Intraspecific genomic divergence and minor structural variations in leishmania (Viannia) panamensis

Leishmania (Viannia) panamensis is one of the most important Leishmania species associated with cutaneous leishmaniasis (CL) in Latin America. Despite its wide geographic distribution and pathogenic potential in humans and animals, the genomic variability of this species is low compared with other L...

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Fecha de publicación:
2020
Institución:
Universidad del Rosario
Repositorio:
Repositorio EdocUR - U. Rosario
Idioma:
eng
OAI Identifier:
oai:repository.urosario.edu.co:10336/24145
Acceso en línea:
https://doi.org/10.3390/genes11030252
https://repository.urosario.edu.co/handle/10336/24145
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Article
Copy number variation
Genetic variability
Genetic variation
Genome
Genomics
Leishmania panamensis
Nonhuman
Phylogenomics
Phylogeny
Ploidy
Sanger sequencing
Single nucleotide polymorphism
Copy number variations
Cutaneous leishmaniasis
DNA-seq
Genomic variability
Leishmania panamensis
Phylogenetic analysis
Single-nucleotide polymorphisms
Rights
License
Abierto (Texto Completo)
id EDOCUR2_1b60d02158f16fd3073919f4227309e4
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spelling b21e2bed-2caa-4b8f-bde4-ef70f15d1937-1453006a5-2ec3-4faf-8e32-a9d7075d519d-194094a23-a4e4-4418-b743-dac06fb0417f-15193546460010117161186002020-05-26T00:09:13Z2020-05-26T00:09:13Z2020Leishmania (Viannia) panamensis is one of the most important Leishmania species associated with cutaneous leishmaniasis (CL) in Latin America. Despite its wide geographic distribution and pathogenic potential in humans and animals, the genomic variability of this species is low compared with other Leishmania species circulating in the same geographical area. No studies have reported a detailed analysis of the whole genome of L. panamensis from clinical isolates using DNA highthroughput sequencing to clarify its intraspecific genomic variability or plausible divergence. Therefore, this study aimed to evaluate the intraspecific genomic variability of L. panamensis from Colombia and Panama. A total of 22 genomes were analyzed, 19 from Colombian patients with CL and three genomes from Panama obtained from public databases. The phylogenomic analysis revealed the potential existence of three well-supported clades as evidence of intraspecific divergence. Additionally, the whole-genome analysis showed low structural variations in terms of ploidy, copy number variations, and single-nucleotide polymorphisms (SNPs). SNPs shared among all clades were identified, revealing their importance in different biological processes of L. panamensis. The findings not only expand our knowledge of intraspecific genomic variability of one of the most important Leishmania species in South America but also highlights the possible existence of different clades/lineages/subpopulations across a geographic scale. © 2020 by the authors. Licensee MDPI, Basel, Switzerland.application/pdfhttps://doi.org/10.3390/genes1103025220734425https://repository.urosario.edu.co/handle/10336/24145engMDPI AGNo. 3GenesVol. 11Genes, ISSN:20734425, Vol.11, No.3 (2020)https://www.scopus.com/inward/record.uri?eid=2-s2.0-85080959829&doi=10.3390%2fgenes11030252&partnerID=40&md5=148432dcc15dd175feb88e8cf39fd7d4Abierto (Texto Completo)http://purl.org/coar/access_right/c_abf2instname:Universidad del Rosarioreponame:Repositorio Institucional EdocURArticleCopy number variationGenetic variabilityGenetic variationGenomeGenomicsLeishmania panamensisNonhumanPhylogenomicsPhylogenyPloidySanger sequencingSingle nucleotide polymorphismCopy number variationsCutaneous leishmaniasisDNA-seqGenomic variabilityLeishmania panamensisPhylogenetic analysisSingle-nucleotide polymorphismsIntraspecific genomic divergence and minor structural variations in leishmania (Viannia) panamensisarticleArtículohttp://purl.org/coar/version/c_970fb48d4fbd8a85http://purl.org/coar/resource_type/c_6501Patino, Luz H.Muñoz, MarinaMuskus, CarlosMéndez-Sarmiento, Claudia Ramírez, Juan DavidORIGINALgenes-11-00252-v2.pdfapplication/pdf2288081https://repository.urosario.edu.co/bitstreams/2e6f76aa-af2f-4994-af1a-e0f0c3d224ff/download48721c32a3525bce7494eca74d52d1bdMD51TEXTgenes-11-00252-v2.pdf.txtgenes-11-00252-v2.pdf.txtExtracted texttext/plain79606https://repository.urosario.edu.co/bitstreams/ca15a85c-7fde-4e47-bd76-dc4b2efb0485/download1312cf9f3e83e2ad746784609aa79280MD52THUMBNAILgenes-11-00252-v2.pdf.jpggenes-11-00252-v2.pdf.jpgGenerated Thumbnailimage/jpeg4900https://repository.urosario.edu.co/bitstreams/a3feb0ed-f363-4fee-8a33-0e5117ee3cf2/downloadc323fbf785886f707b81d9cf4d4a82a0MD5310336/24145oai:repository.urosario.edu.co:10336/241452022-05-02 07:37:21.605072https://repository.urosario.edu.coRepositorio institucional EdocURedocur@urosario.edu.co
