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

Llanes, Alejandro; Restrepo, Carlos M.; Vecchio, Gina Del; Anguizola, Franklin José; Lleonart, Ricardo

doi:10.1038/srep08550

Cited by 73 publications

(87 citation statements)

References 69 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…4). Chromosome 2 had a somy of 3.4, symptomatic of a mosaic cell population, and chromosome 31 was tetrasomic, as expected given it was nearly always tetrasomic in sequenced Leishmania 343536373841. These estimates were confirmed by the heterozygous SNP RDAF distributions for each chromosome (Supplementary Fig.…”

Section: Resultssupporting

confidence: 70%

The genome of Leishmania adleri from a mammalian host highlights chromosome fission in Sauroleishmania

Coughlan

Mulhair

Sanders

et al. 2017

Sci Rep

View full text Add to dashboard Cite

Control of pathogens arising from humans, livestock and wild animals can be enhanced by genome-based investigation. Phylogenetically classifying and optimal construction of these genomes using short sequence reads are key to this process. We examined the mammal-infecting unicellular parasite Leishmania adleri belonging to the lizard-infecting Sauroleishmania subgenus. L. adleri has been associated with cutaneous disease in humans, but can be asymptomatic in wild animals. We sequenced, assembled and investigated the L. adleri genome isolated from an asymptomatic Ethiopian rodent (MARV/ET/75/HO174) and verified it as L. adleri by comparison with other Sauroleishmania species. Chromosome-level scaffolding was achieved by combining reference-guided with de novo assembly followed by extensive improvement steps to produce a final draft genome with contiguity comparable with other references. L. tarentolae and L. major genome annotation was transferred and these gene models were manually verified and improved. This first high-quality draft Leishmania adleri reference genome is also the first Sauroleishmania genome from a non-reptilian host. Comparison of the L. adleri HO174 genome with those of L. tarentolae Parrot-TarII and lizard-infecting L. adleri RLAT/KE/1957/SKINK-7 showed extensive gene amplifications, pervasive aneuploidy, and fission of chromosomes 30 and 36. There was little genetic differentiation between L. adleri extracted from mammals and reptiles, highlighting challenges for leishmaniasis surveillance.

show abstract

Section: Resultssupporting

confidence: 70%

The genome of Leishmania adleri from a mammalian host highlights chromosome fission in Sauroleishmania

Coughlan

Mulhair

Sanders

et al. 2017

Sci Rep

View full text Add to dashboard Cite

show abstract

“…The L. guyanensis LgCL085 genome had more protein coding genes (8,230) than L. naiffi LnCL223 (8,104). These numbers were similar to those for L. panamensis PSC-1 (7,748) [51] and L. braziliensis M2904 (8,357) [48]. The vast majority of protein coding gene models were computationally transferred [81] from the L. braziliensis M2904 reference with perfect matching, and were verified and improved manually.…”

Section: Discussionmentioning

confidence: 57%

“…We identified 22 OGs exclusive to Viannia (Table S12): three OGs contained the RNAi pathway genes (DCL1, DCL2, RIF4). Another OG was the telomere-associated mobile elements (TATE) DNA transposons (OG5_132061), a dynamic feature of Viannia genomes [51] (Supplementary Results). Four OGs encoded a diacylglycerol kinase-like protein (OG5_133291), a nucleoside transporter (OG5_134097), a beta tubulin / amastin (OG5_183241), and a /zinc transporter (OG5_214682).…”

Section: Resultsmentioning

confidence: 99%

Leishmania naiffi and Leishmania guyanensis reference genomes highlight genome structure and gene evolution in the Viannia subgenus

