Transcriptome Profiling of Giardia intestinalis Using Strand-specific RNAseq

• 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 ofthe 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.

Subject headings

Natural Sciences  (hsv)

Biological Sciences  (hsv)

Microbiology  (hsv)

Naturvetenskap  (hsv)

Biologiska vetenskaper  (hsv)

Mikrobiologi  (hsv)

Medical and Health Sciences  (hsv)

Clinical Medicine  (hsv)

Infectious Medicine  (hsv)

Medicin och hälsovetenskap  (hsv)

Klinisk medicin  (hsv)

Infektionsmedicin  (hsv)

Biology with specialization in Microbiology  (uu)

Biologi med inriktning mot mikrobiologi  (uu)

Biologi med inriktning mot evolutionär organismbiologi  (uu)

Biology with specialization in Evolutionary Organismal Biology  (uu)

Keyword

Giardia intestinalis

transcriptome

RNA-seq

poly(A)

intestinal parasite