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...
- Autores:
- Tipo de recurso:
- 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
- Palabra clave:
- 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)
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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 |
dc.type.coarversion.fl_str_mv |
http://purl.org/coar/version/c_970fb48d4fbd8a85 |
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) |
dc.relation.uri.spa.fl_str_mv |
https://www.scopus.com/inward/record.uri?eid=2-s2.0-85080959829&doi=10.3390%2fgenes11030252&partnerID=40&md5=148432dcc15dd175feb88e8cf39fd7d4 |
dc.rights.coar.fl_str_mv |
http://purl.org/coar/access_right/c_abf2 |
dc.rights.acceso.spa.fl_str_mv |
Abierto (Texto Completo) |
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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 |
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Universidad del Rosario |
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reponame:Repositorio Institucional EdocUR |
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