The Comparative Genomics and Phylogenomics of <i>Leishmania Amazonensis</i> Parasite

Tschoeke, Diogo A.; Nunes, Gisele; Jardim, Rodrigo; Lima, Joana Esteves de; Dumaresq, Aline; Gomes, Maria de Lourdes Contente; Pereira, Leandro de Mattos; Loureiro, Daniel R; Stoco, Patrícia Hermes; Guedes, Herbert Leonel de Matos; Miranda, Antônio Basílio de; Ruiz, Jerônimo C.; Pitaluga, André Nóbrega; Silva, Floriano P.; Probst, Christian M.; Dickens, Nicholas J.; Mottram, Jeremy C.; Grisard, Edmundo C.; Dávila, Alberto M. R.

doi:10.4137/ebo.s13759

Cited by 24 publications

(26 citation statements)

References 106 publications

(192 reference statements)

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“…This method resulted in 3,584 and 3,236 contigs with an N50 of 29,346 bp and 26,692 bp for isolates S3 and S6, respectively (Table 1). While still a draft, our assembly is more contiguous than either of the published L. (L.) amazonensis M2269 assemblies1516. These contigs comprised more than 30.5 Mbp, which is slightly larger than the current L. (L.) amazonensis M2269 reference genome (version from 2013-07-25) and closer to the expected size for Leishmania genomes of 32 Mbp19.…”

Section: Resultsmentioning

confidence: 64%

“…. M2269 2 is the L. (L.) amazonensis genome published by Tschoeke16, there are no scaffolds available for this assembly.…”

Section: Figurementioning

confidence: 99%

“…Two different genome assemblies of the same L. (L.) amazonensis isolate (MHOM/BR/71973/M2269) have previously been published1516. The M2269 isolate was obtained from a human cutaneous lesion in Para state, Brazil in 197315.…”

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confidence: 99%

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Comparative genomics of canine-isolated Leishmania (Leishmania) amazonensis from an endemic focus of visceral leishmaniasis in Governador Valadares, southeastern Brazil

Valdivia

Almeida

Roatt

et al. 2017

Sci Rep

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Leishmaniasis is a highly diverse group of diseases caused by kinetoplastid of the genus Leishmania. These parasites are taxonomically diverse, with human pathogenic species separated into two subgenera according to their development site inside the alimentary tract of the sand fly insect vector. The disease encompasses a variable spectrum of clinical manifestations with tegumentary or visceral symptoms. Among the causative species in Brazil, Leishmania (Leishmania) amazonensis is an important etiological agent of human cutaneous leishmaniasis that accounts for more than 8% of all cases in endemic regions. L. (L.) amazonensis is generally found in the north and northeast regions of Brazil. Here, we report the first isolation of L. (L.) amazonensis from dogs with clinical manifestations of visceral leishmaniasis in Governador Valadares, an endemic focus in the southeastern Brazilian State of Minas Gerais where L. (L.) infantum is also endemic. These isolates were characterized in terms of SNPs, chromosome and gene copy number variations, confirming that they are closely related to a previously sequenced isolate obtained in 1973 from the typical Northern range of this species. The results presented in this article will increase our knowledge of L. (L.) amazonensis-specific adaptations to infection, parasite survival and the transmission of this Amazonian species in a new endemic area of Brazil.

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Section: Resultsmentioning

confidence: 64%

“…. M2269 2 is the L. (L.) amazonensis genome published by Tschoeke16, there are no scaffolds available for this assembly.…”

Section: Figurementioning

confidence: 99%

See 1 more Smart Citation

Comparative genomics of canine-isolated Leishmania (Leishmania) amazonensis from an endemic focus of visceral leishmaniasis in Governador Valadares, southeastern Brazil

Valdivia

Almeida

Roatt

et al. 2017

Sci Rep

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“…The presence of the PHA03247 domain is interesting since viral domains, including the domain under discussion, were found to be part of a special type of TEs, the helitrons (Castañera et al 2014). However, PHA03247 is the second most frequently found domain in L. amazonensis (126 copies) in a less stringent search (Tschoeke et al 2014). Thus, the actual existence of this domain may be questioned.…”

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confidence: 99%

Genomic and phylogenetic evidence of VIPER retrotransposon domestication in trypanosomatids

Ludwig

Krieger

2016

Mem. Inst. Oswaldo Cruz

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Transposable elements are important residents of eukaryotic genomes and eventually the host can domesticate them to serve cellular functions. We reported here a possible domestication event of the vestigial interposed retroelement (VIPER) in trypanosomatids. We found a large gene in a syntenic location in Leishmania braziliensis, L. panamensis, Leptomanas pyrrhocoris, and Crithidia fasciculata whose products share similarity in the C-terminal portion with the third protein of VIPER. No remnants of other VIPER regions surrounding the gene sequence were found. We hypothesise that the domestication event occurred more than 50 mya and the conservation of this gene suggests it might perform some function in the host species.

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“…Shotgun sequencing data of thirteen Leishmania isolates (this study) and eleven species available publicly enabled us to mine whole genome datasets for hundreds of thousands of phylogenetically informative sites. Previous molecular datasets used for phylogenetic reconstruction ranged from 1-31 genes 47 . Rather than relying on a few known genes, these data were sampled across the genome.…”

Section: Datamentioning

confidence: 99%

Phylogenomic Reconstruction Supports Supercontinent Origins forLeishmania

Harkins

Schwartz

Cartwright

et al. 2015

Preprint

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Leishmania, a genus of parasites transmitted to human hosts and mammalian/reptilian reservoirs by an insect vector, is the causative agent of the human disease complex leishmaniasis. The evolutionary relationships within the genus Leishmania and its origins are the source of ongoing debate, reflected in conflicting phylogenetic and biogeographic reconstructions. This study employs a recently described bioinformatics method, SISRS, to identify over 200,000 informative sites across the genome from newly sequenced and publicly available Leishmania data. This dataset is used to reconstruct the evolutionary relationships of this genus. Additionally, we constructed a large multi-gene dataset; we used this dataset to reconstruct the phylogeny and estimate divergence dates for species. We conclude that the genus Leishmania evolved at least 90-100 million years ago. Our results support the hypothesis that Leishmania clades separated prior to, and during, the breakup of Gondwana. Additionally, we confirm that reptile-infecting Leishmania are derived from mammalian forms, and that the species that infect porcupines and sloths form a clade long separated from other species. We also firmly place the guinea-pig infecting species, L. enrietti, the globally dispersed L. siamensis, and the newly identified Australia species from kangaroos as sibling species whose distribution arises from the ancient connection between Australia, Antarctica, and South America.

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The Comparative Genomics and Phylogenomics of Leishmania Amazonensis Parasite

Cited by 24 publications

References 106 publications

Comparative genomics of canine-isolated Leishmania (Leishmania) amazonensis from an endemic focus of visceral leishmaniasis in Governador Valadares, southeastern Brazil

Comparative genomics of canine-isolated Leishmania (Leishmania) amazonensis from an endemic focus of visceral leishmaniasis in Governador Valadares, southeastern Brazil

Genomic and phylogenetic evidence of VIPER retrotransposon domestication in trypanosomatids

Phylogenomic Reconstruction Supports Supercontinent Origins forLeishmania

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