The Pinus taeda genome is characterized by diverse and highly diverged repetitive sequences

BMC Genomics

Table 2 Summary of elements in ten annotated pine BACs, as identified by MAKER (white background) and through additional repeat analyses performed in this study (shaded background).

	BAC3	BAC12	BAC15	BAC17	BAC19	BAC20	BAC21	BAC31	BAC37	BAC40	ALL
No. dicot-like genes	0	2	2	2	1	1	2	1	0	7	18
Dicot-like gene content	0	3.0%	4.7%	4.5%	3.7%	2.5%	2.8%	1.5%	-	6.5%	2.6%
No. monocot-like genes	0	2	2	1	1	1	2	1	0	8	18
Monocot-like genes content	0	20%	3.9%	3.7%	11.3%	2.5%	1.9%	1.5%	-	5.8%	4.2%
TRANSPOSONS	72	46	31	73	47	51	64	79	81	55	599
DNA transposons	23	11	11	19	19	15	28	22	24	18	190
ERVs	4	2	2	6	1	1	2	3	0	6	27
Non-LTR retroelement	7	13	6	18	12	16	7	28	18	7	132
LTR retrotransposons	38	20	12	30	15	19	27	26	39	24	250
Gypsy-like	26	7	9	17	6	14	15	13	26	10	143
Named elements*	4	1	2	1	1	1	1	1	1	1	14
Copia-like	17	3	3	13	6	4	12	10	11	13	92
Named elements*	1	0	1	2	1	1	0	2	2	0	10
INTEGRATED VIRUSES	0	0	1	0	0	0	0	1	0	1	3
OTHER REPBASE	0	0	0	1	0	2	2	1	1	1	8
SIMPLE REPEATS	16	10	4	9	12	2	22	18	41	18	152
TOTAL NO. REPBASE HITS	88	56	36	83	59	55	88	99	123	75	762
*Similar to Repbase or RM*	*18%*	*12%*	*12%*	*15%*	*17%*	*19%*	*12%*	*17%*	*15%*	9%	*17%*
Tandem repeats/minisats**	13	11	10	14	23	14	22	45	21	41	214
Direct rpts/potential LTRs**	40	12	10	10	4	6	12	24	27	16	161
Putative ORF elements**	11	5	3	8	5	6	8	3	14	7	70
NO. ADD'L REP. ELEMENTS	64	28	23	32	32	26	42	72	62	64	445
*New Repetitive Content*	*72%*	*54%*	*50%*	*59%*	*34%*	*75%*	*44%*	*93%*	*59%*	*38%*	63%
Repetitive content* at 75% threshold (similarity)**	*81%*	*83%*	*80%*	*82%*	*70%*	*86%*	*76%*	*85%*	*75%*	*82%*	*80%*
Repetitive content* at 99% threshold (identity)**	*25%*	*21%*	*22%*	*24%*	*15%*	*35%*	*19%*	*30%*	*15%*	*29%*	*24%*

*The occurrence of novel gypsy-like and copia-like elements (underlined) was manually examined as described in the text.
**See Methods for a description of the discovery of putative ORF elements, tandem repeats and direct repeats.
***The percentage of sites in each BAC assembly that aligned with one or more WGS reads at thresholds of 75% and 99% identity.

ISSN: 1471-2164