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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)