271-8. 2010
    ..e., phloem, xylem, blood, omnivores, and grain). Particular emphasis is given to the evolutionary functional convergence of phylogenetically distant endosymbionts, which are evolving in hosts with similar diets...
  79. pmc The Gypsy Database (GyDB) of mobile genetic elements: release 2.0
    Carlos Llorens
    Biotechvana, Parc Cientific, Universitat de Valencia, Calle Catedrático José Beltrán 2, 46980 Paterna, Valencia, Spain
    Nucleic Acids Res 39:D70-4. 2011
    ..GyDB 2.0 is available at http://gydb.org...
  80. ncbi request reprint Bacterial endosymbionts of insects: insights from comparative genomics
    Rosario Gil
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva and Departament de Genètica, Universitat de Valencia, Apartado Postal 22085, 46071 Valencia, Spain
    Environ Microbiol 6:1109-22. 2004
    ....
  81. ncbi request reprint Sampling and repeatability in the evaluation of hepatitis C virus genetic variability
    Manuela Torres-Puente
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva and Departament de Genètica, Universitat de Valencia, Apartado Oficial 2085, 46071 Valencia, Spain
    J Gen Virol 84:2343-50. 2003
    ..These results validate the use of relatively small sample sets for the evaluation of genetic variability and for the estimation of phylogenetic relationships of RNA viruses in population and epidemiological studies...
  82. doi request reprint Daily follow-up of bacterial communities in the human gut reveals stable composition and host-specific patterns of interaction
    Ana Durbán
    Joint Research Unit on Genomics and Health, CSISP, University of Valencia Cavanilles Institute of Biodiversity and Evolutionary Biology, Valencia, Spain
    FEMS Microbiol Ecol 81:427-37. 2012
    ..Networks of potential interactions between co-occurring genera were also subject-specific, even for the same bacterial genus, which might be reflecting host-specific selective pressures and historic events...
  83. pmc Determination of the core of a minimal bacterial gene set
    Rosario Gil
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, Apartat Oficial 2085, 46071 Valencia, Spain
    Microbiol Mol Biol Rev 68:518-37, table of contents. 2004
    ..The main features of such a minimal gene set, as well as the metabolic functions that must be present in the hypothetical minimal cell, are discussed...
  84. pmc Mobile genetic element proliferation and gene inactivation impact over the genome structure and metabolic capabilities of Sodalis glossinidius, the secondary endosymbiont of tsetse flies
    Eugeni Belda
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, Spain
    BMC Genomics 11:449. 2010
    ....
  85. pmc Bioinformatic flowchart and database to investigate the origins and diversity of clan AA peptidases
    Carlos Llorens
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, Paterna, Valencia, Spain
    Biol Direct 4:3. 2009
    ..However, clan AA is a difficult case to study due to the low similarity and different rates of evolution. This work is an ongoing attempt to investigate the different clan AA families to understand the cause of their diversity...
  86. ncbi request reprint The evolution of the heat-shock protein GroEL from Buchnera, the primary endosymbiont of aphids, is governed by positive selection
    Mario Ali Fares
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva and Department de Genètica, Universitat de Valencia, Spain
    Mol Biol Evol 19:1162-70. 2002
    ....
  87. ncbi request reprint The evolutionary origin of Xanthomonadales genomes and the nature of the horizontal gene transfer process
    Iñaki Comas
    Instituto Cavanilles de Biodiversidad y Biologia Evolutiva, Universidad de Valencia, Valencia, Spain
    Mol Biol Evol 23:2049-57. 2006
    ....
  88. pmc Selection for robustness in mutagenized RNA viruses
    Rafael Sanjuan
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, Valencia, Spain
    PLoS Genet 3:e93. 2007
    ..These results show that selection can directly favor mutational robustness and reveal a novel viral resistance mechanism against treatment by lethal mutagenesis...
