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3. Population genetics and microevolution of clinical Candida glabrata reveals recombinant sequence types and hyper-variation within mitochondrial genomes, virulence genes and drug-targets

Author

Helmstetter, Nicolas, Chybowska, Aleksandra D., Delaney, Christopher, Da Silva Dantas, Alessandra, Gifford, Hugh, Wacker, Theresa, Munro, Carol, Warris, Adilia, Jones, Brian, Cuomo, Christina A., Wilson, Duncan, Ramage, Gordon, and Farrer, Rhys A.

Abstract

Candida glabrata is the second most common etiological cause of worldwide systemic candidiasis in adult patients. Genome analysis of 68 isolates from 8 hospitals across Scotland, together with 83 global isolates, revealed insights into the population genetics and evolution of C. glabrata. Clinical isolates of C. glabrata from across Scotland are highly-genetically diverse, including at least 19 separate sequence types (STs) that have been recovered previously in globally diverse locations, and one newly discovered ST. Several STs had evidence for ancestral recombination, suggesting transmission between distinct geographical regions has coincided with genetic exchange arising in new clades. Three isolates were missing MATα1, potentially representing a second mating type. Signatures of positive selection were identified in every ST including enrichment for Epithelial Adhesins (EPA) thought to facilitate fungal adhesion to human epithelial cells. In patent microevolution was identified from seven sets of recurrent cases of candidiasis, revealing an enrichment for non-synonymous and frameshift indels in cell surface proteins. Microevolution within patients also affected EPA genes, and several genes involved in drug resistance including the ergosterol synthesis gene ERG4 and the echinocandin target FKS1/2, the latter coinciding with a marked drop in fluconazole MIC. In addition to nuclear genome diversity, the C. glabrata mitochondrial genome was particularly diverse, with reduced conserved sequence and conserved protein encoding genes in all non-reference ST15 isolates. Together, this study highlights the genetic diversity within the C. glabrata population that may impact virulence and drug resistance, and two major mechanisms generating this diversity: microevolution and genetic exchange/recombination.

Published
2022

4. Repeat-driven genome expansion and two-speed genome architecture of amphibian-infecting chytrids

Author

Wacker, Theresa, Helmstetter, Nicolas, Duncan, Wilson, Fisher, Matthew C., Studholme, David J., and Farrer, Rhys A.

Subjects
Chytridiomycosis, infectious disease, pathogenicity, fungal pathogens, two-speed genome evolution
Abstract

Over the past half century, the chytridiomycosis panzootic has led to the decline of over 500 amphibian species with 90 attributed extinctions. Chytridiomycosis of amphibians is caused by two fungal species Batrachochytrium dendrobatidis (Bd) and Batrachochytrium salamandrivorans (Bsal). The genetic mechanisms underlying host-specificity and pathology in the Batrachochytrium genus remain elusive and their evolution and origins of virulence are largely unknown. Using deep nanopore sequencing, we found that Bsal is extremely repeat-rich with high numbers of long terminal repeats, long interspersed nuclear elements and transposable elements. This repeat-driven genome expansion in Bsal has resulted in a tripling of its length compared with Bd. Key pathogenicity genes including M36 metalloproteases have expanded compared with Bd, and are enriched for flanking transposable elements, suggesting its genome expansion is connected to selective evolutionary processes. Both batrachochytrids have evidence of a two speed genome architecture, including an enrichment of functional categories in compartments of repeat richness or sparsity. Furthermore, among Bd lineages, M36 metalloproteases with signatures of positive selection and, both in Bsal and Bd, genes upregulated during infection in vivo are enriched in repeat-rich and gene-sparse compartment of the genome. This is the first evidence for a two-speed genome in an animal pathogen, shedding new light on the role of repetitive sequences on the evolution of fungal pathogens driving global declines and extinctions of amphibians., {"references":["Scheele, B. C.et al., Science 363, 1459-1463 (2019)","Carey, C.et al., EcoHealth 3, 5-21 (2006)","Stegen, G.et al., Nature 544, 353-356 (2017)","Martel, A.et al., Proc. Natl. Acad. Sci. 110, 15325-15329 (2013)","Farrer, R. A. , Trends Microbiol. 27, 892-893 (2019)","Sabino-Pinto, J. et al. , AMRE 36, 411-416 (2015)","Wang, Y. et al. , New Phytol. 220, 922-935 (2018)","Zhang, S.-J. et al., Genomics Proteomics Bioinformatics 18, 321-332 (2020)","Wos, G. et al., Mob. DNA 12, 7 (2021)","Klein, S. J. & O'Neill, R. J. , Chromosome Res. 26, 5-23 (2018)","Oliver, K. R. & Greene, W. K. , BioEssays 31, 703-714 (2009)"]}

