Supplementary Material for: Recombination in pe/ppe genes contributes to genetic variation in Mycobacterium tuberculosis lineages
Type
DatasetAuthors
Phelan, JodyColl, Francesc

Bergval, Indra
Anthony, Richard
Warren, Rob
Sampson, Samantha
Pittius, Nicolaas Gey van
Glynn, Judith R.

Crampin, Amelia
Alves, Adriana
Bessa, Theolis
Campino, Susana
Dheda, Keertan
Grandjean, Louis
Hasan, Rumina
Hasan, Zahra

Miranda, Anabela
Moore, David J.

Panaiotov, Stefan
Perdigao, Joao
Portugal, Isabel
Sheen, Patricia
Sousa, Erivelton de Oliveira
Streicher, Elizabeth
Helden, Paul van
Viveiros, Miguel

Hibberd, Martin L.

Pain, Arnab

McNerney, Ruth

Clark, Taane G.

KAUST Department
Biological and Environmental Sciences and Engineering (BESE) DivisionBioscience Program
Date
2016Permanent link to this record
http://hdl.handle.net/10754/624142
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Abstract Background Approximately 10Â % of the Mycobacterium tuberculosis genome is made up of two families of genes that are poorly characterized due to their high GC content and highly repetitive nature. The PE and PPE families are typified by their highly conserved N-terminal domains that incorporate proline-glutamate (PE) and proline-proline-glutamate (PPE) signature motifs. They are hypothesised to be important virulence factors involved with host-pathogen interactions, but their high genetic variability and complexity of analysis means they are typically disregarded in genome studies. Results To elucidate the structure of these genes, 518 genomes from a diverse international collection of clinical isolates were de novo assembled. A further 21 reference M. tuberculosis complex genomes and long read sequence data were used to validate the approach. SNP analysis revealed that variation in the majority of the 168 pe/ppe genes studied was consistent with lineage. Several recombination hotspots were identified, notably pe_pgrs3 and pe_pgrs17. Evidence of positive selection was revealed in 65 pe/ppe genes, including epitopes potentially binding to major histocompatibility complex molecules. Conclusions This, the first comprehensive study of the pe and ppe genes, provides important insight into M. tuberculosis diversity and has significant implications for vaccine development.Citation
Phelan, J., Coll, F., Bergval, I., Anthony, R., Warren, R., Sampson, S., … Taane Clark. (2016). Recombination in pe/ppe genes contributes to genetic variation in Mycobacterium tuberculosis lineages. Figshare. https://doi.org/10.6084/m9.figshare.c.3645272Publisher
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Recombination in pe/ppe genes contributes to genetic variation in Mycobacterium tuberculosis lineages 2016, 17 (1) BMC Genomics. DOI: 10.1186/s12864-016-2467-y HANDLE: 10754/600452
ae974a485f413a2113503eed53cd6c53
10.6084/m9.figshare.c.3645272