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The genome of Leishmania panamensis: insights into genomics of the L. (Viannia) subgenus.

Llanes A, Restrepo CM, Del Vecchio G, Anguizola FJ, Lleonart R - Sci Rep (2015)

Bottom Line: Species from the Viannia subgenus cause predominantly cutaneous leishmaniasis in Central and South America, occasionally leading to more severe clinical presentations.Although the genomes of several species of Leishmania have been sequenced to date, only one belongs to this rather different subgenus.These differences may in part explain some phenotypic characteristics of the Viannia parasites, including their increased adaptive capacity and enhanced metastatic ability.

View Article: PubMed Central - PubMed

Affiliation: 1] Centro de Biología Celular y Molecular de Enfermedades, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Ciudad del Saber, Panamá, Panamá [2] Facultad de Ciencias de la Salud Dr. William C. Gorgas, Universidad Latina de Panamá, Panamá, Panamá [3] Department of Biotechnology, Acharya Nagarjuna University, Guntur, India.

ABSTRACT
Kinetoplastid parasites of the Leishmania genus cause several forms of leishmaniasis. Leishmania species pathogenic to human are separated into two subgenera, Leishmania (Leishmania) and L. (Viannia). Species from the Viannia subgenus cause predominantly cutaneous leishmaniasis in Central and South America, occasionally leading to more severe clinical presentations. Although the genomes of several species of Leishmania have been sequenced to date, only one belongs to this rather different subgenus. Here we explore the unique features of the Viannia subgenus by sequencing and analyzing the genome of L. (Viannia) panamensis. Against a background of conservation in gene content and synteny, we found key differences at the genomic level that may explain the occurrence of molecular processes involving nucleic acid manipulation and differential modification of surface glycoconjugates. These differences may in part explain some phenotypic characteristics of the Viannia parasites, including their increased adaptive capacity and enhanced metastatic ability.

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Related in: MedlinePlus

Estimates of chromosome somy for L. panamensis strain PSC-1.Normalized median read depth is plotted for each L. panamensis chromosome. Bars are shaded according to estimated chromosome somy: light gray (disomic), medium gray (trisomic) and dark gray (tetrasomic).
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f3: Estimates of chromosome somy for L. panamensis strain PSC-1.Normalized median read depth is plotted for each L. panamensis chromosome. Bars are shaded according to estimated chromosome somy: light gray (disomic), medium gray (trisomic) and dark gray (tetrasomic).

Mentions: Alignments of the Illumina reads to the assembled pseudochromosomes were used for ploidy or chromosome somy estimations. Despite local spikes associated with repetitive features, distribution of read depth is relatively uniform along the sequence of all chromosomes (Supplementary Figure 4). Median read depth does not appear to be globally affected by local variations in depth of coverage or GC content bias (Supplementary Figure 5). Several studies in our laboratory have shown that the PSC-1 strain is mostly diploid, thus we arbitrarily assigned the most frequent value of median read depth within all chromosomes to a disomic state. This value was used to compute a normalized median read depth for each chromosome, which was considered to be an estimation of its somy (Fig. 3 and Supplementary Data 3). Most chromosomes seem to be disomic, with the exception of chromosomes 4 and 23, which appear to be trisomic, and chromosome 31, which seems to be tetrasomic. Chromosome 31 has been previously found to have an unusually larger somy in Leishmania; in fact, this is the only chromosome that has been found to be supernumerary in all Leishmania species in previous studies3038. As reported by Rogers et al.30, we also noticed irregular values for median read depth in some of the smallest chromosomes, suggestive of chromosomes that are not fully disomic or trisomic. However, this situation is likely to be a consequence of mosaic aneuploidy39, a phenomenon recently described for Leishmania, characterized by a variation in the somy of the same chromosomes among cells within the population.


The genome of Leishmania panamensis: insights into genomics of the L. (Viannia) subgenus.

Llanes A, Restrepo CM, Del Vecchio G, Anguizola FJ, Lleonart R - Sci Rep (2015)

Estimates of chromosome somy for L. panamensis strain PSC-1.Normalized median read depth is plotted for each L. panamensis chromosome. Bars are shaded according to estimated chromosome somy: light gray (disomic), medium gray (trisomic) and dark gray (tetrasomic).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4338418&req=5

f3: Estimates of chromosome somy for L. panamensis strain PSC-1.Normalized median read depth is plotted for each L. panamensis chromosome. Bars are shaded according to estimated chromosome somy: light gray (disomic), medium gray (trisomic) and dark gray (tetrasomic).
Mentions: Alignments of the Illumina reads to the assembled pseudochromosomes were used for ploidy or chromosome somy estimations. Despite local spikes associated with repetitive features, distribution of read depth is relatively uniform along the sequence of all chromosomes (Supplementary Figure 4). Median read depth does not appear to be globally affected by local variations in depth of coverage or GC content bias (Supplementary Figure 5). Several studies in our laboratory have shown that the PSC-1 strain is mostly diploid, thus we arbitrarily assigned the most frequent value of median read depth within all chromosomes to a disomic state. This value was used to compute a normalized median read depth for each chromosome, which was considered to be an estimation of its somy (Fig. 3 and Supplementary Data 3). Most chromosomes seem to be disomic, with the exception of chromosomes 4 and 23, which appear to be trisomic, and chromosome 31, which seems to be tetrasomic. Chromosome 31 has been previously found to have an unusually larger somy in Leishmania; in fact, this is the only chromosome that has been found to be supernumerary in all Leishmania species in previous studies3038. As reported by Rogers et al.30, we also noticed irregular values for median read depth in some of the smallest chromosomes, suggestive of chromosomes that are not fully disomic or trisomic. However, this situation is likely to be a consequence of mosaic aneuploidy39, a phenomenon recently described for Leishmania, characterized by a variation in the somy of the same chromosomes among cells within the population.

Bottom Line: Species from the Viannia subgenus cause predominantly cutaneous leishmaniasis in Central and South America, occasionally leading to more severe clinical presentations.Although the genomes of several species of Leishmania have been sequenced to date, only one belongs to this rather different subgenus.These differences may in part explain some phenotypic characteristics of the Viannia parasites, including their increased adaptive capacity and enhanced metastatic ability.

View Article: PubMed Central - PubMed

Affiliation: 1] Centro de Biología Celular y Molecular de Enfermedades, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Ciudad del Saber, Panamá, Panamá [2] Facultad de Ciencias de la Salud Dr. William C. Gorgas, Universidad Latina de Panamá, Panamá, Panamá [3] Department of Biotechnology, Acharya Nagarjuna University, Guntur, India.

ABSTRACT
Kinetoplastid parasites of the Leishmania genus cause several forms of leishmaniasis. Leishmania species pathogenic to human are separated into two subgenera, Leishmania (Leishmania) and L. (Viannia). Species from the Viannia subgenus cause predominantly cutaneous leishmaniasis in Central and South America, occasionally leading to more severe clinical presentations. Although the genomes of several species of Leishmania have been sequenced to date, only one belongs to this rather different subgenus. Here we explore the unique features of the Viannia subgenus by sequencing and analyzing the genome of L. (Viannia) panamensis. Against a background of conservation in gene content and synteny, we found key differences at the genomic level that may explain the occurrence of molecular processes involving nucleic acid manipulation and differential modification of surface glycoconjugates. These differences may in part explain some phenotypic characteristics of the Viannia parasites, including their increased adaptive capacity and enhanced metastatic ability.

Show MeSH
Related in: MedlinePlus