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Table 4 Gene sets used in phylogenetic analysis.*

From: A salmonid EST genomic study: genes, duplications, phylogeny and microarrays

Tree # of Contigs Align Length Salmon Group SubfamilyGroup Duplication Salmonidae Gene Description
       Accession e-value SwissProt Description
1 25 302 Om/Sf - no Q9EPH8 0.0E+00 Polyadenylate-binding protein 1
2 11 287 - - yes Q92572 1.0E-103 AP-3 complex subunit sigma-1
3 18 455 Om/Sf - yes P41134 4.0E-31 DNA-binding protein inhibitor ID-1
4 16 283 - - yes Q24117 2.0E-46 Dynein light chain 1, cytoplasmic
5 11 438 Om/Sf C/T yes P38400 0.0E+00 Guanine nucleotide-binding protein G(i)
6 26 271 - - - P09486 1.0E-138 SPARC precursor
7 12 301 - - no    Unknown
8 17 307 Om/Sf - yes P62161 4.0E-80 Calmodulin
9 12 341 Ss/Sf - no Q9Y5S9 4.0E-80 RNA-binding protein 8A
10 16 370 Om/Sf - no P51410 4.0E-95 60S ribosomal protein L9
11 11 305 Om/Sf - yes Q3MHN0 3.0E-95 Proteasome subunit beta type-6 precursor
12 8 411 - - - O60493 1.0E-82 Sorting nexin-3
13 7 448 Ss/Sf - yes O15247 8.0E-97 Chloride intracellular channel protein 2
14 13 500 Om/Sf - no Q9NPI5 6.0E-73 Nicotinamide riboside kinase 2
15 14 379 Om/Sf S/C no P13668 2.0E-47 Stathmin
16 7 638 Ss/Sf - no Q6IQU6 1.0E-154 Ribosome production factor 1
17 11 713 - - yes Q9D915 6.0E-23 Uncharacterized protein C8orf4 homolog
18 9 438 - - - Q8VHZ7 1.0E-125 U3 small nucleolar ribonucleoprotein
19 10 314 - - yes Q05826 1.0E-35 CCAAT/enhancer-binding protein beta
20 18 313 - - yes P97371 1.0E-68 Proteasome activator complex subunit 1
21 10 505 - C/T yes Q96GG9 1.0E-135 DCN1-like protein 1
22 10 620 - - yes Q3T0B6 1.0E-91 Complement 1 Q subcomponent-binding
23 12 442 - S/C - P05141 1.0E-149 ADP/ATP translocase 2
24 8 517 - - no Q9UM00 2.0E-78 Transmembrane and coiled-coil domain
25 14 471 Om/Sf - yes Q6PC69 1.0E-101 60S ribosomal protein L10a
26 13 409 - - no Q5RE33 2.0E-67 Receptor expression-enhancing protein 5
27 14 308 Om/Sf - yes P50397 0.0E+00 Rab GDP dissociation inhibitor beta
28 19 311 Ss/Sf S/C yes P30044 8.0E-64 Peroxiredoxin-5, mitochondrial prec.
29 6 428 - S/C no P15156 1.0E-115 Calcium-dependent serine proteinase
30 10 355 - S/C yes    Unknown
31 15 486 - - yes Q9CXL1 8.0E-78 Transmembrane protein 50A
32 11 332 - - yes Q62636 2.0E-90 Ras-related protein Rap-1b precursor
33 22 291 Om/Sf - yes Q3T0Q6 3.0E-71 Cellular nucleic acid-binding protein
34 10 268 - - yes O54734 0.0E+00 Dolichyl-diphosphooligosaccharide
35 8 367 Om/Sf S/C no Q9W719 1.0E-117 Hypoxanthine-guanine phosphoribosyltran.
36 9 609 Om/Sf - no O42123 2.0E-48 FK506-binding protein 1A
37 7 379 - - yes Q9Y5K5 1.0E-161 Ubiquitin carboxyl-terminal hydrolase
38 17 599 Ss/Sf C/T yes P50897 1.0E-120 Palmitoyl-protein thioesterase 1 prec.
