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

Luz H. Patino; Marina Muñoz; Carlos Muskus; Claudia Méndez; Juan David Ramírez

doi:10.3390/genes11030252

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

Título traducido de la contribución: Divergencia genómica intraespecífica y variaciones estructurales menores en leishmania (Viannia) panamensis

Luz H. Patino, Marina Muñoz, Carlos Muskus, Claudia Méndez, Juan David Ramírez

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10 Citas (Scopus)

Resumen

Leishmania (Viannia) panamensis es una de las especies de Leishmania más importantes asociadas a la leishmaniosis cutánea (LC) en América Latina. A pesar de su amplia distribución geográfica y su potencial patógeno en humanos y animales, la variabilidad genómica de esta especie es baja en comparación con otras especies de Leishmania que circulan en la misma zona geográfica. Ningún estudio ha informado de un análisis detallado del genoma completo de L. panamensis a partir de aislados clínicos utilizando la secuenciación de alto rendimiento del ADN para aclarar su variabilidad genómica intraespecífica o su divergencia plausible. Por lo tanto, este estudio tuvo como objetivo evaluar la variabilidad genómica intraespecífica de L. panamensis de Colombia y Panamá. Se analizaron un total de 22 genomas, 19 de pacientes colombianos con CL y tres genomas de Panamá obtenidos de bases de datos públicas. El análisis filogenómico reveló la existencia potencial de tres clados bien soportados como evidencia de divergencia intraespecífica. Además, el análisis del genoma completo mostró bajas variaciones estructurales en términos de ploidía, variaciones en el número de copias y polimorfismos de un solo nucleótido (SNP). Se identificaron SNPs compartidos entre todos los clados, revelando su importancia en diferentes procesos biológicos de L. panamensis. Los hallazgos no sólo amplían nuestro conocimiento de la variabilidad genómica intraespecífica de una de las especies de Leishmania más importantes de Sudamérica, sino que también destacan la posible existencia de diferentes clados/linajes/subpoblaciones a escala geográfica.

Título traducido de la contribución	Divergencia genómica intraespecífica y variaciones estructurales menores en leishmania (Viannia) panamensis
Idioma original	Inglés estadounidense
Número de artículo	252
Publicación	Genes
Volumen	11
N.º	3
DOI	https://doi.org/10.3390/genes11030252
Estado	Publicada - feb. 27 2020

Áreas temáticas de ASJC Scopus

Genética
Genética (clínica)

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title = "Intraspecific genomic divergence and minor structural variations in leishmania (Viannia) panamensis",

abstract = "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.",

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T1 - Intraspecific genomic divergence and minor structural variations in leishmania (Viannia) panamensis

AU - Patino, Luz H.

AU - Muñoz, Marina

AU - Muskus, Carlos

AU - Méndez, Claudia

AU - Ramírez, Juan David

PY - 2020/2/27

Y1 - 2020/2/27

N2 - 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.

AB - 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.

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

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