Search

Your search keyword '"Porcelli, Damiano"' showing total 23 results
Start Over Author "Porcelli, Damiano"
23 results on '"Porcelli, Damiano"'

1. Structural and Comparative Analyses of Insects Suggest the Presence of an Ultra-Conserved Regulatory Element of the Genes Encoding Vacuolar-Type ATPase Subunits and Assembly Factors

Author

Lovero, Domenica, primary, Porcelli, Damiano, additional, Giordano, Luca, additional, Lo Giudice, Claudio, additional, Picardi, Ernesto, additional, Pesole, Graziano, additional, Pignataro, Eugenia, additional, Palazzo, Antonio, additional, and Marsano, René Massimiliano, additional

Published
2023
Full Text
View/download PDF

3. Experimental sexual selection reveals rapid evolutionary divergence in sex-specific transcriptomes and their interactions following mating

Author

Veltsos, Paris, Porcelli, Damiano, Fang, Yongxiang, Cossins, Andrew R., Ritchie, Michael G., Snook, Rhonda R., Veltsos, Paris, Porcelli, Damiano, Fang, Yongxiang, Cossins, Andrew R., Ritchie, Michael G., and Snook, Rhonda R.

Abstract

Post copulatory interactions between the sexes in internally fertilizing species elicits both sexual conflict and sexual selection. Macroevolutionary and comparative studies have linked these processes to rapid transcriptomic evolution in sex-specific tissues and substantial transcriptomic post mating responses in females, patterns of which are altered when mating between reproductively isolated species. Here, we tested multiple predictions arising from sexual selection and conflict theory about the evolution of sex-specific and tissue-specific gene expression and the post mating response at the microevolutionary level. Following over 150 generations of experimental evolution under either reduced (enforced monogamy) or elevated (polyandry) sexual selection in Drosophila pseudoobscura, we found a substantial effect of sexual selection treatment on transcriptomic divergence in virgin male and female reproductive tissues (testes, male accessory glands, the female reproductive tract and ovaries). Sexual selection treatment also had a dominant effect on the post mating response, particularly in the female reproductive tract - the main arena for sexual conflict - compared to ovaries. This effect was asymmetric with monandry females typically showing more post mating responses than polyandry females, with enriched gene functions varying across treatments. The evolutionary history of the male partner had a larger effect on the post mating response of monandry females, but females from both sexual selection treatments showed unique patterns of gene expression and gene function when mating with males from the alternate treatment. Our microevolutionary results mostly confirm comparative macroevolutionary predictions on the role of sexual selection on transcriptomic divergence and altered gene regulation arising from divergent coevolutionary trajectories between sexual selection treatments.