39 12 408 - S/C no Q75AA8 7.0E-44 Translation machinery-associated protein
40 15 389 Ss/Sf - yes Q9UL46 4.0E-76 Proteasome activator complex subunit 2
41 8 413 - - no Q96A49 1.0E-100 Synapse-associated protein 1
42 20 333 - S/C yes Q9JK11 8.0E-66 Reticulon-4
43 17 336 - S/T no P67810 5.0E-97 Signal peptidase complex catalytic sub.
44 11 483 - S/C yes Q5XIH7 1.0E-112 Prohibitin-2
45 7 419 Om/Sf - yes P28497 1.0E-136 F-actin-capping protein subunit alpha-2
46 14 465 - - no Q8BLR9 7.0E-16 Hypoxia-inducible factor 1 alpha inhibitor
47 9 610 Om/Sf - yes O75940 9.0E-96 Survival of motor neuron-related-splicing
48 19 604 - C/T yes P60517 4.0E-61 Gamma-aminobutyric acid receptor-
49 17 413 - C/T yes Q6NUC2 1.0E-161 COP9 signalosome complex sub. 6
50 13 350 - S/C yes Q28104 1.0E-141 Coatomer subunit epsilon
51 16 289 - - yes Q2VIU1 7.0E-55 DNA-binding protein inhibitor ID-2
52 12 484 Om/Sf S/C yes P30101 0.0E+00 Protein disulfide-isomerase A3 prec.
53 19 356 - - yes Q6DH65 4.0E-81 Density-regulated protein
54 9 439 Om/Sf S/C yes P26990 4.0E-99 ADP-ribosylation factor 6
55 8 300   - yes Q13491 1.0E-124 Neuronal membrane glycoprotein M6-b
56 10 273 - - yes O93277 0.0E+00 WD repeat-containing protein 1
57 11 304 - S/T yes P08132 1.0E-115 Annexin A4
58 12 562 - - no Q12962 3.0E-63 Transcription initiation factor TFIID sub.
59 7 553 - - yes Q9NS69 2.0E-18 Mitochondrial import receptor subunit
60 8 561 Ss/Sf S/C no Q6AYU1 1.0E-158 Mortality factor 4-like protein 1
61 11 378 - - no P50169 1.0E-95 Retinol dehydrogenase 3
62 16 509 - - yes P59998 2.0E-87 Actin-related protein 2/3 complex sub. 4
63 7 619 - - no    Unknown
64 12 310 - - no P62316 4.0E-52 Small nuclear ribonucleoprotein Sm D2
65 10 398 - - yes P16527 8.0E-23 Myristoylated alanine-rich C-kinase sub.
66 10 277 - S/T yes    Unknown
67 7 388 - - yes O54968 3.0E-80 Nuclear factor erythroid 2-related factor 2
68 8 311 - - no P22232 1.0E-124 rRNA 2'-O-methyltransferase fibrillarin
69 14 300 Om/Sf - yes P40926 1.0E-157 Malate dehydrogenase, mito. prec.
70 9 589 - - yes Q64422 1.0E-138 Glucosamine-6-phosphate isomerase
71 13 577 Ss/Sf S/C yes Q58DU5 1.0E-127 Proteasome subunit alpha type-3
72 14 210 - C/T yes Q15008 0.0E+00 26S proteasome non-ATPase reg. sub.
73 12 348   C/T no    Unknown
74 18 409   - yes Q16799 7.0E-77 Reticulon-1
75 19 462   - yes Q9D1J3 5.0E-39 Nuclear protein Hcc-1
76 8 621   - yes P19387 1.0E-145 DNA-directed RNA polymerase II subunit
77 16 482   - yes Q02878 1.0E-106 60S ribosomal protein L6
78 11 552   C/T yes Q802F2 3.0E-95 Selenoprotein T1a precursor
  1. * Listed is the gene set identifier (tree number) along with the number of contigs used in each data set, the length of the respective nucleotide alignment (no gaps), and tentative identification based on BLASTX hits to the SwissProt database (accession number, E-value and description). For each gene set, the tree support for the various arrangements is listed; for example, Om/Sf supports an Oncorhynchus mykiss/Salvelinus fontinalis grouping; or S/C supports a Salmoninae/Coregoninae grouping. In addition there is an indication whether a tree is consistent (yes/no) with an ancestral Salmonidae gene duplication. "-" indicates that the data provides no clear evidence for any particular tree. All EST accession numbers used to make contig consensus sequences, all alignments and the 70% consensus trees are available [see Additional file 1] or online at the GRASP website [24].