Table 2. Genes within the top 20 genomic islands from each mountain.
| Mt. Ibuki | |||
| Rank | AGI code | Gene | Representative GO terms under ‘Biological Process’ |
| 1 | AT1G67120 | MDN1 | gluconeogenesis; cytoskeleton organization; embryo sac development |
| 2 | AT3G44713 | ||
| 3 | AT2G43160 | ||
| 4* | AT3G58160 | XIJ | actin filament-based movement; Golgi localization; mitochondrion localization |
| 5* | AT4G00310 | EDA8 | seed dormancy process; leaf development; response to freezing |
| 6 | AT2G48060 | ||
| 7* (2) | AT4G31300 | PBA1 | hyperosmotic response; response to temperature stimulus; response to cadmium ion |
| 8 | AT4G34910 | protein import into nucleus | |
| 9* | AT1G80930 | translation | |
| 10* | AT5G66190 | FNR1 | response to cold; detection of biotic stimulus; photosynthesis |
| 11* | AT2G33820 | MBAC1 | mitochondrial transport |
| 12* | AT4G04972 | ||
| 13 | AT1G28240 | ||
| 14* | AT2G41500 | LIS | meristem structural organization; seed dormancy process; response to freezing |
| 15* | AT4G27010 | EMB2788 | embryo sac egg cell differentiation; regulation of flower development; maintenance of meristem identity |
| 16 | AT1G33410 | SAR1 | response to auxin; regulation of flower development; maintenance of meristem identity |
| 17* | AT1G79560 | FTSH12 | chloroplast organization; embryo development ending in seed dormancy; ovule development |
| 18 (1) | AT2G36850 | GSL8 | meristem initiation; trichome morphogenesis; telomere maintenance in response to DNA damage |
| 19 | AT5G16280 | vegetative to reproductive phase transition of meristem; protein desumoylation; hydrogen peroxide biosynthetic process | |
| 20* | AT4G32730 | MYB3R1 | cytokinesis by cell plate formation; regulation of transcription, DNA-templated |
| Mt. Fujiwara | |||
| Rank | AGI code | Gene | Representative GO terms under ‘Biological Process’ |
| 1 (18) | AT2G36850 | GSL8 | meristem initiation; trichome morphogenesis; telomere maintenance in response to DNA damage |
| 2* (7) | AT4G31300 | PBA1 | hyperosmotic response; response to temperature stimulus; response to cadmium ion |
| 3 | AT2G41225 | ||
| 4 | AT4G30990 | ||
| 5 | AT2G40270 | response to bacterium; response to insect; regulation of plant-type hypersensitive response | |
| 6 | AT2G45880 | BAM7 | vernalization response; regulation of shoot system development |
| 7* | AT5G63190 | auxin-activated signaling pathway; response to sucrose; response to fructose | |
| 8* | AT1G06040 | STO | hyperosmotic response; response to temperature stimulus; response to light stimulus |
| 9 | AT1G29400 | ML5 | fatty acid beta-oxidation; positive regulation of meiosis; positive regulation of growth |
| 10* | AT3G03340 | UNE6 | positive regulation of cell proliferation; double fertilization forming a zygote and endosperm |
| 11 | AT1G63440 | HMA5 | response to zinc ion; detoxification of copper ion; response to copper ion |
| 12* | AT2G38823 | ||
| 13* | AT1G15690 | AVP1 | response to water deprivation; response to salt stress; leaf development |
| 14* | AT1G25510 | proteolysis | |
| 15 | AT3G15300 | MVQ4 | |
| 16* | AT1G60780 | HAP13 | intracellular protein transport |
| 17 | AT1G32750 | HAC13 | RNA splicing, via endonucleolytic cleavage and ligation; transcription from RNA polymerase II promoter; DNA mediated transformation |
| 18 | AT4G25530 | FWA | trichome morphogenesis; photoperiodism, flowering; cell wall organization |
| 19 | AT1G52830 | IAA6 | de-etiolation; response to auxin |
| 20 | AT2G46430 | CNGC3 | |
Numbers in parenthesis indicate rank in the other mountain. Asterisks indicate the presence of other genes that are located in the same genomic island. AGI codes in bold indicates genes with nonsynonymous SNPs that were highly differentiated (G’ST > 0.4) between the lowest and highest populations. See S3 Table for the extended list.