Published
2022
Full Text
View/download PDF

6. Pool-seq DrosEU 2014 samples VCF file

Author

Agencia Estatal de Investigación (España), University of Freiburg, Academy of Finland, Russian Foundation for Basic Research, Danish Natural Science Research Council, Ministerio de Economía y Competitividad (España), European Commission, Centre National de la Recherche Scientifique (France), Swedish Research Council, German Research Foundation, National Institutes of Health (US), Ministerio de Ciencia, Innovación y Universidades (España), The Scientific and Technological Research Council of Turkey, Agence Nationale de la Recherche (France), Israel Science Foundation, Austrian Science Fund, Biotechnology and Biological Sciences Research Council (UK), Swiss National Science Foundation, Kapun, Martin [0000-0002-3810-0504], Barrón, Maite G. [0000-0001-6146-6259], Staubach, Fabian [0000-0002-8097-2349], Vieira, Jorge [0000-0001-7032-5220], Obbard, Darren, J. [0000-0001-5392-8142], Rota-Stabelli, Omar [0000-0002-0030-7788], Kankare, Maaria [0000-0003-1541-9050], Haudry, Annabelle [0000-0001-6088-0909], Wiberg, R. Axel W. [0000-0002-8074-8670], Waidele, Lena [0000-0002-6323-6438], Kozeretska, Iryna [0000-0002-6485-1408], Pasyukova, Elena G. [0000-0002-6491-8561], Loeschcke, Volker [0000-0003-1450-0754], Pascual, Marta [0000-0002-6189-0612], Vieira, Cristina P. [0000-0002-7139-2107], Serga, Svitlana [0000-0003-1875-3185], Montchamp-Moreau, Catherine [0000-0002-5044-9709], Abbott, Jessica [0000-0002-8743-2089], Gibert, Patricia [0000-0002-9461-6820], Porcelli, Damiano [0000-0002-9019-5758], Posnien, Nico [0000-0003-0700-5595], Grath, Sonja [0000-0003-3621-736X], Sucena, Élio [0000-0001-8810-870X], Bergland, Alan O. [0000-0001-7145-7575], Onder, Banu Sebnem [0000-0002-3003-248X], Argyridou, Eliza [0000-0002-6890-4642], Guio, Lain [0000-0002-5481-5200], Schou, Mads Fristrup [0000-0001-5521-5269], Deplancke, Bart [0000-0001-9935-843X], Vieira, Cristina [0000-0003-3414-3993], Ritchie, Michael G. [0000-0001-7913-8675], Zwaan, Blas J. [0000-0002-8221-4998], Tauber, Eran [0000-0003-4018-6535], Orengo, Dorcas J. [0000-0001-7911-3224], Puerma, Eva [0000-0001-7261-187X], Aguadé i Porres, Montserrat [0000-0002-3884-7800], Schmidt, Paul S. [0000-0002-8076-6705], Parsch, John [0000-0001-9068-5549], Betancourt, Andrea J. [0000-0001-9351-1413], Flatt, Thomas [0000-0002-5990-1503], González Pérez, Josefa [0000-0001-9824-027X], González Pérez, Josefa [josefa.gonzalez@ibe.upf-csic.es], Kapun, Martin, Barrón, Maite G., Staubach, Fabian, Vieira, Jorge, Obbard, Darren, J., Rota-Stabelli, Omar, Kankare, Maaria, Haudry, Annabelle, Wiberg, R. Axel W., Waidele, Lena, Kozeretska, Iryna, Pasyukova, Elena G., Loeschcke, Volker, Pascual, Marta, Vieira, Cristina P., Serga, Svitlana, Montchamp-Moreau, Catherine, Abbott, Jessica, Gibert, Patricia, Porcelli, Damiano, Posnien, Nico, Grath, Sonja, Sucena, Élio, Bergland, Alan O., Garcia Guerreiro, Maria Pilar, Onder, Banu Sebnem, Argyridou, Eliza, Guio, Lain, Schou, Mads Fristrup, Deplancke, Bart, Vieira, Cristina, Ritchie, Michael G., Zwaan, Blas J., Tauber, Eran, Orengo, Dorcas J., Puerma, Eva, Aguadé i Porres, Montserrat, Schmidt, Paul S., Parsch, John, Betancourt, Andrea J., Flatt, Thomas, González Pérez, Josefa, Agencia Estatal de Investigación (España), University of Freiburg, Academy of Finland, Russian Foundation for Basic Research, Danish Natural Science Research Council, Ministerio de Economía y Competitividad (España), European Commission, Centre National de la Recherche Scientifique (France), Swedish Research Council, German Research Foundation, National Institutes of Health (US), Ministerio de Ciencia, Innovación y Universidades (España), The Scientific and Technological Research Council of Turkey, Agence Nationale de la Recherche (France), Israel Science Foundation, Austrian Science Fund, Biotechnology and Biological Sciences Research Council (UK), Swiss National Science Foundation, Kapun, Martin [0000-0002-3810-0504], Barrón, Maite G. [0000-0001-6146-6259], Staubach, Fabian [0000-0002-8097-2349], Vieira, Jorge [0000-0001-7032-5220], Obbard, Darren, J. [0000-0001-5392-8142], Rota-Stabelli, Omar [0000-0002-0030-7788], Kankare, Maaria [0000-0003-1541-9050], Haudry, Annabelle [0000-0001-6088-0909], Wiberg, R. Axel W. [0000-0002-8074-8670], Waidele, Lena [0000-0002-6323-6438], Kozeretska, Iryna [0000-0002-6485-1408], Pasyukova, Elena G. [0000-0002-6491-8561], Loeschcke, Volker [0000-0003-1450-0754], Pascual, Marta [0000-0002-6189-0612], Vieira, Cristina P. [0000-0002-7139-2107], Serga, Svitlana [0000-0003-1875-3185], Montchamp-Moreau, Catherine [0000-0002-5044-9709], Abbott, Jessica [0000-0002-8743-2089], Gibert, Patricia [0000-0002-9461-6820], Porcelli, Damiano [0000-0002-9019-5758], Posnien, Nico [0000-0003-0700-5595], Grath, Sonja [0000-0003-3621-736X], Sucena, Élio [0000-0001-8810-870X], Bergland, Alan O. [0000-0001-7145-7575], Onder, Banu Sebnem [0000-0002-3003-248X], Argyridou, Eliza [0000-0002-6890-4642], Guio, Lain [0000-0002-5481-5200], Schou, Mads Fristrup [0000-0001-5521-5269], Deplancke, Bart [0000-0001-9935-843X], Vieira, Cristina [0000-0003-3414-3993], Ritchie, Michael G. [0000-0001-7913-8675], Zwaan, Blas J. [0000-0002-8221-4998], Tauber, Eran [0000-0003-4018-6535], Orengo, Dorcas J. [0000-0001-7911-3224], Puerma, Eva [0000-0001-7261-187X], Aguadé i Porres, Montserrat [0000-0002-3884-7800], Schmidt, Paul S. [0000-0002-8076-6705], Parsch, John [0000-0001-9068-5549], Betancourt, Andrea J. [0000-0001-9351-1413], Flatt, Thomas [0000-0002-5990-1503], González Pérez, Josefa [0000-0001-9824-027X], González Pérez, Josefa [josefa.gonzalez@ibe.upf-csic.es], Kapun, Martin, Barrón, Maite G., Staubach, Fabian, Vieira, Jorge, Obbard, Darren, J., Rota-Stabelli, Omar, Kankare, Maaria, Haudry, Annabelle, Wiberg, R. Axel W., Waidele, Lena, Kozeretska, Iryna, Pasyukova, Elena G., Loeschcke, Volker, Pascual, Marta, Vieira, Cristina P., Serga, Svitlana, Montchamp-Moreau, Catherine, Abbott, Jessica, Gibert, Patricia, Porcelli, Damiano, Posnien, Nico, Grath, Sonja, Sucena, Élio, Bergland, Alan O., Garcia Guerreiro, Maria Pilar, Onder, Banu Sebnem, Argyridou, Eliza, Guio, Lain, Schou, Mads Fristrup, Deplancke, Bart, Vieira, Cristina, Ritchie, Michael G., Zwaan, Blas J., Tauber, Eran, Orengo, Dorcas J., Puerma, Eva, Aguadé i Porres, Montserrat, Schmidt, Paul S., Parsch, John, Betancourt, Andrea J., Flatt, Thomas, and González Pérez, Josefa

