Chromosomal copy number variation analysis by next generation sequencing confirms ploidy stability in Trypanosoma brucei subspecies

Abstract

Although aneuploidy usually results in severe abnormalities in multicellular eukaryotes, recent data suggest that it could be beneficial for unicellular eukaryotes, such as yeast and trypanosomatid parasites, providing increased survival under stressful conditions. Among characterized trypanosomatids, Trypanosoma cruzi, Trypanosoma brucei and species from the genus Leishmania stand out due to their importance in public health, infecting around 20 million people worldwide. The presence of aneuploidies in T. cruzi and Leishmania was recently confirmed by analysis based on next generation sequencing (NGS) and fluorescence in situ hybridization, where they have been associated with adaptation during transmission between their insect vectors and mammalian hosts and in promoting drug resistance. Although chromosomal copy number variations (CCNVs) are present in the aforementioned species, PFGE and fluorescence cytophotometry analyses suggest that aneuploidies are absent from T. brucei. A re-evaluation of CCNV in T. b gambiense based on NGS reads confirmed the absence of aneuploidies in this subspecies. However, the presence of aneuploidies in the other two T. brucei subspecies, T. b. brucei and T. b. rhodesiense, has not been evaluated using NGS approaches. In the present work, we tested for aneuploidies in 26 T. brucei isolates, including samples from the three T. brucei subspecies, by both allele frequency and read depth coverage analyses. These analyses showed that none of the T. brucei subspecies presents aneuploidies, which could be related to differences in the mechanisms of DNA replication and recombination in these parasites when compared with Leishmania.

Intraspecific Genomic Divergence and Minor Structural Variations in Leishmania (Viannia) panamensis

“…These results are consistent with the dynamics of ploidy observed in genomes SRR10246848 and SRR10246849 analyzed by Restrepo et al [28]. The lack of genomic plasticity at the chromosomal level observed for L. panamensis has also been reported in other pathogens such as T. brucei; recently, a study has shown that none of the T. brucei subspecies present aneuploidy [62]. The low aneuploidy in these pathogens could be explained as a possible feature of adaptation of these parasites to human hosts or could be related to the loss of recombination events in this species, similar to that proposed for T. brucei [62].…”

“…The lack of genomic plasticity at the chromosomal level observed for L. panamensis has also been reported in other pathogens such as T. brucei; recently, a study has shown that none of the T. brucei subspecies present aneuploidy [62]. The low aneuploidy in these pathogens could be explained as a possible feature of adaptation of these parasites to human hosts or could be related to the loss of recombination events in this species, similar to that proposed for T. brucei [62]. This is also supported by the low number of SNPs found in the L. panamensis genomes analyzed which would explain a plausible mechanism of adaptation to human infection.…”

Replication origin location might contribute to genetic variability in Trypanosoma cruzi

“…Among these families, the trans-sialidase (TS) and dispersed gene family-1 (DGF-1) genes are enriched at subtelomeric regions of chromosomes [33], though other gene arrays are found throughout the chromosomes. Intriguingly, next generation sequencing has suggested that T. cruzi, like Leishmania, displays chromosomes that deviate from diploidy [34], whereas no such aneuploidy is seen in T. brucei [35]. Whether this difference relates to T. cruzi and Leishmania each having their genome housed in large numbers (> 35) of relatively small chromosomes, whereas the T. brucei genome is found in 11 relatively large chromosomes, is unknown.…”

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

“…These aneuploidies are related to drug resistance, gene expression regulation, or host adaptation [ 60 , 61 , 62 ]. Otherwise, in T. brucei a ploidy stability exists, including the subspecies T. b. gambiense and T. b. rhodesiense [ 63 ].…”