  89. ncbi request reprint Molecular systematics of aphids and their primary endosymbionts
    D Martinez-Torres
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, Valencia, Apartado de Correos 2085, 46071, Spain
    Mol Phylogenet Evol 20:437-49. 2001
    ..Finally, we discuss our results in the light of the proposed parallel evolution of aphids and their endosymbionts...
  90. pmc Relationship between within-host fitness and virulence in the vesicular stomatitis virus: correlation with partial decoupling
    Victoria Furió
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, Spain
    J Virol 86:12228-36. 2012
    ....
  91. pmc Relationships of gag-pol diversity between Ty3/Gypsy and Retroviridae LTR retroelements and the three kings hypothesis
    Carlos Llorens
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, Polígono de coma S N, Paterna, Valencia, Spain
    BMC Evol Biol 8:276. 2008
    ..In relation to 3 previously proposed Retroviridae classes I, II and II, investigation of the above proteins conclusively uncovers important insights regarding the ancient history of Ty3/Gypsy and Retroviridae LTR retroelements...
  92. doi request reprint Evolution of reduced prokaryotic genomes and the minimal cell concept: variations on a theme
    Luis Delaye
    Unidad Mixta de Investigación en Genómica y Salud CSISP UVEG Instituto Cavanilles, Valencia, Spain
    Bioessays 32:281-7. 2010
    ..An upcoming challenge for biologists will be to discern, by studying differences and similarities in current biodiversity, how cells with reduced genomes have adapted while retaining all basic life-supporting functions...
  93. pmc The cost of replication fidelity in human immunodeficiency virus type 1
    Victoria Furió
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, PO Box 22085, 46071 Valencia, Spain
    Proc Biol Sci 274:225-30. 2007
    ..Since in RNA viruses fast replication is critical for survival, this could impose a high cost of fidelity and favour the evolution of high mutation rates...
  94. ncbi request reprint Why are the genomes of endosymbiotic bacteria so stable?
    Francisco J Silva
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva and Departament de Genètica, Universitat de Valencia, Apartado 22085, 46071 Valencia, Spain
    Trends Genet 19:176-80. 2003
    ..Gene loss, which was extensive during the initial steps of Buchnera evolution, has continued in the different Buchnera lineages since their divergence...
  95. ncbi request reprint The effect of co- and superinfection on the adaptive dynamics of vesicular stomatitis virus
    Francy Y E Carrillo
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, PO Box 22085, 46071 Valencia, Spain
    Infect Genet Evol 7:69-73. 2007
    ....
  96. doi request reprint Enhanced adaptation of vesicular stomatitis virus in cells infected with vaccinia virus
    Francy Y E Carrillo
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, P O Box 22085, 46071 Valencia, Spain
    Infect Genet Evol 8:614-20. 2008
    ..Further studies are needed to discern whether infections involving different viruses could have an increased ability to escape antiviral strategies...
  97. pmc Effect of ribavirin on the mutation rate and spectrum of hepatitis C virus in vivo
    José M Cuevas
    Departamento de Genetica, Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, Valencia, Spain
    J Virol 83:5760-4. 2009
    ..This result is consistent with the known in vitro mutagenic effect of ribavirin and suggests that the antiviral effect of ribavirin plus interferon treatment is at least partly exerted through lethal mutagenesis...
  98. pmc Modular organization in the reductive evolution of protein-protein interaction networks
    Javier Tamames
    Instituto Cavanilles de Biodiversidad y Biologia Evolutiva, Universitat de Valencia, 46071 Valencia, Spain
    Genome Biol 8:R94. 2007
    ..High-throughput protein interaction data now make it possible to examine the additional complexity generated by the way that protein interactions are organized...
  99. pmc Microbial diversity in the midguts of field and lab-reared populations of the European corn borer Ostrinia nubilalis
    Eugeni Belda
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva, University of Valencia, Valencia, Spain
    PLoS ONE 6:e21751. 2011
    ....