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Additional file 1: Table S1. of Horizontal gene transfer in bdelloid rotifers is ancient, ongoing and more frequent in species from desiccating habitats

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posted on 2015-11-04, 05:00 authored by Isobel Eyres, Chiara Boschetti, Alastair Crisp, Thomas Smith, Diego Fontaneto, Alan Tunnacliffe, Timothy Barraclough
Number of reads/sequences retained at each stage of the assembly process. Table S2. Transcript length and read depth in relation to the number of species in which transcripts were identified. Transcripts from each Rotaria species in turn were used as queries in a BLASTN search of the other three Rotaria transcriptomes (e-value ≤1e-10). Mean transcript length and FPKM is presented in relation to the number of species transcripts were identified in. Table S3. Percentage of transcripts with h u ≥30 with varying HGT detection thresholds. Left: percentage of transcripts with h u ≥30, for decreasing e-value thresholds for accepting transcripts for analysis. Right: percentage of transcripts with h u ≥30, for increasing minimum transcript length for analysis. Red, R. magnacalcarata; blue, R. socialis; green, R. sordida; and black, R. tardigrada. Table S4. The number of orthologs that are unique to different subclades based on presence/absence in transcriptomes for different methods of identifying orthologs and different criteria for assigning orthologs as foreign or not. Table S5. BLASTN matches in the R. magnacalcarata genome of genes inferred to be unique to particular species based on transcriptome presences/absences. Table S6. Best BLASTN matches of scaffolds that contain a foreign gene but no non-foreign gene in R. magnacalcarata in GenBank. Table S7. Reconstruction of numbers and rates of gains and losses of foreign genes on different branches or sets of branches on the Rotaria tree. Results based on two methods of assigning orthologs are shown: 1) reciprocal BLAST and 2) Markov clusters; and excluding or including correction based on R. magnacalcarata genome matches. Table S8. Results of topGO enrichment analysis for GO annotation categories that are over-represented in particular species or sets of species relative to numbers across the whole foreign ortholog dataset. Fisher’s exact tests with P <0.01 are shown in bold. The “Weight01” option was used to correct for significance of nested annotation terms. Only terms with more than five orthologs present in the whole dataset are shown. Table S9. List of foreign transcripts (h U >30), results of the HGT analysis, GO annotation and matches to the R. magnacalcarata draft genome. Table S10. List of nuclear genes used in phylogenetic reconstruction. (XLSX 3668 kb)


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