A search for reverse transcriptase-coding sequences reveals new non-LTR retrotransposons in the genome of Drosophila melanogaster

Table 1 Summary of non-LTR retrotransposon sequences found in the genome of the D. melanogaster isogenic strain y; cn bw sp

	Number of elements^*		Localization^†		Full-size elements^‡		5' truncated^§		D^¶
Family	Total	Unfinished	Euchromatic	?	With TSD	Without TSD	With TSD	Without TSD	>200
BS	19	5	15	4	2	0	5	3	0.055
Doc	128	38	78	50	18	4	20	14	0.095
F	94	25	59	35	2	12	7	10	0.079
G	37	3	22	15	1	0	2	12	0.219
I	48	15	20	28	6	0	6	8	0.097
Jockey	86	16	78	8	7	0	40	6	0.036
JuanDm	8	1	8	0	4	0	2	0	0.003
Waldo-A	82	20	40	42	2	0	10	10	0.119
Waldo-B	48	4	24	24	4	1	3	17	0.137
You	19	3	6	13	3	1	1	2	0.116
QDm	85 sequences matching reverse transcriptase								0.435
LOA	18 sequences matching reverse transcriptase								0.370
HelenaDm	9 sequences matching reverse transcriptase								0.594
TART	11 sequences matching reverse transcriptase								0.374
R1Dm	Only partial elements								0.417
R2Dm	No hit
Bilbo	Only short (70-600 bp) regions with average identity of 55%
HeT-A	Only short (70-600 bp) regions with average identity of 60%

^*The total number of elements of each family and the number of elements that were not completely sequenced are indicated. ^†The localization of elements on chromosomal bands was deduced from the scaffold mapping [14]. Question mark indicates elements whose sequences were found in scaffolds that were not mapped to chromosomal arms. ^‡§The number of full size and 5'-truncated elements, surrounded and not surrounded by TSD, are given. ^¶The mean genetic distance between elements longer than 200 bp.

ISSN: 1474-760X