Published
2019

7. Genomic analysis of European Drosophila populations reveals longitudinal structure and continent-wide selection

Author

Kapun, Martin, Barrón, Maite G., Staubach, Fabian, Vieira, Jorge, Obbard, Darren, J., Rota-Stabelli, Omar, Kankare, Maaria, Haudry, Annabelle, Wiberg, R. Axel W., Waidele, Lena, Kozeretska, Iryna, Pasyukova, Elena G., Loeschcke, Volker, Pascual, Marta, Vieira, Cristina P., Serga, Svitlana, Montchamp-Moreau, Catherine, Abbott, Jessica, Gibert, Patricia, Porcelli, Damiano, Posnien, Nico, Grath, Sonja, Sucena, Élio, Bergland, Alan O., Garcia Guerreiro, Maria Pilar, Onder, Banu Sebnem, Argyridou, Eliza, Guio, Lain, Schou, Mads Fristrup, Deplancke, Bart, Vieira, Cristina, Ritchie, Michael G., Zwaan, Blas J., Tauber, Eran, Orengo, Dorcas J., Puerma, Eva, Aguadé i Porres, Montserrat, Schmidt, Paul S., Parsch, John, Betancourt, Andrea J., Flatt, Thomas, González Pérez, Josefa, Agencia Estatal de Investigación (España), University of Freiburg, Academy of Finland, Russian Foundation for Basic Research, Danish Natural Science Research Council, Ministerio de Economía y Competitividad (España), European Commission, Centre National de la Recherche Scientifique (France), Swedish Research Council, German Research Foundation, National Institutes of Health (US), Ministerio de Ciencia, Innovación y Universidades (España), Agence Nationale de la Recherche (France), Israel Science Foundation, Austrian Science Fund, Biotechnology and Biological Sciences Research Council (UK), Swiss National Science Foundation, Kapun, Martin [0000-0002-3810-0504], Barrón, Maite G. [0000-0001-6146-6259], Staubach, Fabian [0000-0002-8097-2349], Vieira, Jorge [0000-0001-7032-5220], Obbard, Darren, J. [0000-0001-5392-8142], Rota-Stabelli, Omar [0000-0002-0030-7788], Kankare, Maaria [0000-0003-1541-9050], Haudry, Annabelle [0000-0001-6088-0909], Wiberg, R. Axel W. [0000-0002-8074-8670], Waidele, Lena [0000-0002-6323-6438], Kozeretska, Iryna [0000-0002-6485-1408], Pasyukova, Elena G. [0000-0002-6491-8561], Loeschcke, Volker [0000-0003-1450-0754], Pascual, Marta [0000-0002-6189-0612], Vieira, Cristina P. [0000-0002-7139-2107], Serga, Svitlana [0000-0003-1875-3185], Montchamp-Moreau, Catherine [0000-0002-5044-9709], Abbott, Jessica [0000-0002-8743-2089], Gibert, Patricia [0000-0002-9461-6820], Porcelli, Damiano [0000-0002-9019-5758], Posnien, Nico [0000-0003-0700-5595], Grath, Sonja [0000-0003-3621-736X], Sucena, Élio [0000-0001-8810-870X], Bergland, Alan O. [0000-0001-7145-7575], Onder, Banu Sebnem [0000-0002-3003-248X], Argyridou, Eliza [0000-0002-6890-4642], Guio, Lain [0000-0002-5481-5200], Schou, Mads Fristrup [0000-0001-5521-5269], Deplancke, Bart [0000-0001-9935-843X], Vieira, Cristina [0000-0003-3414-3993], Ritchie, Michael G. [0000-0001-7913-8675], Zwaan, Blas J. [0000-0002-8221-4998], Tauber, Eran [0000-0003-4018-6535], Orengo, Dorcas J. [0000-0001-7911-3224], Puerma, Eva [0000-0001-7261-187X], Aguadé i Porres, Montserrat [0000-0002-3884-7800], Schmidt, Paul S. [0000-0002-8076-6705], Parsch, John [0000-0001-9068-5549], Betancourt, Andrea J. [0000-0001-9351-1413], Flatt, Thomas [0000-0002-5990-1503], González Pérez, Josefa [0000-0001-9824-027X], Kapun, Martin, Barrón, Maite G., Staubach, Fabian, Vieira, Jorge, Obbard, Darren, J., Rota-Stabelli, Omar, Kankare, Maaria, Haudry, Annabelle, Wiberg, R. Axel W., Waidele, Lena, Kozeretska, Iryna, Pasyukova, Elena G., Loeschcke, Volker, Pascual, Marta, Vieira, Cristina P., Serga, Svitlana, Montchamp-Moreau, Catherine, Abbott, Jessica, Gibert, Patricia, Porcelli, Damiano, Posnien, Nico, Grath, Sonja, Sucena, Élio, Bergland, Alan O., Onder, Banu Sebnem, Argyridou, Eliza, Guio, Lain, Schou, Mads Fristrup, Deplancke, Bart, Vieira, Cristina, Ritchie, Michael G., Zwaan, Blas J., Tauber, Eran, Orengo, Dorcas J., Puerma, Eva, Aguadé i Porres, Montserrat, Schmidt, Paul S., Parsch, John, Betancourt, Andrea J., Flatt, Thomas, and González Pérez, Josefa

Abstract

Genetic variation is the fuel of evolution. However, analyzing evolutionary dynamics in natural populations is challenging, sequencing of entire populations remains costly and comprehensive sampling logistically difficult. To tackle this issue and to define relevant spatial and temporal scales of variation, we have founded the European Drosophila Population Genomics Consortium (DrosEU). Here we present the first analysis of 48 D. melanogaster population samples collected across Europe in 2014. Our analysis uncovers novel patterns of variation at multiple levels: genome-wide neutral SNPs, mtDNA haplotypes, inversions, and TEs showing previously cryptic longitudinal population structure; signatures of selective sweeps shared among populations; presumably adaptive clines in inversions; and geographic variation in TEs. Additionally, we document highly variable microbiota and identify several new Drosophila viruses. Our study reveals novel aspects of the population biology of D. melanogaster and illustrates the power of extensive sampling and pooled sequencing of populations on a continent-wide scale.

