Evidence of hybridization, mitochondrial introgression and biparental inheritance of the kDNA minicircles in Trypanosoma cruzi I

Abstract

BackgroundGenetic exchange in Trypanosoma cruzi is controversial not only in relation to its frequency, but also to its mechanism. Parasexual genetic exchange has been proposed based on laboratory hybrids, but population genomics strongly suggests meiosis in T. cruzi. In addition, mitochondrial introgression has been reported several times in natural isolates although its mechanism is not fully understood yet. Moreover, hybrid T. cruzi DTUs (TcV and TcVI) have inherited at least part of the kinetoplastic DNA (kDNA = mitochondrial DNA) from both parents. Methodology/Principal findingsIn order to address such topics, we sequenced and analyzed fourteen nuclear DNA fragments and three kDNA maxicircle genes in three TcI stocks which are natural clones potentially involved in events of genetic exchange. We also deep-sequenced (a total of 6,146,686 paired-end reads) the minicircle hypervariable region (mHVR) of the kDNA in such three strains. In addition, we analyzed the DNA content by flow cytometry to address cell ploidy. We observed that most polymorphic sites in nuclear loci showed a hybrid pattern in one cloned strain and the other two cloned strains were compatible as parental strains (or nearly related to the true parents). The three clones had almost the same ploidy and the DNA content was similar to the reference strain Sylvio (a nearly diploid strain). Despite maxicircle genes evolve faster than nuclear housekeeping ones, we detected no polymorphisms in the sequence of three maxicircle genes showing mito-nuclear discordance. Lastly, the hybrid stock shared 66% of its mHVR clusters with one putative parent and 47% with the other one; in contrast, the putative parental stocks shared less than 30% of the mHVR clusters between them.

Guide RNA Repertoires in the Main Lineages of Trypanosoma cruzi: High Diversity and Variable Redundancy Among Strains

“…The TcI strains analyzed here are phylogenetically close according to nuclear and mitochondrial sequences (Tomasini et al, 2014;Rusman et al, 2020). However, they shared just 19.2% of their gRNA classes.…”

“…Since the model of (partial) random segregation as the unique evolutionary force does not fit the high levels of gRNA class redundancy observed in some strains, the genetic exchange would be the most probable force generating gRNA class redundancy. In a previous paper, we proposed biparental inheritance of minicircles in hybrid DTUs of T. cruzi (Rusman et al, 2019) and in an intra TcI hybrid (Rusman et al, 2020). Biparental inheritance has also been proposed for T. brucei (Turner et al, 1995;Gibson et al, 2008).…”

“…In addition, such differences in the number of mHVR clusters may imply redundant gRNAs (gRNAs with relatively different sequences that edit the same region) or mHVRs not encoding gRNAs. We proposed that minicircle inheritance is biparental in hybrid DTUs (Rusman et al, 2019) and hybrid strains (Rusman et al, 2020) despite the uniparental inheritance of maxicircles (Tomasini, 2018). This scenario opens the question on how mixing minicircles from different parents could still lead to correct editing of mitochondrial mRNAs, since maxicircles are inherited from one parental.…”

Trypanosoma cruzi Genome 15 Years Later: What Has Been Accomplished?

“…There are claims of the uniparental contribution of K-DNA in parasexual hybrids [23,66] but with pieces of evidence of exchanges with other clades or DTUs. Little is known about how these inter-DTUs introgression processes occur [30,67,68].…”

High-throughput analysis of the Trypanosoma cruzi minicirculome (mcDNA) unveils structural variation and functional diversity

“…Recent reports using deep sequencing of mHVR amplicons have shown variable clusters of mHVRs across strains, ranging from 71 in TcV (Mncl2 strain) to 373 in TcIII (X109/2 strain). Some of these clusters are shared among strains both intra and within lineages, hinting at potential bi-parental inheritance of minicircles 12 , 19 . This diversity in gRNAs repertoire may contribute to the extreme diversity observed in different lineages of T. cruzi 15 .…”