PhyloSift Reference Marker Genes
New marker download link here:
https://figshare.com/articles/PhyloSift_markers_database/5755404/1
https://figshare.com/articles/PhyloSift_markers_database/5755404/1
In addition to rRNA genes (16S/18S), Phylosift relies on protein coding marker genes for assigning taxonomy to bacteria, archaea, and eukaryotes. Although we’ve computationally identified marker genes via name-independent approaches, gene annotations are listed here for reference and biological ponderings.
We’re working to update PhyloSift with an expanded marker set which will incorporate additional marker genes for eukaryotes (e.g. plastid genes), taxon-specific sets of gene families, and support for viral marker genes.
The following markers (DNGNGWU*) were originally mined from bacterial/archaeal genomes, but our in-house tests show that at least 33 of these markers have full-length eukaryotic homologs (based on searches against the yeast genome). Percentage values given for Bacteria/Archaea indicate the proportion of taxa in each group whose genomes contain each marker gene (obtained from Wu et al. 2013). Asterisk denotes potentially multi-copy markers, as determined by in-house assessments of microbial genome assemblies at UC Davis (NOTE: As of 1/10/14, these three markers with an asterisk – DNGNGWU00004, DNGNGWU00008, and DNGNGWU00038 – are currently disabled during PhyloSift runs, even though they are still included in automatic marker package downloads):
|
PhyloSift Marker |
Gene Name |
| DNGNGWU00001 | ribosomal protein S2 rpsB (Archaea: 100%, Bacteria: 99.5%) |
| DNGNGWU00002 | ribosomal protein S10 rpsJ (Archaea: 100%, Bacteria: 98.51%) |
| DNGNGWU00003 | ribosomal protein L1 rplA (Archaea: 100%, Bacteria: 99.83%) |
| DNGNGWU00004* | translation elongation factor EF-2 (Archaea: 100%, Bacteria: 99.67%) |
| DNGNGWU00005 | translation initiation factor IF-2 (Archaea: 100%, Bacteria: 99.83%) |
| DNGNGWU00006 | metalloendopeptidase (Archaea: 100%, Bacteria: 99.83%) |
| DNGNGWU00007 | ribosomal protein L22 (Archaea: 100%, Bacteria: 99.67%) |
| DNGNGWU00008* | ffh signal recognition particle protein (Archaea: 100%, Bacteria: 98.18%) |
| DNGNGWU00009 | ribosomal protein L4/L1e rplD (Archaea: 100%, Bacteria: 99.67%) |
| DNGNGWU00010 | ribosomal protein L2 rplB (Archaea: 100%, Bacteria: 99.5%) |
| DNGNGWU00011 | ribosomal protein S9 rpsI (Archaea: 100%, Bacteria: 100%) |
| DNGNGWU00012 | ribosomal protein L3 rplC (Archaea: 100%, Bacteria: 99.5%) |
| DNGNGWU00013 | phenylalanyl-tRNA synthetase beta subunit (Archaea: 100%, Bacteria: 99.67%) |
| DNGNGWU00014 | ribosomal protein L14b/L23e rplN (Archaea: 100%, Bacteria: 99.34%) |
| DNGNGWU00015 | ribosomal protein S5 (Archaea: 100%, Bacteria: 99.5%) |
| DNGNGWU00016 | ribosomal protein S19 rpsS (Archaea: 100%, Bacteria: 99.17%) |
| DNGNGWU00017 | ribosomal protein S7 (Archaea: 100%, Bacteria: 99.67%) |
| DNGNGWU00018 | ribosomal protein L16/L10E rplP (Archaea: 100%, Bacteria: 99.67%) |
| DNGNGWU00019 | ribosomal protein S13 rpsM (Archaea: 100%, Bacteria: 99.17%) |
| DNGNGWU00020 | phenylalanyl-tRNA synthetase alpha subunit (Archaea: 100%, Bacteria: 99.83%) |
| DNGNGWU00021 | ribosomal protein L15 (Archaea: 100%, Bacteria: 99.5%) |
| DNGNGWU00022 | ribosomal protein L25/L23 (Archaea: 100%, Bacteria: 99.17%) |
| DNGNGWU00023 | ribosomal protein L6 rplF (Archaea: 100%, Bacteria: 99.5%) |
