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11. Generating genomic platforms to study Candida albicans pathogenesis

Author

Legrand, Mélanie, primary, Bachellier-Bassi, Sophie, additional, Lee, Keunsook K, additional, Chaudhari, Yogesh, additional, Tournu, Hélène, additional, Arbogast, Laurence, additional, Boyer, Hélène, additional, Chauvel, Murielle, additional, Cabral, Vitor, additional, Maufrais, Corinne, additional, Nesseir, Audrey, additional, Maslanka, Irena, additional, Permal, Emmanuelle, additional, Rossignol, Tristan, additional, Walker, Louise A, additional, Zeidler, Ute, additional, Znaidi, Sadri, additional, Schoeters, Floris, additional, Majgier, Charlotte, additional, Julien, Renaud A, additional, Ma, Laurence, additional, Tichit, Magali, additional, Bouchier, Christiane, additional, Van Dijck, Patrick, additional, Munro, Carol A, additional, and d’Enfert, Christophe, additional

Published
2018
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12. Gene flow contributes to diversification of the major fungal pathogen Candida albicans

Author

Ropars, Jeanne, primary, Maufrais, Corinne, additional, Diogo, Dorothée, additional, Marcet-Houben, Marina, additional, Perin, Aurélie, additional, Sertour, Natacha, additional, Mosca, Kevin, additional, Permal, Emmanuelle, additional, Laval, Guillaume, additional, Bouchier, Christiane, additional, Ma, Laurence, additional, Schwartz, Katja, additional, Voelz, Kerstin, additional, May, Robin C., additional, Poulain, Julie, additional, Battail, Christophe, additional, Wincker, Patrick, additional, Borman, Andrew M., additional, Chowdhary, Anuradha, additional, Fan, Shangrong, additional, Kim, Soo Hyun, additional, Le Pape, Patrice, additional, Romeo, Orazio, additional, Shin, Jong Hee, additional, Gabaldon, Toni, additional, Sherlock, Gavin, additional, Bougnoux, Marie-Elisabeth, additional, and d’Enfert, Christophe, additional

Published
2018
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13. Generating genomic platforms to studyCandida albicanspathogenesis

Author

Legrand, Mélanie, primary, Bachellier-Bassi, Sophie, additional, Lee, Keunsook K., additional, Chaudhari, Yogesh, additional, Tournu, Hélène, additional, Arbogast, Laurence, additional, Boyer, Hélène, additional, Chauvel, Murielle, additional, Cabral, Vitor, additional, Maufrais, Corinne, additional, Nesseir, Audrey, additional, Maslanka, Irena, additional, Permal, Emmanuelle, additional, Rossignol, Tristan, additional, Walker, Louise A., additional, Zeidler, Ute, additional, Znaidi, Sadri, additional, Schoeters, Floris, additional, Majgier, Charlotte, additional, Julien, Renaud A., additional, Ma, Laurence, additional, Tichit, Magali, additional, Bouchier, Christiane, additional, Dijck, Patrick Van, additional, Munro, Carol A., additional, and d’Enfert, Christophe, additional

Published
2018
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14. Gene flow contributes to diversification of the major fungal pathogen Candida albicans.

Author

Diogo, Dorothée, Perin, Aurélie, Sertour, Natacha, Mosca, Kevin, Permal, Emmanuelle, d'Enfert, Christophe, Ropars, Jeanne, Bougnoux, Marie-Elisabeth, Maufrais, Corinne, Marcet-Houben, Marina, Battail, Christophe, Poulain, Julie, Wincker, Patrick, Borman, Andrew M., Chowdhary, Anuradha, Fan, Shangrong, Soo Hyun Kim, Jong Hee Shin, Pape, Patrice Le, and Romeo, Orazio

Subjects
POPULATION, GENETICS, CANDIDA albicans, MYCOSES, MORTALITY, GENE flow, MORPHOGENESIS
Abstract

