Dataset Information

Comparative genomic analysis of six Glossina genomes, vectors of African trypanosomes.

ABSTRACT: BACKGROUND:Tsetse flies (Glossina sp.) are the vectors of human and animal trypanosomiasis throughout sub-Saharan Africa. Tsetse flies are distinguished from other Diptera by unique adaptations, including lactation and the birthing of live young (obligate viviparity), a vertebrate blood-specific diet by both sexes, and obligate bacterial symbiosis. This work describes the comparative analysis of six Glossina genomes representing three sub-genera: Morsitans (G. morsitans morsitans, G. pallidipes, G. austeni), Palpalis (G. palpalis, G. fuscipes), and Fusca (G. brevipalpis) which represent different habitats, host preferences, and vectorial capacity. RESULTS:Genomic analyses validate established evolutionary relationships and sub-genera. Syntenic analysis of Glossina relative to Drosophila melanogaster shows reduced structural conservation across the sex-linked X chromosome. Sex-linked scaffolds show increased rates of female-specific gene expression and lower evolutionary rates relative to autosome associated genes. Tsetse-specific genes are enriched in protease, odorant-binding, and helicase activities. Lactation-associated genes are conserved across all Glossina species while male seminal proteins are rapidly evolving. Olfactory and gustatory genes are reduced across the genus relative to other insects. Vision-associated Rhodopsin genes show conservation of motion detection/tracking functions and variance in the Rhodopsin detecting colors in the blue wavelength ranges. CONCLUSIONS:Expanded genomic discoveries reveal the genetics underlying Glossina biology and provide a rich body of knowledge for basic science and disease control. They also provide insight into the evolutionary biology underlying novel adaptations and are relevant to applied aspects of vector control such as trap design and discovery of novel pest and disease control strategies.

SUBMITTER: Attardo GM

PROVIDER: S-EPMC6721284 | biostudies-literature | 2019 Sep

REPOSITORIES: biostudies-literature

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Comparative genomic analysis of six Glossina genomes, vectors of African trypanosomes.

Attardo Geoffrey M GM Abd-Alla Adly M M AMM Acosta-Serrano Alvaro A Allen James E JE Bateta Rosemary R Benoit Joshua B JB Bourtzis Kostas K Caers Jelle J Caljon Guy G Christensen Mikkel B MB Farrow David W DW Friedrich Markus M Hua-Van Aurélie A Jennings Emily C EC Larkin Denis M DM Lawson Daniel D Lehane Michael J MJ Lenis Vasileios P VP Lowy-Gallego Ernesto E Macharia Rosaline W RW Malacrida Anna R AR Marco Heather G HG Masiga Daniel D Maslen Gareth L GL Matetovici Irina I Meisel Richard P RP Meki Irene I Michalkova Veronika V Miller Wolfgang J WJ Minx Patrick P Mireji Paul O PO Ometto Lino L Parker Andrew G AG Rio Rita R Rose Clair C Rosendale Andrew J AJ Rota-Stabelli Omar O Savini Grazia G Schoofs Liliane L Scolari Francesca F Swain Martin T MT Takáč Peter P Tomlinson Chad C Tsiamis George G Van Den Abbeele Jan J Vigneron Aurelien A Wang Jingwen J Warren Wesley C WC Waterhouse Robert M RM Weirauch Matthew T MT Weiss Brian L BL Wilson Richard K RK Zhao Xin X Aksoy Serap S

Genome biology 20190902 1

<h4>Background</h4>Tsetse flies (Glossina sp.) are the vectors of human and animal trypanosomiasis throughout sub-Saharan Africa. Tsetse flies are distinguished from other Diptera by unique adaptations, including lactation and the birthing of live young (obligate viviparity), a vertebrate blood-specific diet by both sexes, and obligate bacterial symbiosis. This work describes the comparative analysis of six Glossina genomes representing three sub-genera: Morsitans (G. morsitans morsitans, G. pal ...[more]

PMID: 31477173

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Project description:BackgroundEmerging infectious disease-causing RNA viruses, such as the SARS-CoV-2 and Ebola viruses, are thought to rely on bats as natural reservoir hosts. Since these zoonotic viruses pose a great threat to humans, it is important to characterize the bat genome from multiple perspectives. Unsupervised machine learning methods for extracting novel information from big sequence data without prior knowledge or particular models are highly desirable for obtaining unexpected insights. We previously established a batch-learning self-organizing map (BLSOM) of the oligonucleotide composition that reveals novel genome characteristics from big sequence data.ResultsIn this study, using the oligonucleotide BLSOM, we conducted a comparative genomic study of humans and six bat species. BLSOM is an explainable-type machine learning algorithm that reveals the diagnostic oligonucleotides contributing to sequence clustering (self-organization). When unsupervised machine learning reveals unexpected and/or characteristic features, these features can be studied in more detail via the much simpler and more direct standard distribution map method. Based on this combined strategy, we identified the Mb-level enrichment of CG dinucleotide (Mb-level CpG islands) around the termini of bat long-scaffold sequences. In addition, a class of CG-containing oligonucleotides were enriched in the centromeric and pericentromeric regions of human chromosomes. Oligonucleotides longer than tetranucleotides often represent binding motifs for a wide variety of proteins (e.g., transcription factor binding sequences (TFBSs)). By analyzing the penta- and hexanucleotide composition, we observed the evident enrichment of a wide range of hexanucleotide TFBSs in centromeric and pericentromeric heterochromatin regions on all human chromosomes.ConclusionFunction of transcription factors (TFs) beyond their known regulation of gene expression (e.g., TF-mediated looping interactions between two different genomic regions) has received wide attention. The Mb-level TFBS and CpG islands are thought to be involved in the large-scale nuclear organization, such as centromere and telomere clustering. TFBSs, which are enriched in centromeric and pericentromeric heterochromatin regions, are thought to play an important role in the formation of nuclear 3D structures. Our machine learning-based analysis will help us to understand the differential features of nuclear 3D structures in the human and bat genomes.

Dataset Information

Comparative genomic analysis of six Glossina genomes, vectors of African trypanosomes.

Publications

Comparative genomic analysis of six Glossina genomes, vectors of African trypanosomes.

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