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Draft Genome Sequencing of Giardia intestinalis Assemblage B Isolate GS: Is Human Giardiasis Caused by Two Different Species?

Franzén, Oscar, Jerlström-Hultqvist, Jon, Castro, Elsie, Sherwood, Ellen, Ankarklev, Johan, Reiner, David S., Palm, Daniel, Andersson, Jan O., Andersson, Björn, Svärd, Staffan G.·2009·PLoS Pathogens
DOI 10.1371/journal.ppat.1000560PMC PMC2723961
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Figure 1 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.
Figure 1 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.CC BY · PubMed Central
Figure 2 Characterization of sequence variations within GS. (A) Individual sequence reads of a portion of the triosephosphate isomerase (tpi) gene aligned to two previously reported sequences from the GS isolate. (B) Distribution in the six possible two-base combinations for the 45153 variable positions with two alternative bases represented among the individual sequence reads. (C) Analysis of the ratio between the numbers of independent reads for the major and minor base in the positions with two alternative bases. (D) Analysis of the frequency of positions with variations for individual genes. Analysis of the distribution of positions with variations along the four largest contigs in the assembly; contig 2890 (E), contig 2435 (F), contig 540 (G), and contig 1134 (H). Sliding windows of 2000 bp were analyzed in steps of 200 bp.
Figure 2 Characterization of sequence variations within GS. (A) Individual sequence reads of a portion of the triosephosphate isomerase (tpi) gene aligned to two previously reported sequences from the GS isolate. (B) Distribution in the six possible two-base combinations for the 45153 variable positions with two alternative bases represented among the individual sequence reads. (C) Analysis of the ratio between the numbers of independent reads for the major and minor base in the positions with two alternative bases. (D) Analysis of the frequency of positions with variations for individual genes. Analysis of the distribution of positions with variations along the four largest contigs in the assembly; contig 2890 (E), contig 2435 (F), contig 540 (G), and contig 1134 (H). Sliding windows of 2000 bp were analyzed in steps of 200 bp.CC BY · PubMed Central
Figure 3 Synteny-break in the GS genome. Comparison of genomic synteny between contig 3082 (upper panel) of the GS assembly and the syntenic region of scaffold CH991782 of the WB genome (lower panel). A 15 kb region is missing from the GS genome. This region contains 7 genes including one VSP, two NEK kinases and one HCMP. Syntenic regions in the two isolates are indicated in green.
Figure 3 Synteny-break in the GS genome. Comparison of genomic synteny between contig 3082 (upper panel) of the GS assembly and the syntenic region of scaffold CH991782 of the WB genome (lower panel). A 15 kb region is missing from the GS genome. This region contains 7 genes including one VSP, two NEK kinases and one HCMP. Syntenic regions in the two isolates are indicated in green.CC BY · PubMed Central
Figure 4 Comparison of encystation-specific promoters. The promoters of the cyst-wall proteins-1 and 2 (CWP-1 and CWP-2), the encystation-specific transcription factor (gMyb2), the key enzymes involved in the synthesis of cyst wall sugars, glucosamine-6 phosphate isomerase (G6PI-B) and UDP-glucosamine-4 epimerase (UG4E) were aligned using the program CLUSTALW. Poly A rich initiator regions and gMyb2 binding-sites are underlined. Note that the G6PI-B and UG4E promoters are missing the gMyb2 binding-sites, whereas they are found in the corresponding positions in the promoters of CWP-1 and –2 and gMyb2.
Figure 4 Comparison of encystation-specific promoters. The promoters of the cyst-wall proteins-1 and 2 (CWP-1 and CWP-2), the encystation-specific transcription factor (gMyb2), the key enzymes involved in the synthesis of cyst wall sugars, glucosamine-6 phosphate isomerase (G6PI-B) and UDP-glucosamine-4 epimerase (UG4E) were aligned using the program CLUSTALW. Poly A rich initiator regions and gMyb2 binding-sites are underlined. Note that the G6PI-B and UG4E promoters are missing the gMyb2 binding-sites, whereas they are found in the corresponding positions in the promoters of CWP-1 and –2 and gMyb2.CC BY · PubMed Central
Figure 5 mRNA degradation pathways in Giardia and yeast. The major mRNA degradation pathways in Giardia compared to the corresponding pathways in yeast. Decapping: Decapping in S. cerevisiae involves the decapping enzymes Dcp1–2, EDC1–3, DHH1, PAT and Lsm1-7. In Giardia only DHH1 and three Lsm proteins were identified. Nonsense-mediated decay: The process involves Dcp1-2, Upf1-3 and eRF1 and 3 in yeast. Giardia has only orthologs to Upf1 and eRF1. Deadenylation: Giardia lacks the PARN and Pan2/Pan3 systems. In the CCR4-NOT complex only Ccr4, Pop2, NOT4 and 5 and PABP are found.
Figure 5 mRNA degradation pathways in Giardia and yeast. The major mRNA degradation pathways in Giardia compared to the corresponding pathways in yeast. Decapping: Decapping in S. cerevisiae involves the decapping enzymes Dcp1–2, EDC1–3, DHH1, PAT and Lsm1-7. In Giardia only DHH1 and three Lsm proteins were identified. Nonsense-mediated decay: The process involves Dcp1-2, Upf1-3 and eRF1 and 3 in yeast. Giardia has only orthologs to Upf1 and eRF1. Deadenylation: Giardia lacks the PARN and Pan2/Pan3 systems. In the CCR4-NOT complex only Ccr4, Pop2, NOT4 and 5 and PABP are found.CC BY · PubMed Central

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Metadata

Authors
Franzén, O., Jerlström-Hultqvist, J., Castro, E., Sherwood, E., Ankarklev, J., Reiner, D. S., Palm, D., Andersson, J. O., Andersson, B., & Svärd, S. G.
Venue
PLoS Pathogens
Publisher
Public Library of Science (PLoS)
Published
2009-08-21
Volume
5
Issue
8
Pages
e1000560
ISSN
1553-7374
DOI
10.1371/journal.ppat.1000560
PMC
PMC2723961
Cited by
232
References
6
Language
en
Licence
creativecommons.org/licenses/by/4.0/ (unspecified)

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Franzén, O., Jerlström-Hultqvist, J., Castro, E., Sherwood, E., Ankarklev, J., Reiner, D. S., Palm, D., Andersson, J. O., Andersson, B., & Svärd, S. G. (2009). Draft Genome Sequencing of Giardia intestinalis Assemblage B Isolate GS: Is Human Giardiasis Caused by Two Different Species? PLoS Pathogens. https://doi.org/10.1371/journal.ppat.1000560