Published
2022
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6. Population genetics and microevolution of clinical Candida glabrata reveals recombinant sequence types and hyper-variation within mitochondrial genomes, virulence genes, and drug targets

Author

Helmstetter, Nicolas, primary, Chybowska, Aleksandra D, additional, Delaney, Christopher, additional, Da Silva Dantas, Alessandra, additional, Gifford, Hugh, additional, Wacker, Theresa, additional, Munro, Carol, additional, Warris, Adilia, additional, Jones, Brian, additional, Cuomo, Christina A, additional, Wilson, Duncan, additional, Ramage, Gordon, additional, and Farrer, Rhys A, additional

Published
2022
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8. The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution

Author

Badouin, Hlne, Gouzy, Jrme, Grassa, Christopher J., Murat, Florent, Staton, S. Evan, Cottret, Ludovic, Lelandais-Brire, Christine, Owens, Gregory L., Carrre, Sbastien, Mayjonade, Baptiste, Legrand, Ludovic, Gill, Navdeep, Kane, Nolan C., Bowers, John E., Hubner, Sariel, Bellec, Arnaud, Brard, Aurlie, Bergs, Hlne, Blanchet, Nicolas, Boniface, Marie-Claude, Brunel, Dominique, Catrice, Olivier, Chaidir, Nadia, Claudel, Clotilde, Donnadieu, Ccile, Faraut, Thomas, Fievet, Ghislain, Helmstetter, Nicolas, King, Matthew, Knapp, Steven J., Lai, Zhao, Le Paslier, Marie-Christine, Lippi, Yannick, Lorenzon, Lolita, Mandel, Jennifer R., Marage, Gwenola, Marchand, Gwenalle, Marquand, Elodie, Bret-Mestries, Emmanuelle, Morien, Evan, Nambeesan, Savithri, Nguyen, Thuy, Pegot-Espagnet, Prune, Pouilly, Nicolas, Raftis, Frances, Sallet, Erika, Schiex, Thomas, Thomas, Justine, Vandecasteele, Cline, Vars, Didier, Vear, Felicity, Vautrin, Sonia, Crespi, Martin, Mangin, Brigitte, Burke, John M., Salse, Jrme, Muos, Stphane, Vincourt, Patrick, Rieseberg, Loren H., and Langlade, Nicolas B.

Subjects
Observations, Genetic aspects, Plant metabolism -- Genetic aspects, Sunflowers -- Genetic aspects, Gene expression -- Observations
Abstract

Author(s): Hlne Badouin [1]; Jrme Gouzy [1]; Christopher J. Grassa [1, 2]; Florent Murat [3]; S. Evan Staton [2]; Ludovic Cottret [1]; Christine Lelandais-Brire [4, 5]; Gregory L. Owens [2]; [...]

Published
2017
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9. Construction and characterization of two BAC libraries representing a deep-coverage of the genome of chicory (Cichorium intybus L., Asteraceae)

Author

Gonthier Lucy, Bellec Arnaud, Blassiau Christelle, Prat Elisa, Helmstetter Nicolas, Rambaud Caroline, Huss Brigitte, Hendriks Theo, Bergès Hélène, and Quillet Marie-Christine

Subjects
Medicine, Biology (General), QH301-705.5, Science (General), Q1-390
Abstract

