Supplementary Material for: Recombination in pe/ppe genes contributes to genetic variation in Mycobacterium tuberculosis lineages

  • Jody Phelan (Creator)
  • Francesc Coll (Creator)
  • Indra Bergval (Creator)
  • Richard Anthony (Creator)
  • Rob Warren (Creator)
  • Samantha Sampson (Creator)
  • Nicolaas Gey van Pittius (Creator)
  • Judith R. Glynn (Creator)
  • Amelia Crampin (Creator)
  • Adriana Alves (Creator)
  • Theolis Bessa (Creator)
  • Susana Campino (Creator)
  • Keertan Dheda (Creator)
  • Louis Grandjean (Creator)
  • Rumina Hasan (Creator)
  • Zahra Hasan (Creator)
  • Anabela Miranda (Creator)
  • David J. Moore (Creator)
  • Stefan Panaiotov (Creator)
  • João Perdigão (Creator)
  • Isabel Portugal (Creator)
  • Patricia Sheen (Creator)
  • Erivelton de Oliveira Sousa (Creator)
  • Elizabeth Streicher (Creator)
  • Paul van Helden (Creator)
  • Miguel Viveiros (Creator)
  • Martin L. Hibberd (Creator)
  • Arnab Pain (Creator)
  • Ruth McNerney (Creator)
  • Taane G Clark (Creator)
  • Jody Phelan (Creator)
  • Francesc Coll (Creator)
  • Indra Bergval (Creator)
  • Richard Anthony (Creator)
  • Rob Warren (Creator)
  • Samantha Sampson (Creator)
  • Nicolaas Gey van Pittius (Creator)
  • Judith R. Glynn (Creator)
  • Amelia Crampin (Creator)
  • Adriana Alves (Creator)
  • Theolis Bessa (Creator)
  • Susana Campino (Creator)
  • Keertan Dheda (Creator)
  • Louis Grandjean (Creator)
  • Rumina Hasan (Creator)
  • Zahra Hasan (Creator)
  • Anabela Miranda (Creator)
  • David J. Moore (Creator)
  • Stefan Panaiotov (Creator)
  • João Perdigão (Creator)
  • Isabel Portugal (Creator)
  • Patricia Sheen (Creator)
  • Erivelton de Oliveira Sousa (Creator)
  • Elizabeth Streicher (Creator)
  • Paul van Helden (Creator)
  • Miguel Viveiros (Creator)
  • Martin L. Hibberd (Creator)
  • Ruth McNerney (Creator)
  • Taane G Clark (Creator)

Dataset

Description

Abstract Background Approximately 10 % 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.
Date made available2016
Publisherfigshare
  • Recombination in pe/ppe genes contributes to genetic variation in Mycobacterium tuberculosis lineages

    Phelan, J. E., Coll, F., Bergval, I., Anthony, R. M., Warren, R., Sampson, S. L., Gey van Pittius, N. C., Glynn, J. R., Crampin, A. C., Alves, A., Bessa, T. B., Campino, S., Dheda, K., Grandjean, L., Hasan, R., Hasan, Z., Miranda, A., Moore, D. J., Panaiotov, S., Perdigao, J. & 10 others, Portugal, I., Sheen, P., de Oliveira Sousa, E., Streicher, E. M., van Helden, P. D., Viveiros, M., Hibberd, M. L., Pain, A., McNerney, R. & Clark, T. G., Feb 29 2016, In: BMC Genomics. 17, 1

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    Open Access
    38 Scopus citations

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