Genome-wide analysis of LTR-retrotransposons in oil palm

BMC Genomics

Table 1 Structural characteristics of the full-length LTR retrotransposons of oil palm E. guineensis

Superfamily/lineage	Groups	Elements		LTR		Copies (70–70 %)
		Number	Avg. length (bp) (min-max)	Avg. % identity	Avg. length (bp) (min-max)	Number	Genome coverage (%)
Copia
Oryco	25	36	4796	91.85	338
Oryco			4536–5627		240–469
Sire	8	8	9063	89.34	1170
Sire			4538–11,043		347–1475
Retrofit	74	97	5075	91.62	269
Retrofit			2198–9109		83–414
Tork	66	73	7539	88.43	1069
Tork			4118–10,744		131–248
Undefined clade	26	27	8108	89.21	1473
Undefined clade			1408–10,381		168–2668
Subtotal	199	241	6252	90.34	863	4816	2.32
Subtotal			1408–11,043		83–2668
Gypsy
Athila	10	10	10,438	91.07	1411
Athila			1171–9780		875–1697
Tat	58	84	10,078	90.64	666
Tat			5572–11,478		350–1129
CRM	16	20	6455	89.51	712
CRM			8463–5084		296–1380
Del	3	3	8624	86.07	1454
Del			6730–10,443		305–2468
Galadriel	3	3	7463	90.83	1777
Galadriel			5826–10,130		533–3861
G-Rhodo	1	1	5506	90.40	448
G-Rhodo					447–450
Reina	15	16	5921	91.62	607
Reina			5085–10,286		266–2490
Undefined clade	13	14	6561	88.07	824
Undefined clade			2113–11,900		110–1413
Subtotal	119	151	8744	90.30	987	1934	1.06
Subtotal			2113–11,900		110–3861
Putative non autonomous (RXX-NA)	174	191	4911	88.20	828	3804	1.01
Putative non autonomous (RXX-NA)			1279–11,793		83–5259
Total	492	583	6458	89.63	753	10,554	4.39
Total			1279–11,900		83–5259

ISSN: 1471-2164