dc.title.spa.fl_str_mv Intraspecific genomic divergence and minor structural variations in leishmania (Viannia) panamensis
title Intraspecific genomic divergence and minor structural variations in leishmania (Viannia) panamensis
spellingShingle Intraspecific genomic divergence and minor structural variations in leishmania (Viannia) panamensis
Article
Copy number variation
Genetic variability
Genetic variation
Genome
Genomics
Leishmania panamensis
Nonhuman
Phylogenomics
Phylogeny
Ploidy
Sanger sequencing
Single nucleotide polymorphism
Copy number variations
Cutaneous leishmaniasis
DNA-seq
Genomic variability
Leishmania panamensis
Phylogenetic analysis
Single-nucleotide polymorphisms
title_short Intraspecific genomic divergence and minor structural variations in leishmania (Viannia) panamensis
title_full Intraspecific genomic divergence and minor structural variations in leishmania (Viannia) panamensis
title_fullStr Intraspecific genomic divergence and minor structural variations in leishmania (Viannia) panamensis
title_full_unstemmed Intraspecific genomic divergence and minor structural variations in leishmania (Viannia) panamensis
title_sort Intraspecific genomic divergence and minor structural variations in leishmania (Viannia) panamensis
dc.subject.keyword.spa.fl_str_mv Article
Copy number variation
Genetic variability
Genetic variation
Genome
Genomics
Leishmania panamensis
Nonhuman
Phylogenomics
Phylogeny
Ploidy
Sanger sequencing
Single nucleotide polymorphism
Copy number variations
Cutaneous leishmaniasis
DNA-seq
Genomic variability
Leishmania panamensis
Phylogenetic analysis
Single-nucleotide polymorphisms
topic Article
Copy number variation
Genetic variability
Genetic variation
Genome
Genomics
Leishmania panamensis
Nonhuman
Phylogenomics
Phylogeny
Ploidy
Sanger sequencing
Single nucleotide polymorphism
Copy number variations
Cutaneous leishmaniasis
DNA-seq
Genomic variability
Leishmania panamensis
Phylogenetic analysis
Single-nucleotide polymorphisms
description Leishmania (Viannia) panamensis is one of the most important Leishmania species associated with cutaneous leishmaniasis (CL) in Latin America. Despite its wide geographic distribution and pathogenic potential in humans and animals, the genomic variability of this species is low compared with other Leishmania species circulating in the same geographical area. No studies have reported a detailed analysis of the whole genome of L. panamensis from clinical isolates using DNA highthroughput sequencing to clarify its intraspecific genomic variability or plausible divergence. Therefore, this study aimed to evaluate the intraspecific genomic variability of L. panamensis from Colombia and Panama. A total of 22 genomes were analyzed, 19 from Colombian patients with CL and three genomes from Panama obtained from public databases. The phylogenomic analysis revealed the potential existence of three well-supported clades as evidence of intraspecific divergence. Additionally, the whole-genome analysis showed low structural variations in terms of ploidy, copy number variations, and single-nucleotide polymorphisms (SNPs). SNPs shared among all clades were identified, revealing their importance in different biological processes of L. panamensis. The findings not only expand our knowledge of intraspecific genomic variability of one of the most important Leishmania species in South America but also highlights the possible existence of different clades/lineages/subpopulations across a geographic scale. © 2020 by the authors. Licensee MDPI, Basel, Switzerland.
publishDate 2020
dc.date.accessioned.none.fl_str_mv 2020-05-26T00:09:13Z
dc.date.available.none.fl_str_mv 2020-05-26T00:09:13Z
dc.date.created.spa.fl_str_mv 2020
dc.type.eng.fl_str_mv article
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dc.type.coar.fl_str_mv http://purl.org/coar/resource_type/c_6501
dc.type.spa.spa.fl_str_mv Artículo
dc.identifier.doi.none.fl_str_mv https://doi.org/10.3390/genes11030252
dc.identifier.issn.none.fl_str_mv 20734425
dc.identifier.uri.none.fl_str_mv https://repository.urosario.edu.co/handle/10336/24145
url https://doi.org/10.3390/genes11030252
https://repository.urosario.edu.co/handle/10336/24145
identifier_str_mv 20734425
dc.language.iso.spa.fl_str_mv eng
language eng
dc.relation.citationIssue.none.fl_str_mv No. 3
dc.relation.citationTitle.none.fl_str_mv Genes
dc.relation.citationVolume.none.fl_str_mv Vol. 11
dc.relation.ispartof.spa.fl_str_mv Genes, ISSN:20734425, Vol.11, No.3 (2020)
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dc.rights.acceso.spa.fl_str_mv Abierto (Texto Completo)
rights_invalid_str_mv Abierto (Texto Completo)
http://purl.org/coar/access_right/c_abf2
dc.format.mimetype.none.fl_str_mv application/pdf
dc.publisher.spa.fl_str_mv MDPI AG
institution Universidad del Rosario
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dc.source.reponame.spa.fl_str_mv reponame:Repositorio Institucional EdocUR
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