A yeast model for target-primed (non-LTR) retrotransposition

Goodwin, Timothy JD; Busby, Jason N; Poulter, Russell TM

doi:10.1186/1471-2164-8-263

BMC Genomics

Table 1 Features of retrotransposed copies of tagged Zorro3.

From: A yeast model for target-primed (non-LTR) retrotransposition

Insert no.	Assembly 19 contig^A	Chromo- some	Length of target poly-A tract (bp)	5' end^B	Length of 5' poly-A tract (bp)	3' end^C	Length of 3' poly-A tract (bp)
12.1	x0254 (94830 F)	3	10	5' truncated (ORF2)	10	Native	20
12.2	x0257 (1660 F)	2^D	9/11^E	ACT1 promoter (52–53)	6	URA3 promoter	31
12.4	10119 (254650 F)	2	12	Native (recombinant)	26^F	Native	20
22.1	x0163 (134670 R)	1	12	Native (recombinant)	20^F	Native	20
13.3	x0234 (49865 R)	2	9	Native (recombinant)	26^F	Native	20
13.4	10231 (18975 F)	4	10	Native	22	Native	13
13.5	x0143 (96420 F)	2	12	Native	28	3' UTR	7
13.6	x0163 (203035 F)	1	13	Native (recombinant)	20^F	URA3 promoter	43
13.7	x0119 (244340 F)	2	12	Native (recombinant)	26^F	Native	20
13.11	10063 (36770 F)	R	11	Native (recombinant)	34^F	Native	20
13.13	x0216 (94130 R)	1	9	None (recombinant?)^G	NA	Native	12
13.14	10212 (133650 R)	4	10	None (recombinant?)^G	NA	Native	11
13.15	x0196 (22910 F)	2	21	ACT1 promoter (20–27)	20	Native	17
13.17	x0166 (27780 R)	4	12	None (recombinant)	NA	Native	25
13.18	x0163 (15740 F)	1	12	Native	~160^H	Native	24
14.1	x0087 (72350 R)	1	10	Native	19	Native	18
14.4	20236 (26790 R)	3	7	ACT1 promoter (48–51)	30	Native	17
14.5	x0218 (144180 R)	1	17	Native	~100	Native	24
14.7	x0188 (25725 F)	R	9	Native	52	Native	18
14.11	x0139 (200180 F)	2	11	None (recombinant)	NA	Native	15
14.13	10020 (2820 R)	1	10	ACT1 promoter (20–27)	87	Native	24
14.15	x0087 (72350 R)	1	10	None (recombinant)	NA	Native	12
14.16	2500 (72900 R)	3	11	ACT1 promoter (20–27)	10	Native	14
14.17	x0073 (13260 R)	1	10	Native	36	Native	14
14.18	x0163 (134670 R)	1	12	Native	24	Native	25
14.19	2506 (28525 R)	7	4	Native	27	Native	16
14.20	20161 (92640 R)	R	10	Native	27	Native	16
14.21	20216 (97180 F)	1	18	Native	51	Native	17
14.22	10119 (254650 F)	2	12	ACT1 promoter (20–27)	25	Native	15
14.24	20155 (47610 R)	5	10	Native	37	Native	21

^A Assembly 19 contigs generally come in pairs of similar sequence representing portions of putative homologous chromosome pairs. Members of the pairs are distinguished by either a 1 or 2 at the start of the contig number, eg. 10254 and 20254. In the cases where the Zorro3 insertion site can be assigned to a particular homolog the number of that contig is shown. In cases where the insertion could lie on either of the homologs the first digit of the contig number is replaced by an x. The positions of the insertions within the contigs and their orientations, forward (F) or reverse (R), are shown in parentheses.
^B The nature of the 5' end of each element is given. For a majority of elements the 5' ends are the same as those of the full-length endogenous insertions (Native). Several elements were greater than full-length, i.e., extending back into the ACT1 promoter sequence. The precise lengths of ACT1 promoter sequences in these elements could not be determined as in all cases the similarity between the retrotransposed sequences and the ACT1 promoter sequences ended within runs of A residues. Some elements had recombined with endogenous full-length Zorro3 elements (Native (recombinant)). Some elements had recombined with an endogenous 5' truncated/inverted Zorro3 element in such a way that the resulting insertion lacks a 5' end (None (recombinant); see text).
^C The nature of the 3' end of each element is given. For most elements the 3' ends are the same as those of the endogenous insertions (Native). Some end earlier within either the Zorro3 3' UTR or within the URA3 promoter sequence.
^D Insertion site corresponds to chromosome 2 in C. albicans strain WO-1. The chromosomal origin of contigs 19–10257 and 19–20257 in strain SC5314 is not known due to conflicing data.
^E The length of the target poly-A tract varies in the two homologs.
^F The length of the 5' poly-A tract in each of these insertions is determined by the length of the 5' poly-A tract of the endogenous element that was involved in the recombination event.
^G Data not conclusive for these two insertions.
^H Several T residues are found within the 5' poly-A tract of this element. NA Not applicable.

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ISSN: 1471-2164

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