Published
2018

8. Genomic analysis of European Drosophila populations reveals longitudinal structure and continent-wide selection

Author

Agencia Estatal de Investigación (España), University of Freiburg, Academy of Finland, Russian Foundation for Basic Research, Danish Natural Science Research Council, Ministerio de Economía y Competitividad (España), European Commission, Centre National de la Recherche Scientifique (France), Swedish Research Council, German Research Foundation, National Institutes of Health (US), Ministerio de Ciencia, Innovación y Universidades (España), Agence Nationale de la Recherche (France), Israel Science Foundation, Austrian Science Fund, Biotechnology and Biological Sciences Research Council (UK), Swiss National Science Foundation, Kapun, Martin [0000-0002-3810-0504], Barrón, Maite G. [0000-0001-6146-6259], Staubach, Fabian [0000-0002-8097-2349], Vieira, Jorge [0000-0001-7032-5220], Obbard, Darren, J. [0000-0001-5392-8142], Rota-Stabelli, Omar [0000-0002-0030-7788], Kankare, Maaria [0000-0003-1541-9050], Haudry, Annabelle [0000-0001-6088-0909], Wiberg, R. Axel W. [0000-0002-8074-8670], Waidele, Lena [0000-0002-6323-6438], Kozeretska, Iryna [0000-0002-6485-1408], Pasyukova, Elena G. [0000-0002-6491-8561], Loeschcke, Volker [0000-0003-1450-0754], Pascual, Marta [0000-0002-6189-0612], Vieira, Cristina P. [0000-0002-7139-2107], Serga, Svitlana [0000-0003-1875-3185], Montchamp-Moreau, Catherine [0000-0002-5044-9709], Abbott, Jessica [0000-0002-8743-2089], Gibert, Patricia [0000-0002-9461-6820], Porcelli, Damiano [0000-0002-9019-5758], Posnien, Nico [0000-0003-0700-5595], Grath, Sonja [0000-0003-3621-736X], Sucena, Élio [0000-0001-8810-870X], Bergland, Alan O. [0000-0001-7145-7575], Onder, Banu Sebnem [0000-0002-3003-248X], Argyridou, Eliza [0000-0002-6890-4642], Guio, Lain [0000-0002-5481-5200], Schou, Mads Fristrup [0000-0001-5521-5269], Deplancke, Bart [0000-0001-9935-843X], Vieira, Cristina [0000-0003-3414-3993], Ritchie, Michael G. [0000-0001-7913-8675], Zwaan, Blas J. [0000-0002-8221-4998], Tauber, Eran [0000-0003-4018-6535], Orengo, Dorcas J. [0000-0001-7911-3224], Puerma, Eva [0000-0001-7261-187X], Aguadé i Porres, Montserrat [0000-0002-3884-7800], Schmidt, Paul S. [0000-0002-8076-6705], Parsch, John [0000-0001-9068-5549], Betancourt, Andrea J. [0000-0001-9351-1413], Flatt, Thomas [0000-0002-5990-1503], González Pérez, Josefa [0000-0001-9824-027X], Kapun, Martin, Barrón, Maite G., Staubach, Fabian, Vieira, Jorge, Obbard, Darren, J., Rota-Stabelli, Omar, Kankare, Maaria, Haudry, Annabelle, Wiberg, R. Axel W., Waidele, Lena, Kozeretska, Iryna, Pasyukova, Elena G., Loeschcke, Volker, Pascual, Marta, Vieira, Cristina P., Serga, Svitlana, Montchamp-Moreau, Catherine, Abbott, Jessica, Gibert, Patricia, Porcelli, Damiano, Posnien, Nico, Grath, Sonja, Sucena, Élio, Bergland, Alan O., Garcia Guerreiro, Maria Pilar, Onder, Banu Sebnem, Argyridou, Eliza, Guio, Lain, Schou, Mads Fristrup, Deplancke, Bart, Vieira, Cristina, Ritchie, Michael G., Zwaan, Blas J., Tauber, Eran, Orengo, Dorcas J., Puerma, Eva, Aguadé i Porres, Montserrat, Schmidt, Paul S., Parsch, John, Betancourt, Andrea J., Flatt, Thomas, González Pérez, Josefa, Agencia Estatal de Investigación (España), University of Freiburg, Academy of Finland, Russian Foundation for Basic Research, Danish Natural Science Research Council, Ministerio de Economía y Competitividad (España), European Commission, Centre National de la Recherche Scientifique (France), Swedish Research Council, German Research Foundation, National Institutes of Health (US), Ministerio de Ciencia, Innovación y Universidades (España), Agence Nationale de la Recherche (France), Israel Science Foundation, Austrian Science Fund, Biotechnology and Biological Sciences Research Council (UK), Swiss National Science Foundation, Kapun, Martin [0000-0002-3810-0504], Barrón, Maite G. [0000-0001-6146-6259], Staubach, Fabian [0000-0002-8097-2349], Vieira, Jorge [0000-0001-7032-5220], Obbard, Darren, J. [0000-0001-5392-8142], Rota-Stabelli, Omar [0000-0002-0030-7788], Kankare, Maaria [0000-0003-1541-9050], Haudry, Annabelle [0000-0001-6088-0909], Wiberg, R. Axel W. [0000-0002-8074-8670], Waidele, Lena [0000-0002-6323-6438], Kozeretska, Iryna [0000-0002-6485-1408], Pasyukova, Elena G. [0000-0002-6491-8561], Loeschcke, Volker [0000-0003-1450-0754], Pascual, Marta [0000-0002-6189-0612], Vieira, Cristina P. [0000-0002-7139-2107], Serga, Svitlana [0000-0003-1875-3185], Montchamp-Moreau, Catherine [0000-0002-5044-9709], Abbott, Jessica [0000-0002-8743-2089], Gibert, Patricia [0000-0002-9461-6820], Porcelli, Damiano [0000-0002-9019-5758], Posnien, Nico [0000-0003-0700-5595], Grath, Sonja [0000-0003-3621-736X], Sucena, Élio [0000-0001-8810-870X], Bergland, Alan O. [0000-0001-7145-7575], Onder, Banu Sebnem [0000-0002-3003-248X], Argyridou, Eliza [0000-0002-6890-4642], Guio, Lain [0000-0002-5481-5200], Schou, Mads Fristrup [0000-0001-5521-5269], Deplancke, Bart [0000-0001-9935-843X], Vieira, Cristina [0000-0003-3414-3993], Ritchie, Michael G. [0000-0001-7913-8675], Zwaan, Blas J. [0000-0002-8221-4998], Tauber, Eran [0000-0003-4018-6535], Orengo, Dorcas J. [0000-0001-7911-3224], Puerma, Eva [0000-0001-7261-187X], Aguadé i Porres, Montserrat [0000-0002-3884-7800], Schmidt, Paul S. [0000-0002-8076-6705], Parsch, John [0000-0001-9068-5549], Betancourt, Andrea J. [0000-0001-9351-1413], Flatt, Thomas [0000-0002-5990-1503], González Pérez, Josefa [0000-0001-9824-027X], Kapun, Martin, Barrón, Maite G., Staubach, Fabian, Vieira, Jorge, Obbard, Darren, J., Rota-Stabelli, Omar, Kankare, Maaria, Haudry, Annabelle, Wiberg, R. Axel W., Waidele, Lena, Kozeretska, Iryna, Pasyukova, Elena G., Loeschcke, Volker, Pascual, Marta, Vieira, Cristina P., Serga, Svitlana, Montchamp-Moreau, Catherine, Abbott, Jessica, Gibert, Patricia, Porcelli, Damiano, Posnien, Nico, Grath, Sonja, Sucena, Élio, Bergland, Alan O., Garcia Guerreiro, Maria Pilar, Onder, Banu Sebnem, Argyridou, Eliza, Guio, Lain, Schou, Mads Fristrup, Deplancke, Bart, Vieira, Cristina, Ritchie, Michael G., Zwaan, Blas J., Tauber, Eran, Orengo, Dorcas J., Puerma, Eva, Aguadé i Porres, Montserrat, Schmidt, Paul S., Parsch, John, Betancourt, Andrea J., Flatt, Thomas, and González Pérez, Josefa

Abstract

Genetic variation is the fuel of evolution. However, analyzing evolutionary dynamics in natural populations is challenging, sequencing of entire populations remains costly and comprehensive sampling logistically difficult. To tackle this issue and to define relevant spatial and temporal scales of variation, we have founded the European Drosophila Population Genomics Consortium (DrosEU). Here we present the first analysis of 48 D. melanogaster population samples collected across Europe in 2014. Our analysis uncovers novel patterns of variation at multiple levels: genome-wide neutral SNPs, mtDNA haplotypes, inversions, and TEs showing previously cryptic longitudinal population structure; signatures of selective sweeps shared among populations; presumably adaptive clines in inversions; and geographic variation in TEs. Additionally, we document highly variable microbiota and identify several new Drosophila viruses. Our study reveals novel aspects of the population biology of D. melanogaster and illustrates the power of extensive sampling and pooled sequencing of populations on a continent-wide scale.

