Table 1 TE content of species in the D. pseudoobscura group

From: Extensive exchange of transposable elements in the Drosophila pseudoobscura group

			Reads			Reference	PPTE2
Species	TE Order	Families	Percent reads	Est. copy number	dnapipeTE (%)	Reference masked (%)	Num. ins
D. pseudoobscura	TIR	31	1.745	414	1.65	0.98	292
	LTR	72	8.875	2230	12.67	7.21	1846
	LINE	35	3.633	1121	5.02	2.85	927
	RC	3	1.852	978	2.83	1.21	978
	Polinton	1	0.417	149	0.65	0.081	29
	Unknown	2	0.332	22	0.8	0.017	6
	Total known	142	16.522	4892	22.82	12.33	4072
	Total	144	16.854	4914	23.62	12.5	4078
D. persimilis	TIR	31	1.547	413	1.47	1.29	392
	LTR	72	14.273	2260	15.24	12.95	1919
	LINE	35	6.956	1301	6.92	5.76	958
	RC	3	4.43	1781	4.11	3.41	1755
	Polinton	1	0.034	46	0.49	0.18	46
	Unknown	2	0.543	76	0.86	0.025	7
	Total known	142	27.24	5801	28.23	23.59	5070
	Total	144	27.78	5877	29.09	23.62	5077
D. miranda	TIR	31	0.892	262	1.85	0.87	258
	LTR	67	7.19	973	10.86	2.21	925
	LINE	36	5.367	1431	9.26	1.25	1059
	RC	5	1.484	1934	2.34	1.16	1934
	Polinton	1	0.054	9	0.03	0.024	9
	Unknown	2	0.337	4	0.27	0.015	4
	Total known	140	14.987	4609	24.34	5.51	4185
	Total	142	15.324	4613	24.61	5.53	4189
D. lowei	TIR	31	1.396	495	1.46	0.382	381
	LTR	74	6.883	1366	6.71	1.55	740
	LINE	34	3.839	933	4.03	0.799	449
	RC	5	1.245	813	1.83	0.363	523
	Polinton	1	0.054	7	0.094	0.013	7
	Unknown	9	0.641	265	3.9	0.087	241
	Total known	145	13.417	3614	14.12	3.1	2100
	Total	154	14.058	3879	18.024	3.187	2341
D. affinis	TIR	9	0.872	278	3.25	0.177	230
	LTR	47	4.328	630	8.4	1.427	832
	LINE	13	5.223	530	6.4	0.406	339
	RC	4	1.351	369	2.26	0.245	369
	Polinton	1	0.068	35	0.77	0.041	35
	Unknown	10	1.192	206	1.36	0.098	206
	Total known	74	11.842	1842	21.08	2.29	1805
	Total	84	13.034	2048	22.44	2.39	2011

For each species, the table shows the number of TE families annotated for each order, and five metrics of TE content. These are: the proportion of Illumina reads mapping to TE sequences from each order (% reads), the total number of copies from all families of that order, estimated from coverage relative to chromosome 3 (est. copy number), the proportion of the reference genome masked by each order, the proportion of reads (% reads) per TE order as estimated by dnaPipeTE, and the number of insertions found using PopoolationTE2 [90]. As LTR elements often exist not as complete insertions, but as solo-LTRs resulting from illegitimate recombination, coverage for the LTR elements was estimated for both solo LTRs and LTR bodies separately, with the mean taken across the combined sequences. We tested for extrachromosomal circular DNAs such as from Helitrons and Polintons via comparisons between copy numbers and insertion numbers

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ISSN: 1759-8753

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