Determination and Analyses of the Complete Genome Sequences of Apple Stem Grooving Virus Isolates Infecting Tree Peony

doi:10.16420/j.issn.0513-353x.2023-0277

Acta Horticulturae Sinica ›› 2023, Vol. 50 ›› Issue (12): 2735-2747.doi: 10.16420/j.issn.0513-353x.2023-0277

• Plant Protection • Previous Articles Next Articles

Determination and Analyses of the Complete Genome Sequences of Apple Stem Grooving Virus Isolates Infecting Tree Peony

CHEN Ling¹, GUO Cheng¹, JIA Anning², DENG Congliang³, CHONG Yan³, SHI Xiju³, LI Yongqiang²^,^*()

¹ School of Grassland Science，Beijing Forestry University，Beijing 100083，China
² College of Biological Science and Resources Environment，Beijing University of Agriculture，Beijing 102206，China
³ China Customs Science and Technology Research Center，Beijing 100026，China

Received:2023-06-19 Revised:2023-10-24 Online:2023-12-25 Published:2023-12-29
Contact: LI Yongqiang

Abstract

Abstract:

Apple stem grooving virus（ASGV）was detected in tree peony（Paeonia sect. moutan）plants cultivated in Beijing region in previous study，and the complete genome sequence of one ASGV-tree peony isolate was obtained. To analyze the genetic diversity of tree peony-infecting ASGV，the complete genome sequences of nine ASGV-tree peony isolates were obtained using overlapping RT-PCR and rapid amplification of cDNA ends（RACE）techniques with specific primers designed according to the conserved regions of 118 reported ASGV complete genome sequences. Pairwise alignment of the complete genome sequences of total ten ASGV-tree peony isolates showed the nucleotide identity of 81.9%-97.6%. Alignment of ASGV-tree peony isolates and other isolates showed the nucleotide identity of 80.8%-91.2%. Sequence analyses indicated that the molecular diversity of ASGV-tree peony isolates mainly located in the regions between Mtr and P-Pro，RdRp and CP，which were the conserved domains of ASGV-encoded polyprotein. Five ASGV-tree peony isolates were identified as recombinants，including one recombinant whose recombinant parents developed from different host plants in different countries，performed by recombination analyses using the complete genome sequences of 127 ASGV isolates. Phylogenetic tree constructed using 79 non-recombinant ASGV complete genome sequences suggested that ASGV-tree peony isolates clustered into the first group closely with ASGV isolates from apple，pear，citrus and so on，and ASGV-tree peony isolates clustered into different clades. These results revealed the genetic diversity of tree peony-infecting ASGV，and recombination is a factor that likely contributes to this diversity.

Key words: apple stem grooving virus, tree peony, complete genome sequence, sequence analyses, recombination, phylogeny

CHEN Ling, GUO Cheng, JIA Anning, DENG Congliang, CHONG Yan, SHI Xiju, LI Yongqiang. Determination and Analyses of the Complete Genome Sequences of Apple Stem Grooving Virus Isolates Infecting Tree Peony[J]. Acta Horticulturae Sinica, 2023, 50(12): 2735-2747.

Figures/Tables 10

References 30

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产物/bp Product	引物位置/nt Location	引物名称 Primer name	引物序列（5′-3′） Primer sequence
1 953	494 ~ 513	ASGV-F1	TGGTCTGAGGAACCAATGCC
	2 446 ~ 2 427	ASGV-R1	ATCCTCTTGACGTTTGGCGT
2 342	1 533 ~ 1 552	ASGV-F2	TCAAAGCTGGTCAGAGCGAG
	3 874 ~ 3 855	ASGV-R2	AAAGCATGGTCGAGCTTCCA
2 083	3 498 ~ 3 517	ASGV-F3	TCCATACTCGGCCTCTCCAA
	5 580 ~ 5 561	ASGV-R3	TTGGAGTTTGGCCCCCTTTT
	1 413 ~ 1 392	5ʹ RACE	GATTACGCCAAGCTT-AACCTGCGGCCAAGCAGGTCCAA
	5 128 ~ 5 152	3ʹ RACE	GATTACGCCAAGCTT-TGCCTGTTTGGACCCAGAAAGGGGT