Published
2018

9. Genomic Analysis of European Drosophila melanogaster Populations Reveals Longitudinal Structure, Continent-Wide Selection, and Previously Unknown DNA Viruses

Author

Kapun, Martin, Barrón, Maite G, Staubach, Fabian, Obbard, Darren J, Wiberg, R Axel W, Vieira, Jorge, Goubert, Clément, Rota-Stabelli, Omar, Kankare, Maaria, Bogaerts-Márquez, María, Haudry, Annabelle, Waidele, Lena, Kozeretska, Iryna, Pasyukova, Elena G, Loeschcke, Volker, Pascual, Marta, Vieira, Cristina P, Serga, Svitlana, Montchamp-Moreau, Catherine, Abbott, Jessica, Gibert, Patricia, Porcelli, Damiano, Posnien, Nico, Sánchez-Gracia, Alejandro, Grath, Sonja, Sucena, Élio, Bergland, Alan O, Guerreiro, Maria Pilar Garcia, Onder, Banu Sebnem, Argyridou, Eliza, University of Zurich, Falush, Daniel, and Kapun, Martin

Subjects
10127 Institute of Evolutionary Biology and Environmental Studies, 1105 Ecology, Evolution, Behavior and Systematics, 1311 Genetics, Ecology, Behavior and Systematics, Evolution, 1312 Molecular Biology, Genetics, 570 Life sciences, biology, 590 Animals (Zoology), Molecular Biology
Published
2020

10. Evolution of genes and genomes on the Drosophila phylogeny

Author

Clark, Andrew G., Eisen, Michael B., Smith, Douglas R., Bergman, Casey M., Oliver, Brian, Markow, Therese A., Kaufman, Thomas C., Kellis, Manolis, Gelbart, William, Iyer, Venky N., Pollard, Daniel A., Sackton, Timothy B., Larracuente, Amanda M., Singh, Nadia D., Abad, Jose P., Abt, Dawn N., Adryan, Boris, Aguade, Montserrat, Akashi, Hiroshi, Anderson, Wyatt W., Aquadro, Charles F., Ardell, David H., Arguello, Roman, Artieri, Carlo G., Barbash, Daniel A., Barker, Daniel, Barsanti, Paolo, Batterham, Phil, Batzoglou, Serafim, Begun, Dave, Bhutkar, Arjun, Blanco, Enrico, Bosak, Stephanie A., Bradley, Robert K., Brand, Adrianne D., Brent, Michael R., Brooks, Angela N., Brown, Randall H., Butlin, Roger K., Caggese, Corrado, Calvi, Brian R., Bernardo de Carvalho, A., Caspi, Anat, Castrezana, Sergio, Celniker, Susan E., Chang, Jean L., Chapple, Charles, Chatterji, Sourav, Chinwalla, Asif, Civetta, Alberto, Clifton, Sandra W., Comeron, Josep M., Costello, James C., Coyne, Jerry A., Daub, Jennifer, David, Robert G., Delcher, Arthur L., Delehaunty, Kim, Do, Chuong B., Ebling, Heather, Edwards, Kevin, Eickbush, Thomas, Evans, Jay D., Filipski, Alan, Findeiß, Sven, Freyhult, Eva, Fulton, Lucinda, Fulton, Robert, Garcia, Ana C. L., Gardiner, Anastasia, Garfield, David A., Garvin, Barry E., Gibson, Greg, Gilbert, Don, Gnerre, Sante, Godfrey, Jennifer, Good, Robert, Gotea, Valer, Gravely, Brenton, Greenberg, Anthony J., Griffiths-Jones, Sam, Gross, Samuel, Guigo, Roderic, Gustafson, Erik A., Haerty, Wilfried, Hahn, Matthew W., Halligan, Daniel L., Halpern, Aaron L., Halter, Gillian M., Han, Mira V., Heger, Andreas, Hillier, LaDeana, Hinrichs, Angie S., Holmes, Ian, Hoskins, Roger A., Hubisz, Melissa J., Hultmark, Dan, Huntley, Melanie A., Jaffe, David B., Jagadeeshan, Santosh, Jeck, William R., Johnson, Justin, Jones, Corbin D., Jordan, William C., Karpen, Gary H., Kataoka, Eiko, Keightley, Peter D., Kheradpour, Pouya, Kirkness, Ewen F., Koerich, Leonardo B., Kristiansen, Karsten, Kudrna, Dave, Kulathinal, Rob J., Kumar, Sudhir, Kwok, Roberta, Lander, Eric, Langley, Charles H., Lapoint, Richard, Lazzaro, Brian P., Lee, So-Jeong, Levesque, Lisa, Li, Ruiqiang, Lin, Chiao-Feng, Lin, Michael F., Lindblad-Toh, Kerstin, Llopart, Ana, Long, Manyuan, Low, Lloyd, Lozovsky, Elena, Lu, Jian, Luo, Meizhong, Machado, Carlos A., Makalowski, Wojciech, Marzo, Mar, Matsuda, Muneo, Matzkin, Luciano, McAllister, Bryant, McBride, Carolyn S., McKernan, Brendan, McKernan, Kevin, Mendez-Lago, Maria, Minx, Patrick, Mollenhauer, Michael U., Montooth, Kristi, Mount, Stephen M., Mu, Xu, Myers, Eugene, Negre, Barbara, Newfeld, Stuart, Nielsen, Rasmus, Noor, Mohamed A. F., O'Grady, Patrick, Pachter, Lior, Papaceit, Montserrat, Parisi, Matthew J., Parisi, Michael, Parts, Leopold, Pedersen, Jakob S., Pesole, Graziano, Phillippy, Adam M., Ponting, Chris P., Pop, Mihai, Porcelli, Damiano, Powell, Jeffrey R., Prohaska, Sonja, Pruitt, Kim, Puig, Marta, Quesneville, Hadi, Ravi Ram, Kristipati, Rand, David, Rasmussen, Matthew D., Reed, Laura K., Reenan, Robert, Reily, Amy, Remington, Karin A., Rieger, Tania T., Ritchie, Michael G., Robin, Charles, Rogers, Yu-Hui, Rohde, Claudia, Rozas, Julio, Rubenfield, Marc J., Ruiz, Alfredo, Russo, Susan, Salzberg, Steven L., Sanchez-Gracia, Alejandro, Saranga, David J., Sato, Hajime, Schaeffer, Stephen W., Schatz, Michael C., Schlenke, Todd, Schwartz, Russell, Segarra, Carmen, Singh, Rama S., Sirot, Laura, Sirota, Marina, Sisneros, Nicholas B., Smith, Chris D., Smith, Temple F., Spieth, John, Stage, Deborah E., Stark, Alexander, Stephan, Wolfgang, Strausberg, Robert L., Strempel, Sebastian, Sturgill, David, Sutton, Granger, Sutton, Granger G., Tao, Wei, Teichmann, Sarah, Tobari, Yoshiko N., Tomimura, Yoshihiko, Tsolas, Jason M., Valente, Vera L. S., Venter, Eli, Craig Venter, J., Vicario, Saverio, Vieira, Filipe G., Vilella, Albert J., Villasante, Alfredo, Walenz, Brian, Wang, Jun, Wasserman, Marvin, Watts, Thomas, Wilson, Derek, Wilson, Richard K., Wing, Rod A., Wolfner, Mariana F., Wong, Alex, Ka-Shu Wong, Gane, Wu, Chung-I, Wu, Gabriel, Yamamoto, Daisuke, Yang, Hsiao-Pei, Yang, Shiaw-Pyng, Yorke, James A., Yoshida, Kiyohito, Zdobnov, Evgeny, Zhang, Peili, Zhang, Yu, Zimin, Aleksey V., Baldwin, Jennifer, Abdouelleil, Amr, Abdulkadir, Jamal, Abebe, Adal, Abera, Brikti, Abreu, Justin, Christophe Acer, St, Aftuck, Lynne, Alexander, Allen, An, Peter, Anderson, Erica, Anderson, Scott, Arachi, Harindra, Azer, Marc, Bachantsang, Pasang, Barry, Andrew, Bayul, Tashi, Berlin, Aaron, Bessette, Daniel, Bloom, Toby, Blye, Jason, Boguslavskiy, Leonid, Bonnet, Claude, Boukhgalter, Boris, Bourzgui, Imane, Brown, Adam, Cahill, Patrick, Channer, Sheridon, Cheshatsang, Yama, Chuda, Lisa, Citroen, Mieke, Collymore, Alville, Cooke, Patrick, Costello, Maura, D'Aco, Katie, Daza, Riza, De Haan, Georgius, DeGray, Stuart, DeMaso, Christina, Dhargay, Norbu, Dooley, Kimberly, Dooley, Erin, Doricent, Missole, Dorje, Passang, Dorjee, Kunsang, Dupes, Alan, Elong, Richard, Falk, Jill, Farina, Abderrahim, Faro, Susan, Ferguson, Diallo, Fisher, Sheila, Foley, Chelsea D., Franke, Alicia, Friedrich, Dennis, Gadbois, Loryn, Gearin, Gary, Gearin, Christina R., Giannoukos, Georgia, Goode, Tina, Graham, Joseph, Grandbois, Edward, Grewal, Sharleen, Gyaltsen, Kunsang, Hafez, Nabil, Hagos, Birhane, Hall, Jennifer, Henson, Charlotte, Hollinger, Andrew, Honan, Tracey, Huard, Monika D., Hughes, Leanne, Hurhula, Brian, Erii Husby, M, Kamat, Asha, Kanga, Ben, Kashin, Seva, Khazanovich, Dmitry, Kisner, Peter, Lance, Krista, Lara, Marcia, Lee, William, Lennon, Niall, Letendre, Frances, LeVine, Rosie, Lipovsky, Alex, Liu, Xiaohong, Liu, Jinlei, Liu, Shangtao, Lokyitsang, Tashi, Lokyitsang, Yeshi, Lubonja, Rakela, Lui, Annie, MacDonald, Pen, Magnisalis, Vasilia, Maru, Kebede, Matthews, Charles, McCusker, William, McDonough, Susan, Mehta, Teena, Meldrim, James, Meneus, Louis, Mihai, Oana, Mihalev, Atanas, Mihova, Tanya, Mittelman, Rachel, Mlenga, Valentine, Montmayeur, Anna, Mulrain, Leonidas, Navidi, Adam, Naylor, Jerome, Negash, Tamrat, Nguyen, Thu, Nguyen, Nga, Nicol, Robert, Norbu, Choe, Norbu, Nyima, Novod, Nathaniel, O'Neill, Barry, Osman, Sahal, Markiewicz, Eva, Oyono, Otero L., Patti, Christopher, Phunkhang, Pema, Pierre, Fritz, Priest, Margaret, Raghuraman, Sujaa, Rege, Filip, Reyes, Rebecca, Rise, Cecil, Rogov, Peter, Ross, Keenan, Ryan, Elizabeth, Settipalli, Sampath, Shea, Terry, Sherpa, Ngawang, Shi, Lu, Shih, Diana, Sparrow, Todd, Spaulding, Jessica, Stalker, John, Stange-Thomann, Nicole, Stavropoulos, Sharon, Stone, Catherine, Strader, Christopher, Tesfaye, Senait, Thomson, Talene, Thoulutsang, Yama, Thoulutsang, Dawa, Topham, Kerri, Topping, Ira, Tsamla, Tsamla, Vassiliev, Helen, Vo, Andy, Wangchuk, Tsering, Wangdi, Tsering, Weiand, Michael, Wilkinson, Jane, Wilson, Adam, Yadav, Shailendra, Young, Geneva, Yu, Qing, Zembek, Lisa, Zhong, Danni, Zimmer, Andrew, Zwirko, Zac, Alvarez, Pablo, Brockman, Will, Butler, Jonathan, Chin, CheeWhye, Grabherr, Manfred, Kleber, Michael, Mauceli, Evan, and MacCallum, Iain

