Transposable element distribution, abundance and role in genome size variation in the genus Oryza

Table 2 Abundance of major classes of repeats in different Oryza genomes.

	O. nivara [AA; 448 Mbp]	O. rufipogon [AA; 439 Mbp	O. glaberrima [AA; 357 Mbp]	O. punctata [BB; 425 Mbp]	O. officinalis [CC; 651 Mbp	O. minuta [BBCC; 1124 Mbp]	O. alta [CCDD; 1008 Mbp]	O. australiensis [EE; 965 Mbp]	O. brachyantha [FF; 362 Mbp]	O. granulata [GG; 882 Mbp]	O. ridleyi [HHJJ; 1283 Mbp]	O. coarctata [HHKK]
Centromeric	0.64	0.59	2.29	4.39	3.84	3.66	6.22	0.91	2.04	0.30	0.25	0.16
Helitron	0.71	0.78	0.89	1.02	0.39	0.55	0.44	0.08	0.03	0.16	0.09	0.20
LINEs	1.10	1.17	1.09	0.83	0.47	0.68	0.81	0.86	0.36	0.28	0.39	0.58
MITEs	11.73	14.36	17.00	5.09	5.20	5.88	5.28	1.83	15.28	2.14	3.33	2.08
LTR-Retroelement (a)	3.87	4.38	4.49	5.38	6.60	5.26	7.95	5.25	2.34	4.65	8.75	2.73
Ty1-copia	2.32	1.92	2.78	3.47	3.96	5.10	5.35	9.84	2.49	4.74	4.59	7.44
Ty3-gypsy	23.27	19.69	13.31	20.42	31.31	24.27	18.81	35.59	7.88	45.60	19.38	7.74
Ribosomal	1.22	0.27	0.94	1.24	1.24	0.94	1.10	0.64	3.85	0.82	0.99	0.56
DNA-Transposon (b)	7.38	10.80	9.70	9.83	11.90	11.28	8.33	7.42	4.26	4.81	11.93	3.44
SINEs	0.35	0.63	0.49	0.03	0.21	0.23	0.25	0.01	0.18	0.07	0.11	0.00
Telomeric	0.06	0.16	0.00	0.10	0.27	0.12	0.16	0.26	0.00	0.01	0.08	0.04
Other (c)	0.68	0.94	0.97	0.22	1.03	0.38	2.84	0.10	0.03	0.07	0.21	0.07
Total	53.34	55.69	53.95	52.00	66.42	58.35	57.54	62.79	38.73	63.67	50.10	25.04

Occurrences are expressed as percentage of sequence reads having significant similarity out of the total.
(a) Refers to LTR-RTs that could not be classified as Ty3-gypsy or Ty1-copia (so non autonomous, tracts of LTRs from non autonomous etc.)
(b) Includes all the autonomous DNA elements; non autonomous ones such MITEs are excluded; helitrons are reported separately
(c) Unclassified repeats

ISSN: 2730-7182