| DNGNGWU00024 | ribosomal protein L11 rplK (Archaea: 100%, Bacteria: 99.83%) |
| DNGNGWU00025 | ribosomal protein L5 rplE (Archaea: 100%, Bacteria: 99.83%) |
| DNGNGWU00026 | ribosomal protein S12/S23 (Archaea: 100%, Bacteria: 99.17%) |
| DNGNGWU00027 | ribosomal protein L29 (Archaea: 98.39%, Bacteria: 98.68%) |
| DNGNGWU00028 | ribosomal protein S3 rpsC (Archaea: 100%, Bacteria: 99.83%) |
| DNGNGWU00029 | ribosomal protein S11 rpsK (Archaea: 100%, Bacteria: 99.17%) |
| DNGNGWU00030 | ribosomal protein L10 (Archaea: 98.39%, Bacteria: 99.67%) |
| DNGNGWU00031 | ribosomal protein S8 (Archaea: 100%, Bacteria: 99.5%) |
| DNGNGWU00032 | tRNA pseudouridine synthase B (Archaea: 95.16%, Bacteria: 97.35%) |
| DNGNGWU00033 | ribosomal protein L18P/L5E (Archaea: 100%, Bacteria: 99.83%) |
| DNGNGWU00034 | ribosomal protein S15P/S13e (Archaea: 100%, Bacteria: 99.84%) |
| DNGNGWU00035 | Porphobilinogen deaminase (Archaea: 85.48%, Bacteria: 86.59%) |
| DNGNGWU00036 | ribosomal protein S17 (Archaea: 100%, Bacteria: 99.17%) |
| DNGNGWU00037 | ribosomal protein L13 rplM (Archaea: 100%, Bacteria: 99.83%) |
| DNGNGWU00038* | phosphoribosylformylglycinamidine cyclo-ligase rpsE (Archaea: 90.32%, Bacteria: 92.38%) |
| DNGNGWU00039 | ribonuclease HII (Archaea: 100%, Bacteria: 98.51%) |
| DNGNGWU00040 | ribosomal protein L24 (Archaea: 100%, Bacteria: 99.5%) |
PhyloSift also includes a suite of markers that are more narrowly focused on eukaryotes, including both nuclear and mitochondrial markers:
|
PhyloSift Marker (Eukaryotic) |
Gene Name |
| 14-3-3 | 5-monooxygenase activation protein (HomoloGene ID: 100743) |
| 40S | 40S ribosomal protein S4 (HomoloGene ID: 90857) |
| Actin | actin, beta (HomoloGene ID: 110648) |
| Atub | tubulin, alpha 4a (HomoloGene ID: 68496) |
| Btub | tubulin, beta 4 (HomoloGene ID: 55952) |
| ef1aLike | eukaryotic translation elongation factor 1, alpha 1 (HomoloGene ID: 105313) |
| ef2 | eukaryotic translation elongation factor 2 (HomoloGene ID: 100816) |
| enolase | enolase 1 (HomoloGene ID: 68183) |
| gamma | tubulin, gamma |
| grc5 | 60S ribosomal protein L10 (HomoloGene ID: 68830) |
| hsp70 | Hsp70 protein |
| hsp70cyt | heat shock 70kDa protein 8 (HomoloGene ID: 68524) |
| hsp70er | predicted Hsp70 protein |
| Hsp90 | heat shock protein 90kDa alpha (cytosolic) (HomoloGene ID: 74306) |
| metk | methionine adenosyltransferase II alpha, S-adenosylmethionine synthetase (HomoloGene ID: 38112) |
| Rad51 | RAD-associated protein |
| rps22 | Rps15a (ribosomal protein S15A) (HomoloGene ID: 128371) |
| Rps23a | 40S ribosomal protein S23 (HomoloGene ID: 799) |
| TFIIH | (hypothetical protein) |
| Tsec61 | Sec61 alpha 1 subunit (HomoloGene ID: 55537) |
| U5 | splicing factor Prp8 |
| mtDNA_ATP6 | Mitochondrial ATP synthase subunit 6 |
| mtDNA_ATP8 | Mitochondrial ATP synthase subunit 8 |
| mtDNA_Cox1 | Mitochondrial cytochrome c oxidase subunit 1 |
| mtDNA_Cox2 | Mitochondrial cytochrome c oxidase subunit 2 |
| mtDNA_Cox3 | Mitochondrial cytochrome c oxidase subunit 3 |
| mtDNA_CytB | Mitochondrial Cytochrome b |
| mtDNA_ND1 | Mitochondrial NADH Deyhydrogenase subunit 1 |
| mtDNA_ND2 | Mitochondrial NADH Deyhydrogenase subunit 2 |
| mtDNA_ND4 | Mitochondrial NADH Deyhydrogenase subunit 4 |
| mtDNA_ND4L | Mitochondrial NADH Deyhydrogenase subunit 4L |
| mtDNA_ND5 | Mitochondrial NADH Deyhydrogenase subunit 5 |
| mtDNA_ND6 | Mitochondrial NADH Deyhydrogenase subunit 6 |
PhyloSift 