title: Transcriptome profiling of Giardia intestinalis using strand-specific RNA-seq.
abstract: 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.
authors.affiliation: Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.
authors.forename: Oscar
authors.initials: O
authors.lastname: Franzén
authors.forename: Jon
authors.initials: J
authors.lastname: Jerlström-Hultqvist
authors.forename: Elin
authors.initials: E
authors.lastname: Einarsson
authors.forename: Johan
authors.initials: J
authors.lastname: Ankarklev
authors.forename: Marcela
authors.initials: M
authors.lastname: Ferella
authors.forename: Björn
authors.initials: B
authors.lastname: Andersson
authors.forename: Staffan G
authors.initials: SG
authors.lastname: Svärd
mesh_terms: D000953:Antigens, Protozoan / Q000235:genetics; D019295:Computational Biology; D030541:Databases, Genetic; D020869:Gene Expression Profiling / Q000379:methods*; D005786:Gene Expression Regulation; D016829:Giardia lamblia / Q000235:genetics* / Q000378:metabolism; D005873:Giardiasis / Q000469:parasitology; D006801:Humans; D010802:Phylogeny; D026723:Polyadenylation; D015800:Protozoan Proteins / Q000235:genetics; D012333:RNA, Messenger / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017423:Sequence Analysis, RNA / Q000379:methods*; D018709:Statistics, Nonparametric
chemical_list: D000953:Antigens, Protozoan; D015800:Protozoan Proteins; D012333:RNA, Messenger; C072464:variant surface protein H7, Giardia lamblia
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