Evolutionary Insight into the Trypanosomatidae Using Alignment-Free Phylogenomics of the Kinetoplast

Abstract

Advancements in next-generation sequencing techniques have led to a substantial increase in the genomic information available for analyses in evolutionary biology. As such, this data requires the exponential growth in bioinformatic methods and expertise required to understand such vast quantities of genomic data. Alignment-free phylogenomics offer an alternative approach for large-scale analyses that may have the potential to address these challenges. The evolutionary relationships between various species within the trypanosomatid family, specifically members belonging to the genera Leishmania and Trypanosoma have been extensively studies over the last 30 years. However, there is a need for a more exhaustive analysis of the Trypanosomatidae, summarising the evolutionary patterns amongst the entire family of these important protists. The mitochondrial DNA of the trypanosomatids, better known as the kinetoplast, represents a valuable taxonomic marker given its unique presence across all kinetoplastid protozoans. The aim of this study was to validate the reliability and robustness of alignment-free approaches for phylogenomic analyses and its applicability to reconstruct the evolutionary relationships between the trypanosomatid family. In the present study, alignment-free analyses demonstrated the strength of these methods, particularly when dealing with large datasets compared to the traditional phylogenetic approaches. We present a maxicircle genome phylogeny of 46 species spanning the trypanosomatid family, demonstrating the superiority of the maxicircle for the analysis and taxonomic resolution of the Trypanosomatidae.

Novel organization of mitochondrial minicircles and guide RNAs in the zoonotic pathogen Trypanosoma lewisi

“…Interestingly, the minicircle-based phylogeny clusters T. rangeli , T. copemani and T. lewisi within the T. cruzi clade. This clustering corroborates previous phylogenetic analyses using the maxicircle conserved region, 18S rRNA and the glycosomal glyceraldehyde-3-phosphate dehydrogenase genes ( 69–71 ). This divergent pattern of minicircle organization within the Stercorarian group, which is characterized by transmission via insect feces ( 1 , 72 ), indicates that these trypanosomes might share a degree of similarity in features such as life cycle, growth requirements, virulence and pathogenicity.…”

Genome Analysis of Endotrypanum and Porcisia spp., Closest Phylogenetic Relatives of Leishmania, Highlights the Role of Amastins in Shaping Pathogenicity

“…The maximum likelihood and Bayesian phylogenomic trees inferred using the supermatrix of 410 proteins encoded by single-copy genes have the same topology and demonstrate maximal supports for almost all branches ( Figure 1 ). This topology is compatible with those inferred previously [ 2 , 9 , 96 , 97 ], which confirms the position of the genera Endotrypanum and Porcisia as the closest known relatives of the genus Leishmania .…”

Assembly of a Large Collection of Maxicircle Sequences and Their Usefulness for Leishmania Taxonomy and Strain Typing

“…A significant portion of the maxicircle (around 12 kb), named “divergent region” or DR, consists of low-complexity, tandemly repeats and its complete sequence remains undetermined for most species, but it is considered to be non-coding [ 48 ]. In contrast, the “coding region” (CR), completely sequenced years ago [ 49 ], has a remarkable conservation, in terms of both sequence and gene order among the trypanosomatids [ 19 , 22 , 25 ]. Figure 1 illustrates the absolute conservation in gene order (and strain polarity) in the maxicircles of evolutionary distant species such as L. tarentolae , L. infantum , and T. cruzi.…”

“…The low sequence complexity and repeated nature of the DR have been insurmountable hurdles to determining its complete sequence and length until the use of long-range PCR [ 23 ], or a combination of short and long reads from massive sequence technologies [ 22 , 24 ]. However, the gene order (synteny) in the maxicircle CR is highly conserved among the trypanosomatids [ 19 , 23 ], a feature that enables maxicircles to be reliable markers to determine evolutionary relationships among members of this order of organisms [ 25 ]. Now, when whole-genome sequencing (WGS) technologies are widely used for determining the nuclear genomic sequences of an increasing number of Leishmania species and strains [ 26 , 27 , 28 , 29 , 30 , 31 , 32 , 33 ], and their raw data are in publicly available databases [ 34 ], it is feasible to use those data to assemble the corresponding maxicircle sequences.…”