Evolution of plant genome architecture

Wendel, Jonathan F.; Jackson, Scott A.; Meyers, Blake C.; Wing, Rod A.

doi:10.1186/s13059-016-0908-1

Table 1 Sequenced crop genomes with their estimated genome size, number of annotated genes and percentage of globally consumed kilocalories that they are responsible for

From: Evolution of plant genome architecture

Species	Common name	Genome size (Mbp)	Number of annotated genes	Genome multiples^a	Percentage kcal production [104]	Percentage genome captured^b	Percentage transposon/repeat^c	References
Nelumbo nucifera	Sacred lotus	929	26,685			86.5	57	[105]
Beta vulgaris	Sugar beet	758	27,421		1.2	74.8	63	[106]
Solanum lycopersicum	Tomato	900	34,727	36×	0.21	84.4	63.3	[107]
Solanum tuberosum	Potato	844	39,031	72×	1.51	86	62.2	[108]
Solanum melongena	Eggplant	1125	85,446	36×	0.07	74	70.4	[109]
Capsicum annum	Pepper	3480	34,903	36×	0.14	87.9	76.4	[110]
Nicotiana benthamiana	Tobacco	3000	ND			86.7	ND	[107]
Vaccinium macrocarpon	Cranberry	470	36,364		0.002	89.4	39.5^b	[111]
Actinidia chinensis	Kiwifruit	758	39,040		0.005	81.3	36	[112]
Coffea canephora	Coffee	710	25,574	24×		80	50^b	[113]
Vitis vinifera	Grape	475	30,434		0.36	102.5	41.4	[114]
Populus trichocharpa	Poplar	485	41,377			84.5	41	[115]
Linum usitatissimum	Flax	350	43,384			81	24.3^b	[116]
Ricinus communis	Castor bean	320	31,237			100	50	[117]
Manihot esculenta	Cassava	742	30,666		2.05	70	36.9	[118]
Hevea brasiliensis	Rubber tree	2150	68,955			51	78	[119]
Cucumis sativus	Cucumber	367	26,682		0.04	70	24	[120]
Cucumis melo	Melon	450	27,427		0.04	83.3	19.7^b	[121]
Citrullus lanatus	Watermelon	425	23,440		0.11	83.2	45.2	[122]
Fragaria vesca	Strawberry	240	34,809		0.009	95	22^b	[123]
Malus x domestica	Apple	742	57,386	24×	0.22	81.3	38^b	[124]
Pyrus bretschneideri	Pear	528	42,812		0.07	97.1	53.1	[125]
Cannabis sativa	Cannabis	818–843	ND			65.1	ND	[126]
Humulus lupulus	Hops	2570	41,228			80	34.7^b	[127]
Ziziphus jujuba	Jujube	440	32,808			98.6	49.5	[128]
Prunus persica	Peach	265	27,582		0.06	84.8	18.6^b	[129]
Medicago truncatula	Medicago	450	47,845	24×		54.6	31	[130]
Cicer arietinum	Chickpea	738	28,269	24×	0.29	73.8	49.4	[131]
Lotus japonicus	Lotus	472	30,799	24×		67	29.7^b	[132]
Glycine max	Soybean	1100	46,430	48×	7.43	85	42^b	[133]
Cajanus cajan	Pigeonpea	833	46,680	24×	0.11	72.7	51.67	[134]
Phaseolus vulgaris	Common bean	587	27,197	24×	0.754	80.6	45^b	[135]
Vigna radiata	Mung bean	579	22,427	24×		80	50.1	[136]
Lupinus angustifolius	Lupin	1153	57,806			51.9	50	[137]
Gossypium raimondii	Cotton	630–880	37,505	72×	1.6	~100	61	[95]
Gossypium hirsutum	Cotton	2400	76,943	144×		~90	67.2	[96, 138]
Theobroma cacao	Chocolate	430	28,798	12×		76	41.8^b	[139]
Citrus x clementina	Orange	367	25,376		0.17	82.1	45	[140]
Carica papaya	Papaya	372	28,629		0.02	73.8	41.9	[141]
Brassica rapa	Chinese cabbage	468–516	41,174	144×	1	59	39.5	[142]
Brassica napus	Oilseed rape	1130	101,040	288×	2.23	79	ND	[143]
Brassica oleracea	Vegetables	630	45,758	144×		85	38.8^b	[128]
Raphanus raphanistrum	Wild radish	515	38,174			49.3	ND	[144]
Phoenix dactylifera	Date palm	658	28,890		0.08	60	ND	[145]
Elaeis guineensis	Oil palm	1800	34,802		5.09	85.3	50	[146]
Musa acuminata	Diploid banana	523	36,542	64×	0.41	90	32	[147]
Oryza sativa	Asian rice	389	37,544	32×	17.2	95	35	[51]
Oryza glaberrima	African rice	358	33,164	32×		88.3	34.3	[148]
Hordeum vulgare	Barley	5100	26,159	32×	3.23	37.3	84	[149]
Triticum aestivum	Wheat	17,000	124,201	96×	15.98	60	76.6	[150]
Zea mays	Maize	2500	32,540	64×	23.56	81.9	85	[151]
Sorghum bicolor	Sorghum	730	34,496	32×	1.99	89.7	61	[152]
Setaria italica	Foxtail millet	490	38,801	32×	1.01	86	46	[153]
Eragrostis tef	Tef	772	ND	64×		87	14^b	[154]

^aReported whole-genome doublings from base of angiosperms as reported in [155] and inferred from phylogenetic position. ^bAs determined from the amount of sequence represented in the assembly compared to estimated genome size. For some species, these percentages were reported in the referenced articles, whereas for others we calculated the percentages using genome size estimates from articles in which sequences were published or from public databases. ^cThese percentages are likely to be underestimates. Abbreviations: ND No data/data not reported

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