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

Abstract

We recently published the first genomic diversity study of Trypanosoma congolense, a major aetiological agent of Animal African Trypanosomiasis. We demonstrated striking levels of SNP and indel diversity in the Eastern province of Zambia as a consequence of hybridization between divergent trypanosome lineages. We concluded that these and earlier findings in T. congolense challenge the predominant clonal evolution (PCE) model. In a recent comment, Tibayrenc and Ayala claim that there are many features in T. congolense supporting their theory of clonality. While we can follow the reasoning of the authors, we also identify major limitations in their theory and interpretations that resulted in incorrect conclusions. First, we argue that each T. congolense subgroup should be analysed independently as they may represent different (sub)species rather than "near-clades". Second, the authors neglect major findings of two robust population genetic studies on Savannah T. congolense that provide clear evidence of frequent recombination. Third, we reveal additional events of introgressive hybridization in T. congolense by analysing the maxicircle coding region using next-generation sequencing analyses. At last, we pinpoint two important misinterpretations by the authors and show that there are no spatially and temporally widespread clones in T. congolense. We stand by our earlier conclusions that the clonal framework is unlikely to accurately model the population structure of T. congolense. Other theoretical frameworks such as Maynard Smith's epidemic model may better represent the complex ancestry seen in T. congolense, where clones delimited in space and time arise against a background of recombination.

Meiotic sex in Chagas disease parasite Trypanosoma cruzi

“…Establishing the occurrence of regular meiotic recombination in T. b. brucei has taken decades of laboratory and field research; not until 2014 was haploid gamete production (coincident to peak meiosis-specific gene expression) confirmed by fluorescence microscopy as a normal phase of development in the vector’s salivary gland 9–11 . More recently, genome-scale signatures of meiosis have also been detected in T. congolense 12,13 . In contrast, robust genomic evidence now suggests that the human-infective T. b. gambiense subspecies is completely asexual 14 .…”

rKOMICS: an R package for processing mitochondrial minicircle assemblies in population-scale genome projects

“…Reads that did not align against the reference genome are putative extranuclear sequences and should be extracted from the alignment file. When a reference maxicircle sequence of the same or a closely related species is available, unaligned reads are mapped against the maxicircle sequence to assist reference-guided assembly or genotyping of the conserved coding region (see [ 14 , 16 , 20 , 21 ] for examples).…”

“… Extract putative maxicircle sequences using a BLAST [ 32 ] approach with several build-in maxicircle sequences of Leishmania braziliensis M2904 [ 21 ] (available on www.tritrypdb.org ), Trypanosoma lewisi [ 36 ] (GenBank: KR072974.1), Trypanosoma brucei brucei (GenBank: M94286.1) and Trypanosoma equiperdum STIB842 [ 37 ] (GenBank: EU185800.1) as subjects. Identified maxicircle sequences may be further extended using NOVOPlasty [ 7 ], circularized using a BLAST approach and annotated using a homology-based search of known maxicircle genes with RATT [ 38 ] (see [ 16 ] for a detailed example on how to assemble a complete maxicircle sequence using deep-sequencing data of 250 bp paired-end reads). However, depending on sequencing depth and the complexity of the divergent (variable) region of the maxicircle, assembly of a complete maxicircle may prove challenging.…”

“…Hence, bioinformatic and downstream phylogenetic analyses of the mitochondrial maxicircle resemble those used for analyzing the mitochondrial genome in higher eukaryotes. Reference maxicircle sequences can be assembled using either short- or long-read sequencing datasets (see [ 16 ] for an example on how to sequence, assemble and annotate a complete reference maxicircle genome using paired-end 250-bp Illumina reads). Once a reference maxicircle sequence is available from the species of interest (or from a closely related organism), it can be used in population-scale genome studies for reference-guided assembly (e.g.…”

“…[ 25 ]) or genotyping (e.g. [ 16 ]). This approach has been used widely to recover the maxicircles from whole genome sequencing datasets of various protozoan parasites [ 14 , 16 , 20 , 21 ].…”