Supplemental information for "Compact genome of Giardia muris reveals important steps in the evolution of intestinal protozoan parasites” by Xu et al. Xu et al (2019)
Creators: name: Feifei Xu
name: Jiménez-González, Alejandro
name: Einarsson, Elin
name: Ástvaldsson, Ásgeir
name: Peirasmaki, Dimitra
name: Eckmann, Lars
name: Andersson, Jan O.
name: Svärd, Staffan G.
name: Hultqvist, Jon Jerlström
Publisher: name: figshare
Year: 2020
Subjects: subject: 60408 Genomics
subject: FOS: Biological sciences
subject: FOS: Biological sciences
subject: Parasitology
subject: Microbiology
subject: 70708 Veterinary Parasitology
subject: FOS: Veterinary sciences
subject: FOS: Veterinary sciences

description: <b>Figure S1.</b> <b>A)</b> <i>G. muris</i> cells propagate as trophozoites in the mice small intestine. The cell trophozoites undergo encystation into cysts and are shed in the feces. The cysts are prompted to excyst as they encounter the conditions of the digestive tract. The excyzoites transition into the vegetative trophozoites. Cell material for genomic DNA was harvested from <i>G. muris</i> cysts from infected mice. <b>B)</b> Sub-telomeric regions in <i>G. muris.</i> Sequence motifs in the 10 unitigs terminating in (TAGGG)n telomeric sequences (purple). Ribosomal DNA sequences (black). Satellite-like repeated sequences (green). <b><br></b><b>Figure S2.</b> Chromosome-scale synteny between <i>G. muris</i> and <i>G. intestinalis</i> WB. <i>G. muris</i> chromosomes are color coded. The links between the two genomes representing sequence similarity identified by MUMmer promer(95), are colored after the <i>G. muris</i> chromosomal color. Circular plot was drawn with circlize(93). <br><b>Figure S3. </b>Sequence logo around start codon <b>(A)</b> and stop codon <b>(B)</b> in <i>G. muris</i>. <b>C)</b> <i>G. muris</i> gene expression from in vivo trophozoites. Genes showing top-ranked FPKM ratios (log2 (Trophs/Cysts)) between <i>in vivo</i> derived trophozoites and cysts (cut-off value ≥4). The value is indicated in the teal circle. An orange dot indicates that the ortholog of this gene is upregulated (&gt;2 fold) in <i>G. intestinalis</i> at 7 hrs, 12 hrs or 22 hrs into encystation (40). <b><br></b><b>Figure S4.</b> <i>Trans-</i> and <i>cis</i>-introns in <i>G. muris</i>. <b>A)</b> Aligned <i>trans</i>- and <i>cis</i>-splice junctions in <i>G. muris</i>. <b>B)</b> Splice-site associated motifs in <i>trans</i>-spliced exons. Base-pairing stems are underlined. Bases in red denote the predicted cleavage motif. <b>C)</b> Consensus alignment of the cleavage motifs in <i>G. muris</i>. <b>D-E)</b> Predicted secondary structures of <b>D)</b> <i>cis</i>-spliced and <b>E)</b> <i>trans</i>-spliced genes. The secondary structure was predicted using the mfold webserver using default settings and manually curated. GU-rich stretches and cleavage motifs are boxed. <br><b>Figure S5.</b> <b>A)</b> Conservation of the VSP C-terminal in <i>G. muris</i> and <i>G. intestinalis</i>. Sequence logos of conserved motifs in the C-terminal of VSPs in <i>G. muris</i> (n=25) (upper panel) and <i>G. intestinalis</i> WB (n=183) (lower panel) were generated using MEME v5.0.5. Transmembrane and cytosolic pentapeptides were predicted by the Phobius webserver. <b>B)</b> VSP and ψVSP evolutionary dynamics. The ψVSP arrays (defined as &gt;3 ψVSP genes arrayed) in the <i>G. muris</i> genome arranged by chromosome, termini arranged to the right. Arrays of ψVSPs without chromosomal context are shown below as orphan arrays. <b>C)</b> VSP cluster mostly together in a phylogeny whereas most ψVSP gene arrays show relaxed clustering. Intact VSP genes are colored red, while ψVSP genes are colored according to their resident ψVSP array in panel <b>A.</b> Genes with black label are not found in arrays. <b>D)</b> Expression measurements of VSP and ψVSP in <i>G. muris</i>. VSP and ψVSP RNA-seq read counts (FPKM) from trophozoites, cysts and excyzoites. Size of the circle corresponds to expression level.<b><br></b><b>Figure S6.</b> <b>A)</b> Phylogenetic tree of <i>G. muris</i> and <i>G. intestinalis </i>NEKs. <b>B)</b> Phylogenetic tree of <i>G. muris</i> and <i>G. intestinalis</i> ARPs. <b>C)</b> Network analysis of <i>G. muris</i> and <i>G. intestinalis</i> NEKs and ARPs. <i>G. muris</i> genes are represented in circle whereas <i>G. intestinalis</i> genes are shown in triangle. Blue indicates NEK and pink as ARP. Edges are weighted and scaled by reciprocal BLAST scores with evalue 1e-05 as the cutoff. <br><b>Figure S7.</b> Phylogenetic tree of C1 family cysteine proteases in diplomonads. Black: <i>G. muris</i>, Red: <i>S. salmonicida,</i> Cyan: <i>G. intestinalis</i> GS/M, Green: <i>G. intestinalis</i> P15, Purple: <i>G. intestinalis</i> WB. <br><b>Figure S8. </b>Phylogenetic analyses of HGT genes. <b>A)</b> Fructokinase. <b>B)</b> Mannose-6-phosphate isomerase. <b>C)</b> Transcriptional regulator/sugar kinase. <b>D)</b> Arginase. <b>E)</b> 2,5-diketo-D-gluconic acid reductase 1. <b>F)</b> 2,5-diketo-D-gluconic acid reductase 2. <b>G)</b> Carboxymuconolactone decarboxylase. <b>H)</b> Ketosteroid isomerase. <b>I)</b> Tryptophanase. <b>J)</b> Tae4. <b>K)</b> Quorum-quenching N-acyl-homoserine lactonase. <br><b>Table S1. A)</b> One-to-one ortholog list between <i>G. muris</i> and <i>G. intestinalis </i>WB. Orthologs inferred by OrthoMCL. <b>B)</b> RNA-Seq expression values in excel file. Sorted according to FPKM values. <b>C)</b> VSP and ψVSP gene metadata. ‘-’ in the pentapeptide motif represents lack of the 3’ end sequence. <b>D)</b> List of ventral disc proteins in <i>G. muris</i>. <b>E)</b> Proteases detected in <i>G. muris</i> and <i>G. intestinalis</i>. <b>F)</b> Detailed information about hits of unique genes in <i>G. muris</i>.<br><b>Methods S1.</b> Additional methods section<br>