Abstract Background The Asteraceae represents an important plant family with respect to the numbers of species present in the wild and used by man. Nonetheless, genomic resources for Asteraceae species are relatively underdeveloped, hampering within species genetic studies as well as comparative genomics studies at the family level. So far, six BAC libraries have been described for the main crops of the family, i.e. lettuce and sunflower. Here we present the characterization of BAC libraries of chicory (Cichorium intybus L.) constructed from two genotypes differing in traits related to sexual and vegetative reproduction. Resolving the molecular mechanisms underlying traits controlling the reproductive system of chicory is a key determinant for hybrid development, and more generally will provide new insights into these traits, which are poorly investigated so far at the molecular level in Asteraceae. Findings Two bacterial artificial chromosome (BAC) libraries, CinS2S2 and CinS1S4, were constructed from HindIII-digested high molecular weight DNA of the contrasting genotypes C15 and C30.01, respectively. C15 was hermaphrodite, non-embryogenic, and S2S2 for the S-locus implicated in self-incompatibility, whereas C30.01 was male sterile, embryogenic, and S1S4. The CinS2S2 and CinS1S4 libraries contain 89,088 and 81,408 clones. Mean insert sizes of the CinS2S2 and CinS1S4 clones are 90 and 120 kb, respectively, and provide together a coverage of 12.3 haploid genome equivalents. Contamination with mitochondrial and chloroplast DNA sequences was evaluated with four mitochondrial and four chloroplast specific probes, and was estimated to be 0.024% and 1.00% for the CinS2S2 library, and 0.028% and 2.35% for the CinS1S4 library. Using two single copy genes putatively implicated in somatic embryogenesis, screening of both libraries resulted in detection of 12 and 13 positive clones for each gene, in accordance with expected numbers. Conclusions This indicated that both BAC libraries are valuable tools for molecular studies in chicory, one goal being the positional cloning of the S-locus in this Asteraceae species.

Published
2010
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10. The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution

