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Draft genome sequencing of giardia intestinalis assemblage B isolate GS: is human giardiasis caused by two different species?

Franzén O, Jerlström-Hultqvist J, Castro E, Sherwood E, Ankarklev J, Reiner DS, Palm D, Andersson JO, Andersson B, Svärd SG - PLoS Pathog. (2009)

Bottom Line: We here performed 454 sequencing to 16x coverage of the assemblage B isolate GS, the only Giardia isolate successfully used to experimentally infect animals and humans.The tetraploid GS genome shows higher levels of overall allelic sequence polymorphism (0.5 versus <0.01% in WB).The genomic differences between WB and GS may explain some of the observed biological and clinical differences between the two isolates, and it suggests that assemblage A and B Giardia can be two different species.

View Article: PubMed Central - PubMed

Affiliation: Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.

ABSTRACT
Giardia intestinalis is a major cause of diarrheal disease worldwide and two major Giardia genotypes, assemblages A and B, infect humans. The genome of assemblage A parasite WB was recently sequenced, and the structurally compact 11.7 Mbp genome contains simplified basic cellular machineries and metabolism. We here performed 454 sequencing to 16x coverage of the assemblage B isolate GS, the only Giardia isolate successfully used to experimentally infect animals and humans. The two genomes show 77% nucleotide and 78% amino-acid identity in protein coding regions. Comparative analysis identified 28 unique GS and 3 unique WB protein coding genes, and the variable surface protein (VSP) repertoires of the two isolates are completely different. The promoters of several enzymes involved in the synthesis of the cyst-wall lack binding sites for encystation-specific transcription factors in GS. Several synteny-breaks were detected and verified. The tetraploid GS genome shows higher levels of overall allelic sequence polymorphism (0.5 versus <0.01% in WB). The genomic differences between WB and GS may explain some of the observed biological and clinical differences between the two isolates, and it suggests that assemblage A and B Giardia can be two different species.

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Characterization of a recently introduced chromosomal region in GS.(A) Overview of contig 2921 showing identified genes and pseudogenes. Diagonal bars indicate approximate positions of frameshift mutations in the putative proteins. Vertical bar indicate putative deletion causing loss of the 3′ end of the FtsY gene and 5′ end of a gene coding for Copine-1. Arrows indicate positions of primers used in PCR reactions to connect contig 2921 with contig 2545. Protein maximum likelihood tree based on 125 unambiguously aligned position between the conserved hypothetical protein and all available homologs (B). Giardia sequence is shown in red, proteobacterial sequences in green, and sequences belonging to Bacteroidetes in blue. Protein maximum likelihood trees of carboxynorspermidine decarboxylase (C) and signal recognition particle-docking protein FtsY (D) based on 322 and 297 unambiguously aligned positions, respectively. The Giardia sequences were reconstructed based on alignments of the translation in all three reading frames to functional homologs of the pseudogenes. Only bootstrap support values above 50% are shown.
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ppat-1000560-g001: Characterization of a recently introduced chromosomal region in GS.(A) Overview of contig 2921 showing identified genes and pseudogenes. Diagonal bars indicate approximate positions of frameshift mutations in the putative proteins. Vertical bar indicate putative deletion causing loss of the 3′ end of the FtsY gene and 5′ end of a gene coding for Copine-1. Arrows indicate positions of primers used in PCR reactions to connect contig 2921 with contig 2545. Protein maximum likelihood tree based on 125 unambiguously aligned position between the conserved hypothetical protein and all available homologs (B). Giardia sequence is shown in red, proteobacterial sequences in green, and sequences belonging to Bacteroidetes in blue. Protein maximum likelihood trees of carboxynorspermidine decarboxylase (C) and signal recognition particle-docking protein FtsY (D) based on 322 and 297 unambiguously aligned positions, respectively. The Giardia sequences were reconstructed based on alignments of the translation in all three reading frames to functional homologs of the pseudogenes. Only bootstrap support values above 50% are shown.

Mentions: Thus, 28 protein-coding genes were found to be unique for the GS isolate. Although the majority of these genes code for hypothetical proteins, eight showed sequence similarity to genes present in the public databases. Four of these appear to be of bacterial origin, since the best BLAST matches were to bacterial sequences, and they branched with bacterial genes in phylogenetic trees (Table 1; Fig. 1B; Fig. S1A,B,C). Another four showed similarity to a gene family associated with rolling circle replication and mostly found in viruses (Table 1; Fig. S1D). Homologs to these proteins of putative viral origin have previously been shown to be present in a G. intestinalis isolate BRIS/92/HEPU/1541 [28], but they are not present in the WB genome (Table 1). Interestingly, three additional gene families were detected among the unique genes coding for hypothetical proteins, resulting in a total of 19 genes and gene families that were only present in the GS/M-H7 genome (Table 1).


