Table 6.

Genomic Resources for Six Allotetraploid Species Complexes.

Species complex	Species	Ploidy	Version/Accession	Reference
Brachypodium	Hordeum vulgare a	2x	GCA_901482405.1	Mascher et al. (2017)
	Brachypodium distachyon	2x	GCA_000005505.4	Gordon et al. (2017)
	Brachypodium stacei b	2x	B_stacei_v1_1	Gordon et al. (2020)
	Brachypodium hybridum	4x	B_hybridum_v1_1	Gordon et al. (2020)
Coffee	Gardenia jasminoides a	2x	GCA_013103745.1	Xu et al. (2020)
	Coffea canephora	2x	GCA_900059795.1	Denoeud et al. (2014)
	Coffea eugenioides c	2x	GCA_003713205.1	Gaitán et al. (2019)
	Coffea arabica	4x	GCA_003713225.1	Tran et al. (2018); Gaitán et al. (2019)
Cotton	Gossypioides kirkii a	2x	Gossypioides_kirkii_ISU-v3.0	Udall et al. (2019b)
	Gossypium raimondii	2x	G.raimondii_JGI_221_v2.0	Paterson et al. (2012)
	Gossypium arboreum d	2x	G.arboreum_CRI-A2_assembly_v1.0	Jia et al. (2018)
	Gossypium hirsutum	4x	Ghirsutum_458_v1.0	Saski et al. (2017)
Quinoa	Spinacia oleracea a	2x	GCA_002007265.1	Xu et al. (2017)
	Chenopodium suecicum	2x	Csuecicum_DT_PBjellyM2
	Chenopodium pallidicaule e	2x	PGA_assembly_final_assembly_Cpallidicaule	Mangelson et al. (2019)
	Chenopodium quinoa	4x	quinoa_pb_chicago-2-final_PBJELLY_pilon	Jarvis et al. (2017)
Tobacco	Solanum lycopersicum a	2x	ITAG4.0	Hosmani et al. (2019)
	Nicotiana tomentosiformis	2x	GCA_000390325.2	Sierro et al. (2013)
	Nicotiana sylvestris f	2x	GCA_000393655.1	Sierro et al. (2013)
	Nicotiana tabacum	4x	GCA_002210045.1	Edwards et al. (2017)
Wheat	Hordeum vulgare a	2x	GCA_901482405.1	Mascher et al. (2017)
	Triticum urartu	2x	GCA_003073215.1	Ling et al. (2018)
	Aegilops speltoides g	2x	SRR949822
	Triticum dicoccoides	4x	GCA_002162155.2	Zhu et al. (2019)

^aSpecies used as outgroup sequence.

^bClosest extant relative to maternal progenitor inferred from the plastid genome data (Gordon et al. 2020).

^cClosest extant relative to maternal progenitor inferred from the plastid genome data (Cros et al. 1998).

^dClosest extant relative to maternal progenitor inferred from the mitochondrial and plastid genome data (Wendel 1989; Chen et al. 2017b).

^eClosest extant relative to maternal progenitor inferred from the mitochondrial and plastid genome data (Kolano et al. 2016).

^fClosest extant relative to maternal progenitor inferred from the mitochondrial and plastid genome data (Bland et al. 1985; Sasaki et al. 2003).

^gClosest extant relative to maternal progenitor inferred from the plastid genome data (Gornicki et al. 2014).