Author

BADOUIN, Hélène, Gouzy, Jerome, GRASSA, Christopher, Murat, Florent, Staton, S Evan, Cottret, Ludovic, Lelandais-briere, Christine, Owens, Gregory L, Carrere, Sebastien, mayjonade, Baptiste, Legrand, Ludovic, Gill, Navdeep, Kane, Nolan C, Bowers, John E, Hubner, Sariel, Bellec, Arnaud, Berard, Aurélie, Berges, Helene, BLANCHET, Nicolas, Boniface, Marie-Claude, Brunel, Dominique, Catrice, Olivier, Chaidir, Nadia, Claudel, Clotilde, Donnadieu, Cecile, Faraut, Thomas, Fievet, Ghislain, Helmstetter, Nicolas, King, Matthew, Knapp, Steven J, Lai, Zhao, Le Paslier, Marie-Christine, Lippi, Yannick, LORENZON, Lolita, Mandel, Jennifer R, Marage, Gwenola, MARCHAND, Gwenaëlle, MARQUAND, Elodie, MESTRIES, Emmanuelle, Morien, Evan, Nambeesan, Savithri, Nguyen, Thuy, Pegot - Espagnet, Prune, Pouilly, Nicolas, Raftis, Frances, Sallet, Erika, Schiex, Thomas, Thomas, Justine, Vandecasteele, Céline, Vares, Didier, Vear, Felicity, Vautrin, Sonia, Crespi, Martin, Mangin, Brigitte, Burke, John M, Salse, Jerome, Munos, Stephane, Vincourt, Patrick, Rieseberg, Loren H, Langlade, Nicolas, Laboratoire des interactions plantes micro-organismes (LIPM), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Department of Botany and Biodiversity Research Centre, University of British Columbia (UBC), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Department of Ecology and Evolutionary Biology (Faculty of Biology), University of Science-Vietnam National Universities, Department of Plant Biology, Miller Plant Sciences, University of Georgia [USA], Department of Biotechnology, Tel-Hai Academic College, Galilee Research Institute (Migal), Centre National de Ressources Génomiques Végétales (CNRGV), Institut National de la Recherche Agronomique (INRA), Etude du Polymorphisme des Génomes Végétaux (EPGV), Dow AgroSciences LLC, Biogemma, GeT PlaGe, Genotoul, Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT], Department of Plant Sciences, University of California, Department of Biology, Northern Arizona University [Flagstaff], Center for Genomics and Bioinformatics, Indiana University [Bloomington], Indiana University System-Indiana University System, Department of Biological Sciences, The Open University [Milton Keynes] (OU), UMR : AGroécologie, Innovations, TeRritoires, Ecole Nationale Supérieure Agronomique de Toulouse, Department of Horticulture, University of Wisconsin-Madison, The Wellcome Trust Sanger Institute [Cambridge], Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), French National Research Agency : SUNYFUEL/ANR-07-GPLA-0022, SUNRISE/ANR-11-BTBR-0005 Midi-Pyrenees Region, European Fund for Regional Development, French Fund for Competitiveness Clusters (FUI), Genoscope SystemSun project, Genome Canada, Genome BC's Applied Genomics Research in Bioproducts or Crops (ABC) Competition, NSF Plant Genome Program : DBI-082045, International Consortium for Sunflower Genomics Resources, Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Tel-Hai College, Génome et Transcriptome - Plateforme Génomique (GeT-PlaGe), Institut National de la Recherche Agronomique (INRA)-Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, AGroécologie, Innovations, teRritoires (AGIR), Institut National de la Recherche Agronomique (INRA)-Institut National Polytechnique (Toulouse) (Toulouse INP), ANR-07-GPLA-0022,SUNYFUEL,Improving sunflower yield and quality for biofuel production by genomics and genetics(2007), ANR-11-BTBR-0005,SUNRISE,Ressources génétiques de tournesol pour l'amélioration de la stabilité de production d'huile sous c(2011), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Galilee Research Institute [Israël] (MIGAL), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université de Toulouse (UT)-Université de Toulouse (UT)-École nationale supérieure agronomique de Toulouse (ENSAT), Université de Toulouse (UT)-Université de Toulouse (UT), University of California (UC), Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Institut National de la Recherche Agronomique (INRA), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Interactions plantes-microorganismes et santé végétale, Institut National de la Recherche Agronomique ( INRA ) -Université Nice Sophia Antipolis ( UNS ), Université Côte d'Azur ( UCA ) -Université Côte d'Azur ( UCA ) -Centre National de la Recherche Scientifique ( CNRS ), University of British Columbia ( UBC ), Génétique Diversité et Ecophysiologie des Céréales ( GDEC ), Université Blaise Pascal - Clermont-Ferrand 2 ( UBP ) -Institut National de la Recherche Agronomique ( INRA ), UMR 1403 Institut des Sciences des Plantes de Paris Saclay, Institut National de la Recherche Agronomique ( INRA ) -Université Paris Diderot - Paris 7 ( UPD7 ), Department of Ecology and Evolutionary Biology ( Faculty of Biology ), University of Georgia, Galilee Research Institute ( Migal ), Centre National de Ressources Génomiques Végétales ( CNRGV ), Institut National de la Recherche Agronomique ( INRA ), Etude du Polymorphisme des Génomes Végétaux ( EPGV ), GenPhySE - UMR 1388 ( Génétique Physiologie et Systèmes d'Elevage ), Institut National de la Recherche Agronomique ( INRA ) -École nationale supérieure agronomique de Toulouse [ENSAT]-ENVT, The Open University [Milton Keynes] ( OU ), University of Wisconsin-Madison [Madison], Wellcome Trust Sanger Institute, and Unité de Mathématiques et Informatique Appliquées de Toulouse ( MIAT INRA )

Subjects
[ SDV.BV ] Life Sciences [q-bio]/Vegetal Biology, sunflower, Acclimatization, résistance au stress, génome végétal, Flowers, genome evolution, résilience, Evolution, Molecular, Gene Expression Regulation, Plant, Stress, Physiological, Gene Duplication, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Plant Oils, Sunflower Oil, genome, food and beverages, Genetic Variation, Genomics, Sequence Analysis, DNA, tournesol, genêtic variation, stress biotique, diversité génétique, Helianthus, Transcriptome, Genome, Plant
Abstract