Draft genome sequencing of giardia intestinalis assemblage B isolate GS: is human giardiasis caused by two different species?

Franzén O, Jerlström-Hultqvist J, Castro E, Sherwood E, Ankarklev J, Reiner DS, Palm D, Andersson JO, Andersson B, Svärd SG - PLoS Pathog. (2009)

Characterization of a recently introduced chromosomal region in GS.(A) Overview of contig 2921 showing identified genes and pseudogenes. Diagonal bars indicate approximate positions of frameshift mutations in the putative proteins. Vertical bar indicate putative deletion causing loss of the 3′ end of the FtsY gene and 5′ end of a gene coding for Copine-1. Arrows indicate positions of primers used in PCR reactions to connect contig 2921 with contig 2545. Protein maximum likelihood tree based on 125 unambiguously aligned position between the conserved hypothetical protein and all available homologs (B). Giardia sequence is shown in red, proteobacterial sequences in green, and sequences belonging to Bacteroidetes in blue. Protein maximum likelihood trees of carboxynorspermidine decarboxylase (C) and signal recognition particle-docking protein FtsY (D) based on 322 and 297 unambiguously aligned positions, respectively. The Giardia sequences were reconstructed based on alignments of the translation in all three reading frames to functional homologs of the pseudogenes. Only bootstrap support values above 50% are shown.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2723961&req=5

ppat-1000560-g001: Characterization of a recently introduced chromosomal region in GS.(A) Overview of contig 2921 showing identified genes and pseudogenes. Diagonal bars indicate approximate positions of frameshift mutations in the putative proteins. Vertical bar indicate putative deletion causing loss of the 3′ end of the FtsY gene and 5′ end of a gene coding for Copine-1. Arrows indicate positions of primers used in PCR reactions to connect contig 2921 with contig 2545. Protein maximum likelihood tree based on 125 unambiguously aligned position between the conserved hypothetical protein and all available homologs (B). Giardia sequence is shown in red, proteobacterial sequences in green, and sequences belonging to Bacteroidetes in blue. Protein maximum likelihood trees of carboxynorspermidine decarboxylase (C) and signal recognition particle-docking protein FtsY (D) based on 322 and 297 unambiguously aligned positions, respectively. The Giardia sequences were reconstructed based on alignments of the translation in all three reading frames to functional homologs of the pseudogenes. Only bootstrap support values above 50% are shown.
Mentions: Thus, 28 protein-coding genes were found to be unique for the GS isolate. Although the majority of these genes code for hypothetical proteins, eight showed sequence similarity to genes present in the public databases. Four of these appear to be of bacterial origin, since the best BLAST matches were to bacterial sequences, and they branched with bacterial genes in phylogenetic trees (Table 1; Fig. 1B; Fig. S1A,B,C). Another four showed similarity to a gene family associated with rolling circle replication and mostly found in viruses (Table 1; Fig. S1D). Homologs to these proteins of putative viral origin have previously been shown to be present in a G. intestinalis isolate BRIS/92/HEPU/1541 [28], but they are not present in the WB genome (Table 1). Interestingly, three additional gene families were detected among the unique genes coding for hypothetical proteins, resulting in a total of 19 genes and gene families that were only present in the GS/M-H7 genome (Table 1).

Bottom Line: We here performed 454 sequencing to 16x coverage of the assemblage B isolate GS, the only Giardia isolate successfully used to experimentally infect animals and humans.The tetraploid GS genome shows higher levels of overall allelic sequence polymorphism (0.5 versus <0.01% in WB).The genomic differences between WB and GS may explain some of the observed biological and clinical differences between the two isolates, and it suggests that assemblage A and B Giardia can be two different species.

View Article: PubMed Central - PubMed

Affiliation: Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.

ABSTRACT
Giardia intestinalis is a major cause of diarrheal disease worldwide and two major Giardia genotypes, assemblages A and B, infect humans. The genome of assemblage A parasite WB was recently sequenced, and the structurally compact 11.7 Mbp genome contains simplified basic cellular machineries and metabolism. We here performed 454 sequencing to 16x coverage of the assemblage B isolate GS, the only Giardia isolate successfully used to experimentally infect animals and humans. The two genomes show 77% nucleotide and 78% amino-acid identity in protein coding regions. Comparative analysis identified 28 unique GS and 3 unique WB protein coding genes, and the variable surface protein (VSP) repertoires of the two isolates are completely different. The promoters of several enzymes involved in the synthesis of the cyst-wall lack binding sites for encystation-specific transcription factors in GS. Several synteny-breaks were detected and verified. The tetraploid GS genome shows higher levels of overall allelic sequence polymorphism (0.5 versus <0.01% in WB). The genomic differences between WB and GS may explain some of the observed biological and clinical differences between the two isolates, and it suggests that assemblage A and B Giardia can be two different species.

Show MeSH
Related in: MedlinePlus