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

Jon Jerlström-Hultqvist,Staffan G Svärd,Feifei Xu,Eva Nohýnková,Björn Andersson,Johan Ankarklev,Jan O Andersson,Oscar Franzén

doi:10.1186/1471-2164-11-543

Jon Jerlström-Hultqvist, Staffan G Svärd + Show 6 more

Open Access

https://doi.org/10.1186/1471-2164-11-543

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Abstract

BackgroundGiardia 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.ResultsWe 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.ConclusionsOur 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.

Highlights

Giardia intestinalis is a protozoan parasite that causes diarrhea in a wide range of mammalian species
Genome assembly and allelic sequence heterozygosity Clustering of the shotgun reads (Table 1, Additional file 1) and manual finishing of the assembly resulted in 820 contiguous sequences with an N50 of 71,261 bp and an average genome coverage of 47×
Average read length relatively large number of contigs is likely to be caused by the presence of genomic repeats rather than areas of insufficient sampling

Summary

Introduction

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. Giardia intestinalis (syn G. lamblia and G. duodenalis) is a flagellated protozoan parasite that belongs to the diplomonad group, which includes both parasitic and free living species. G. intestinalis infects humans and a broad range of other mammals including wild and domestic animals, and causes diarrhea. Substantial karyotype variability has been reported among G. intestinalis isolates, most likely caused by the hypervariable subtelomeric regions [14]. The genome of G. intestinalis is compact in terms of intergenic space and non-coding regions. Promoters and untranslated regions are minimal and only four introns have been identified [11], which is consistent with the features of a compact genome

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