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Drosophila 12 Genomes Consortium; Project Leaders; Andrew G. Clark (corresponding author) [1]; Michael B. Eisen (corresponding author) [2, 3]; Douglas R. Smith (corresponding author) [4]; Casey M. Bergman (corresponding [...]

Published
2007
Full Text
View/download PDF

11. Genomic Analysis of European Drosophila melanogaster Populations Reveals Longitudinal Structure, Continent-Wide Selection, and Previously Unknown DNA Viruses

Author

CSIC - Unidad de Recursos de Información Científica para la Investigación (URICI), Stanford University, European Society for Evolutionary Biology, Wellcome Trust, University of Freiburg, German Research Foundation, Academy of Finland, Russian Foundation for Basic Research, Danish Natural Science Research Council, Ministerio de Economía y Competitividad (España), Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Centre National de la Recherche Scientifique (France), Swedish Research Council, National Institutes of Health (US), The Scientific and Technological Research Council of Turkey, Agence Nationale de la Recherche (France), European Commission, Israel Science Foundation, Austrian Science Fund, Biotechnology and Biological Sciences Research Council (UK), Swiss National Science Foundation, European Research Council, Generalitat de Catalunya, Kapun, Martin, Barrón, Maite G., Staubach, Fabian, Obbard, Darren, J., Wiberg, R. Axel W., Vieira, Jorge, Goubert, Clément, Rota-Stabelli, Omar, Kankare, Maaria, Bogaerts-Márquez, María, Haudry, Annabelle, Waidele, Lena, Kozeretska, Iryna, Pasyukova, Elena G., Loeschcke, Volker, Pascual, Marta, Vieira, Cristina P., Serga, Svitlana, Montchamp-Moreau, Catherine, Abbott, Jessica, Gibert, Patricia, Porcelli, Damiano, Posnien, Nico, Sánchez-Gracia, Alejandro, Grath, Sonja, Sucena, Élio, Bergland, Alan O., Garcia Guerreiro, Maria Pilar, Onder, Banu Sebnem, Argyridou, Eliza, Guio, Lain, Schou, Mads Fristrup, Deplancke, Bart, Vieira, Cristina, Ritchie, Michael G., Zwaan, Blas J., Tauber, Eran, Orengo, Dorcas J., Puerma, Eva, Aguadé i Porres, Montserrat, Schmidt, Paul S., Parsch, John, Betancourt, Andrea J., Flatt, Thomas, González Pérez, Josefa, CSIC - Unidad de Recursos de Información Científica para la Investigación (URICI), Stanford University, European Society for Evolutionary Biology, Wellcome Trust, University of Freiburg, German Research Foundation, Academy of Finland, Russian Foundation for Basic Research, Danish Natural Science Research Council, Ministerio de Economía y Competitividad (España), Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Centre National de la Recherche Scientifique (France), Swedish Research Council, National Institutes of Health (US), The Scientific and Technological Research Council of Turkey, Agence Nationale de la Recherche (France), European Commission, Israel Science Foundation, Austrian Science Fund, Biotechnology and Biological Sciences Research Council (UK), Swiss National Science Foundation, European Research Council, Generalitat de Catalunya, Kapun, Martin, Barrón, Maite G., Staubach, Fabian, Obbard, Darren, J., Wiberg, R. Axel W., Vieira, Jorge, Goubert, Clément, Rota-Stabelli, Omar, Kankare, Maaria, Bogaerts-Márquez, María, Haudry, Annabelle, Waidele, Lena, Kozeretska, Iryna, Pasyukova, Elena G., Loeschcke, Volker, Pascual, Marta, Vieira, Cristina P., Serga, Svitlana, Montchamp-Moreau, Catherine, Abbott, Jessica, Gibert, Patricia, Porcelli, Damiano, Posnien, Nico, Sánchez-Gracia, Alejandro, Grath, Sonja, Sucena, Élio, Bergland, Alan O., Garcia Guerreiro, Maria Pilar, Onder, Banu Sebnem, Argyridou, Eliza, Guio, Lain, Schou, Mads Fristrup, Deplancke, Bart, Vieira, Cristina, Ritchie, Michael G., Zwaan, Blas J., Tauber, Eran, Orengo, Dorcas J., Puerma, Eva, Aguadé i Porres, Montserrat, Schmidt, Paul S., Parsch, John, Betancourt, Andrea J., Flatt, Thomas, and González Pérez, Josefa

