Reconstruction of putative DNA virus from endogenous rice tungro bacilliform virus-like sequences in the rice genome: implications for integration and evolution

Kunii, Motoyuki; Kanda, Masanori; Nagano, Hironori; Uyeda, Ichiro; Kishima, Yuji; Sano, Yoshio

doi:10.1186/1471-2164-5-80

Table 1 Summary of the ERTBV structures in the rice genomes¹.

From: Reconstruction of putative DNA virus from endogenous rice tungro bacilliform virus-like sequences in the rice genome: implications for integration and evolution

Chr.²	Accession Number	ERTBV position (length)³	Cluster⁴	alignment of gene⁵					AT-repeated sequence⁶
				Intergenic region	Region x	ORF y (MP/CP/PR)	ORF y (RT/RH)	ORF z	5'-end	3'-end
	[Japonica]
1	AP003338	31237-38745 (7509)	C	32277-31237	38711-38217	38259-34814	34534-33094	33127-32278	34 (2)	153 (0)
				38745-38712
2	AP006160^a	128189-135399^a	C	128189-128420^a	128421-128915^a	128873-129447^a	134248-132808^a	132841-131989^a	97 (0)^a	12 (0)^b
	AP004842^b	1-7610^b(11686)		131988-131526^a	7379-6885^b	130212-131451^a
				135399-134914^a		134913-134534^a
				7610-7380^b		5595-3136^b
						6927-6352^b
4	AL606628	47001-48868 (1868)	B	-	-	47001-47054	47334-48768	48756-48868	16 (0)	45 (391)
	AL606618	82165-88112 (5948)	B	-	88112-87631	87673-84239	83959-82532	82544-82165	13 (678)	156 (48)
	AL606592	36282-40413 (4132)	B	39437-40413	-	36282-36894	37174-38614	38602-39436	65 (0)	101 (17)
	AL662971	104278-111739 (7462)	C	105283-104278	111720-111226	111268-107823	107543-106102	106135-105284	65 (727)	-
				111739-111721
	AL607003	63290-71598 (8309)	A	63406-64469	64470-64882	64846-68248	68532-69972	63290-63405	52 (68)	151 (265)
				70794-71598				69939-70793
5	AC107085	22244-29756 (7513)	B	22436-22244	28859-28374	28416-24971	24691-23258	23270-22437	25 (0)	55 (64)
				29756-28860
6	AP002542	33961-41438 (7478)	B	39087-38121	38120-37636	37678-34233	39121-40541	40529-41362	216 (2)	252 (1)
				41363-41438
	AP006056	28996-33700 (4705)	C	29562-28996	-	33700-32101	31821-30381	30414-29563	93 (10)	337 (87)
	AP004750	97242-104472 (7231)	A	98061-97242	104472-103986	104022-100607	100323-98883	98916-98062	39 (178)	52 (694)
7	AP006163	118513-126010 (7498)	C	118513-118518	118519-119013	118971-122416	122696-124136	124103-124954	82 (502)	224 (129)
				124955-126010
	AP005719	363-7932 (7570)	C	3278-2211	2210-1716	1758-363	5526-4096	4129-3279	65 (100)	33 (2)
						7932-5806
	AP004348	17568-24897 (7330)	A	18513-17568	24897-24437	24473-21059	20775-19335	19368-18514	96 (100)	37 (20)
8	AP005164	171654-179236 (7583)	C	173775-174838	174839-175333	175291-178760	171654-172956	172923-173774	52 (284)	274 (11)
							179071-179236
	AP003883	117668-125143 (7476)	C	117668-117743	117744-118238	118196-121641	121921-123361	123328-124179	54 (612)	41 (16)
				124180-125143
	AP003914	22973-25201 (2229)	A	-	-	-	23074-24514	24481-25201	373 (14)	1136 (0)
	AP005301	34330-41566 (7237)	A	34330-34741	34742-35228	35192-38611	38895-40314	40281-41135	153 (14)	34 (23)
				41136-41566
	AP005159	88879-97300 (8422)	B	88879-89828	89829-90315	90273-93716	93996-95435	95423-96256	179 (0)	34 (19)
				96257-97300
9	AP005424	11998-18576 (6579)	C	18576-17867	11998-12492	12450-15849	16129-17569	17536-17833	57 (10)	95 (225)
	AP005860	50709-58281 (7573)	A	50709-50806	50807-51295	51259-54579	54863-56304	56271-57124	218 (0)	8 (3)
				57125-58281
10	AC119147	89355-102382 (13028)	B	90235-89355	101319-100834	99260-96143	95863-94424	94436-93603	71 (0)	183 (68)
				93602-93432		100876-100548
				102382-101320
	AC027660	24299-31769 (7471)	A	29370-28257	28256-27768	27804-24390	31632-30192	30225-29371	-	28 (520)
	AC069300	89901-96619 (6719)	A	90209-89901	96619-96133	96169-92755	92471-91031	91064-90210	21 (162)	21 (688)
11	AC135957	69527-81251 (11725)	A	73392-74286	81251-80765	69527-70846	71130-72570	72537-73391	368 (619)	-
				75398-74475		80801-77387		75444-75410
12	AL713945	45991-49426 (3436)	B	47029-45991	-	-	49291-47851	47863-47030	55 (1)	261 (9)
	AL731743	14231-18608 (4378)	B	17596-18608	14768-14283	14325-14231	15333-16774	16762-17595	-	44 (40)
						14791-15053
	AL928780	103187-110757 (7571)	A	103187-103406	103407-103893	103857-107273	107665-109105	109072-109926	44 (25)	25 (32)
				109927-110757
	AL928749	6275-11538 (5264)	A	7149-6275	-	11538-9695	9411-7971	8004-7150	479 (127)	624 (0)
	[Indica]
4	AB124591	554-4677(4124)	B	3709-4677	-	554-1166	1446-2886	2874-3708	43(0)	105(26)
ND	AB124592	8867-14510(5644)	C	10990-12051	12052-12546	12504-14510	8867-10171	10138-10989	64(273)	unknown
ND	AB124593	158-5914(5757)	C	4214-5914	-	158-1677	1957-3397	3364-4213	157(0)	62(2)

1 The sequences were mined from Japonica database or investigated from phage clones isolated from Indica (IR36) genomic library.
2 Chromosome no. on which the ERTBV segment resides.
3 Nucleotide positions of ERTBV in the registered genomic clone. Parenthesis indicates a length of ERTBV sequence.
4 Clusters into which the individual ERTBV sequences were phylogenetically grouped.
5 The region belongs to the part of ERTBV, and their nucleotide positions in the clone registered in the database.
6 The numbers indicate repetition times of AT at both the ends of ERTBV, and parenthesis indicates distance (bp) from the ERTBV.
a and b These clones contain the identical ERTBV, but both the clones ended within the ERTBV sequence.

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ISSN: 1471-2164

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