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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

From: Genomic changes associated with adaptation to arid environments in cactophilic Drosophila species

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