Table 4.
Top 10 genes driving differential expression in six most divergent clusters between D. hydei and D. buzzatii, along with the membership coefficient ranges of the genes in parentheses. Functional information for each gene was summarised based on Flybase descriptions for D. melanogaster orthologues, where available, and otherwise, domain classification of the protein sequence using gene ontology and Pfam family annotations
| Gene ID | Gene name | Gene function |
|---|---|---|
| Cluster 1: Initial upregulation & late downregulation (0.51, 0.59); D. buzzatii in excess, mainly response to stimuli | ||
| DBUZO2014318 | Odorant receptor 10a (Or10a) | Chemoreceptor that mediates response to volatile chemicals |
| DBUZO2013263 | Ucp4C (Ucp4C) | Protein uncouples respiration and energy dissipation |
| DBUZO2011185 | CG17387 | Involved in cilium dependent cell motility |
| DBUZO2010006 | CG11475 (DUF89) | May be involved in protein methylation in response to DNA damage |
| DBUZO2009533 | Ppm1 | Involved in protein serine/threonine phosphatase activity |
| DBUZO2005585 | CG9702 | Transmembrane transporter involved in sulfate transport and regulation of intracellular pH |
| DBUZO2002166 | NA | |
| DBUZO2001878 | Gustatory receptor 97a (Gr97a) | Involved in sensory perception of taste |
| DBUZO2001291 | CG5538 | Voltage gates chloride channel |
| DBUZO2001235 | NA | |
| Cluster 2: Initial upregulation & then stable (0.41, 0.45); D. hydei in excess, mainly stress response | ||
| DHYD012352 | Heat shock protein 83 (Hsp83) | Heat shock protein 90 family, regulates response to abiotic stress and circadian behaviour |
| DHYD011340 | NA | Heat Shock protein 70 family |
| DHYD011253 | CG14516 | Zing ion binding peptidase |
| DHYD011218 | frayed (fray) | Protein serine/threonine kinase involved in several development processes |
| DHYD007159 | Egg-derived tyrosine phosphatase (EDTP) | Protein-tyrosine phosphatase-like gene involved in oogenesis and dephosphorylation |
| DHYD006916 | CG8944 | DNA binding zinc finger domain gene |
| DHYD005532 | NA | |
| DHYD003416 | CG4950 | |
| DHYD001898 | tramtrack (ttk) | DNA binding RNA polymerase promoter involved in response to external stimulus |
| DHYD000023 | Cyclin E (CycE) | Cyclin dependent protein kinase, positively regulates cell cycle and morphogenesis |
| Cluster 4: Bimodal upregulation (0.69, 0.76); D. buzzatii in excess, mainly enzymes involved in detox | ||
| DBUZO2012733 | NA | Cytochrome P450 |
| DBUZO2012084 | NA | S1 peptidase |
| DBUZO2011594 | CG3699 | Short-chain dehydrogenase/reductase, involved in fatty-acid beta-oxidation |
| DBUZO2009194 | NA | Cytochrome P450 |
| DBUZO2005738 | CG31087 (DUF227) | Involved in neurogenesis |
| DBUZO2005447 | alpha-Esterase-5 (alpha-Est5) | Type B carboxylesterase |
| DBUZO2002940 | Maltase A4 (Mal-A4) | Glycosyl hydrolase, involved in carbohydrate metabolism |
| DBUZO2002034 | Tetraspanin 42 Eq (Tsp42Eq) | Cell surface receptor |
| DBUZO2001132 | CG42335 | M1 peptidase involved in proteolysis |
| DBUZO2000745 | CG31198 | M1 peptidase involved in proteolysis |
| Cluster 6: Ongoing upregulation &-mid-recovery downregulation (0.50, 0.53); D. hydei in excess, mainly regulation & stress response | ||
| DHYD014524 | Hira (Hira) | Histone H3-H4 chaperone, involved in various replication-independent nucleosome assembly processes |
| DHYD014213 | ellipsoid body open (ebo) | Complexes with actin, chic, and Ran-GTPase to mediate actin nuclear export |
| DHYD014093 | Ajuba LIM protein (jub) | Protein inhibits activation of the Hippo pathway kinase |
| DHYD011516 | CG7065 | |
| DHYD011485 | maroon-like (mal) | Molybdenum cofactor sulfurase involved in ommochrome biosynthesis |
| DHYD010172 | slow as molasses (slam) | Involved in protein localisation and migration |
| DHYD008182 | withered (whd) | Involved in response to starvation, ethanol, oxidative stress and metal ions |
| DHYD007200 | Enigma (Egm) | Involved in response to endoplasmic reticulum stress; fatty acid beta-oxidation; lipid homeostasis and cellular response to oxidative stress |
| DHYD006980 | CG8611 | Involved in unwinding RNA secondary structure |
| DHYD001526 | Hillarin (Hil) | W180-domain protein, affects cytokinesis, developing nervous system |
| Cluster 7: Initial downregulation & early upregulation (0.42, 0.44); D. hydei in excess, mainly regulation & stress response | ||
| DHYD015984 | Catalytic subunit 3B of the oligosaccharyltransferase complex (Stt3B) | Involved in post-translational protein modification |
| DHYD015297 | Ror | Involved in protein phosphorylation; central nervous system development and transmembrane receptor protein tyrosine kinase signalling pathway |
| DHYD012423 | Myocardin-related transcription factor (Mrtf) | Transcription factor with roles in cell migration during development |
| DHYD009550 | pasilla (ps) | A nuclear RNA binding protein implicated in splicing |
| DHYD008649 | epithelial membrane protein (emp) | Associated with autophagic cell death |
| DHYD006908 | NA | |
| DHYD006727 | NA | Involved in fatty acid elongation |
| DHYD004130 | CG31522 | Involved in fatty acid elongation |
| DHYD004039 | Heterogeneous nuclear ribonucleoprotein at 87F (Hrb87F) | Involved in regulation of alternative mRNA splicing and responses to starvation and heat |
| DHYD001282 | CG16713 | Pancreatic trypsin inhibitor involved in development and signalling |
| Cluster 8: Initial upregulation & late upregulation (0.40, 0.43); D. hydei in excess, mainly development & stress response | ||
| DHYD018935 | short stop (shot) | Cytoskeletal linker molecule in the nervous system and other tissues |
| DHYD016713 | Gp150 (Gp150) | Transmembrane glycoprotein; regulates Notch signalling in development |
| DHYD016696 | acyl-Coenzyme A oxidase at 57D distal (Acox57D-d) | fatty acid beta-oxidation |
| DHYD014956 | rugose (rg) | Involved in olfactory learning and short-term memory |
| DHYD012466 | Laminin A (LanA) | Regulates growth and locomotion of cells |
| DHYD009427 | Glutathione S transferase Z2 (GstZ2) | Involved in aromatic amino acid and glutathione metabolic process |
| DHYD009383 | CG43222 | |
| DHYD001387 | Not1 | Muscular development, morphogenesis, mRNA catabolic processes |
| DHYD001006 | CG42500 | Induced during the immune response of Drosophila |
| DHYD000649 | NA | |