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Table 4 Genes affected differently between S10-P3 and S10-P9 by frameshift changes, stop codon changes and non-synonymous SNPs

From: Genome-wide variation in the pinewood nematode Bursaphelenchus xylophilus and its relationship with pathogenic traits

Gene ID S10-P3a S10-P9a BLAST tophit E-value Coverage (%) GO Annotation Signal-P
Frameshift changes
BUX.s00036.207 0/1 1/1 Filamin abp280 repeat-containing domain protein 1.06E-60 48.27 F: transferase activity, transferring phosphorus-containing groups; F: kinase activity; P: phosphorylation  
BUX.s00116.453b 1/0 0/0 Na (+)–dependent inorganic phosphate co-transporter 6.31E-101 55.9 C: cell; P: transport SignalP-NN (euk)
BUX.s00172.1 0/1 0/0 protein srt-52 3.75E-16 55.9 P: biological_process  
BUX.s00358.10 0/1 1/1 Degenerin unc-8 2.28E-18 51.75 C: cell; C: plasma membrane; P: biological_process; F: ion channel activity; P: behavior; P: response to external stimulus; P: response to abiotic stimulus; P: ion transport  
BUX.s00460.315 0/1 1/1 Protein ugt-15 4.018E-71 50.5 P: metabolic process SignalP-NN (euk)
BUX.s01066.84 0/1 1/1 Protein kinase 1.90E-05 51.82 F: ATP binding; F: protein kinase activity; F: transferase activity; P: protein phosphorylation; F: transferase activity, transferring phosphorus-containing groups; F: protein serine/threonine kinase activity; F: kinase activity; P: phosphorylation  
BUX.s01092.23 0/1 0/0 Protein nkcc-isoform e 9.34E-28 72.8 C: cell; P: transport  
BUX.s01133.2 1/1 0/0 Protein-tyrosine phosphatase-containing protein 3.76E-49 56.3 F: phosphoprotein phosphatase activity; P: cellular protein modification process  
BUX.s01144.298 0/0 1/1 Discoidin domain-containing receptor 2-like 2.87E-113 52.25 P: cell adhesion; F: ATP binding; P: protein phosphorylation; F: protein tyrosine kinase activity  
BUX.s01144.7 0/1 0/0 Protein lgx- isoform a 1.18E-119 51.5 F: protein binding; P: carbohydrate metabolic process; F: catalytic activity; F: metal ion binding  
BUX.s01147.248 1/1 0/1 Cysteine-rich motor neuron 1 protein 6.71E-19 46.65 P: multicellular organismal development; F: protein binding  
Stop changes
BUX.s00116.766 1/1 0/1 Hypothetical protein CAEBREN_14873 (protein isoform a) 2.54E-31 48.95 C: membrane; P: molting cycle, collagen and cuticulin-based cuticle; P: locomotion; P: positive regulation of growth rate; P: nematode larval development; P: growth  
BUX.s00351.27 0/0 0/1 Uncharacterised oxidoreductase–like 7.92E-51 57.7 P: metabolic process; F: catalytic activity  
BUX.s00460.265 1/1 0/1 gdp-d-glucose phosphorylase 1 9.86E-127 58.35 C: cytoplasm; P: embryo development; F: transferase activity; P: carbohydrate metabolic process  
Genes with possible functional effect by homozygotic non-synonymous SNPsc
BUX.s00119.53 (SIFT + align-GVGD) 1/1 0/0 Pot family protein 0.0E0 57.3 F: transporter activity; P: ion transport; F: ion channel activity; P: cell cycle; P: transport  
BUX.s00422.86 (SIFT + align-GVGD) 1/1 0/0 Kap family p-loop domain-containing protein 0.0E0 62.35 -  
BUX.s00713.1105 (SIFT + align-GVGD) 1/1 0/0 No hit - - - SignalP-NN (euk)
BUX.s00770.54 (SIFT + SIFT + align-GVGD, inter-medium (class C25)) 1/1 0/0 Innexin unc-7 0.0E0 82.6 P: behavior; P: reproduction; P: regulation of biological process; C: cell; C: plasma membrane; P: biological_process; P: cellular component organization; F: transporter activity; P: ion transport; P: protein metabolic process; P: catabolic process  
BUX.s01281.204 (SIFT + SIFT + align-GVGD, inter-medium (class C25)) 1/1 0/0 No hit - - - SignalP-NN (euk)
  1. a0/0: equal to the genome reference, 0/1: heterozygous, 1/1: homozygotically different to the genome reference; bvariants found to be heterozygotic in the validation process; cSIFT (first) and align-GVGD were used to find the putative effects on the proteins; Genes underlined are homozygotic at the SNP sites; −: no information available)