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Open Access Highly Accessed Research article

Genome analysis and comparative genomics of a Giardia intestinalis assemblage E isolate

Jon Jerlström-Hultqvist1, Oscar Franzén23, Johan Ankarklev1, Feifei Xu4, Eva Nohýnková5, Jan O Andersson4, Staffan G Svärd1 and Björn Andersson23*

Author Affiliations

1 Department of Cell and Molecular Biology, BMC, Box 596, Uppsala University, SE-751 24 Uppsala, Sweden

2 Department of Cell and Molecular Biology, Karolinska Institutet, Box 285, SE-171 77 Stockholm, Sweden

3 Science for Life Laboratory, KISP, Tomtebodavägen 23A, 171 65 Solna, Sweden

4 Department of Evolution, Genomics and Systematics, EBC, Uppsala University, SE-752 36 Uppsala, Sweden

5 Department of Tropical Medicine, 1st Faculty of Medicine, Charles University, 128 00 Prague 2, Czech Republic

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BMC Genomics 2010, 11:543  doi:10.1186/1471-2164-11-543

Published: 7 October 2010

Abstract

Background

Giardia intestinalis is a protozoan parasite that causes diarrhea in a wide range of mammalian species. To further understand the genetic diversity between the Giardia intestinalis species, we have performed genome sequencing and analysis of a wild-type Giardia intestinalis sample from the assemblage E group, isolated from a pig.

Results

We identified 5012 protein coding genes, the majority of which are conserved compared to the previously sequenced genomes of the WB and GS strains in terms of microsynteny and sequence identity. Despite this, there is an unexpectedly large number of chromosomal rearrangements and several smaller structural changes that are present in all chromosomes. Novel members of the VSP, NEK Kinase and HCMP gene families were identified, which may reveal possible mechanisms for host specificity and new avenues for antigenic variation. We used comparative genomics of the three diverse Giardia intestinalis isolates P15, GS and WB to define a core proteome for this species complex and to identify lineage-specific genes. Extensive analyses of polymorphisms in the core proteome of Giardia revealed differential rates of divergence among cellular processes.

Conclusions

Our results indicate that despite a well conserved core of genes there is significant genome variation between Giardia isolates, both in terms of gene content, gene polymorphisms, structural chromosomal variations and surface molecule repertoires. This study improves the annotation of the Giardia genomes and enables the identification of functionally important variation.