Table 1.
O. europaea genomes used in the analysis. The columns show the sample origin, analysis in which it was used, plastid group [17], nuclear group [12], ploidy level, and the source of the data. *Cultivars that are duplicated and are excluded from the main analysis (see “Methods”)
| O. europaea subsp. | Origin | Analysis | Plastid group | Nuclear group | Ploidy level | Source |
|---|---|---|---|---|---|---|
| europaea var. europaea cv. “Farga” | Spain (Boadilla/La Senia) | Nuclear, plastid, mitochondrial | E3.1 | Central MB (Q2) | 2x | ENA (PRJEB4992) |
| europaea var. europaea cv. “Arbequina” | Spain (BGMO_UCO) | Nuclear, plastid, mitochondrial | E1.1 | Central MB (Q2) | 2x | This study |
| europaea var. europaea cv. “Picual” | Spain (BGMO_UCO) | Nuclear, plastid, mitochondrial | E1.1 | Western MB (Q1) | 2x | This study |
| europaea var. europaea cv. “Beladi” | Lebanon (BGMO_UCO) | Nuclear, plastid, mitochondrial | E1.1 | Eastern MB (Q3) | 2x | This study |
| europaea var. europaea cv. “Sorani” | Syria (BGMO_UCO) | Nuclear, plastid, mitochondrial | E1.1 | Eastern MB (Q3) | 2x | This study |
| europaea var. europaea cv. “Manzanilla” | Spain | Plastid | E1.1 | – | 2x | NCBI (FN996972) |
| europaea var. europaea cv. “Bianchera” | Italy | Plastid | E1.1 | – | 2x | NCBI (NC_013707) |
| europaea var. europaea cv. “Chemlal de Kabilye” | Algeria (BGMO_UCO) | Nuclear, plastid, mitochondrial | E3.2 | Mosaic (Q2 + Q1) | 2x | This study |
| europaea var. europaea cv. “Megaritiki” | Greece (BGMO_UCO) | Nuclear, plastid, mitochondrial | E2.2 | Central (Q2) | 2x | This study |
| europaea var. europaea cv. “Lechin de Sevilla” | Spain (BGMO_UCO) | Nuclear, plastid, mitochondrial | E2.3 | Mosaic (Q1 + Q2) | 2x | This study |
| europaea var. europaea cv. “Lechin de Granada” | Spain (BGMO_UCO) | Nuclear, plastid, mitochondrial | E1.1 | Western MB (Q1) | 2x | This study |
| europaea var. europaea cv. “Frantoio” | Italy (BGMO_UCO) | Nuclear, plastid, mitochondrial | E1.1 | Central (Q2) | 2x | This study |
| europaea var. europaea cv. “Koroneiki” | Greece (BGMO_UCO) | Nuclear, plastid, mitochondrial | E1.1 | Central (Q2) | 2x | This study |
| europaea var. sylvestris “sylvestris-T” | Turkey | Nuclear, plastid, mitochondrial | E1.1 | – | 2x | NCBI (PRJNA417827) |
| europaea var. sylvestris “sylvestris-S” | Spain (Pechón) | Nuclear, plastid, mitochondrial | E3 | – | 2x | This study |
| europaea var. sylvestris “W7R224” | Morocco | Nuclear, plastid, mitochondrial | E3 | – | 2x | SRR9860491 |
| europaea var. sylvestris “W11R37” | Spain | Nuclear, plastid, mitochondrial | E3 | – | 2x | SRR9860496 |
| europaea var. sylvestris “W9R302” | Albania | Nuclear, plastid, mitochondrial | E2 | – | 2x | SRR9860497 |
| europaea var. sylvestris “W8R225” | Morocco | Nuclear, plastid, mitochondrial | E1 | – | 2x | SRR9860498 |
| europaea var. sylvestris “W4R183” | Spain | Nuclear, plastid, mitochondrial | E1 | – | 2x | SRR9860503 |
| europaea var. sylvestris “W3R78” | Spain (Menorca island) | Nuclear, plastid, mitochondrial | E2 | – | 2x | SRR9860505 |
