Variant antigen repertoires in Trypanosoma congolense populations and experimental infections can be profiled from deep sequence data using universal protein motifs
African trypanosomes are vector-borne hemoparasites of humans and animals. In the mammal, parasites evade the immune response through antigenic variation. Periodic switching of the variant surface glycoprotein (VSG) coat covering their cell surface allows sequential expansion of serologically distin...
| Autores principales: | , , , , , , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Cold Spring Harbor Laboratory
2018
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| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/98962 |
| _version_ | 1855518011113340928 |
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| author | Silva Pereira, S. Casas-Sánchez, A. Haines, L.R. Ogugo, Moses W. Kihara, Absolomon Sanders, M. Kemp, Stephen J. Acosta-Serrano, Á. Noyes, H. Berriman, M. Jackson, A.P. |
| author_browse | Acosta-Serrano, Á. Berriman, M. Casas-Sánchez, A. Haines, L.R. Jackson, A.P. Kemp, Stephen J. Kihara, Absolomon Noyes, H. Ogugo, Moses W. Sanders, M. Silva Pereira, S. |
| author_facet | Silva Pereira, S. Casas-Sánchez, A. Haines, L.R. Ogugo, Moses W. Kihara, Absolomon Sanders, M. Kemp, Stephen J. Acosta-Serrano, Á. Noyes, H. Berriman, M. Jackson, A.P. |
| author_sort | Silva Pereira, S. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | African trypanosomes are vector-borne hemoparasites of humans and animals. In the mammal, parasites evade the immune response through antigenic variation. Periodic switching of the variant surface glycoprotein (VSG) coat covering their cell surface allows sequential expansion of serologically distinct parasite clones. Trypanosome genomes contain many hundreds ofVSGgenes, subject to rapid changes in nucleotide sequence, copy number, and chromosomal position. Thus, analyzing, or even quantifying, VSG diversity over space and time presents an enormous challenge to conventional techniques. Indeed, previous population genomic studies have overlooked this vital aspect of pathogen biology for lack of analytical tools. Here we present a method for analyzing population-scale VSG diversity inTrypanosoma congolensefrom deep sequencing data. Previously, we suggested thatT. congolenseVSGs segregate into defined “phylotypes” that do not recombine. In our data set comprising 41T. congolensegenome sequences from across Africa, these phylotypes are universal and exhaustive. Screening sequence contigs with diagnostic protein motifs accurately quantifies relative phylotype frequencies, providing a metric of VSG diversity, called the “variant antigen profile.” We applied our metric to VSG expression in the tsetse fly, showing that certain, rare VSG phylotypes may be preferentially expressed in infective, metacyclic-stage parasites. Hence, variant antigen profiling accurately and rapidly determines theT. congolense VSGgene and transcript repertoire from sequence data, without need for manual curation or highly contiguous sequences. It offers a tractable approach to measuring VSG diversity across strains and during infections, which is imperative to understanding the host–parasite interaction at population and individual scales. |
| format | Journal Article |
| id | CGSpace98962 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2018 |
| publishDateRange | 2018 |
| publishDateSort | 2018 |
| publisher | Cold Spring Harbor Laboratory |
| publisherStr | Cold Spring Harbor Laboratory |
| record_format | dspace |
| spelling | CGSpace989622025-12-08T09:54:28Z Variant antigen repertoires in Trypanosoma congolense populations and experimental infections can be profiled from deep sequence data using universal protein motifs Silva Pereira, S. Casas-Sánchez, A. Haines, L.R. Ogugo, Moses W. Kihara, Absolomon Sanders, M. Kemp, Stephen J. Acosta-Serrano, Á. Noyes, H. Berriman, M. Jackson, A.P. antigens trypanosoma congolense data research genomes genetics health African trypanosomes are vector-borne hemoparasites of humans and animals. In the mammal, parasites evade the immune response through antigenic variation. Periodic switching of the variant surface glycoprotein (VSG) coat covering their cell surface allows sequential expansion of serologically distinct parasite clones. Trypanosome genomes contain many hundreds ofVSGgenes, subject to rapid changes in nucleotide sequence, copy number, and chromosomal position. Thus, analyzing, or even quantifying, VSG diversity over space and time presents an enormous challenge to conventional techniques. Indeed, previous population genomic studies have overlooked this vital aspect of pathogen biology for lack of analytical tools. Here we present a method for analyzing population-scale VSG diversity inTrypanosoma congolensefrom deep sequencing data. Previously, we suggested thatT. congolenseVSGs segregate into defined “phylotypes” that do not recombine. In our data set comprising 41T. congolensegenome sequences from across Africa, these phylotypes are universal and exhaustive. Screening sequence contigs with diagnostic protein motifs accurately quantifies relative phylotype frequencies, providing a metric of VSG diversity, called the “variant antigen profile.” We applied our metric to VSG expression in the tsetse fly, showing that certain, rare VSG phylotypes may be preferentially expressed in infective, metacyclic-stage parasites. Hence, variant antigen profiling accurately and rapidly determines theT. congolense VSGgene and transcript repertoire from sequence data, without need for manual curation or highly contiguous sequences. It offers a tractable approach to measuring VSG diversity across strains and during infections, which is imperative to understanding the host–parasite interaction at population and individual scales. 2018-09 2019-01-08T09:43:58Z 2019-01-08T09:43:58Z Journal Article https://hdl.handle.net/10568/98962 en Open Access Cold Spring Harbor Laboratory Silva Pereira, S., Casas-Sánchez, A., Haines, L.R., Ogugo, M., Absolomon, K., Sanders, M., Kemp, S., Acosta-Serrano, Á., Noyes, H., Berriman, M. and Jackson, A.P. 2018. Variant antigen repertoires in Trypanosoma congolense populations and experimental infections can be profiled from deep sequence data using universal protein motifs. Genome Research 28:1383-1394. |
| spellingShingle | antigens trypanosoma congolense data research genomes genetics health Silva Pereira, S. Casas-Sánchez, A. Haines, L.R. Ogugo, Moses W. Kihara, Absolomon Sanders, M. Kemp, Stephen J. Acosta-Serrano, Á. Noyes, H. Berriman, M. Jackson, A.P. Variant antigen repertoires in Trypanosoma congolense populations and experimental infections can be profiled from deep sequence data using universal protein motifs |
| title | Variant antigen repertoires in Trypanosoma congolense populations and experimental infections can be profiled from deep sequence data using universal protein motifs |
| title_full | Variant antigen repertoires in Trypanosoma congolense populations and experimental infections can be profiled from deep sequence data using universal protein motifs |
| title_fullStr | Variant antigen repertoires in Trypanosoma congolense populations and experimental infections can be profiled from deep sequence data using universal protein motifs |
| title_full_unstemmed | Variant antigen repertoires in Trypanosoma congolense populations and experimental infections can be profiled from deep sequence data using universal protein motifs |
| title_short | Variant antigen repertoires in Trypanosoma congolense populations and experimental infections can be profiled from deep sequence data using universal protein motifs |
| title_sort | variant antigen repertoires in trypanosoma congolense populations and experimental infections can be profiled from deep sequence data using universal protein motifs |
| topic | antigens trypanosoma congolense data research genomes genetics health |
| url | https://hdl.handle.net/10568/98962 |
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