The domesticated sunflower, Helianthus annuus L., is a global oil crop that has promise for climate change adaptation, because it can maintain stable yields across a wide variety of environmental conditions, including drought. Even greater resilience is achievable through the mining of resistance alleles from compatible wild sunflower relatives, including numerous extremophile species. Here we report a high-quality reference for the sunflower genome (3.6 gigabases), together with extensive transcriptomic data from vegetative and floral organs. The genome mostly consists of highly similar, related sequences and required single-molecule real-time sequencing technologies for successful assembly. Genome analyses enabled the reconstruction of the evolutionary history of the Asterids, further establishing the existence of a whole-genome triplication at the base of the Asterids II clade and a sunflower-specific whole-genome duplication around 29 million years ago. An integrative approach combining quantitative genetics, expression and diversity data permitted development of comprehensive gene networks for two major breeding traits, flowering time and oil metabolism, and revealed new candidate genes in these networks. We found that the genomic architecture of flowering time has been shaped by the most recent whole-genome duplication, which suggests that ancient paralogues can remain in the same regulatory networks for dozens of millions of years. This genome represents a cornerstone for future research programs aiming to exploit genetic diversity to improve biotic and abiotic stress resistance and oil production, while also considering agricultural constraints and human nutritional needs.

Published
2016
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12. Contrasted Patterns of Molecular Evolution in Dominant and Recessive Self-Incompatibility Haplotypes in Arabidopsis

Author

Goubet, Pauline M., primary, Bergès, Hélène, additional, Bellec, Arnaud, additional, Prat, Elisa, additional, Helmstetter, Nicolas, additional, Mangenot, Sophie, additional, Gallina, Sophie, additional, Holl, Anne-Catherine, additional, Fobis-Loisy, Isabelle, additional, Vekemans, Xavier, additional, and Castric, Vincent, additional

Published
2012
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13. Construction and characterization of two BAC libraries representing a deep-coverage of the genome of chicory (Cichorium intybusL., Asteraceae).

Author

Gonthier, Lucy, Bellec, Arnaud, Blassiau, Christelle, Prat, Elisa, Helmstetter, Nicolas, Rambaud, Caroline, Huss, Brigitte, Hendriks, Theo, Bergès, Hélène, and Quillet, Marie-Christine

Subjects
ASTERACEAE, GENES, GENETIC polymorphisms, GENOMES, NUCLEOTIDE sequence, GENOMICS, SYNTHETIC seeds, SOMATIC embryogenesis, GENETICS
Abstract

Background: The Asteraceae represents an important plant family with respect to the numbers of species present in the wild and used by man. Nonetheless, genomic resources for Asteraceae species are relatively underdeveloped, hampering within species genetic studies as well as comparative genomics studies at the family level. So far, six BAC libraries have been described for the main crops of the family, i.e. lettuce and sunflower. Here we present the characterization of BAC libraries of chicory (Cichorium intybus L.) constructed from two genotypes differing in traits related to sexual and vegetative reproduction. Resolving the molecular mechanisms underlying traits controlling the reproductive system of chicory is a key determinant for hybrid development, and more generally will provide new insights into these traits, which are poorly investigated so far at the molecular level in Asteraceae. Findings: Two bacterial artificial chromosome (BAC) libraries, CinS2S2 and CinS1S4, were constructed from HindIII-digested high molecular weight DNA of the contrasting genotypes C15 and C30.01, respectively. C15 was hermaphrodite, non-embryogenic, and S2S2 for the S-locus implicated in self-incompatibility, whereas C30.01 was male sterile, embryogenic, and S1S4. The CinS2S2 and CinS1S4 libraries contain 89,088 and 81,408 clones. Mean insert sizes of the CinS2S2 and CinS1S4 clones are 90 and 120 kb, respectively, and provide together a coverage of 12.3 haploid genome equivalents. Contamination with mitochondrial and chloroplast DNA sequences was evaluated with four mitochondrial and four chloroplast specific probes, and was estimated to be 0.024% and 1.00% for the CinS2S2 library, and 0.028% and 2.35% for the CinS1S4 library. Using two single copy genes putatively implicated in somatic embryogenesis, screening of both libraries resulted in detection of 12 and 13 positive clones for each gene, in accordance with expected numbers. Conclusions: This indicated that both BAC libraries are valuable tools for molecular studies in chicory, one goal being the positional cloning of the S-locus in this Asteraceae species. [ABSTRACT FROM AUTHOR]