Abstract

Genetic variation is the fuel of evolution, with standing genetic variation especially important for short-term evolution and local adaptation. To date, studies of spatiotemporal patterns of genetic variation in natural populations have been challenging, as comprehensive sampling is logistically difficult, and sequencing of entire populations costly. Here, we address these issues using a collaborative approach, sequencing 48 pooled population samples from 32 locations, and perform the first continent-wide genomic analysis of genetic variation in European Drosophila melanogaster. Our analyses uncover longitudinal population structure, provide evidence for continent-wide selective sweeps, identify candidate genes for local climate adaptation, and document clines in chromosomal inversion and transposable element frequencies. We also characterize variation among populations in the composition of the fly microbiome, and identify five new DNA viruses in our samples.

Published
2020

12. Genomic Analysis of European Drosophila melanogaster Populations Reveals Longitudinal Structure, Continent-Wide Selection, and Previously Unknown DNA Viruses

Author

Falush, Daniel, Falush, D ( Daniel ), Kapun, Martin; https://orcid.org/0000-0002-3810-0504, Barrón, Maite G, Staubach, Fabian, Obbard, Darren J, Wiberg, R Axel W; https://orcid.org/0000-0001-5392-8142, Vieira, Jorge, Goubert, Clément, Rota-Stabelli, Omar, Kankare, Maaria; https://orcid.org/0000-0003-1541-9050, Bogaerts-Márquez, María, Haudry, Annabelle, Waidele, Lena, Kozeretska, Iryna, Pasyukova, Elena G, Loeschcke, Volker, Pascual, Marta, Vieira, Cristina P, Serga, Svitlana, Montchamp-Moreau, Catherine, Abbott, Jessica, Gibert, Patricia, Porcelli, Damiano, Posnien, Nico; https://orcid.org/0000-0003-0700-5595, Sánchez-Gracia, Alejandro, Grath, Sonja, Sucena, Élio, Bergland, Alan O, Guerreiro, Maria Pilar Garcia, Onder, Banu Sebnem, Argyridou, Eliza, Falush, Daniel, Falush, D ( Daniel ), Kapun, Martin; https://orcid.org/0000-0002-3810-0504, Barrón, Maite G, Staubach, Fabian, Obbard, Darren J, Wiberg, R Axel W; https://orcid.org/0000-0001-5392-8142, Vieira, Jorge, Goubert, Clément, Rota-Stabelli, Omar, Kankare, Maaria; https://orcid.org/0000-0003-1541-9050, Bogaerts-Márquez, María, Haudry, Annabelle, Waidele, Lena, Kozeretska, Iryna, Pasyukova, Elena G, Loeschcke, Volker, Pascual, Marta, Vieira, Cristina P, Serga, Svitlana, Montchamp-Moreau, Catherine, Abbott, Jessica, Gibert, Patricia, Porcelli, Damiano, Posnien, Nico; https://orcid.org/0000-0003-0700-5595, Sánchez-Gracia, Alejandro, Grath, Sonja, Sucena, Élio, Bergland, Alan O, Guerreiro, Maria Pilar Garcia, Onder, Banu Sebnem, and Argyridou, Eliza

Abstract

Genetic variation is the fuel of evolution, with standing genetic variation especially important for short-term evolution and local adaptation. To date, studies of spatiotemporal patterns of genetic variation in natural populations have been challenging, as comprehensive sampling is logistically difficult, and sequencing of entire populations costly. Here, we address these issues using a collaborative approach, sequencing 48 pooled population samples from 32 locations, and perform the first continent-wide genomic analysis of genetic variation in European Drosophila melanogaster. Our analyses uncover longitudinal population structure, provide evidence for continent-wide selective sweeps, identify candidate genes for local climate adaptation, and document clines in chromosomal inversion and transposable element frequencies. We also characterize variation among populations in the composition of the fly microbiome, and identify five new DNA viruses in our samples.

Published
2020

14. Genomic Analysis of European Drosophila melanogaster Populations Reveals Longitudinal Structure, Continent-Wide Selection, and Previously Unknown DNA Viruses

Author

Kapun, Martin, primary, Barrón, Maite G, additional, Staubach, Fabian, additional, Obbard, Darren J, additional, Wiberg, R Axel W, additional, Vieira, Jorge, additional, Goubert, Clément, additional, Rota-Stabelli, Omar, additional, Kankare, Maaria, additional, Bogaerts-Márquez, María, additional, Haudry, Annabelle, additional, Waidele, Lena, additional, Kozeretska, Iryna, additional, Pasyukova, Elena G, additional, Loeschcke, Volker, additional, Pascual, Marta, additional, Vieira, Cristina P, additional, Serga, Svitlana, additional, Montchamp-Moreau, Catherine, additional, Abbott, Jessica, additional, Gibert, Patricia, additional, Porcelli, Damiano, additional, Posnien, Nico, additional, Sánchez-Gracia, Alejandro, additional, Grath, Sonja, additional, Sucena, Élio, additional, Bergland, Alan O, additional, Guerreiro, Maria Pilar Garcia, additional, Onder, Banu Sebnem, additional, Argyridou, Eliza, additional, Guio, Lain, additional, Schou, Mads Fristrup, additional, Deplancke, Bart, additional, Vieira, Cristina, additional, Ritchie, Michael G, additional, Zwaan, Bas J, additional, Tauber, Eran, additional, Orengo, Dorcas J, additional, Puerma, Eva, additional, Aguadé, Montserrat, additional, Schmidt, Paul, additional, Parsch, John, additional, Betancourt, Andrea J, additional, Flatt, Thomas, additional, and González, Josefa, additional

