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

Handle URI:
http://hdl.handle.net/10754/624142
Title:
Supplementary Material for: Recombination in pe/ppe genes contributes to genetic variation in Mycobacterium tuberculosis lineages
Authors:
Phelan, Jody; Coll, Francesc; Bergval, Indra; Anthony, Richard; Warren, Rob; Sampson, Samantha; Pittius, Nicolaas Gey van; Glynn, Judith; Crampin, Amelia; Alves, Adriana; Bessa, Theolis; Campino, Susana; Dheda, Keertan; Grandjean, Louis; Hasan, Rumina; Hasan, Zahra; Miranda, Anabela; Moore, David; Panaiotov, Stefan; Perdigao, Joao; Portugal, Isabel; Sheen, Patricia; Sousa, Erivelton de Oliveira; Streicher, Elizabeth; Helden, Paul van; Viveiros, Miguel; Hibberd, Martin; Pain, Arnab ( 0000-0002-1755-2819 ) ; McNerney, Ruth; Clark, Taane
Abstract:
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.
KAUST Department:
Biological and Environmental Sciences and Engineering (BESE) Division
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.3645272
Publisher:
Figshare
Issue Date:
2016
DOI:
10.6084/m9.figshare.c.3645272
Type:
Dataset
Is Supplement To:
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:http://hdl.handle.net/10754/600452
Appears in Collections:
Datasets; Biological and Environmental Sciences and Engineering (BESE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorPhelan, Jodyen
dc.contributor.authorColl, Francescen
dc.contributor.authorBergval, Indraen
dc.contributor.authorAnthony, Richarden
dc.contributor.authorWarren, Roben
dc.contributor.authorSampson, Samanthaen
dc.contributor.authorPittius, Nicolaas Gey vanen
dc.contributor.authorGlynn, Judithen
dc.contributor.authorCrampin, Ameliaen
dc.contributor.authorAlves, Adrianaen
dc.contributor.authorBessa, Theolisen
dc.contributor.authorCampino, Susanaen
dc.contributor.authorDheda, Keertanen
dc.contributor.authorGrandjean, Louisen
dc.contributor.authorHasan, Ruminaen
dc.contributor.authorHasan, Zahraen
dc.contributor.authorMiranda, Anabelaen
dc.contributor.authorMoore, Daviden
dc.contributor.authorPanaiotov, Stefanen
dc.contributor.authorPerdigao, Joaoen
dc.contributor.authorPortugal, Isabelen
dc.contributor.authorSheen, Patriciaen
dc.contributor.authorSousa, Erivelton de Oliveiraen
dc.contributor.authorStreicher, Elizabethen
dc.contributor.authorHelden, Paul vanen
dc.contributor.authorViveiros, Miguelen
dc.contributor.authorHibberd, Martinen
dc.contributor.authorPain, Arnaben
dc.contributor.authorMcNerney, Ruthen
dc.contributor.authorClark, Taaneen
dc.date.accessioned2017-06-06T07:44:33Z-
dc.date.available2017-06-06T07:44:33Z-
dc.date.created2016-12-16en
dc.date.issued2016en
dc.identifier.citationPhelan, 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.3645272en
dc.identifier.doi10.6084/m9.figshare.c.3645272en
dc.identifier.urihttp://hdl.handle.net/10754/624142-
dc.description.abstractAbstract 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.en
dc.publisherFigshareen
dc.rightsCC BYen
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/en
dc.subjectMedicineen
dc.subjectMicrobiologyen
dc.subjectCell Biologyen
dc.subjectGeneticsen
dc.subjectMolecular Biologyen
dc.subjectImmunologyen
dc.subjectInfectious Diseasesen
dc.subjectVirologyen
dc.titleSupplementary Material for: Recombination in pe/ppe genes contributes to genetic variation in Mycobacterium tuberculosis lineagesen
dc.typeDataseten
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Divisionen
kaust.authorPain, Arnaben
dc.type.resourceCollectionen
dc.relation.isSupplementToRecombination in pe/ppe genes contributes to genetic variation in Mycobacterium tuberculosis lineages 2016, 17 (1) BMC Genomicsen
dc.relation.isSupplementToDOI:10.1186/s12864-016-2467-yen
dc.relation.isSupplementToHANDLE:http://hdl.handle.net/10754/600452en
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