Elucidating population structure and levels of genetic diversity and recombination is necessary to understand the evolution and adaptation of species. Candida albicans is the second most frequent agent of human fungal infections worldwide, causing high-mortality rates. Here we present the genomic sequences of 182 C. albicans isolates collected worldwide, including commensal isolates, as well as ones responsible for superficial and invasive infections, constituting the largest dataset to date for this major fungal pathogen. Although, C. albicans shows a predominantly clonal population structure, we find evidence of gene flow between previously known and newly identified genetic clusters, supporting the occurrence of (para) sexuality in nature. A highly clonal lineage, which experimentally shows reduced fitness, has undergone pseudogenization in genes required for virulence and morphogenesis, which may explain its niche restriction. Candida albicans thus takes advantage of both clonality and gene flow to diversify. [ABSTRACT FROM AUTHOR]

Published
2018
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15. Lepido-DB, a new bioinformatic resource for the annotation and cross-comparisons of lepidopteran genomes

Author

Legeai, Fabrice, D'Alençon, Emmanuelle, Cousserans, François, Sezutsu, Hideki, Permal, Emmanuelle, Gordon, Karl, Quesneville, Hadi, Feyereisen, René, Fournier, Philippe, Biologie des organismes et des populations appliquées à la protection des plantes (BIO3P), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Biological systems and models, bioinformatics and sequences (SYMBIOSE), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria), Biologie Intégrative et Virologie des Insectes [Univ. de Montpellier II] (BIVI), Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2), National Institute of Agrobiological Sciences (NIAS), National Institute of Agrobiological Sciences, Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), CSIRO Entomology [Canberra], CSIRO Entomology, Institut Jacques Monod (IJM (UMR_7592)), Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7), Institut Sophia Agrobiotech [Sophia Antipolis] (ISA), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), Université Montpellier 2 - Sciences et Techniques (UM2)-Institut National de la Recherche Agronomique (INRA), Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Inria Rennes – Bretagne Atlantique, Institut Sophia Agrobiotech (ISA), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), and COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Recherche Agronomique (INRA)

Subjects
[INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]
Abstract

International audience; Lepido-DB is a centralized bioinformatic resource that was first developed to facilitate the comparative genomics of two major lepidopteran pests, the noctuid moths Helicoverpa armigera and Spodoptera frugiperda, by the analyzis of syntenic relationships and genome rearrangements of 15 pairs of BACs sequences and their corresponding colinear regions extracted from 10 Bombyx mori chromosomes. In this context, Lepido-DB Information System was designed to store, organize, display and distribute various genomic data and annotations of the three species. For instance, we supplied Lepido-DB with the KAIKOGAAS automatic annotations, the comparisons to insects proteomes and UniProt, the alignments of transcript sequences (retrieved from the Spodoptera SpodoBase, from CSIRO Helicoverpa ESTs or from NCBI Bombyx ESTs), the REPET pipeline's transposable elements predictions, or results of different cross-comparisons process to emphasize conserved regions and orthologous genes. The system was constructed using open source software tools from the Generic Model Organism Database (GMOD, http://www.gmod.org) including - a Chado database, - Gbrowse, a simple but rapid genome browser, - CMAP a graphical tool which facilitates the navigation within multiple maps or genome sequences, - Apollo, an application for the manual curation. Finally, beside a blast search and a full text search facilities, we released a gene report system offering gene information at a glance, such as transcripts and peptides sequences, functional annotations, or expression level based on its EST coverage. Lepido-DB can be accessed at http://www.inra.fr/lepidodb. In a larger scope, ensuing the AphidBase experience, this system may definitely support complete genomes sequencing and annotation projects, or any other project based on deep sequencing strategies (expression profiling by RNA-Seq, variability studies, ChIP- Seq, ...) for various Lep species.

