Table 2.

Drought genes that contain variants that are “fixed” in Q. engelmannii and at low frequency and under-represented across 20 scrub oak samples

Gene (transcriptome contig)	Biallelic variants	engelmannii-fixed variants	Scrub oak variants with less than 10% engelmannii	% Identity to Arabidopsis protein	Uniprot Protein Name	Gene	Uniprot Function Description
m01oak10430CC	163	138	8	80%	CHY-type/CTCHY-type/RING-type Zinc finger protein	None	none
m01oak03512CC	71	55	7	71%	Monosaccharide-sensing protein 3	MSSP3	Sugar transport
m01oak02926cC	109	42	7	87%	Phosphoenolpyruvate carboxylase 1	PPC1	Through the carboxylation of phosphoenolpyruvate (PEP) it forms oxaloacetate, a four-carbon dicarboxylic acid source for the tricarboxylic acid cycle. Contributes probably to the adaptation to inorganic phosophate (Pi) deprivation
m01oak01922jc	71	49	5	92%	Cellulose synthase A catalytic subunit 2	CESA2	Catalytic subunit of cellulose synthase terminal complexes (‘rosettes’), required for beta-1,4-glucan microfibril crystallization, a major mechanism of the cell wall formation. Involved in the primary cell wall formation.
m01oak00521CC	61	53	3	87%	Heat shock 70 kDa protein 10, mitochondrial;Mitochondrial HSO70 2 isoform 2	HSP70	In cooperation with other chaperones, Hsp70s stabilize preexistent proteins against aggregation and mediate the folding of newly translated polypeptides in the cytosol as well as within organelles. These chaperones participate in all these processes through their ability to recognize nonnative conformations of other proteins. They bind extended peptide segments with a net hydrophobic character exposed by polypeptides during translation and membrane translocation, or following stress-induced damage (By similarity).
m01oak09381CC	22	21	2	81%	Amino acid permease 3	AAP3	Amino acid-proton symporter. Stereospecific transporter with a broad specificity for GABA, tryptophan and both neutral and basic amino acids. High affinity transport of cationic amino acids.
m01oak03200CC	66	46	2	79%	Polyol transporter 5	PLT5	Plasma membrane broad-spectrum sugar-proton symporter. Mediates the uptake of linear polyols such as sorbitol, xylitol, erythritol or glycerol. Can transport the cyclic polyol myo-inositol and different hexoses, pentoses (including ribose), tetroses and sugar alcohols.
m01oak01473cC	42	33	1	77%	Aspartic proteinase A1	APA1	Involved in the breakdown of propeptides of storage proteins in protein-storage vacuoles (By similarity). Possesses aspartic protease activity in vitro
m01oak03575jC	32	29	1	88%	Cryptochrome-1	CRY1	Photoreceptor that mediates primarily blue light inhibition of hypocotyl elongation and photoperiodic control of floral initiation, and regulates other light responses, including circadian rhythms, tropic growth, stomata opening, guard cell development, root development, bacterial and viral pathogen responses, abiotic stress responses, cell cycles, programmed cell death, apical dominance, fruit and ovule development, seed dormancy, and magnetoreception
m01oak00924cC	53	34	1	84%	Auxin-responsive protein IAA8	IAA8	Aux/IAA proteins are short-lived transcriptional factors that function as repressors of early auxin response genes at low auxin concentrations. Repression is thought to result from the interaction with auxin response factors (ARFs), proteins that bind to the auxin-responsive promoter element (AuxRE). Formation of heterodimers with ARF proteins may alter their ability to modulate early auxin response genes expression
m01oak01539cC	15	10	4	84%	Translation initiation factor SUI1 family protein (TAIR database)	AT5G11900	none