Horizontally Transferred Genetic Elements in the Tsetse Fly Genome: An Alignment-Free Clustering Approach Using Batch Learning Self-Organising Map (BLSOM).

Chihiro Sugimoto,Ryo Nakao,Takashi Abe,Shunsuke Funayama

doi:10.1155/2016/3164624

Chihiro Sugimoto, Ryo Nakao + Show 2 more

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https://doi.org/10.1155/2016/3164624

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Abstract

Tsetse flies (Glossina spp.) are the primary vectors of trypanosomes, which can cause human and animal African trypanosomiasis in Sub-Saharan African countries. The objective of this study was to explore the genome of Glossina morsitans morsitans for evidence of horizontal gene transfer (HGT) from microorganisms. We employed an alignment-free clustering method, that is, batch learning self-organising map (BLSOM), in which sequence fragments are clustered based on the similarity of oligonucleotide frequencies independently of sequence homology. After an initial scan of HGT events using BLSOM, we identified 3.8% of the tsetse fly genome as HGT candidates. The predicted donors of these HGT candidates included known symbionts, such as Wolbachia, as well as bacteria that have not previously been associated with the tsetse fly. We detected HGT candidates from diverse bacteria such as Bacillus and Flavobacteria, suggesting a past association between these taxa. Functional annotation revealed that the HGT candidates encoded loci in various functional pathways, such as metabolic and antibiotic biosynthesis pathways. These findings provide a basis for understanding the coevolutionary history of the tsetse fly and its microbes and establish the effectiveness of BLSOM for the detection of HGT events.

Highlights

Tsetse flies (Glossina spp.) are the primary vectors of trypanosome parasites; they cause human African trypanosomiasis and animal African trypanosomiasis in Sub-Saharan African countries
Of 303,250 sequence segments obtained from the tsetse genome, we found that 11,524 sequences (3.8%) clustered with reads from prokaryotes and were horizontal gene transfer (HGT) candidates according to Tsetse+Prokaryotes-batch learning self-organising map (BLSOM) (Figure 2)
It is possible that these candidates were introduced by ancient HGT events, and their oligonucleotide compositions drifted over time [30], limiting the use of composition-based methods for classification

Summary

Introduction

Tsetse flies (Glossina spp.) are the primary vectors of trypanosome parasites; they cause human African trypanosomiasis (or sleeping sickness) and animal African trypanosomiasis (or nagana) in Sub-Saharan African countries. The flies harbour three maternally transmitted endosymbionts, Wigglesworthia glossinidia, Sodalis glossinidius, and Wolbachia pipientis, which influence host physiology. The precise role of Sodalis in the tsetse fly is not clear, it appears to influence various host properties, such as longevity and susceptibility to trypanosome infections [4,5,6]. In many arthropod species [7, 8], Wolbachia induces strong cytoplasmic incompatibility, which was observed in the tsetse fly [9]. In addition to these common bacteria, a recent microbial population analysis using a deep-sequencing approach revealed other facultative microorganisms from diverse bacterial families in the guts of tsetse flies, though

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