Analysis of the mitochondrial maxicircle of Trypanosoma lewisi, a neglected human pathogen

Abstract

BackgroundThe haemoflagellate Trypanosoma lewisi is a kinetoplastid parasite which, as it has been recently reported to cause human disease, deserves increased attention. Characteristic features of all kinetoplastid flagellates are a uniquely structured mitochondrial DNA or kinetoplast, comprised of a network of catenated DNA circles, and RNA editing of mitochondrial transcripts. The aim of this study was to describe the kinetoplast DNA of T. lewisi.Methods/ResultsIn this study, purified kinetoplast DNA from T. lewisi was sequenced using high-throughput sequencing in combination with sequencing of PCR amplicons. This allowed the assembly of the T. lewisi kinetoplast maxicircle DNA, which is a homologue of the mitochondrial genome in other eukaryotes. The assembly of 23,745 bp comprises the non-coding and coding regions. Comparative analysis of the maxicircle sequence of T. lewisi with Trypanosoma cruzi, Trypanosoma rangeli, Trypanosoma brucei and Leishmania tarentolae revealed that it shares 78 %, 77 %, 74 % and 66 % sequence identity with these parasites, respectively. The high GC content in at least 9 maxicircle genes of T. lewisi (ATPase6; NADH dehydrogenase subunits ND3, ND7, ND8 and ND9; G-rich regions GR3 and GR4; cytochrome oxidase subunit COIII and ribosomal protein RPS12) implies that their products may be extensively edited. A detailed analysis of the non-coding region revealed that it contains numerous repeat motifs and palindromes.ConclusionsWe have sequenced and comprehensively annotated the kinetoplast maxicircle of T. lewisi. Our analysis reveals that T. lewisi is closely related to T. cruzi and T. brucei, and may share similar RNA editing patterns with them rather than with L. tarentolae. These findings provide novel insight into the biological features of this emerging human pathogen.Electronic supplementary materialThe online version of this article (doi:10.1186/s13071-015-1281-8) contains supplementary material, which is available to authorized users.

Mitonuclear genomics challenges the theory of clonality in Trypanosoma congolense: Reply to Tibayrenc and Ayala

“…The maxicircle was de novo assembled with SPAdes (Bankevich et al., ), elongated with NOVOplasty (Dierckxsens, Mardulyn, & Smits, ), chopped in two and circularized by assembling overlapping ends with CAP3 (Huang & Madan, ) (Figure a). The final assembly was annotated with RATT (Otto, Dillon, Degrave, & Berriman, ) using the T. lewisi annotation file (Lin et al., ) (Figure b). The T. congolense sequence data (Tihon et al., ) were aligned against this novel maxicircle reference using SMALT (https://www.sanger.ac.uk/science/tools/smalt-0) and SNPs were called with SAMTOOLS mpileup and bcftools (Li et al., ), including only reads with a minimum mapping quality of 20.…”

Cell cycle and cleavage events during in vitro cultivation of bloodstream forms of Trypanosoma lewisi, a zoonotic pathogen

“…Trypanosoma cruzi [41]. The dramatic differences in the ways which the bloodstream forms divide when comparing T. rangeli and other Herpetosoma members support the suggestion of reclassification of T. rangeli from the subgenus Herpetosoma into Schizotrypanum as suggested from studies based on molecular data [42,43].…”

PCR-based identification of Trypanosoma lewisi and Trypanosoma musculi using maxicircle kinetoplast DNA

“…T. evansi was also separated from other trypanosoma genus (Masiga and Gibson, 1990), but the kDNA test could not distinguish dyskinetoplastic strains of T. evansi. Our laboratory described the maxicircle sequence of T. lewisi (Lin et al, 2015) and partially a divergent region of T. musculi. Herein, species-specific primers 9 were designed on this region.…”

“…lewisi-like trypanosomes have been reported, suggesting it may be an underestimated human pathogen (Doke and Kar, 2011;Howie et al, 2006;Johnson, 1933;Kaur et al, 2007;Lin et al, 2015;Lun et al, 2009;Lun et al, 2015;Sarataphan et al, 2007;Shrivastava and Shrivastava, 1974;Verma et al, 2011). Serological surveys in last century observed a 1% positivity in healthy human populations in Northeast China (Liu and Liu, 1990), suggesting a high frequency of direct contact between humans (likely villagers) with this pathogen.…”