Pathogens

17 pages, 3991 KiB

Open AccessArticle

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

by Alexa Kaufer, Damien Stark and John Ellis

Pathogens 2019, 8(3), 157; https://doi.org/10.3390/pathogens8030157 - 18 Sep 2019

Cited by 12 | Viewed by 5198

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. [...] Read more.

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. Full article

(This article belongs to the Special Issue Kinetoplastid Phylogenomics and Evolution)

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12 pages, 4546 KiB

Open AccessEditor’s ChoiceArticle

New Taxon-Specific Heterobasidion PCR Primers Detect and Differentiate North American Heterobasidion spp. in Various Substrates and Led to the Discovery of Heterobasidion irregulare in British Columbia, Canada

by Simon Francis Shamoun, Craig Hammett, Grace Sumampong, Xiang Li and Matteo Garbelotto

Pathogens 2019, 8(3), 156; https://doi.org/10.3390/pathogens8030156 - 18 Sep 2019

Cited by 5 | Viewed by 4873

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Pathogens, Volume 8, Issue 3 (September 2019) – 70 articles

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