| europaea var. sylvestris “W2R74” | Spain | Nuclear, plastid, mitochondrial | E3 | – | 2x | SRR9860532 |
| europaea var. sylvestris “W1R198” | Croatia | Nuclear, plastid, mitochondrial | E2 | – | 2x | SRR9860533 |
| europaea var. europaea cv. “Myrtolia” | Greece | Nuclear, plastid, mitochondrial | E1 | – | 2x | SRR9860492 |
| europaea var. europaea cv. “Klon-14-1812” | Albania | Nuclear, plastid, mitochondrial | E1 | – | 2x | SRR9860493 |
| europaea var. europaea cv. “Barri” | Syria | Nuclear, plastid, mitochondrial | E1 | – | 2x | SRR9860494 |
| europaea var. europaea cv. “Grappolo” | Italy | Nuclear, plastid, mitochondrial | E1 | – | 2x | SRR9860495 |
| europaea var. europaea cv. “Mari” | Iran | Nuclear, plastid, mitochondrial | E1 | – | 2x | SRR9860499 |
| europaea var. europaea cv. “Lianolia Kerkyras” | Greece | Nuclear, plastid, mitochondrial | E2 | – | 2x | SRR9860500 |
| europaea var. europaea cv. “Piñonera” | Spain | Nuclear, plastid, mitochondrial | E1 | – | 2x | SRR9860501 |
| europaea var. europaea cv. “Mavreya” | Greece | Nuclear, plastid, mitochondrial | E1 | – | 2x | SRR9860502 |
| europaea var. europaea cv. “Royal” | Spain | Nuclear, plastid, mitochondrial | E1 | – | 2x | SRR9860504 |
| europaea var. europaea cv. “Llumeta” | Spain | Nuclear, plastid, mitochondrial | E3 | – | 2x | SRR9860506 |
| europaea var. europaea cv. “Barnea” | Israel | Nuclear, plastid, mitochondrial | E1 | – | 2x | SRR9860507 |
| europaea var. europaea cv. “Majhol-1013” | Syria | Nuclear, plastid, mitochondrial | E1 | – | 2x | SRR9860508 |
| europaea var. europaea cv. “Mastoidis” | Greece | Nuclear, plastid, mitochondrial | E1 | – | 2x | SRR9860509 |
| europaea var. europaea cv. “Abbadi Abou Gabra-842” | Syria | Nuclear, plastid, mitochondrial | E1 | – | 2x | SRR9860510 |
| europaea var. europaea cv. “Fishomi” | Iran | Nuclear, plastid, mitochondrial | E1 | – | 2x | SRR9860511 |
| europaea var. europaea cv. “Abou Satl Mohazam” | Syria | Nuclear, plastid, mitochondrial | E1 | – | 2x | SRR9860512 |
| europaea var. europaea cv. “Forastera de Tortosa” | Spain | Nuclear, plastid, mitochondrial | E3 | – | 2x | SRR9860514 |
| europaea var. europaea cv. “Dokkar” | Tunisia | Nuclear, plastid, mitochondrial | E3 | – | 2x | SRR9860516 |
| europaea var. europaea cv. “Jabali” | Syria | Nuclear, plastid, mitochondrial | E1 | – | 2x | SRR9860517 |
| europaea var. europaea cv. “Majhol-152” | Syria | Nuclear, plastid, mitochondrial | E1 | – | 2x | SRR9860518 |
| europaea var. europaea cv. “Picudo” | Spain | Nuclear, plastid, mitochondrial | E1 | – | 2x | SRR9860519 |
| europaea var. europaea cv. “Maarri” | Syria | Nuclear, plastid, mitochondrial | E1 | – | 2x | SRR9860520 |
| europaea var. europaea cv. “Temprano” | Spain | Nuclear, plastid, mitochondrial | E2 | – | 2x | SRR9860521 |
| europaea var. europaea cv. “Menya” | Spain | Nuclear, plastid, mitochondrial | E2 | – | 2x | SRR9860522 |
| europaea var. europaea cv. “Koroneiki”* | Greece | Nuclear, plastid, mitochondrial | E1.1 | – | 2x | SRR9860523 |
