Table 1.
Core gene clusters with ≥2-fold expression differences between species (MBARI-HTCC2255/ MBARI-C16) in MBARI-HTCC2255 genomes (16 genes) and MBARI-C16 genomes (35 genes), organized by functional assignment.
| Gene Cluster ID | MBARI Clade | Representative IMG Gene ID | Transcripts per Gene Copy | Functional Assignment | Annotation |
|---|---|---|---|---|---|
| GC_00000821 | HTCC2255 | 2517702172 | 2.22 | cell surface | lipoprotein |
| GC_00001797 | HTCC2255 | 2517701166 | 4.03 | cofactor | adenosylmethionine-8-amino-7-oxononanoate transaminase (bioA) |
| GC_00002130* | HTCC2255 | 2517702682 | 2.64 | detoxification/stress | LamB YcsF family protein |
| GC_00001582 | HTCC2255 | 2517701925 | 2.17 | DNA/RNA related | ribosome-binding factor A |
| GC_00002206 | HTCC2255 | Ga0315366_1131 | 3.21 | electron transfer | cytochrome B561 |
| GC_00002263 | HTCC2255 | Ga0315446_1343 | 2.05 | metabolism | alcohol dehydrogenase |
| GC_00001518 | HTCC2255 | 2517702423 | 2.10 | metabolism | acetyltransferase GNAT family |
| GC_00001461 | HTCC2255 | 2517702566 | 2.06 | metabolism (choline) | sarcosine oxidase alpha subunit |
| GC_00001635 | HTCC2255 | 2517701161 | 2.79 | metabolism | oxidoreductase |
| GC_00000705 | HTCC2255 | 2517701188 | 2.02 | metabolism (2o met) | 2og-fe(ii) oxygenase |
| GC_00002277 | HTCC2255 | 2517701018 | 2.32 | metabolism (sugar) | glycosyl transferase, family 25 |
| GC_00000600 | HTCC2255 | 2517702623 | 2.40 | regulation | response regulator |
| GC_00002104 | HTCC2255 | 2517702580 | 3.08 | transport | transporter, RhaT family, DMT superfamily |
| GC_00001120 | HTCC2255 | 2517701563 | 2.02 | transport | phosphate transporter |
| GC_00000895 | HTCC2255 | 2517701818 | 2.00 | unknown/other | thioesterase |
| GC_00000814 | HTCC2255 | 2517702318 | 2.08 | unknown/other | cupin protein |
| GC_00000115 | MBARI-C16 | 2517702112 | 0.43 | cell cycle | Maf-like septum formation protein |
| GC_00002052§ | MBARI-C16 | 2517701230 | 0.19 | cell surface | spore coat protein U domain (pilin) |
| GC_00002223§ | MBARI-C16 | n/a | 0.25 | cell surface | spore coat protein U domain (pilin) |
| GC_00000585 | MBARI-C16 | 2517701653 | 0.44 | cell surface | SmpA OmlA lipoprotein |
| GC_00001895 | MBARI-C16 | 2517702558 | 0.42 | cofactor | CoA-binding domain protein |
| GC_00002185 | MBARI-C16 | 3300032478 | 0.46 | cofactor | dihydrolipoyl dehydrogenase |
| GC_00001331 | MBARI-C16 | 2517701226 | 0.05 | detoxification/stress | copper binding, copC |
| GC_00001317 | MBARI-C16 | 2517701227 | 0.06 | detoxification/stress | copper resistance, copD |
| GC_00001072 | MBARI-C16 | 2517702209 | 0.33 | detoxification/stress | NTP pyrophosphohydrolases |
| GC_00000844 | MBARI-C16 | 2517702103 | 0.47 | detoxification/stress | ATP-dependent HslUV protease |
| GC_00001148 | MBARI-C16 | 2517702914 | 0.49 | detoxification/stress | stress responsive alpha-beta barrel domain |
| GC_00001832 | MBARI-C16 | 2517700903 | 0.49 | DNA/RNA related | deoxyribodipyrimidine photo-lyase |
| GC_00000902 | MBARI-C16 | 2517701225 | 0.15 | electron transfer | cytochrome C family protein |
| GC_00001837 | MBARI-C16 | 2517701218 | 0.33 | electron transfer | cytochrome |
| GC_00001790 | MBARI-C16 | 2517702559 | 0.34 | electron transfer | ferredoxin |
| GC_00001063 | MBARI-C16 | 2517701726 | 0.50 | electron transfer | potential cyctchrome biogenesis |
| GC_00001625 | MBARI-C16 | 2517702800 | 0.18 | metabolism (amino acid) | decarboxylase |
| GC_00002149 | MBARI-C16 | 2517701746 | 0.47 | metabolism (amino acid) | deiminase |
| GC_00001233§ | MBARI-C16 | 2517702249 | 0.32 | metabolism (polyamine) | agmatinase |
| GC_00001576 | MBARI-C16 | 2517702141 | 0.48 | metabolism (2o met) | polyprenyl synthetase |
| GC_00001813 | MBARI-C16 | 2517701728 | 0.49 | metabolism (2o met) | isoprenylcysteine carboxyl methyltransferase |
| GC_00002276§ | MBARI-C16 | 2517702021 | 0.47 | metabolism (sugar) | CDP-6-deoxy-D-xylo-4-hexulose-3-dehydrase |
| GC_00001670 | MBARI-C16 | 2517701066 | 0.48 | metabolism (sugar) | xylose isomerase domain protein TIM barrel |
| GC_00001567 | MBARI-C16 | 2517701660 | 0.49 | metabolism (sugar) | dTDP-4-amino-4,6-dideoxygalactose transaminase |
| GC_00000961† | MBARI-C16 | 2517702609 | 0.49 | metabolism (sugar) | ribokinase |
| GC_00001926 | MBARI-C16 | 2517700965 | 0.42 | regulation | transcriptional regulator, LysR family |
| GC_00000837 | MBARI-C16 | 2517702729 | 0.44 | regulation | regulatory protein SoxS |
| GC_00000868 | MBARI-C16 | 2517701134 | 0.45 | regulation | transcriptional regulator, LysR family |
| GC_00001621 | MBARI-C16 | 2517701264 | 0.46 | regulation | transcriptional regulator, LysR family |
| GC_00000824 | MBARI-C16 | 2236439675 | 0.42 | regulation (pilin) | peptide-methionine (R)-S-oxide reductase |
| GC_00001628 | MBARI-C16 | 2517702208 | 0.41 | transcription | polyA polymerase |
| GC_00000610 | MBARI-C16 | 2236438639 | 0.45 | transport | ABC transporter permease protein |
| GC_00002178 | MBARI-C16 | Ga0315456_1082 | 0.38 | transport (carboxylate) | TRAP transporter solute receptor TAXI family |
| GC_00001275 | MBARI-C16 | 2517701302 | 0.44 | unknown/other | hypothetical protein |
| GC_00001341 | MBARI-C16 | 2517702560 | 0.47 | unknown/other | selenium-binding protein |
The expression ratio (transcripts per gene copy) is the mean across all sample dates. See Table S6 for annotation details. All are significantly different at p < 0.05 based on the Benjamini-Hochberg FDR adjustment. MBARI Clade, species with the higher gene expression; n/a, gene is from MAG not available in IMG; 2o met = secondary metabolite. Genes with LGT signatures are indicated by *, Rhizobiaceae; †, Hyphomicrobiales; and §, Gammaproteobacteria.