PwRn1, a novel Ty3/gypsy-like retrotransposon of Paragonimus westermani: molecular characters and its differentially preserved mobile potential according to host chromosomal polyploidy

Table 1 CsRn1-like retrotransposons of Anopheles gambiae isolated in this study

Element	Contig No. (nucleotide position)^a	Nucleotide lengths (bp)				LTR identity (%)	TSD	Note^d
		5'-/3'-LTR	Full unit	ORF1^b	ORF2^{b, c}
AgCR1	AAAB01008980 (3956962–3961632)	264/264	4671	978	2961 (0)	98.1	AAGC
AgCR2	AAAB01008810 (41113–47019)	368/368	5907	978	3168 (0)	100	AACT	GYPSY51AG
AgCR3	AAAB01008968 (1135463–1139639)	146/146	4177	756	3090 (-1)	100	AATG	GYPSY50AG
AgCR4	AAAB01008984 (9436961–9442636)	356/356	5676	948	3135 (0)	100	AACT	GYPSY70AG
AgCR5	AAAB01008831 (1206–6507)	202/202	5302	882	2993 (-1)	100	CGTC
AgCR6	AAAB01008880 (20632–25306)	300/300	4675	888	3087 (0)	99.7	CACC	GYPSY53AG
AgCR7	AAAB01008850 (51014–56635)	266/267	5622	876	2856 (-1)	97.3	AAGT
AgCR8	AAAB01008888 (3231118–3237246)	394/394	6126	984	3249 (0)	100	GCAT	GYPSY52AG
AgCR9	AAAB01008851 (1315535–1320623)	260/260	5089	915	2964 (-1)	100	GGTT
AgCR10	AAAB01008869 (24283–30418)	319/316	6136	885	2991 (-1)	99.1	ATGT	GYPSY49AG
AgCR11	AAAB01008957 (186235–192486)	407/407	6252	909	3081 (-1)	98.5	TATC
AgCR12	AAAB01008964 (2714632–2720796)	370/370	6165	894	3084 (-1)	100	AGTT	GYPSY48AG
AgCR13	AAAB01008849 (1694453–1699416)	219/206^e	4964	933	2946 (-1)	99.5	AGGG^e
AgCR14	AAAB01008944 (738407–744580)	383/383	6174	984	2970 (-1)	100	ACCC

^aContig sequence containing a representative copy is listed.
^bThe lengths of ORFs were estimated from each of the elements, after correcting the corrupted nucleotide sequences (see text).
^cNumber in parentheses indicates a shift in the reading frame of ORF2 compared to that of ORF1.
^dSynonymous names, as have been designated in a previous report [15].
^eNucleotides comprising the end of the 3'-LTR and TSD were deleted in the contig and thus, TSD sequence found at the 5'-flanking region was presented.

ISSN: 1471-2164