产物/bp Product	引物位置/nt Location	引物名称 Primer name	引物序列（5′-3′） Primer sequence
1 953	494 ~ 513	ASGV-F1	TGGTCTGAGGAACCAATGCC
	2 446 ~ 2 427	ASGV-R1	ATCCTCTTGACGTTTGGCGT
2 342	1 533 ~ 1 552	ASGV-F2	TCAAAGCTGGTCAGAGCGAG
	3 874 ~ 3 855	ASGV-R2	AAAGCATGGTCGAGCTTCCA
2 083	3 498 ~ 3 517	ASGV-F3	TCCATACTCGGCCTCTCCAA
	5 580 ~ 5 561	ASGV-R3	TTGGAGTTTGGCCCCCTTTT
	1 413 ~ 1 392	5ʹ RACE	GATTACGCCAAGCTT-AACCTGCGGCCAAGCAGGTCCAA
	5 128 ~ 5 152	3ʹ RACE	GATTACGCCAAGCTT-TGCCTGTTTGGACCCAGAAAGGGGT

取样位置 Sampling location	植株症状 Plant symptom	分离物 Isolate	基因组大小/nt Genome size	登录号 Accession No.
海淀公园Haidian Park	褪绿Chlorosis	Peony BJ2	6 470	OQ658829
	卷叶Leafroll	Peony BJ3	6 470	OQ658830
景山公园Jingshan Park	褪绿Chlorosis	Peony BJ4	6 469	OQ658831
	皱缩、节间缩短Crinkle，internode shortening	Peony BJ5	6 467	OQ658832
	卷叶Leafroll	Peony BJ6	6 467	OQ658833
北京植物园Beijing Botanical Garden	红叶Leaf reddening	Peony BJ7	6 495	OQ658834
	卷叶Leafroll	Peony BJ8	6 495	OQ658835
圆明园Yuanmingyuan Garden	褪绿Chlorosis	Peony BJ9	6 469	OQ658836
	皱缩Crinkle	Peony BJ10	6 469	OQ658837

取样位置 Sampling location	植株症状 Plant symptom	分离物 Isolate	基因组大小/nt Genome size	登录号 Accession No.
海淀公园Haidian Park	褪绿Chlorosis	Peony BJ2	6 470	OQ658829
	卷叶Leafroll	Peony BJ3	6 470	OQ658830
景山公园Jingshan Park	褪绿Chlorosis	Peony BJ4	6 469	OQ658831
	皱缩、节间缩短Crinkle，internode shortening	Peony BJ5	6 467	OQ658832
	卷叶Leafroll	Peony BJ6	6 467	OQ658833
北京植物园Beijing Botanical Garden	红叶Leaf reddening	Peony BJ7	6 495	OQ658834
	卷叶Leafroll	Peony BJ8	6 495	OQ658835
圆明园Yuanmingyuan Garden	褪绿Chlorosis	Peony BJ9	6 469	OQ658836
	皱缩Crinkle	Peony BJ10	6 469	OQ658837

分离物Isolate	Peony BJ2	Peony BJ3	Peony BJ4	Peony BJ5	Peony BJ6	Peony BJ	Peony BJ7	Peony BJ8	Peony BJ9
Peony BJ3	96.4
Peony BJ4	87.4	87.6
Peony BJ5	87.4	86.8	92.2
Peony BJ6	83.3	83.5	90.3	97.0
Peony BJ	82.1	82.1	90.2	87.3	88.7
Peony BJ7	83.2	83.1	83.0	87.4	86.5	87.3
Peony BJ8	82.3	82.2	83.6	85.5	86.8	88.6	91.6
Peony BJ9	94.8	95.2	87.0	86.4	83.5	81.9	83.1	82.2
Peony BJ10	94.8	95.1	86.8	86.1	83.2	82.0	83.0	82.2	97.6
其他Other	82.4 ~ 912	82.3 ~ 91.3	81.9 ~ 86.8	81.8 ~ 87.2	82.6 ~ 87.9	81.2 ~ 89.0	82.1 ~ 90.5	80.8 ~ 91.0	82.0 ~ 90.7