Published
2009

17. Genome Sequence of the Pea Aphid Acyrthosiphon pisum

Author

Richards, Stephen, Gibbs, Richard A., Gerardo, Nicole M., Moran, Nancy, Nakabachi, Atsushi, Stern, David, Tagu, Denis, Wilson, Alex C. C., Muzny, Donna, Kovar, Christie, Cree, Andy, Chacko, Joseph, Chandrabose, Mimi N., Dao, Marvin Diep, Dinh, Huyen H., Gabisi, Ramatu Ayiesha, Hines, Sandra, Hume, Jennifer, Jhangian, Shalini N., Joshi, Vandita, Lewis, Lora R., Liu, Yih-shin, Lopez, John, Morgan, Margaret B., Nguyen, Ngoc Bich, Okwuonu, Geoffrey O., Ruiz, San Juana, Santibanez, Jireh, Wright, Rita A., Fowler, Gerald R., Hitchens, Matthew E., Lozado, Ryan J., Moen, Charles, Steffen, David, Warren, James T., Zhang, Jingkun, Nazareth, Lynne V., Chavez, Dean, Davis, Clay, Lee, Sandra L., Patel, Bella Mayurkumar, Pu, Ling-Ling, Bell, Stephanie N., Johnson, Angela Jolivet, Vattathil, Selina, Williams, Rex L., Jr., Shigenobu, Shuji, Dang, Phat M., Morioka, Mizue, Fukatsu, Takema, Kudo, Toshiaki, Miyagishima, Shin-ya, Jiang, Huaiyang, Worley, Kim C., Legeai, Fabrice, Gauthier, Jean-Pierre, Collin, Olivier, Zhang, Lan, Chen, Hsiu-Chuan, Ermolaeva, Olga, Hlavina, Wratko, Kapustin, Yuri, Kiryutin, Boris, Kitts, Paul, Maglott, Donna, Murphy, Terence, Pruitt, Kim, Sapojnikov, Victor, Souvorov, Alexandre, Thibaud-Nissen, Francoise, Camara, Francisco, Guigo, Roderic, Stanke, Mario, Solovyev, Victor, Kosarev, Peter, Gilbert, Don, Gabaldon, Toni, Huerta-Cepas, Jaime, Marcet-Houben, Marina, Pignatelli, Miguel, Moya, Andres, Rispe, Claude, Ollivier, Morgane, Quesneville, Hadi, Permal, Emmanuelle, Llorens, Carlos, Futami, Ricardo, Hedges, Dale, Robertson, Hugh M., Alioto, Tyler, Mariotti, Marco, Nikoh, Naruo, McCutcheon, John P., Burke, Gaelen, Kamins, Alexandra, Latorre, Amparo, Moran, Nancy A., Ashton, Peter, Calevro, Federica, Charles, Hubert, Colella, Stefano, Douglas, Angela, Jander, Georg, Jones, Derek H., Febvay, Gerard, Kamphuis, Lars G., Kushlan, Philip F., Macdonald, Sandy, Ramsey, John, Schwartz, Julia, Seah, Stuart, Thomas, Gavin, Vellozo, Augusto, Cass, Bodil, Degnan, Patrick, Hurwitz, Bonnie, Leonardo, Teresa, Koga, Ryuichi, Altincicek, Boran, Anselme, Caroline, Atamian, Hagop, Barribeau, Seth M., de Vos, Martin, Duncan, Elizabeth J., Evans, Jay, Ghanim, Murad, Heddi, Abdelaziz, Kaloshian, Isgouhi, Vincent-Monegat, Carole, Parker, Ben J., Perez-Brocal, Vicente, Rahbe, Yvan, Spragg, Chelsea J., Tamames, Javier, Tamarit, Daniel, Tamborindeguy, Cecilia, Vilcinskas, Andreas, Bickel, Ryan D., Brisson, Jennifer A., Butts, Thomas, Chang, Chun-che, Christiaens, Olivier, Davis, Gregory K., Duncan, Elizabeth, Ferrier, David, Iga, Masatoshi, Janssen, Ralf, Lu, Hsiao-Ling, McGregor, Alistair, Miura, Toru, Smagghe, Guy, Smith, James, van der Zee, Maurijn, Velarde, Rodrigo, Wilson, Megan, Dearden, Peter, Edwards, Owain R., Gordon, Karl, Hilgarth, Roland S., Rider, Stanley Dean, Jr., Srinivasan, Dayalan, Walsh, Thomas K., Ishikawa, Asano, Jaubert-Possamai, Stephanie, Fenton, Brian, Huang, Wenting, Rizk, Guillaume, Lavenier, Dominique, Nicolas, Jacques, Smadja, Carole, Zhou, Jing-Jiang, Vieira, Filipe G., He, Xiao-Li, Liu, Renhu, Rozas, Julio, Field, Linda M., Ashton, Peter D., Campbell, Peter, Carolan, James C., Douglas, Angela E., Fitzroy, Carol I. J., Reardon, Karen T., Reeck, Gerald R., Singh, Karam, Wilkinson, Thomas L., Huybrechts, Jurgen, Abdel-latief, Mohatmed, Robichon, Alain, Veenstra, Jan A., Hauser, Frank, Cazzamali, Giuseppe, Schneider, Martina, Williamson, Michael, Stafflinger, Elisabeth, Hansen, Karina K., Grimmelikhuijzen, Cornelis J. P., Price, Daniel R. G., Caillaud, Marina, van Fleet, Eric, Ren, Qinghu, Gatehouse, John A., Brault, Veronique, Monsion, Baptiste, Diaz, Jason, Hunnicutt, Laura, Ju, Ho-Jong, Pechuan, Ximo, Aguilar, Jose, Cortes, Teresa, Ortiz-Rivas, Benjamin, Martinez-Torres, David, Dombrovsky, Aviv, Dale, Richard P., Davies, T. G. Emyr, Williamson, Martin S., Jones, Andrew, Sattelle, David, Williamson, Sally, Wolstenholme, Adrian, Cottret, Ludovic, Sagot, Marie