Table 3.
Genes, detected both as xenologs and as core genes
| Gene name | Protein product | Core genes* | Xenologs¥ | Comment | |||||
|---|---|---|---|---|---|---|---|---|---|
| 1) | 2) | 3) | 4) | A) | B) | C) | |||
| Synpcc7942_0056 | perosamine synthetase | yes | 29 | -2 | yes | Next to a genomic island, also detected by SIGI-HMM method, true prediction of xenology. | |||
| Synpcc7942_0587 | valyl-tRNA synthetase | yes | yes | yes | 35 | -1 | yes | No further phylogenetic evidence of xenology, false positive prediction of xenology. | |
| Synpcc7942_1007 | fumarate hydratase | yes | yes | 35 | -1 | N-J | yes | The phylogenetic evidence suggests a true prediction of xenology. | |
| Synpcc7942_1008 | formyltetrahydrofolate deformylase | yes | 33 | -1 | No phylogenetic evidence of xenology, false positive. | ||||
| Synpcc7942_1064 | type I restriction-modification | yes | 1 | Blast | yes | The phylogenetic evidence suggests a true prediction of xenology. | |||
| Synpcc7942_1080 | K+ transporter Trk | yes | yes | yes | 35 | -2 | yes | No further phylogenetic evidence of xenology, false positive prediction. | |
| Synpcc7942_1081 | hypothetical protein | yes | yes | yes | 35 | -1 | No further phylogenetic evidence of xenology, false positive prediction. | ||
| Synpcc7942_1132 | hypothetical protein | yes | 4 | -2 | yes | No phylogenetic evidence of xenology, false positive prediction. | |||
| Synpcc7942_1660 | potassium channel protein | yes | 23 | -1 | Blast | No phylogenetic evidence of xenology, false positive prediction. | |||
| Synpcc7942_1851 | ferredoxin--nitrite reductase | 27 | -2 | Maby transferred among Cyanobacteria. | |||||
| Synpcc7942_1852 | precorrin-8X methylmutase | yes | yes | 35 | -1 | Likely transferred among Cyanobacteria. | |||
| Synpcc7942_1853 | cobalt-factor II C20-methyltransferase | yes | yes | 35 | -1 | Likely related to alpha-proteobacteria. | |||
| Synpcc7942_1854 | precorrin-3 methyltransferase | yes | 26 | -2 | N-J | Closely related to alpha proteobacteria. | |||
| Synpcc7942_1855 | cobyrinic acid a,c-diamide synthase | yes | yes | 34 | -2 | Likely transferred among cyanobacteria. | |||
| Synpcc7942_1873 | two component transcriptional regulator | 35 | -2 | Likely transferred among cyanobacteria. | |||||
| Synpcc7942_1887 | mannosyltransferase | yes | 8 | -1 | N-J | Likely transferred among cyanobacteria. | |||
| Synpcc7942_2188 | isochorismate synthase | yes | yes | yes | 33 | 1 | N-J | Further phylogenetic analyses does not support evidence of xenology, false positive. | |
| Synpcc7942_2436 | peptide methionine sulfoxide reductase | yes | 22 | -1 | N-J | Further phylogenetic evidence suggests a true prediction of xenology. | |||
* Criteria to detect coregenes. For each gene, it is shown if it is conserved in 1) chromatophore of P. chromathophora; 2) P. marinus SS 120; 3) CyOGs database; and 4) number of cyanobacterial genomes with homologous genes. ¥Criteria to detect xenologs. A) G+C content in number of SD from the mean; B) unusual phylogenetic relationship by BLAST or Neighbor-joining; and C) Putative Alien (PA) genes.