Genome Diversity in Maize

Table 1

Distribution and proportion of features in the annotated genomes of 4 grasses. Table shows a comparison of major genomic element types between 4 published references. N/A indicates these data were not available.

Reference sequence completed*	Brachypodium [17]		Rice [15, 115]		Sorghum [16]		Maize [9]
	Bd21		Indica + japonica		Bxt623		B73
	271 Mb		420 Mb		739 Mb		2160 Mb
	Copies	% Genome	Copies	% Genome	Copies	% Genome	Copies*	% Genome
Class I (retroelements)	50,419	23.33	61,900	19.36	216,519	54.47	1,139,990	75.6
LTR Ty1/copia	12,426	4.86	11,600	3.85	19,844	5.18	404,000	23.7
LTR Ty3/gypsy	32,978	16.05	23,500	10.9	38,652	19	477,000	46.4
LTR other	1,870	0.48	N/A	N/A	156,304	30.25	222,000	4.5
Non-LTR (LINE)	3,145	1.94	9,600	1.12	513	0.04	35,000	1
Non-LTR (SINE)	N/A	N/A	1,800	0.06	0	0	1,990	0
Other Class I	N/A	N/A	15,400	3.43	1,206	N/A	N/A	N/A
Class II (DNA Transposon)	29,630	4.78	163,800	12.96	76,883	7.57	142,800	8.6
CACTA	1,523	2.18	10,800	2.69	15,006	4.69	12,400	3.2
hAT	658	0.24	1,100	0.38	296	0.02	31,800	1.1
Mutator	2,854	0.63	8,800	3.64	440	0.06	N/A	N/A
Tc1/mariner	50	0.07	67,000	2.26	22	0	N/A	N/A
PIF/harbinger	862	0.42	N/A	N/A	389	0.13	N/A	N/A
MULE	N/A	N/A	N/A	N/A	N/A	N/A	12,900	1
MITE (Stowaway)	N/A	N/A	N/A	N/A	7,191	0.19	14,000	0.1
MITE (Tourist)	23,563	1.06	57,900	3.26	27,724	0.94	49,700	1
Helitron	120	0.18	N/A	N/A	1,017	0.81	22,000	2.2
Other Class II	N/A	N/A	18,200	0.73	24,798	0.73	N/A	N/A
Protein-encoding genes	25,532	37	29,717	29	27,640	15	32,540	6