France, Heckel, David G., Hunter, Wayne, Richards, Stephen, Gibbs, Richard A., Gerardo, Nicole M., Moran, Nancy, Nakabachi, Atsushi, Stern, David, Tagu, Denis, Wilson, Alex C. C., Muzny, Donna, Kovar, Christie, Cree, Andy, Chacko, Joseph, Chandrabose, Mimi N., Dao, Marvin Diep, Dinh, Huyen H., Gabisi, Ramatu Ayiesha, Hines, Sandra, Hume, Jennifer, Jhangian, Shalini N., Joshi, Vandita, Lewis, Lora R., Liu, Yih-shin, Lopez, John, Morgan, Margaret B., Nguyen, Ngoc Bich, Okwuonu, Geoffrey O., Ruiz, San Juana, Santibanez, Jireh, Wright, Rita A., Fowler, Gerald R., Hitchens, Matthew E., Lozado, Ryan J., Moen, Charles, Steffen, David, Warren, James T., Zhang, Jingkun, Nazareth, Lynne V., Chavez, Dean, Davis, Clay, Lee, Sandra L., Patel, Bella Mayurkumar, Pu, Ling-Ling, Bell, Stephanie N., Johnson, Angela Jolivet, Vattathil, Selina, Williams, Rex L., Jr., Shigenobu, Shuji, Dang, Phat M., Morioka, Mizue, Fukatsu, Takema, Kudo, Toshiaki, Miyagishima, Shin-ya, Jiang, Huaiyang, Worley, Kim C., Legeai, Fabrice, Gauthier, Jean-Pierre, Collin, Olivier, Zhang, Lan, Chen, Hsiu-Chuan, Ermolaeva, Olga, Hlavina, Wratko, Kapustin, Yuri, Kiryutin, Boris, Kitts, Paul, Maglott, Donna, Murphy, Terence, Pruitt, Kim, Sapojnikov, Victor, Souvorov, Alexandre, Thibaud-Nissen, Francoise, Camara, Francisco, Guigo, Roderic, Stanke, Mario, Solovyev, Victor, Kosarev, Peter, Gilbert, Don, Gabaldon, Toni, Huerta-Cepas, Jaime, Marcet-Houben, Marina, Pignatelli, Miguel, Moya, Andres, Rispe, Claude, Ollivier, Morgane, Quesneville, Hadi, Permal, Emmanuelle, Llorens, Carlos, Futami, Ricardo, Hedges, Dale, Robertson, Hugh M., Alioto, Tyler, Mariotti, Marco, Nikoh, Naruo, McCutcheon, John P., Burke, Gaelen, Kamins, Alexandra, Latorre, Amparo, Moran, Nancy A., Ashton, Peter, Calevro, Federica, Charles, Hubert, Colella, Stefano, Douglas, Angela, Jander, Georg, Jones, Derek H., Febvay, Gerard, Kamphuis, Lars G., Kushlan, Philip F., Macdonald, Sandy, Ramsey, John, Schwartz, Julia, Seah, Stuart, Thomas, Gavin, Vellozo, Augusto, Cass, Bodil, Degnan, Patrick, Hurwitz, Bonnie, Leonardo, Teresa, Koga, Ryuichi, Altincicek, Boran, Anselme, Caroline, Atamian, Hagop, Barribeau, Seth M., de Vos, Martin, Duncan, Elizabeth J., Evans, Jay, Ghanim, Murad, Heddi, Abdelaziz, Kaloshian, Isgouhi, Vincent-Monegat, Carole, Parker, Ben J., Perez-Brocal, Vicente, Rahbe, Yvan, Spragg, Chelsea J., Tamames, Javier, Tamarit, Daniel, Tamborindeguy, Cecilia, Vilcinskas, Andreas, Bickel, Ryan D., Brisson, Jennifer A., Butts, Thomas, Chang, Chun-che, Christiaens, Olivier, Davis, Gregory K., Duncan, Elizabeth, Ferrier, David, Iga, Masatoshi, Janssen, Ralf, Lu, Hsiao-Ling, McGregor, Alistair, Miura, Toru, Smagghe, Guy, Smith, James, van der Zee, Maurijn, Velarde, Rodrigo, Wilson, Megan, Dearden, Peter, Edwards, Owain R., Gordon, Karl, Hilgarth, Roland S., Rider, Stanley Dean, Jr., Srinivasan, Dayalan, Walsh, Thomas K., Ishikawa, Asano, Jaubert-Possamai, Stephanie, Fenton, Brian, Huang, Wenting, Rizk, Guillaume, Lavenier, Dominique, Nicolas, Jacques, Smadja, Carole, Zhou, Jing-Jiang, Vieira, Filipe G., He, Xiao-Li, Liu, Renhu, Rozas, Julio, Field, Linda M., Ashton, Peter D., Campbell, Peter, Carolan, James C., Douglas, Angela E., Fitzroy, Carol I. J., Reardon, Karen T., Reeck, Gerald R., Singh, Karam, Wilkinson, Thomas L., Huybrechts, Jurgen, Abdel-latief, Mohatmed, Robichon, Alain, Veenstra, Jan A., Hauser, Frank, Cazzamali, Giuseppe, Schneider, Martina, Williamson, Michael, Stafflinger, Elisabeth, Hansen, Karina K., Grimmelikhuijzen, Cornelis J. P., Price, Daniel R. G., Caillaud, Marina, van Fleet, Eric, Ren, Qinghu, Gatehouse, John A., Brault, Veronique, Monsion, Baptiste, Diaz, Jason, Hunnicutt, Laura, Ju, Ho-Jong, Pechuan, Ximo, Aguilar, Jose, Cortes, Teresa, Ortiz-Rivas, Benjamin, Martinez-Torres, David, Dombrovsky, Aviv, Dale, Richard P., Davies, T. G. Emyr, Williamson, Martin S., Jones, Andrew, Sattelle, David, Williamson, Sally, Wolstenholme, Adrian, Cottret, Ludovic, Sagot, Marie France, Heckel, David G., and Hunter, Wayne

