Genomic Characterization of a Totiviridae from the Ustilaginoidea virens Strain GZ-14-07

doi:10.13560/j.cnki.biotech.bull.1985.2020-0479

Abstract

Abstract:

Ustilaginoidea virens is a pathogen that causes fungi-like disease Ustilaginoidea oryzae. A mycovirus isolated from strain GZ-14-07 of U. virens was designated as Ustilaginoidea virens RNA virus 6（UvRV6）and sequenced. Mycovirus UvRV6 was extracted from the strain GZ-14-07 using CF-11 cellulose powder method and its full-length genomic sequence was obtained by random-primer amplification method. Sequence analysis,alignment and phylogenetic tree of the UvRV6 were performed using DNAMAN,BlastP and MEGA software. The complete genome sequence of the UvRV6 was determined to be 5 043 bp in length,with a GC content of 48.8%,and contained two open reading frames（ORF1 and ORF2）. ORF1 had a length of 2 280 bp and encoded a 760-amino-acid protein（79.6 kD）,and ORF2 was 2 385 bp long and encoded a 830-amino-acid protein（91.5 kD）. ORF1- and ORF2-encoded protein had a high percentage of sequence similarity to the capsid protein and the RNA-dependent RNA polymerases（RdRps）of genus Victorivirus in the family Totiviridae,respectively. Moreover,there was an AUGA between ORF1 and ORF2,and a sequence forming H-type pseudo-knot existed in the upstream of the AUGA. These 2 sequence elements allowed ORF1 and ORF2 to be merged as a bigger ORF via a mechanism of re-initiating translation after translation ended. A phylogenetic analysis based on the alignment of RdRps of UvRV6 and other totiviruses showed the UvRV6 was clustered with the members of Victorivirus in the family Totiviridae. Therefore,UvRV6 is confirmed as a new member of Victorivirus in the family Totiviridae.

Key words: Ustilaginoidea virens, mycovirus, dsRNA, Totiviridae, Victorivirus

ZHANG Ting-ting, TENG Li, CAI Xiao-yao, LONG Hui, LI Sheng-yu, LIU Hong-mei. Genomic Characterization of a Totiviridae from the Ustilaginoidea virens Strain GZ-14-07[J]. Biotechnology Bulletin, 2020, 36(10): 80-87.

Figures/Tables 5

References 33

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Virus names	Complete genome	Overlapping motif	5'UTR motif	3'UTR motif	Identity（CP）	Identity（RdRp）	H- type pseudoknot or stem-loop structure	Citation
U. virens RNA virus 6	5043	AUGA	GGGCU	CAUCG	/	/	GAUGCggccAcagcCACUgcugggccUGCGC- CGCAAGUAUGA（stem-loop structure）	This study
U. virens RNA virus 5	5221	UAAUG	UGAAA	UCAAA	38%	38%	GAAGGggcgACcggccGCCGAGAGCCUggc- cgcgccGAAUAAUG（stem-loop structure）	[30]
U. virens RNA virus L	5654	UAAUG	CGAAA	UUUUU	40%	32%	CCCCAagcgCUgccccgcuGAGCgggcCGACU- CAAUCGUAAUG（H- type pseudoknot）	[19]
U. virens RNA virus 3	5075	UAAUG	CGAAA	GCCAA	73%	75%	ggacACggcCACUGCCGguccUGCgccCAGG- AUAUAAUG（H- type pseudoknot）	[31]
U. virens RNA virus 1 strain Uv0901	5220	UAAUG	UGAAA	GGCAA	39%	31%	UAGCGcugccccgcagAGUgggCCGACCCC- CGAGUAAUG（H- type pseudoknot）	[31]
U. virens RNA virus 1 strain JYH-ZT	5567	UAAUG	UGAAA	GGCAA	39%	31%	ACCUAgcgCUGccccgcAGAGUgggCCGAC- CCCCGAGUAAUG（H- type pseudoknot）	[17]
U. virens RNA virus 1 strain HNHS-1	5142	UAAUG	AAGAU	ACAAA	39%	31%	UCAGUcgcugcUGCUCCgcaGgcgGGUGCU- GCUCAGUAAUG（stem-loop structure）	[24]

Virus names	Complete genome	Overlapping motif	5'UTR motif	3'UTR motif	Identity（CP）	Identity（RdRp）	H- type pseudoknot or stem-loop structure	Citation
U. virens RNA virus 6	5043	AUGA	GGGCU	CAUCG	/	/	GAUGCggccAcagcCACUgcugggccUGCGC- CGCAAGUAUGA（stem-loop structure）	This study
U. virens RNA virus 5	5221	UAAUG	UGAAA	UCAAA	38%	38%	GAAGGggcgACcggccGCCGAGAGCCUggc- cgcgccGAAUAAUG（stem-loop structure）	[30]
U. virens RNA virus L	5654	UAAUG	CGAAA	UUUUU	40%	32%	CCCCAagcgCUgccccgcuGAGCgggcCGACU- CAAUCGUAAUG（H- type pseudoknot）	[19]
U. virens RNA virus 3	5075	UAAUG	CGAAA	GCCAA	73%	75%	ggacACggcCACUGCCGguccUGCgccCAGG- AUAUAAUG（H- type pseudoknot）	[31]
U. virens RNA virus 1 strain Uv0901	5220	UAAUG	UGAAA	GGCAA	39%	31%	UAGCGcugccccgcagAGUgggCCGACCCC- CGAGUAAUG（H- type pseudoknot）	[31]
U. virens RNA virus 1 strain JYH-ZT	5567	UAAUG	UGAAA	GGCAA	39%	31%	ACCUAgcgCUGccccgcAGAGUgggCCGAC- CCCCGAGUAAUG（H- type pseudoknot）	[17]
U. virens RNA virus 1 strain HNHS-1	5142	UAAUG	AAGAU	ACAAA	39%	31%	UCAGUcgcugcUGCUCCgcaGgcgGGUGCU- GCUCAGUAAUG（stem-loop structure）	[24]