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

Abstract

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.

Evidence that interspeciesLeishmaniahybrids contribute to changes in disease pathology

“…As there is only one reference L. tropica strain, samples SRR6257366, SRR6257367 and SRR6257369 (SL2 B) all clustered to this one reference. With respect to the SL3 group, the reconstructed genes from SRR6257368, SRR6257370 and SRR6257371 were almost exclusively derived from the African LdLV9 reference strain 34 .…”

“…Genetic comparison of the genome of L. donovani origin in those hybrids is most similar to the LV9 strain of Ethiopian origin 34 rather than the reference Sri Lankan or Indian/Nepalese sequences while also assigning the genomic sequences of L. major origin to a Senegalese reference (Table 2, Fig. 1B, Supplementary Fig S3, Fig.…”

Trypanosoma Cruzi Genome: Organization, Multi-Gene Families, Transcription, and Biological Implications

“…This could lead to over-, under- or miss-representation of genes or complete chromosomic regions. In this regard, long-read sequencing methods (i.e., PacBio, Nanopore) could be a better choice for the trypanosomatids genomes [ 52 ], as the case of Bug2148 strain [ 53 ]. This technology allows the sequencing of long genetic fragments avoiding the complex and repetitive nature of the parasite.…”

Genomic and Transcriptomic Analysis for Identification of Genes and Interlinked Pathways Mediating Artemisinin Resistance in Leishmania donovani

“…Normalized read depth data are generally used to assess copy number variation as somy estimation does not always show a result in integral values, since it depicts the average of a population of the cell that does not strictly show identical karyotypes. To determine somy, the two-loop method was used [38,63]. Chromosomal somy data analysis of K133WT and K133AS-R shows that most of the chromosomes were disomic.…”

“…The genes that were observed to be downregulated included phosphoacetylglucosamine mutase-like protein (LinJ07_V30930/LdBPK_070930) and pteridine transporter (LinJ06_V3.1320/LdBPK_061320). Cathepsin L-like protease, a type of lysosomal endopeptidases, is present in both the promastigote and amastimogote stage of Leishmania species and involved in crucial biological process of parasites, such as evasion of the host immune system [63][64][65].…”