Abstract

Aphids are important agricultural pests and also biological models for studies of insect-plant interactions, symbiosis, virus vectoring, and the developmental causes of extreme phenotypic plasticity. Here we present the 464 Mb draft genome assembly of the pea aphid Acyrthosiphon pisum. This first published whole genome sequence of a basal hemimetabolous insect provides an outgroup to the multiple published genomes of holometabolous insects. Pea aphids are host-plant specialists, they can reproduce both sexually and asexually, and they have coevolved with an obligate bacterial symbiont. Here we highlight findings from whole genome analysis that may be related to these unusual biological features. These findings include discovery of extensive gene duplication in more than 2000 gene families as well as loss of evolutionarily conserved genes. Gene family expansions relative to other published genomes include genes involved in chromatin modification, miRNA synthesis, and sugar transport. Gene losses include genes central to the IMD immune pathway, selenoprotein utilization, purine salvage, and the entire urea cycle. The pea aphid genome reveals that only a limited number of genes have been acquired from bacteria; thus the reduced gene count of Buchnera does not reflect gene transfer to the host genome. The inventory of metabolic genes in the pea aphid genome suggests that there is extensive metabolite exchange between the aphid and Buchnera, including sharing of amino acid biosynthesis between the aphid and Buchnera. The pea aphid genome provides a foundation for post-genomic studies of fundamental biological questions and applied agricultural problems.

