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Table 1 Sequence homology of the F. hepatica transcripts with the secondary databases and virulence-related transcripts of the parasite

From: Comparative transcriptome profiling approach to glean virulence and immunomodulation-related genes of Fasciola hepatica

a) F. hepatica transcripts predicted to be similar to:

Number

Percentage (%)

Data type

Analysis/Database

Dugesia sp.

15,784

39.21

Non-parasite-associated

Blast/DDBJ

Schmidtea sp.

15,546

38.61

Non-parasite-associated

Blast/DDBJ

other trematodes (Cura sp., Girardia sp., Neppia sp., Romankenkius sp.)

524

1.30

Non-parasite-associated

Blast/DDBJ

Dugesiidae family (in total, excluding common transcripts)

18,663

46.36

Non-parasite-associated

Blast/DDBJ

C. elegans

15,208

37.77

Non-parasite-associated

Blast/WormBase

C. elegans specific (not associated with Dugesiidae family)

2,218

5.51

Non-parasite-associated

Blast/WormBase

Free-living worms (in total)

20,881

51.87

Non-parasite-associated

Blast/WormBase

Positive selection related transcripts (Dugesiidae or C. elegans orthologous)

377

1.04

Virulence-associated

Ka/Ks//DDBJ/WormBase

Cytokine signaling related transcripts (Dugesiidae or C. elegans orthologous)

21

0.05

Virulence-associated

InterProScan/EBI

NVTs (excluding the positive selection and cytokine signaling related transcripts)

20,483

50.88

Non-parasite-associated

-

HSD data

10,694

26.56

Pathogen-associated

Blast/HSD

Violin data

1,731

4.30

Pathogen-associated

Blast/Violin

b) Virulence-related F. hepatica transcripts (VRs)

Number

Percentage (%)

  

HTs (HSD related transcripts, not identified as NVTs)

1,251

3.11

  

VTs (Violin related transcripts, not identified as NVTs)

117

0.29

  

HTs/VTs (transcripts homologous to both HSD and Violin data, not identified as NVTs)

23

0.06

  

PDRs (pathogen database related transcripts, including HTs and VTs or HTs/VTs)

1,391

3.46

  

PSRs (positive selection related transcripts; PSR subgroup)

246

0.61

  

CSRs (cytokine signaling related transcripts; CSR subgroup)

31

0.08

  

PSRs and PDRs (common for PSR and PDR subgroups)

168

0.42

  

PSRs and CSRs (common for PSR and CSR subgroups)

3

0.007

  

PDR, PSR and CSR (common for all subgroups)

1

0.002

  

Virulence-related transcripts (VRs) identified as PDRs, PSRs or CSRs

1,671

4.15

  
  1. Numerical values for the F. hepatica transcripts which show similarity with nucleotide/protein sequences of the pathogen-associated and non-pathogen-associated databases (a) and the numbers of the virulence-related F. hepatica transcripts (VRs) (b) are listed. A total of 18,663 liver fluke transcripts (46.36%) and an additional 2,218 transcripts (5.51%) showed homology with sequences of Dugesiidae species and C. elegans, respectively, yielding a total of 20,881 transcripts (51.87%) (E value < 10−5) (a). Overall, 20,483 liver fluke transcripts (50.88%) (orthologous to the non-parasitic organisms, E value < 10−5) were determined to be non-virulence-related (NVTs) after excluding the transcripts showing the signs of positive selection (Ka/Ks > 1) (n = 377) and the relationship with cytokine signaling (n = 21). Approximately a quarter of the total liver fluke transcripts (n = 10,694) showed sequence homology with the HSD data and 4.30% of the total liver fluke transcripts showed sequential similarity with the Violin data. A total of 1,251 transcripts (3.11%) and another set of 117 transcripts (0.29%) were exclusively homologous to the HSD (HTs) and Violin data (VTs), respectively but not identified in the category of NVTs (b). A small number of VRs (n = 23) were common for both HTs and VTs (HTs/VTs). In total, 1,391 VRs (HTs, VTs and HTs/VTs) were included in PDR subgroup (containing pathogen database related transcripts). A total of 246 VRs showing the signs of positive selection (Ka/Ks > 1) were observed in PSR group alone. Some of VRs (n = 31) were only identified by CSR subgroup. A number of PSRs (n = 168) were common for PDR subgroup. Three of VRs were detected by both PSR and CSR subgroups. Only one of VRs was determined by all the subgroups (PDR, PSR and CSR). Overall, a total of 1,671 transcripts, identified at least by one of the subgroups, were predicted to be virulence-related. The percentage values indicate the ratio of transcript number to total transcript number (n = 40,260). NVTs: Non-virulence-related transcripts.
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BMC Genomics

ISSN: 1471-2164

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