| europaea var. europaea cv. “Manzanilla de Sevilla” | Spain | Nuclear, plastid, mitochondrial | E1 | – | 2x | SRR9860524 |
| europaea var. europaea cv. “Uslu” | Turkey | Nuclear, plastid, mitochondrial | E1 | – | 2x | SRR9860525 |
| europaea var. europaea cv. “Lechin de Sevilla”* | Spain | Nuclear, plastid, mitochondrial | E2.3 | – | 2x | SRR9860526 |
| europaea var. europaea cv. “Ocal” | Spain | Nuclear, plastid, mitochondrial | E1 | – | 2x | SRR9860527 |
| europaea var. europaea cv. “Abou Kanani” | Syria | Nuclear, plastid, mitochondrial | E1 | – | 2x | SRR9860528 |
| europaea var. europaea cv. “Verdial de Velez-Malaga-1” | Spain | Nuclear, plastid, mitochondrial | E1 | – | 2x | SRR9860529 |
| europaea var. europaea cv. “Arbequina”* | Spain | Nuclear, plastid, mitochondrial | E1.1 | – | 2x | SRR9860530 |
| europaea var. europaea cv. “Chemlal de Kabylie”* | Algeria | Nuclear, plastid, mitochondrial | E3.2 | – | 2x | SRR9860531 |
| europaea var. europaea cv. “Leccino” | Italy | Nuclear, plastid, mitochondrial | E1 | – | 2x | SRR9860534 |
| europaea var. europaea cv. “Manzanillera de Huercal Overa” | Spain | Nuclear, plastid, mitochondrial | E2 | – | 2x | SRR9860535 |
| europaea var. europaea cv. “Hojiblanca” | Spain | Nuclear, plastid, mitochondrial | E1 | – | 2x | SRR9860536 |
| europaea var. europaea cv. “Kalamon” | Greece | Nuclear, plastid, mitochondrial | E1 | – | 2x | SRR9860537 |
| europaea var. europaea cv. “Picual”* | Spain | Nuclear, plastid, mitochondrial | E1.1 | – | 2x | SRR9860538 |
| europaea var. europaea cv. “Zarza” | Spain | Nuclear, plastid, mitochondrial | E2 | – | 2x | SRR9860539 |
| europaea var. europaea cv. “Morrut” | Spain | Nuclear, plastid, mitochondrial | E1 | – | 2x | SRR9860540 |
| europaea var. europaea cv. “Frantoio”* | Italy | Nuclear, plastid, mitochondrial | E1.1 | – | 2x | SRR9860541 |
| europaea var. sylvestris “Stavrovouni 11” | Cyprus | Plastid | E1.4 | – | 2x | NCBI (HF558645) |
| europaea var. sylvestris “Haut Atlas 1” | Morocco (High Atlas) | Plastid | E2 | – | 2x | NCBI (NC_015401) |
| europaea var. sylvestris “Gue de Constantine 20” | Algeria: Gue de Constantine, Algiers | Plastid | E3 | – | 2x | NCBI (FN997651) |
| europaea var. sylvestris “Oeiras 1” | Portugal | Plastid | E3.1 | – | 2x | NCBI (MG255763) |
| europaea var. sylvestris “Vallee du Fango 5” | France | Plastid | E2.1 | – | 2x | NCBI (MG255762) |
| maroccana “Immouzzer S1” | Morocco (High Atlas) | Plastid | M | – | 6x | NCBI (NC_015623) |
| guanchica “La Gomera 10” | Spain | Plastid | M-g1 | – | 2x | NCBI (MG255764) |
| laperrinei “Adjelella 10” | Algeria | Plastid | E1-l1 | – | 2x | NCBI (MG255765) |
| cuspidata - R | Reunion island | Nuclear, plastid, mitochondrial | A | – | 2x | This study |
| cuspidata “Almihwit 5.1” | Yemen | Plastid | C2 | – | 2x | NCBI (FN996943) |
| cuspidata “Guanghzou 1” | China | Plastid | C1 | – | 2x | NCBI (FN996944) |
| cuspidata “Maui 1” | USA (Hawaii-Maui) | Plastid | A | – | 2x | NCBI (NC_015604) |
| cuspidata “Menagesha Forest 14” | Ethiopia | Plastid | C2 | – | 2x | NCBI (MG255760) |