Table 1.
Salient characteristics of the transcriptomic and predicted proteomic data sets for the adult stages of Dictyocaulus filaria and Dictyocaulus viviparus.
| D. filaria | D. viviparus | |
|---|---|---|
| Transcriptome assemblies: | ||
| Total number of reads | 29,405,140 | 120,808,829 |
| Contigs of > 150 nucleotides (mean ± S.D.; range) | 16,987 (1,042.6 ± 1,000.9; 150–14,409) | 21,230 (1,594.9 ± 2,120.0; 150–43,105) |
| Number of reads that mapped to contigs (%) | 23,787,556 (86.7) | 103,122,222 (89.4) |
| Number of non-redundant proteins of > 50 amino acids predicted (mean ± S.D.; range) | 13,271 (295.1± 291.4;50–4,779) | 15,642 (244.1± 267.1;50–7,258) |
| Complete/partial matches to 248 CEGs proteins in % | 81.5/92.7 | 85.1/96.0 |
| Numbers of proteins homologous (BLASTp; E-value cut-off of ≤ 10−5) to entries in various databases (01 Jan and 30 June 2013) (% of predicted proteome): | ||
| NCBI (non-redundant, nr) | 9,116 (68.7) | 8,577 (54.8) |
| SwissProt | 7,211 (54.3) | 6,820 (43.6) |
| MEROPS peptidase | 599 (4.5) | 561 (3.6) |
| MEROPS peptidase inhibitor | 223 (1.7) | 203 (1.3) |
| ChEMBL | 2,947 (22.2) | 2,900 (18.5) |
| Numbers of proteins homologous (BLASTp; E-value cut-off of ≤ 10−5) to entries in KEGG databases (E-value cut-off of ≤ 10−15) (% of predicted proteome; number of conserved KEGG protein classes or pathways): | ||
| KEGG BRITE | 7,944 (59.9; 40) | 8,834 (0.56; 45) |
| KEGG PATHWAY | 4,553 (34.3; 288) | 4,875 (31.1; 306) |
| Numbers of predicted proteins with conserved domains or GO annotations (% of predicted proteome; number of unique InterProScan domains or GO terms): | ||
| InterProScan conserved domains | 5,731 (43.2; 876) | 6,284 (40.2; 973) |
| GO terms | 5,431 (40.9; 1,537) | 6,032 (38.6; 1748) |
| Biological process | 3,298 (24.9; 571) | 3,834 (24.5; 667) |
| Cellular component | 1,860 (14.0; 209) | 2,114 (13.5; 214) |
| Molecular function | 4,710 (35.5; 757) | 5,235 (33.5; 867) |
| Numbers of proteins with a signal peptide, one or more transmembrane domains and predicted to be excreted/secreted (% of predicted proteome): | ||
| Predicted signal peptide | 1,624 (12.2) | 1,470 (9.4) |
| At least one transmembrane domain | 2,904 (21.9) | 4,111 (26.3) |
CEG, conserved eukaryotic genes; GO, gene ontology; KEGG, Kyoto Encyclopedia of Genes and Genomes.