Genome Sequence of Tomato mottle mosaic virus Isolated from Tomato in Hainan, China

doi:10.3969/j.issn.1000-2561.2019.01.020

Abstract

Abstract:

Small RNA deep sequencing and RT-PCR techniques were used to detect the viral pathogen infecting cherry tomato (Lycopersicon esculentum) samples collected from Lingshui County, Hainan Province in 2016. Tomato mottle mosaic virus (ToMMV) was identified from the plants showing dwarf, leaf chlorotic and mottle symptoms. The virus was preserved on the Nicotiana benthamiana by mechanical inoculation, and named as tomato mottle mosaic virus Hainan isolate (ToMMV-HN). Then its whole genome sequence was obtained by RT-PCR. It was determined that the complete genome of ToMMV-HN was 6399 nt in length and contained 4 open reading frames. The identity of nucleotide and encoded amino acid of this isolate with other reported 9 ToMMV isolates was 98.0%-100% and 99.2%-100%, respectively. The identity of nucleotide with Tomato mosaic virus (ToMV), Tomato brown rugose fruit virus (TBRFV) and Tobacco mosaic virus (TMV) which belonging to the genus Tobamovirus was 84.7%, 80.7% and 79.0%, respectively. Phylogenetic analysis showed that ToMMV-HN shared the closest relationship with pepper isolates from Tibetan and Yunnan, China, followed by tomato isolates from California and South Carolina, USA, and relatively distant from Spanish and Brazilian tomato isolates of this virus. This is the first report of the whole genome sequence of ToMMV isolated from tomato in China, which would provide basic information for the diagnosis and prevention of tomato viral disease in China, especially for disease-resistant variety breeding.

Key words: Tomato mottle mosaic virus, siRNA sequencing, virus genome sequence

LIU Xiaoxuan,LI Weilin,ZHANG Tong,ZHOU Guohui. Genome Sequence of Tomato mottle mosaic virus Isolated from Tomato in Hainan, China[J]. Chinese Journal of Tropical Crops, 2019, 40(1): 139-144.

Figures/Tables 6

References 21

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引物名称及检测病毒 Primer name	引物序列 Primer sequence (5′-3′)	预期扩增片段大小 Expected product length/bp
ToMMV-F	CTGGAGAA ACTGGGTCTTG	1152
ToMMV-R	TTCGGTAAGTTCAATGGGACCT	1152
TMV-F	TAGACCCGCTAGTCACAG	237
TMV-R	CAGAGGTCCAAACCAAAC	237
ToMV-F	GGCTGGATCCTAATACCTTGGTCAACGATC	373
ToMV-R	GGCTAAGCTTGCATTATGTCGCGGACATCC	373

引物名称及检测病毒 Primer name	引物序列 Primer sequence (5′-3′)	预期扩增片段大小 Expected product length/bp
ToMMV-F	CTGGAGAA ACTGGGTCTTG	1152
ToMMV-R	TTCGGTAAGTTCAATGGGACCT	1152
TMV-F	TAGACCCGCTAGTCACAG	237
TMV-R	CAGAGGTCCAAACCAAAC	237
ToMV-F	GGCTGGATCCTAATACCTTGGTCAACGATC	373
ToMV-R	GGCTAAGCTTGCATTATGTCGCGGACATCC	373

扩增片段 Amplified fragment	引物序列 Primer sequence (5′-3′)	方向 Direction	位置 Position	预期扩增片段大小 Expected product length/bp
F1	GCGCGTATTTATTATTACAACAATTACC	+	1~1677	1677
F1	CTCGGAAACCAACCTATCATGG	-	1~1677	1677
F2	TATCGTTAGCGTTTGGCAATGCC	+	1538~3237	1699
F2	TCTGACTAACGACACATCCGCA	-	1538~3237	1699
F3	CCAAACCACTCAGTGGAAAGGT	+	3081~4783	1702
F3	CACAATTGTTCAACGAGCCAGC	-	3081~4783	1702
F4	CTCGGTGCAAAACACATCAAGG	+	4696~6399	1703
F4	TGGGCCCCTACCGGGG	-	4696~6399	1703

扩增片段 Amplified fragment	引物序列 Primer sequence (5′-3′)	方向 Direction	位置 Position	预期扩增片段大小 Expected product length/bp
F1	GCGCGTATTTATTATTACAACAATTACC	+	1~1677	1677
F1	CTCGGAAACCAACCTATCATGG	-	1~1677	1677
F2	TATCGTTAGCGTTTGGCAATGCC	+	1538~3237	1699
F2	TCTGACTAACGACACATCCGCA	-	1538~3237	1699
F3	CCAAACCACTCAGTGGAAAGGT	+	3081~4783	1702
F3	CACAATTGTTCAACGAGCCAGC	-	3081~4783	1702
F4	CTCGGTGCAAAACACATCAAGG	+	4696~6399	1703
F4	TGGGCCCCTACCGGGG	-	4696~6399	1703

分离物 Isolate	登录号 Accession number	国家 Country	相似性Identity/%
			基因组 Genome	126 ku复制酶 126 ku viral replicase		183 ku复制酶 183 ku viral replicase		运动蛋白 Movement protein		外壳蛋白 Coat protein		5′非编码区 5′ noncoding region	3′非编码区 3′ noncoding region
			nt	nt	aa	nt	aa	nt	aa	nt	aa	nt	nt
ToMMV- MX5	KF477193	墨西哥	99.5	99.4	99.3	99.5	99.5	99.4	99.3	99.8	100.0	100.0	100.0
ToMMV- 10-100	KP202857	美国	99.4	99.3	99.6	99.4	99.6	99.3	99.3	99.6	100.0	100.0	98.0
ToMMV- NY-13	KT810183	美国	99.4	99.3	99.2	99.3	99.4	99.6	99.6	99.6	99.4	98.7	100.0
ToMMV- SC13-05	KX898033	美国	99.5	99.4	99.4	99.4	99.6	99.4	99.3	100	100.0	98.7	100.0
ToMMV- CA16-01	KX898034	美国	99.2	99.2	99.6	99.2	99.7	98.8	99.3	99.8	100.0	100.0	100.0
ToMMV- YYMLJ	KR824950	中国	99.6	99.6	99.6	99.6	99.8	99.6	99.6	99.4	100.0	100.0	100.0
ToMMV- TiLhaLJ	KR824951	中国	99.7	99.6	99.6	99.6	99.8	99.6	99.6	99.6	100.0	100.0	100.0
ToMMV- VLC-1	KU594507	西班牙	98.9	98.7	99.3	98.8	99.3	99.4	99.6	99.0	100.0	100.0	99.5
ToMMV- CpB1	MH128145	巴西	99.0	98.8	99.1	98.8	99.3	99.1	99.3	99.6	100.0	100.0	100.0
ToMV- SL-1	KY912162	斯洛伐克	84.7	85.1	94.3	85.4	94.7	78.7	81.4	85.8	91.2	95.8	81.9
TBRFV- Tom1-Jo	KT383474	约旦	80.7	80.4	91.5	81.7	92.2	73.8	72.9	80.2	86.2	82.4	82.7
TMV- Hejiang	HE818427	中国	79.0	79.3	90.5	80.4	84.7	71.0	72.8	75.4	81.8	88.1	82.1