Published
2010
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20. Variations in candidalysin amino acid sequence influence toxicity and host responses.

Author

Wickramasinghe DN, Lyon CM, Lee S, Hepworth OW, Priest EL, Maufrais C, Ryan AP, Permal E, Sullivan D, McManus BA, Hube B, Butler G, d'Enfert C, Naglik JR, and Richardson JP

Subjects
Humans, Candidiasis microbiology, Candidiasis immunology, Amino Acid Sequence, Genetic Variation, Candida genetics, Candida pathogenicity, Candida tropicalis genetics, Candida tropicalis metabolism, Fungal Proteins genetics, Fungal Proteins metabolism, Fungal Proteins chemistry, Candida albicans genetics, Candida albicans drug effects, Epithelial Cells microbiology
Abstract

Candida albicans causes millions of mucosal infections in humans annually. Hyphal overgrowth on mucosal surfaces is frequently associated with tissue damage caused by candidalysin, a secreted peptide toxin that destabilizes the plasma membrane of host cells thereby promoting disease and immunopathology. Candidalysin was first identified in C. albicans strain SC5314, but recent investigations have revealed candidalysin "variants" of differing amino acid sequence in isolates of C. albicans , and the related species C. dubliniensis , and C tropicalis , suggesting that sequence variation among candidalysins may be widespread in natural populations of these Candida species. Here, we analyzed ECE1 gene sequences from 182 C . albicans isolates, 10 C . dubliniensis isolates, and 78 C . tropicalis isolates and identified 10, 3, and 2 candidalysin variants in these species, respectively. Application of candidalysin variants to epithelial cells revealed differences in the ability to cause cellular damage, changes in metabolic activity, calcium influx, MAPK signalling, and cytokine secretion, while biophysical analyses indicated that variants exhibited differences in their ability to interact with and permeabilize a membrane. This study identifies candidalysin variants with differences in biological activity that are present in medically relevant Candida species., Importance: Fungal infections are a significant burden to health. Candidalysin is a toxin produced by Candida albicans that damages host tissues, facilitating infection. Previously, we demonstrated that candidalysins exist in the related species C. dubliniensis and C. tropicalis , thereby identifying these molecules as a toxin family. Recent genomic analyses have highlighted the presence of a small number of candidalysin "variant" toxins, which have different amino acid sequences to those originally identified. Here, we screened genome sequences of isolates of C. albicans , C. dubliniensis , and C. tropicalis and identified candidalysin variants in all three species. When applied to epithelial cells, candidalysin variants differed in their ability to cause damage, activate intracellular signaling pathways, and induce innate immune responses, while biophysical analysis revealed differences in the ability of candidalysin variants to interact with lipid bilayers. These findings suggest that intraspecies variation in candidalysin amino acid sequence may influence fungal pathogenicity., Competing Interests: The authors declare no conflict of interest.

Published
2024
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22. Roadmap for annotating transposable elements in eukaryote genomes.

Author

Permal E, Flutre T, and Quesneville H

Subjects
Algorithms, Animals, Cluster Analysis, Humans, Sequence Alignment methods, Software, DNA Transposable Elements genetics, Eukaryota genetics, Genome, Molecular Sequence Annotation methods, Sequence Analysis, DNA methods
Abstract

Current high-throughput techniques have made it feasible to sequence even the genomes of non-model organisms. However, the annotation process now represents a bottleneck to genome analysis, especially when dealing with transposable elements (TE). Combined approaches, using both de novo and knowledge-based methods to detect TEs, are likely to produce reasonably comprehensive and sensitive results. This chapter provides a roadmap for researchers involved in genome projects to address this issue. At each step of the TE annotation process, from the identification of TE families to the annotation of TE copies, we outline the tools and good practices to be used.

Published
2012
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