Published
2010
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14. Population genetics and microevolution of clinical Candida glabratareveals recombinant sequence types and hyper-variation within mitochondrial genomes, virulence genes, and drug targets

Author

Helmstetter, Nicolas, Chybowska, Aleksandra D, Delaney, Christopher, Da Silva Dantas, Alessandra, Gifford, Hugh, Wacker, Theresa, Munro, Carol, Warris, Adilia, Jones, Brian, Cuomo, Christina A, Wilson, Duncan, Ramage, Gordon, and Farrer, Rhys A

Abstract

Candida glabratais the second most common etiological cause of worldwide systemic candidiasis in adult patients. Genome analysis of 68 isolates from 8 hospitals across Scotland, together with 83 global isolates, revealed insights into the population genetics and evolution of C. glabrata. Clinical isolates of C. glabratafrom across Scotland are highly genetically diverse, including at least 19 separate sequence types that have been recovered previously in globally diverse locations, and 1 newly discovered sequence type. Several sequence types had evidence for ancestral recombination, suggesting transmission between distinct geographical regions has coincided with genetic exchange arising in new clades. Three isolates were missing MATα1, potentially representing a second mating type. Signatures of positive selection were identified in every sequence type including enrichment for epithelial adhesins thought to facilitate fungal adhesin to human epithelial cells. In patent microevolution was identified from 7 sets of recurrent cases of candidiasis, revealing an enrichment for nonsynonymous and frameshift indels in cell surface proteins. Microevolution within patients also affected epithelial adhesins genes, and several genes involved in drug resistance including the ergosterol synthesis gene ERG4and the echinocandin target FKS1/2, the latter coinciding with a marked drop in fluconazole minimum inhibitory concentration. In addition to nuclear genome diversity, the C. glabratamitochondrial genome was particularly diverse, with reduced conserved sequence and conserved protein-encoding genes in all nonreference ST15 isolates. Together, this study highlights the genetic diversity within the C. glabratapopulation that may impact virulence and drug resistance, and 2 major mechanisms generating this diversity: microevolution and genetic exchange/recombination.

Published
2022
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15. A near-complete telomere-to-telomere genome assembly for Batrachochytrium dendrobatidis GPL JEL423 reveals a larger CBM18 gene family and a smaller M36 metalloprotease gene family than previously recognised.

Author

Helmstetter N, Harrison K, Gregory J, Harrison J, Ballou E, and Farrer RA

Abstract

Batrachochytrium dendrobatidis (Bd) is responsible for mass extinctions and extirpations of amphibians, mainly driven by the Global Panzootic Lineage (BdGPL). BdGPL isolate JEL423 is a commonly used reference strain in studies exploring the evolution, epidemiology and pathogenicity of chytrid pathogens. These studies have been hampered by the fragmented, erroneous and incomplete B. dendrobatidis JEL423 genome assembly, which includes long stretches of ambiguous positions, and poorly resolved telomeric regions. Here we present and describe a substantially improved, near telomere-to-telomere genome assembly and gene annotation for B. dendrobatidis JEL423. Our new assembly is 24.5 Mb in length, ∼800 kb longer than the previously published assembly for this organism, comprising 18 nuclear scaffolds and 2 mitochondrial scaffolds and including an extra 839 kb of repetitive sequence. We discovered that the patterns of aneuploidy in B. dendrobatidis JEL423 have remained stable over approximately 5 years. We found that our updated assembly encodes fewer than half the number of M36 metalloprotease genes predicted in the previous assembly. In contrast, members of the crinkling and necrosis gene family were found in similar numbers to the previous assembly. We also identified a more extensive carbohydrate binding module 18 gene family than previously observed. We anticipate our findings, and the updated genome assembly will be a useful tool for further investigation of the genome evolution of the pathogenic chytrids., (© The Author(s) 2024. Published by Oxford University Press on behalf of The Genetics Society of America.)

Published
2024
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