Coughlan

Taylor

Feane

et al. 2017

Preprint

View full text Add to dashboard Cite

The unicellular protozoan parasite Leishmania causes the neglected tropical disease leishmaniasis, affecting 12 million people in 98 countries. In South America where the Viannia subgenus predominates, so far only L. (Viannia) braziliensis and L. (V.) panamensis have been sequenced, assembled and annotated as reference genomes. Addressing this deficit in molecular information can inform species typing, epidemiological monitoring and clinical treatment. Here, L. (V.) naiffi and L. (V.) guyanensis genomic DNA was sequenced to assemble these two genomes as draft references from short sequence reads. The methods used were tested using short sequence reads for L. braziliensis M2904 against its published reference as a comparison. This assembly and annotation pipeline identified 70 additional genes not annotated on the original M2904 reference. Phylogenetic and evolutionary comparisons of L. guyanensis and L. naiffi with ten other Viannia genomes revealed four traits common to all Viannia: aneuploidy, 22 orthologous groups of genes absent in other Leishmania subgenera, elevated TATE transposon copies, and a high NADH-dependent fumarate reductase gene copy number. Within the Viannia, there were limited structural changes in genome architecture specific to individual species: a 45 Kb amplification on chromosome 34 was present in all bar L. lainsoni, L. naiffi had a higher copy number of the virulence factor leishmanolysin, and laboratory isolate L. shawi M8408 had a possible minichromosome derived from the 3’ end of chromosome 34. This combination of genome assembly, phylogenetics and comparative analysis across an extended panel of diverse Viannia has uncovered new insights into the origin and evolution of this subgenus and can help improve diagnostics for leishmaniasis surveillance.

show abstract

“…Several other species presented degenerate copies of VIPER. In L. braziliensis, L. panamensis and L. peruviana, which are three closely related species [40,41], one of the significant hits corresponds to a VIPER-derived gene that was already reported [42].…”

Section: Viper and Tate Present A Discontinuous Distribution In Trypamentioning

confidence: 94%

Study of VIPER and TATE in kinetoplastids and the evolution of tyrosine recombinase retrotransposons

et al. 2019

View full text Add to dashboard Cite

Background Kinetoplastids are a flagellated group of protists, including some parasites, such as Trypanosoma and Leishmania species, that can cause diseases in humans and other animals. The genomes of these species enclose a fraction of retrotransposons including VIPER and TATE , two poorly studied transposable elements that encode a tyrosine recombinase (YR) and were previously classified as DIRS elements. This study investigated the distribution and evolution of VIPER and TATE in kinetoplastids to understand the relationships of these elements with other retrotransposons. Results We observed that VIPER and TATE have a discontinuous distribution among Trypanosomatidae, with several events of loss and degeneration occurring during a vertical transfer evolution. We were able to identify the terminal repeats of these elements for the first time, and we showed that these elements are potentially active in some species, including T. cruzi copies of VIPER . We found that VIPER and TATE are strictly related elements, which were named in this study as VIPER-like . The reverse transcriptase (RT) tree presented a low resolution, and the origin and relationships among YR groups remain uncertain. Conversely, for RH, VIPER-like grouped with Hepadnavirus , whereas for YR, VIPER-like sequences constituted two different clades that are closely allied to Crypton . Distinct topologies among RT, RH and YR trees suggest ancient rearrangements/exchanges in domains and a modular pattern of evolution with putative independent origins for each ORF. Conclusions Due to the presence of both elements in Bodo saltans, a nontrypanosomatid species, we suggested that VIPER and TATE have survived and remained active for more than 400 million years or were reactivated during the evolution of the host species. We did not find clear evidence of independent origins of VIPER-like from the other YR retroelements, supporting the maintenance of the DIRS group of retrotransposons. Nevertheless, according to phylogenetic findings and sequence structure obtained by this study and other works, we proposed separating DIRS elements into four subgroups: DIRS-like, PAT-like, Ngaro-like, and VIPER-like. Electronic supplementary material The online version of this article (10.1186/s13100-019-0175-2) contains supplementary material, which is available to authori...

show abstract

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

Cited by 73 publications

References 69 publications

The genome of Leishmania adleri from a mammalian host highlights chromosome fission in Sauroleishmania

The genome of Leishmania adleri from a mammalian host highlights chromosome fission in Sauroleishmania

Leishmania naiffi and Leishmania guyanensis reference genomes highlight genome structure and gene evolution in the Viannia subgenus

Study of VIPER and TATE in kinetoplastids and the evolution of tyrosine recombinase retrotransposons

Contact Info

Product

Resources

About