Table 1.

Examples of domesticated crops with domestication origin, available reference genomes and sequencing strategies.

Crop	Botanical name	Lifecycle	Ploidy level	Time of domestication	Geographical origin	Reference genome	Genome size	Sequencing strategy
African rice	Oryza glaberrima	Annual	Diploid	~3 000 BP	Upper Niger River?	Wang et al. [200]	~860 Mb	Sanger, Roche/454
Amaranth	Amaranthus spp.	Annual	Tetraploid	Aztecs? ~13th – 15th century	Mesoamerica	Clouse et al. [46]	~456 Mb	Illumina, physical map
Apple	Malus x domestica	Perennial	Diploid; polyploid karyotypes exist	Late Bronze Age? ~2 000 – 1 500 BC	West-Asia	Daccord et al. [157]	~651 Mb	Illumina, PacBio, optical map
Asian rice	Oryza sativa	Annual	Diploid	>6 200 BC	China	Kawahara et al. [201]	~500 Mb	Sanger, Illumina, Roche/ 454, optical mapping
Barley	Hordeum vulgare	Annual	Diploid	~10 000 BC	Southwest Asia	Mascher et al. [52]	~5 Gb	Illumina, optical mapping, genetic map, HiC
Beet	Beta vulgaris	Biennial	Diploid	Before 800 BC	Middle East	Dohm et al. [202]	~750 Mb	Roche/454, Illumina, Sanger
Bread wheat	Triticum aestivum	Annual	Hexaploid	~10 000 BC	Southwest Asia	Zimin et al. [65]	~17 Gb	Illumina, PacBio
Carrot	Daucus carota	Annual/bie-nnial	Diploid	Classical antiquity	Central Asia (south-west Asia)	Iorizzo et al. [49]	~473 Mb	Illumina, Roche/454, linkage map
Cassava	Manihot esculenta	Annual	Diploid	10 000 – 5 000 BC in South America	Amazon basin	Wang et al. [203]	~770 Mb	Illumina, Roche/454
Chickpea	Cicer arientinum	Annual	Diploid	~10 000 BC	Fertile Crescent	Varshney et al. [204]	~740 Mb	Illumina
Cotton	Gossypium hirsutum	Perennial	Tetraploid	~6 000 – 5 000BC	India/Mexico	Li et al. [205]	~2.4 Gb	Illumina, genetic map
Cowpea	Vigna unguiculata	Annual	Diploid	~4 000 BC	West Africa	Muñoz-Amatriaín et al. [206]	~620 Mb	Illumina, physical map, genetic map
Emmer wheat	Triticum dicoccon	Annual	Tetraploid	~10 000 BC	Southwest Asia	Avni et al. [58]	~12 Gb	Illumina, genetic map, HiC
Ginseng	Panax ginseng	Perennial	Tetraploid	Cultivated since ~3000 BC	China	Jayakodi et al. [207]	~3.5 Gb	Illumina
Intermediate wheatgrass	Thinopyrum intermedium	Perennial	Hexaploid	~6 000 BC	Central and south-eastern Europe to Anatolia	No reference available	~12.75 Gb	Genetic map [208]
Maize	Zea mays	Annual	Diploid	~6 700 BC	Mexico	Jiao et la. [63]	~2.4 Gb	PacBio, optical mapping, Illumina
Oat	Avena sativa	Annual	Hexaploid	European Bronze Age ~1 800 BC	Fertile Crescent	In progress: The Oat Genome Project [209]	~12 Gb
Pepper	Capsicum spp.	Annual	Diploid	~4 000 BC	South and Middle America	Qin et al. [99]	~3.5 Gb	Illumina, 10X, genetic map
Potato	Solanum tuberosum	Annual	Autotetraploid	~ 7 000 – 6 000 BC	Andean region	The Potato Genome Sequencing Consortium 2011 [210]	~844 Mb	Illumina, Roche/454, Sanger
Pumpkin	Cucurbita maxima	Annual	Tetraploid	~8 000 BC	South America	Sun et al. [47]	~378 Mb	Illumina, genet map
Quinoa	Chenopodium quinoa	Annual	Tetraploid	> 5 000 BC	Mesoamerica	Jarvis et al. [32]	~ 1.5 Gb	PacBio, Illumina, optical mapping
Rapeseed	Brassica napus	Annual	Tetraploid	~400 – 500 BP	Europe	Yang et al. [211]	~1.13 Gb	Illumina, PacBio, optical mapping
Raspberry	Rubus idaeus	Perennial	Tetraploid	~450 BP	Europe and northern Asia	Van Buren et al. [48]	~293 Mb (black raspberry)	Illumina, genetic map
Rye	Secale cereale	Annual	Diploid	European Bronze Age ~1 500 – 1 000 BC	Europe	Bauer et al. [212]	~7.9 Gb	Illumina, genetic map
Sorghum	Sorghum bicolor	Annual	Diploid	~7 100 – 6 900 BC	Sahel	McCormick et al. [213]	~730 Mb	Illumina, Roche/454, Sanger
Sugar cane	Saccharum spp.	Perennial	Allopolyploid	~8 000 BC	Southeast Asia	Riaño-Pachón et al. [214]	~10 Gb	Illumina
Sunflower	Helianthus annuus	Annual	Diploid	~6 000 BC	Eastern North America	Badouin et al. [215]	~3.6 Gb	PacBio, genetic map
Tomato	Solanum lycopersicum	Annual	Diploid	Before 15th century	Andean region	The Tomato Genome Sequencing Consortium 2012 [216]	~900 Mb	Roche/454, Illumina