Table 2. Genomic positions, gene names, annotations for 32 selected candidate genes for intrinsic and ecological functions driving reproductive isolation.
All other annotations are available in Table S3 (see Dataset S1 for details, including references). Species patterns were determined from the analysis of the most outlier-enriched windows between pairs, as detailed in Table S5.
| chr. | positions (regions) | Candidate gene | Gene name | Gene functions | #Paralogs | Pattern |
|---|---|---|---|---|---|---|
| Intrinsic barriers | ||||||
| Flowering | ||||||
| Chr08 | 62493250-62513250 | Qrob_P0412860.2 | Two-component response regulator-like PRR73 | photoperiodic flowering response, circadian clock | 1 | Complex |
| Chr08 | 62673250-62693250 | Qrob_P0749650.2 | Floral homeotic protein APETALA 2 | Transcr. factor RAP2-7 | Delay transition to flowering time, biotic/abiotic stresses | 0 | Complex |
| Chr07 | 44592072-44632072 | Qrob_P0088630.2 | Transcr. activator DEMETER (DME) / protein ROS1-like | Transcriptional activator required for floral development | 1 | Complex |
| Pollen development (Cycloartenol synthases) | ||||||
| Chr06 | 28660694-28680694 | Qrob_P0684330.2 | Cycloartenol synthase 2 | Sterol or triterpenoid synthesis, pollen development | 13 | Complex |
| Chr06 | 28690694-28710694 | Qrob_P0684400.2 | Cycloartenol synthase 2 | Sterol or triterpenoid synthesis, pollen development | 13 | Shared |
| Chr06 | 28770694-28810694 | Qrob_P0684360.2 | Cycloartenol synthase 2 | Sterol or triterpenoid synthesis, pollen development | 13 | Shared |
| Pollen recognition & seed germination (G-type lectin S-receptor-like Serine/threonine kinase genes) | ||||||
| Chr03 | 26118565-26138565 | Qrob_P0538230.2 | G-type lectin S-receptor-like STK At2g19130 | Putatively involved in recognition of pollen | 0 | Complex |
| Chr05 | 4001785-4021785 | Qrob_P0641650.2 | G-type lectin S-receptor-like STK At1g11300 | Putatively involved in recognition of pollen | 190 | Complex |
| Chr06 | 1453464-1473464 | Qrob_P0430150.2 | G-type lectin S-receptor-like STK LECRK | Regulates expression of immunity genes & seed germination | 36 | Q. pyrenaica-specific |
| Chr06 | 1513464-1563464 | Qrob_P0430190.2 | G-type lectin S-receptor-like STK LECRK | Regulates expression of immunity genes & seed germination | 36 | Q. pyrenaica-specific |
| Chr08 | 1749735-1769735 | Qrob_P0138480.2 | G-type lectin S-receptor-like STK LECRK | Regulates expression of immunity genes & seed germination | 36 | Q. pyrenaica-specific |
| Embryo development & organogenesis | ||||||
| Chr12 | 30514806-30534806 | Qrob_P0436820.2 | Transcriptional corepressor LEUNIG-like isoform | Leaf, flower (gynoecium) and embryo development | 5 | All except. Q. pub/Q.pyr |
| Chr02 | 31611918-31651918 | Qrob_P0297580.2 | CHD3-type chromatin-remodeling factor PICKLE | Repressor of LEC1, activator of embryo development | 0 | Complex |
| Chr06 | 43006752-43026752 | Qrob_P0309300.2 | Probable N-acetyltransferase HLS1-like | Auxin-responsive gene expression, shoot organogenesis | 1 | All except. Q. rob/Q.pet |
| Chr08 | 49805801-49825801 | Qrob_P0248780.2 | Receptor-like protein 12 (RLP12) | Meristem maintenance control, organogenesis | 0 | Complex |
| Photoreceptor & UV-B tolerance | ||||||
| Chr02 | 37788250-37808250 | Qrob_P0338870.2 | Ultraviolet-B receptor UVR8 | Photoreceptor/response to UV, circadian clock, stomata | 2 | Shared |
| Chr03 | 34667252-34687252 | Qrob_P0500290.2 | DNA mismatch repair protein MSH2 | UV-B-induced DNA damage response pathway | 0 | Shared |
| Chr06 | 11400887-11420887 | Qrob_P0577750.2 | Transcription factor MYB12 | Positive regulator of flavonoid biosynthesis, UV-B tolerance | 0 | All except. Q. rob/Q.pet |
| Ecological barriers - abiotic stresses | ||||||
| Nramp metal transporters | ||||||
| Chr09 | 7739510-7759510 | Qrob_P0191830.2 | Metal transporter Nramp5 | Manganese and cadmium uptake | 8 | Q. pubescens-specific |
| Chr06 | 38764748-38784748 | Qrob_P0097150.2 | Metal transporter Nramp6 | Involved in iron ion homeostasis | 1 | All except. Q. rob/Q.pet |
| Dehydration/lateral root growth | ||||||
| Chr08 | 68418235-68443235 | Qrob_P0457680.2 | Protein DEHYDRATION-INDUCED 19-like | Stress-induced sensor, interacting with CPK11 & S-Rnase | 0 | All except. Q. rob/Q.pet |
| Chr02 | 27061274-27081274 | Qrob_P0304800.2 | Transcription factor WER | Controls cell fate specification, e.g. hairy roots or stomata | 0 | All except. Q. rob/Q.pet |
| Chr02 | 28240136-28260136 | Qrob_P0299670.2 | Root Primordium Defective 1 (RPD1) | Lateral root morphogenesis; active cell proliferation | 0 | Complex |
| Chr02 | 36392234-36442234 | Qrob_P0422470.2 | Alkaline/neutral invertase CINV2 | Regulator of root growth, sucrose catabolism | 7 | Shared |
| Chr09 | 19506093-19526093 | Qrob_P0418880.2 | 1-aminocyclopropane-1-carboxylate synthase | Ethylene biosynthetic process, lateral root formation | 4 | All except. Q. rob/Q.pet |
| Chr04 | 19182244-19222244 | Qrob_P0652510.2 | Phosphatidylinositol-3-phosphatase myotubularin-1 (or 2) | Role in soil-water-deficit stress | 2 | Shared |
| Chr02 | 96008743-96028743 | Qrob_P0387640.2 | Protein WVD2-like 6 | Organ stockiness (periph. root cap, trichomes & leafs) | 0 | All except. Q. rob/Q.pet |
| Freezing/cold adaptation | ||||||
| Chr09 | 18536093-18556093 | Qrob_P0768740.2 | Dehydration-responsive element-binding protein 1 | Key role in freezing tolerance and cold acclimation | 6 | Complex |
| Chr02 | 112153196-112173196 | Qrob_P0339800.2 | B3 domain-containing transcription factor VRN1 | Vernalization responsiveness, repressor of FLC | 3 | All except. Q. pub/Q.pyr |
| Ecological barriers - biotic stresses | ||||||
| Pathogen resistance/mycorrhization | ||||||
| Chr10 | 12310682-12340682 | Qrob_P0070130.2 | Transportin MOS14 | Plant immunity (splicing of resistant genes) | 0 | Q. pyrenaica-specific |
| Chr01 | 26763631-26783631 | Qrob_P0648170.2 | Ubiquitin carboxyl-terminal hydrolase 12-like | Protein deubiquitination, regulator of disease resistance | 3 | Complex |
| Chr05 | 3053435-3073435 | Qrob_P0622110.2 | Nodulation-signaling pathway 1 (NSP1) | Nodulation & mycorrhization | 0 | Complex |