Transcriptome profiling of Giardia intestinalis using strand-specific RNA-seq.

Giardia intestinalis is a common cause of diarrheal disease and it consists of eight genetically distinct genotypes or assemblages (A-H). Only assemblages A and B infect humans and are suggested to represent two different Giardia species. Correlations exist between assemblage type and host-specifici...

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Autores principales:	Oscar Franzén, Jon Jerlström-Hultqvist, Elin Einarsson, Johan Ankarklev, Marcela Ferella, Björn Andersson, Staffan G Svärd
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/49648a6c295d4c7fba6a853f0f09a459
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spelling	oai:doaj.org-article:49648a6c295d4c7fba6a853f0f09a4592021-11-18T05:52:16ZTranscriptome profiling of Giardia intestinalis using strand-specific RNA-seq.1553-734X1553-735810.1371/journal.pcbi.1003000https://doaj.org/article/49648a6c295d4c7fba6a853f0f09a4592013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23555231/?tool=EBIhttps://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358Giardia intestinalis is a common cause of diarrheal disease and it consists of eight genetically distinct genotypes or assemblages (A-H). Only assemblages A and B infect humans and are suggested to represent two different Giardia species. Correlations exist between assemblage type and host-specificity and to some extent symptoms. Phenotypical differences have been documented between assemblages and genome sequences are available for A, B and E. We have characterized and compared the polyadenylated transcriptomes of assemblages A, B and E. Four genetically different isolates were studied (WB (AI), AS175 (AII), P15 (E) and GS (B)) using paired-end, strand-specific RNA-seq. Most of the genome was transcribed in trophozoites grown in vitro, but at vastly different levels. RNA-seq confirmed many of the present annotations and refined the current genome annotation. Gene expression divergence was found to recapitulate the known phylogeny, and uncovered lineage-specific differences in expression. Polyadenylation sites were mapped for over 70% of the genes and revealed many examples of conserved and unexpectedly long 3' UTRs. 28 open reading frames were found in a non-transcribed gene cluster on chromosome 5 of the WB isolate. Analysis of allele-specific expression revealed a correlation between allele-dosage and allele expression in the GS isolate. Previously reported cis-splicing events were confirmed and global mapping of cis-splicing identified only one novel intron. These observations can possibly explain differences in host-preference and symptoms, and it will be the basis for further studies of Giardia pathogenesis and biology.Oscar FranzénJon Jerlström-HultqvistElin EinarssonJohan AnkarklevMarcela FerellaBjörn AnderssonStaffan G SvärdPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 9, Iss 3, p e1003000 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Oscar Franzén Jon Jerlström-Hultqvist Elin Einarsson Johan Ankarklev Marcela Ferella Björn Andersson Staffan G Svärd Transcriptome profiling of Giardia intestinalis using strand-specific RNA-seq.
description	Giardia intestinalis is a common cause of diarrheal disease and it consists of eight genetically distinct genotypes or assemblages (A-H). Only assemblages A and B infect humans and are suggested to represent two different Giardia species. Correlations exist between assemblage type and host-specificity and to some extent symptoms. Phenotypical differences have been documented between assemblages and genome sequences are available for A, B and E. We have characterized and compared the polyadenylated transcriptomes of assemblages A, B and E. Four genetically different isolates were studied (WB (AI), AS175 (AII), P15 (E) and GS (B)) using paired-end, strand-specific RNA-seq. Most of the genome was transcribed in trophozoites grown in vitro, but at vastly different levels. RNA-seq confirmed many of the present annotations and refined the current genome annotation. Gene expression divergence was found to recapitulate the known phylogeny, and uncovered lineage-specific differences in expression. Polyadenylation sites were mapped for over 70% of the genes and revealed many examples of conserved and unexpectedly long 3' UTRs. 28 open reading frames were found in a non-transcribed gene cluster on chromosome 5 of the WB isolate. Analysis of allele-specific expression revealed a correlation between allele-dosage and allele expression in the GS isolate. Previously reported cis-splicing events were confirmed and global mapping of cis-splicing identified only one novel intron. These observations can possibly explain differences in host-preference and symptoms, and it will be the basis for further studies of Giardia pathogenesis and biology.
format	article
author	Oscar Franzén Jon Jerlström-Hultqvist Elin Einarsson Johan Ankarklev Marcela Ferella Björn Andersson Staffan G Svärd
author_facet	Oscar Franzén Jon Jerlström-Hultqvist Elin Einarsson Johan Ankarklev Marcela Ferella Björn Andersson Staffan G Svärd
author_sort	Oscar Franzén
title	Transcriptome profiling of Giardia intestinalis using strand-specific RNA-seq.
title_short	Transcriptome profiling of Giardia intestinalis using strand-specific RNA-seq.
title_full	Transcriptome profiling of Giardia intestinalis using strand-specific RNA-seq.
title_fullStr	Transcriptome profiling of Giardia intestinalis using strand-specific RNA-seq.
title_full_unstemmed	Transcriptome profiling of Giardia intestinalis using strand-specific RNA-seq.
title_sort	transcriptome profiling of giardia intestinalis using strand-specific rna-seq.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/49648a6c295d4c7fba6a853f0f09a459
work_keys_str_mv	AT oscarfranzen transcriptomeprofilingofgiardiaintestinalisusingstrandspecificrnaseq AT jonjerlstromhultqvist transcriptomeprofilingofgiardiaintestinalisusingstrandspecificrnaseq AT elineinarsson transcriptomeprofilingofgiardiaintestinalisusingstrandspecificrnaseq AT johanankarklev transcriptomeprofilingofgiardiaintestinalisusingstrandspecificrnaseq AT marcelaferella transcriptomeprofilingofgiardiaintestinalisusingstrandspecificrnaseq AT bjornandersson transcriptomeprofilingofgiardiaintestinalisusingstrandspecificrnaseq AT staffangsvard transcriptomeprofilingofgiardiaintestinalisusingstrandspecificrnaseq
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Transcriptome profiling of Giardia intestinalis using strand-specific RNA-seq.

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