A bioinformatics approach to reanalyze the genome annotation of kinetoplastid protozoan parasite Leishmania donovani

Pawar, Harsh; Kulkarni, Aditi; Dixit, Tanwi; Chaphekar, Deepa; Patole, Milind S.

doi:10.1016/j.ygeno.2014.09.008

Cited by 15 publications

(7 citation statements)

References 15 publications

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“…donovani assemblies published to date. This new assembly represents an improved genome regarding the current reference genome (BPK strain 67 ), which is incomplete and presents some annotation deficiencies 75 . Thus, apart from eliminating the gaps, the genome size has been extended about 1.8 Mb in length and the total number of annotated genes has been increased by 400 genes, regarding the current reference L .…”

Section: Resultsmentioning

confidence: 99%

Complete assembly of the Leishmania donovani (HU3 strain) genome and transcriptome annotation

Camacho

Fuente

Rastrojo

et al. 2019

Sci Rep

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Leishmania donovani is a unicellular parasite that causes visceral leishmaniasis, a fatal disease in humans. In this study, a complete assembly of the genome of L . donovani is provided. Apart from being the first published genome of this strain (HU3), this constitutes the best assembly for an L . donovani genome attained to date. The use of a combination of sequencing platforms enabled to assemble, without any sequence gap, the 36 chromosomes for this species. Additionally, based on this assembly and using RNA-seq reads derived from poly-A + RNA, the transcriptome for this species, not yet available, was delineated. Alternative SL addition sites and heterogeneity in the poly-A addition sites were commonly observed for most of the genes. After a complete annotation of the transcriptome, 2,410 novel transcripts were defined. Additionally, the relative expression for all transcripts present in the promastigote stage was determined. Events of cis- splicing have been documented to occur during the maturation of the transcripts derived from genes LDHU3_07.0430 and LDHU3_29.3990. The complete genome assembly and the availability of the gene models (including annotation of untranslated regions) are important pieces to understand how differential gene expression occurs in this pathogen, and to decipher phenotypic peculiarities like tissue tropism, clinical disease, and drug susceptibility.

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Section: Resultsmentioning

confidence: 99%

Complete assembly of the Leishmania donovani (HU3 strain) genome and transcriptome annotation

Camacho

Fuente

Rastrojo

et al. 2019

Sci Rep

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“…One new aspect of this work is the discovery of chromosomal translocations which have not been observed before in old world Leishmania species [ 70 – 72 ]. Studies in yeast have also indicated an increase of translocations events and chromosomal rearrangements when either MRE11 or RAD50 are mutated [ 2 ].…”

Section: Discussionmentioning

confidence: 99%

Chromosomal Translocations in the Parasite Leishmania by a MRE11/RAD50-Independent Microhomology-Mediated End Joining Mechanism

Laffitte

Leprohon

Maripier³

et al. 2016

PLoS Genet

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The parasite Leishmania often relies on gene rearrangements to survive stressful environments. However, safeguarding a minimum level of genome integrity is important for cell survival. We hypothesized that maintenance of genomic integrity in Leishmania would imply a leading role of the MRE11 and RAD50 proteins considering their role in DNA repair, chromosomal organization and protection of chromosomes ends in other organisms. Attempts to generate RAD50 null mutants in a wild-type background failed and we provide evidence that this gene is essential. Remarkably, inactivation of RAD50 was possible in a MRE11 null mutant that we had previously generated, providing good evidence that RAD50 may be dispensable in the absence of MRE11. Inactivation of the MRE11 and RAD50 genes led to a decreased frequency of homologous recombination and analysis of the null mutants by whole genome sequencing revealed several chromosomal translocations. Sequencing of the junction between translocated chromosomes highlighted microhomology sequences at the level of breakpoint regions. Sequencing data also showed a decreased coverage at subtelomeric locations in many chromosomes in the MRE11-/-RAD50-/- parasites. This study demonstrates an MRE11-independent microhomology-mediated end-joining mechanism and a prominent role for MRE11 and RAD50 in the maintenance of genomic integrity. Moreover, we suggest the possible involvement of RAD50 in subtelomeric regions stability.

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“…This finding led to the use of L. major (Friedlin) genome as a template to facilitate the assembly process of most of the Leishmania genomes reported afterwards. However, as demonstrated in this and other works 32 , that approach may lead to introduce assembly errors that would compromise future studies regarding gene content, gene models and genome architecture. Here, we present a de novo assembly of the L. infantum (JPCM5) genome based on sequence data derived from both long (PacBio) and short (Illumina) reads that yielded the expected 36 chromosomal-size contigs, without discontinuities and undetermined sequence (Ns), which are abundant in the current genome (GeneDB.org).…”

Section: Resultsmentioning

confidence: 89%

Resequencing of the Leishmania infantum (strain JPCM5) genome and de novo assembly into 36 contigs

Fuente

Peiró‐Pastor

Rastrojo

et al. 2017

Sci Rep

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Leishmania parasites are the causative of leishmaniasis, a group of potentially fatal human diseases. Control strategies for leishmaniasis can be enhanced by genome based investigations. The publication in 2005 of the Leishmania major genome sequence, and two years later the genomes for the species Leishmania braziliensis and Leishmania infantum were major milestones. Since then, the L. infantum genome, although highly fragmented and incomplete, has been used widely as the reference genome to address whole transcriptomics and proteomics studies. Here, we report the sequencing of the L. infantum genome by two NGS methodologies and, as a result, the complete genome assembly on 36 contigs (chromosomes). Regarding the present L. infantum genome-draft, 495 new genes have been annotated, a hundred have been corrected and 75 previous annotated genes have been discontinued. These changes are not only the result of an increase in the genome size, but a significant contribution derives from the existence of a large number of incorrectly assembled regions in current chromosomal scaffolds. Furthermore, an improved assembly of tandemly repeated genes has been obtained. All these analyses support that the de novo assembled L. infantum genome represents a robust assembly and should replace the currently available in the databases.

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A bioinformatics approach to reanalyze the genome annotation of kinetoplastid protozoan parasite Leishmania donovani

Cited by 15 publications

References 15 publications

Complete assembly of the Leishmania donovani (HU3 strain) genome and transcriptome annotation

Complete assembly of the Leishmania donovani (HU3 strain) genome and transcriptome annotation

Chromosomal Translocations in the Parasite Leishmania by a MRE11/RAD50-Independent Microhomology-Mediated End Joining Mechanism

Resequencing of the Leishmania infantum (strain JPCM5) genome and de novo assembly into 36 contigs

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