<italic toggle="yes">Leishmania</italic> Genome Dynamics during Environmental Adaptation Reveal Strain-Specific Differences in Gene Copy Number Variation, Karyotype Instability, and Telomeric Amplification
ABSTRACT Protozoan parasites of the genus Leishmania adapt to environmental change through chromosome and gene copy number variations. Only little is known about external or intrinsic factors that govern Leishmania genomic adaptation. Here, by conducting longitudinal genome analyses of 10 new Leishm...
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American Society for Microbiology
2018
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oai:doaj.org-article:56d904b3382f42ed88d1c4dbf455eff62021-11-15T15:52:19Z<italic toggle="yes">Leishmania</italic> Genome Dynamics during Environmental Adaptation Reveal Strain-Specific Differences in Gene Copy Number Variation, Karyotype Instability, and Telomeric Amplification10.1128/mBio.01399-182150-7511https://doaj.org/article/56d904b3382f42ed88d1c4dbf455eff62018-12-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mBio.01399-18https://doaj.org/toc/2150-7511ABSTRACT Protozoan parasites of the genus Leishmania adapt to environmental change through chromosome and gene copy number variations. Only little is known about external or intrinsic factors that govern Leishmania genomic adaptation. Here, by conducting longitudinal genome analyses of 10 new Leishmania clinical isolates, we uncovered important differences in gene copy number among genetically highly related strains and revealed gain and loss of gene copies as potential drivers of long-term environmental adaptation in the field. In contrast, chromosome rather than gene amplification was associated with short-term environmental adaptation to in vitro culture. Karyotypic solutions were highly reproducible but unique for a given strain, suggesting that chromosome amplification is under positive selection and dependent on species- and strain-specific intrinsic factors. We revealed a progressive increase in read depth towards the chromosome ends for various Leishmania isolates, which may represent a nonclassical mechanism of telomere maintenance that can preserve integrity of chromosome ends during selection for fast in vitro growth. Together our data draw a complex picture of Leishmania genomic adaptation in the field and in culture, which is driven by a combination of intrinsic genetic factors that generate strain-specific phenotypic variations, which are under environmental selection and allow for fitness gain. IMPORTANCE Protozoan parasites of the genus Leishmania cause severe human and veterinary diseases worldwide, termed leishmaniases. A hallmark of Leishmania biology is its capacity to adapt to a variety of unpredictable fluctuations inside its human host, notably pharmacological interventions, thus, causing drug resistance. Here we investigated mechanisms of environmental adaptation using a comparative genomics approach by sequencing 10 new clinical isolates of the L. donovani, L. major, and L. tropica complexes that were sampled across eight distinct geographical regions. Our data provide new evidence that parasites adapt to environmental change in the field and in culture through a combination of chromosome and gene amplification that likely causes phenotypic variation and drives parasite fitness gains in response to environmental constraints. This novel form of gene expression regulation through genomic change compensates for the absence of classical transcriptional control in these early-branching eukaryotes and opens new venues for biomarker discovery.Giovanni BussottiEvi GouzelouMariana Côrtes BoitéIhcen KherachiZoubir HarratNaouel EddaikraJeremy C. MottramMaria AntoniouVasiliki ChristodoulouAymen BaliFatma Z. GuerfaliDhafer LaouiniMaowia MukhtarFranck DumetzJean-Claude DujardinDespina SmirlisPierre LechatPascale PescherAdil El HamouchiMeryem LemraniCarmen ChicharroIvonne Pamela Llanes-AcevedoLaura BotanaIsrael CruzJavier MorenoFakhri JeddiKarim AounAïda BouratbineElisa CupolilloGerald F. SpäthAmerican Society for MicrobiologyarticleLeishmaniaaneuploidyevolutiongene copy number variationgenomic adaptationtelomeric amplificationMicrobiologyQR1-502ENmBio, Vol 9, Iss 6 (2018) |
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Leishmania aneuploidy evolution gene copy number variation genomic adaptation telomeric amplification Microbiology QR1-502 |
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Leishmania aneuploidy evolution gene copy number variation genomic adaptation telomeric amplification Microbiology QR1-502 Giovanni Bussotti Evi Gouzelou Mariana Côrtes Boité Ihcen Kherachi Zoubir Harrat Naouel Eddaikra Jeremy C. Mottram Maria Antoniou Vasiliki Christodoulou Aymen Bali Fatma Z. Guerfali Dhafer Laouini Maowia Mukhtar Franck Dumetz Jean-Claude Dujardin Despina Smirlis Pierre Lechat Pascale Pescher Adil El Hamouchi Meryem Lemrani Carmen Chicharro Ivonne Pamela Llanes-Acevedo Laura Botana Israel Cruz Javier Moreno Fakhri Jeddi Karim Aoun Aïda Bouratbine Elisa Cupolillo Gerald F. Späth <italic toggle="yes">Leishmania</italic> Genome Dynamics during Environmental Adaptation Reveal Strain-Specific Differences in Gene Copy Number Variation, Karyotype Instability, and Telomeric Amplification |
