Table 1.
Examples (n = 26) of the 41 ecologically relevant gene families in which functional transitions are in line with niche shifts. Families involved in different categories are marked with superscript c.
| Gene namea | Functionb | Niche shift | Functional transition |
|---|---|---|---|
| Resource recovery and energy acquisition | |||
| murQ | N-acetylmuramic acid 6-phosphate etherase MurQ | C-sk -> M-sd | P |
| mltE | Membrane-bound lytic murein transglycosylase E | C-sk -> C-tis | P |
| coxS | Carbon monoxide dehydrogenase small chain CoxS | C-sk -> M-tis | P |
| Nitrogen metabolism and carbohydrate utilization | |||
| ntrY | Nitrogen regulation sensor histidine kinase ntrY | M-sd -> C-sk | P |
| rpiA | Ribose 5-phosphate isomerase A | M-sd -> C-sk | P |
| c | Sugar ABC transporter, permease protein | M-sd -> C-mu | P |
| Transport system | |||
| TRAP transporter | C-sk -> M-sd | P | |
| TAXI family TRAP transporter solute-binding subunit | C-sk -> M-sd | P | |
| nhaGc | Na+/H+antiporter | C-sk -> M-sd | P |
| Na+/solute symporter | C-sk -> M-tis | P | |
| c | Sugar ABC transporter, permease protein | M-sd -> C-mu | P |
| ABC-type peptide/nickel transport system permease protein | M-sd -> C-sk | P | |
| ntpF/atpF | V/A-type H+/Na+-transporting ATPase subunit F | M-sd -> C-sk | P |
| Stress response | |||
| Thioredoxin | C-sk -> M-sd | P | |
| nhaGc | Na+/H+antiporter | C-sk -> M-sd | P |
| phaA | pH adaption potassium efflux system protein PhaA | C-sk -> M-sd | P |
| nsrRd | Nitrite-sensitive transcriptional repressor NsrR | M-sd -> C-sk | P |
| General stress protein A | M-sd -> C-sk | P | |
| gstA | Glutathione S-transferase | M-sd -> C-mu | P |
| gstAd | Glutathione S-transferase | C-sk -> M-tis & M-sw | P |
| Bacteria–host and bacteria–bacteria interactions | |||
| pulF | Type II secretory pathway, component PulF | C-sk -> M-tis | P |
| trbE | Type IV secretion system protein TrbE | C-sk -> C-mu | P |
| virB11 | Type IV secretion system protein VirB11 | M-sd -> M-tis | P |
| impB | Type VI secretion system protein ImpB | M-sd -> C-sk | P |
| tipF | Flagellum assembly factor TipF | M-sd -> C-sk | P |
| flaA | Flagellin protein FlaA | M-sd -> C-sk | P |
| flgD | Flagellar basal-body rod modification protein FlgD | M-sd -> C-sk | B |
| fliI | Flagellum-specific ATP synthase FliI | C-sk -> M-sd | P |
C-mu Coral mucus, C-tis Coral tissue, C-sk Coral skeleton, M-tis Macroalgal tissue, M-sw Macroalgal ambient seawater, M-sd Macroalgal ambient sediment, P pseudogenization, B back event
aThe gene family is indicated by the gene name.
bFunction of each gene family is based on a combination of annotations from CDD, RAST, KEGG, and Prokka.
cThese gene families are involved in two different categories.
dRepeated pseudogenization or back events occurred in these gene families.