Published
2020
Full Text
View/download PDF

15. Additional file 1: of Chromatin accessibility plays a key role in selective targeting of Hox proteins

Author

Porcelli, Damiano, Fischer, Bettina, Russell, Steven, and White, Robert

Subjects
animal structures
Abstract

Figure S1. The association between Hox specificity and binding site affinity, binding region numbers and chromatin accessibility profiles; Figure S2. Hox, Hox+Hth, Hth and Exd binding in open and closed chromatin; Figure S3. Motif analysis showing individual motifs; Figure S4. De-novo motif analysis of Exd/Hth cofactor enhanced binding regions; Figure S5. Comparing the effects of Exd/Hth and Gcm: Chromatin accessibility in Hox + Exd/Hth compared to Hox + Gcm; Figure S6. Hox occupancy is more strongly associated with binding region chromatin accessibility than with binding affinity; Figure S7. The presence of Exd/Hth leads to both enhanced and reduced Abd-B binding; Figure S8. Comparison of Ubx and Dfd binding in presence of Gcm for regions in basal Kc167 closed chromatin; Table S1. ChIP-seq read overview; Table S2. ChIP-Seq binding region numbers; Table S3. Stable cell lines ATAC-seq read overview; Table S4. Cofactor-enhanced binding analysis of transient data in Hox group peak regions; Table S5. Increased chromatin accessibility analysis. (PDF 5942 kb)

Published
2019
Full Text
View/download PDF

16. The nuclear OXPHOS genes in insecta: a common evolutionary origin, a common cis-regulatory motif, a common destiny for gene duplicates

Author

Pesole Graziano, Barsanti Paolo, Porcelli Damiano, and Caggese Corrado

Subjects
Evolution, QH359-425
Abstract

Abstract Background When orthologous sequences from species distributed throughout an optimal range of divergence times are available, comparative genomics is a powerful tool to address problems such as the identification of the forces that shape gene structure during evolution, although the functional constraints involved may vary in different genes and lineages. Results We identified and annotated in the MitoComp2 dataset the orthologs of 68 nuclear genes controlling oxidative phosphorylation in 11 Drosophilidae species and in five non-Drosophilidae insects, and compared them with each other and with their counterparts in three vertebrates (Fugu rubripes, Danio rerio and Homo sapiens) and in the cnidarian Nematostella vectensis, taking into account conservation of gene structure and regulatory motifs, and preservation of gene paralogs in the genome. Comparative analysis indicates that the ancestral insect OXPHOS genes were intron rich and that extensive intron loss and lineage-specific intron gain occurred during evolution. Comparison with vertebrates and cnidarians also shows that many OXPHOS gene introns predate the cnidarian/Bilateria evolutionary split. The nuclear respiratory gene element (NRG) has played a key role in the evolution of the insect OXPHOS genes; it is constantly conserved in the OXPHOS orthologs of all the insect species examined, while their duplicates either completely lack the element or possess only relics of the motif. Conclusion Our observations reinforce the notion that the common ancestor of most animal phyla had intron-rich gene, and suggest that changes in the pattern of expression of the gene facilitate the fixation of duplications in the genome and the development of novel genetic functions.

Published
2007
Full Text
View/download PDF

19. Genomic analysis of EuropeanDrosophila melanogasterpopulations reveals longitudinal structure, continent-wide selection, and previously unknown DNA viruses

Author

Kapun, Martin, primary, Barrón, Maite G., additional, Staubach, Fabian, additional, Obbard, Darren J., additional, Wiberg, R. Axel W., additional, Vieira, Jorge, additional, Goubert, Clément, additional, Rota-Stabelli, Omar, additional, Kankare, Maaria, additional, Bogaerts-Márquez, María, additional, Haudry, Annabelle, additional, Waidele, Lena, additional, Kozeretska, Iryna, additional, Pasyukova, Elena G., additional, Loeschcke, Volker, additional, Pascual, Marta, additional, Vieira, Cristina P., additional, Serga, Svitlana, additional, Montchamp-Moreau, Catherine, additional, Abbott, Jessica, additional, Gibert, Patricia, additional, Porcelli, Damiano, additional, Posnien, Nico, additional, Sánchez-Gracia, Alejandro, additional, Grath, Sonja, additional, Sucena, Élio, additional, Bergland, Alan O., additional, Guerreiro, Maria Pilar Garcia, additional, Onder, Banu Sebnem, additional, Argyridou, Eliza, additional, Guio, Lain, additional, Schou, Mads Fristrup, additional, Deplancke, Bart, additional, Vieira, Cristina, additional, Ritchie, Michael G., additional, Zwaan, Bas J., additional, Tauber, Eran, additional, Orengo, Dorcas J., additional, Puerma, Eva, additional, Aguadé, Montserrat, additional, Schmidt, Paul S., additional, Parsch, John, additional, Betancourt, Andrea J., additional, Flatt, Thomas, additional, and González, Josefa, additional

Published
2018
Full Text
View/download PDF

23. The MitoDrome database annotates and compares the OXPHOS nuclear genes of Drosophila melanogaster, Drosophila pseudoobscura and Anopheles gambiae.

Author

D'Elia D, Catalano D, Licciulli F, Turi A, Tripoli G, Porcelli D, Saccone C, and Caggese C

Subjects
Animals, Biological Evolution, Drosophila melanogaster genetics, Humans, Mitochondria genetics, User-Computer Interface, Anopheles genetics, Databases, Nucleic Acid, Drosophila genetics, Genes, Insect, Oxidative Phosphorylation
Abstract

The oxidative phosphorylation (OXPHOS) is the primary energy-producing process of all aerobic organisms and the only cellular function under the dual control of both the mitochondrial and the nuclear genomes. Functional characterization and evolutionary study of the OXPHOS system is of great importance for the understanding of many as yet unclear aspects of nucleus-mitochondrion genomic co-evolution and co-regulation gene networks. The MitoDrome database is a web-based database which provides genomic annotations about nuclear genes of Drosophila melanogaster encoding for mitochondrial proteins. Recently, MitoDrome has included a new section annotating genomic information about OXPHOS genes in Drosophila pseudoobscura and Anopheles gambiae and their comparative analysis with their Drosophila melanogaster and human counterparts. The introduction of this new comparative annotation section into MitoDrome is expected to be a useful resource for both functional and structural genomics related to the OXPHOS system.

Published
2006
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results