| description |
ABSTRACT Protozoan parasites of the genus Leishmania adapt to environmental change through chromosome and gene copy number variations. Only little is known about external or intrinsic factors that govern Leishmania genomic adaptation. Here, by conducting longitudinal genome analyses of 10 new Leishmania clinical isolates, we uncovered important differences in gene copy number among genetically highly related strains and revealed gain and loss of gene copies as potential drivers of long-term environmental adaptation in the field. In contrast, chromosome rather than gene amplification was associated with short-term environmental adaptation to in vitro culture. Karyotypic solutions were highly reproducible but unique for a given strain, suggesting that chromosome amplification is under positive selection and dependent on species- and strain-specific intrinsic factors. We revealed a progressive increase in read depth towards the chromosome ends for various Leishmania isolates, which may represent a nonclassical mechanism of telomere maintenance that can preserve integrity of chromosome ends during selection for fast in vitro growth. Together our data draw a complex picture of Leishmania genomic adaptation in the field and in culture, which is driven by a combination of intrinsic genetic factors that generate strain-specific phenotypic variations, which are under environmental selection and allow for fitness gain. IMPORTANCE Protozoan parasites of the genus Leishmania cause severe human and veterinary diseases worldwide, termed leishmaniases. A hallmark of Leishmania biology is its capacity to adapt to a variety of unpredictable fluctuations inside its human host, notably pharmacological interventions, thus, causing drug resistance. Here we investigated mechanisms of environmental adaptation using a comparative genomics approach by sequencing 10 new clinical isolates of the L. donovani, L. major, and L. tropica complexes that were sampled across eight distinct geographical regions. Our data provide new evidence that parasites adapt to environmental change in the field and in culture through a combination of chromosome and gene amplification that likely causes phenotypic variation and drives parasite fitness gains in response to environmental constraints. This novel form of gene expression regulation through genomic change compensates for the absence of classical transcriptional control in these early-branching eukaryotes and opens new venues for biomarker discovery. |
| format |
article |
| author |
Giovanni Bussotti Evi Gouzelou Mariana Côrtes Boité Ihcen Kherachi Zoubir Harrat Naouel Eddaikra Jeremy C. Mottram Maria Antoniou Vasiliki Christodoulou Aymen Bali Fatma Z. Guerfali Dhafer Laouini Maowia Mukhtar Franck Dumetz Jean-Claude Dujardin Despina Smirlis Pierre Lechat Pascale Pescher Adil El Hamouchi Meryem Lemrani Carmen Chicharro Ivonne Pamela Llanes-Acevedo Laura Botana Israel Cruz Javier Moreno Fakhri Jeddi Karim Aoun Aïda Bouratbine Elisa Cupolillo Gerald F. Späth |
| author_facet |
Giovanni Bussotti Evi Gouzelou Mariana Côrtes Boité Ihcen Kherachi Zoubir Harrat Naouel Eddaikra Jeremy C. Mottram Maria Antoniou Vasiliki Christodoulou Aymen Bali Fatma Z. Guerfali Dhafer Laouini Maowia Mukhtar Franck Dumetz Jean-Claude Dujardin Despina Smirlis Pierre Lechat Pascale Pescher Adil El Hamouchi Meryem Lemrani Carmen Chicharro Ivonne Pamela Llanes-Acevedo Laura Botana Israel Cruz Javier Moreno Fakhri Jeddi Karim Aoun Aïda Bouratbine Elisa Cupolillo Gerald F. Späth |
| author_sort |
Giovanni Bussotti |
| title |
<italic toggle="yes">Leishmania</italic> Genome Dynamics during Environmental Adaptation Reveal Strain-Specific Differences in Gene Copy Number Variation, Karyotype Instability, and Telomeric Amplification |
| title_short |
<italic toggle="yes">Leishmania</italic> Genome Dynamics during Environmental Adaptation Reveal Strain-Specific Differences in Gene Copy Number Variation, Karyotype Instability, and Telomeric Amplification |
| title_full |
<italic toggle="yes">Leishmania</italic> Genome Dynamics during Environmental Adaptation Reveal Strain-Specific Differences in Gene Copy Number Variation, Karyotype Instability, and Telomeric Amplification |
| title_fullStr |
<italic toggle="yes">Leishmania</italic> Genome Dynamics during Environmental Adaptation Reveal Strain-Specific Differences in Gene Copy Number Variation, Karyotype Instability, and Telomeric Amplification |
| title_full_unstemmed |
<italic toggle="yes">Leishmania</italic> Genome Dynamics during Environmental Adaptation Reveal Strain-Specific Differences in Gene Copy Number Variation, Karyotype Instability, and Telomeric Amplification |
| title_sort |
<italic toggle="yes">leishmania</italic> genome dynamics during environmental adaptation reveal strain-specific differences in gene copy number variation, karyotype instability, and telomeric amplification |
| publisher |
American Society for Microbiology |
| publishDate |
2018 |
| url |
https://doaj.org/article/56d904b3382f42ed88d1c4dbf455eff6 |
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