De novo assembly of the olive fruit fly (Bactrocera oleae) genome with linked-reads and long-read technologies minimizes gaps and provides exceptional Y chromosome assembly

Table 2 Classification of transposable elements (TE) identified in B. oleae genome

Class	Order	Number	Percentage
Class I	DIRS	30	0.06
	LARD	1111	2.12
	LINE	7802	14.85
	LTR	8339	15.88
	PLE	5	0.01
	SINE	206	0.39
	TRIM	831	1.58
	No order	78	0.15
	Several orders	11	0.02
	Total	18,413	34.99
Class II	Helitron	7700	14.66
	MITE	113	0.21
	Maverick	133	0.25
	TIR	15,301	29.13
	No order	481	0.92
	Several orders	21	0.04
	Total	23,749	45.13
Simple Sequence Repeats		100	0.19
No category		10,361	19.73
Total		52,623	100

Nine de novo and similarity based TE identification tools included in the PiRATE pipeline [67] were used to generate a library of TE followed by classification using PASTEC [69]

ISSN: 1471-2164