Determination and Analyses of the Complete Genome Sequences of Apple Stem Grooving Virus Isolates Infecting Tree Peony

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分离物Isolate	核苷酸序列Nucleotide sequence					氨基酸序列Amino acid sequence
分离物Isolate	5ʹ UTR	ORF1	CP	ORF2	3ʹ UTR	Polyprotein	CP	MP
Peony BJ2	—	81.8 ~ 91.1	92.9 ~ 97.8	85.8 ~ 92.9	96.5 ~ 100	84.1 ~ 94.5	96.2 ~ 98.7	92.5 ~ 98.4
Peony BJ3	—	82.8 ~ 91.4	92.6 ~ 97.2	85.8 ~ 93.3	96.5 ~ 100	85.8 ~ 94.8	96.6 ~ 99.2	91.9 ~ 97.5
Peony BJ4	100	81.5 ~ 86.6	91.2 ~ 94.0	85.3 ~ 88.4	95.6 ~ 99.1	86.7 ~ 92.1	94.1 ~ 97.9	92.8 ~ 98.1
Peony BJ5	97.0 ~ 100	81.5 ~ 86.4	91.5 ~ 94.3	83.8 ~ 87.5	95.6 ~ 99.1	86.4 ~ 91.2	96.2 ~ 99.2	89.4 ~ 94.7
Peony BJ6	97.1 ~ 100	82.3 ~ 87.7	91.9 ~ 94.1	85.3 ~ 88.7	95.6 ~ 99.1	86.5 ~ 90.9	94.9 ~ 98.3	92.2 ~ 98.1
Peony BJ	97.1 ~ 100	81.1 ~ 88.9	91.4 ~ 94.3	85.0 ~ 88.7	93.0 ~ 96.5	86.6 ~ 92.5	94.9 ~ 98.3	91.9 ~ 97.5
Peony BJ7	97.1 ~ 100	80.6 ~ 90.4	91.5 ~ 93.6	85.5 ~ 92.8	95.1 ~ 99.3	85.6 ~ 91.9	94.1 ~ 97.1	92.5 ~ 98.1
Peony BJ8	97.1 ~ 100	81.5 ~ 90.9	91.9 ~ 97.2	84.8 ~ 88.0	95.7 ~ 99.3	85.9 ~ 90.9	94.5 ~ 98.3	92.2 ~ 97.2
Peony BJ9	97.1 ~ 100	81.7 ~ 90.6	91.7 ~ 98.6	86.0 ~ 92.9	94.8 ~ 99.1	85.7 ~ 94.0	94.5 ~ 98.7	92.8 ~ 98.8
Peony BJ10	97.1 ~ 100	81.7 ~ 90.7	91.3 ~ 98.0	85.6 ~ 92.9	94.8 ~ 99.1	85.7 ~ 94.2	94.5 ~ 98.7	91.9 ~ 97.8

重组序列 Recombination sequence	主、次要亲本 Major and minor parents	重组发生的比对起、终点/nt Breakpoint positions in alignment（Begin，End）	RDP v.4.101软件中7种检测方法的P值
			P-value for the seven detection methods in RDP v.4.101
			RDP GENECONV	BootScan MaxChi	Chimaera SiScan	3Seq
OQ658832	OQ658833 OQ658829	待定Undetermined 2 022	3.064 × 10^-87 3.681 × 10^-104	3.083 × 10^-100 1.879 × 10^-42	3.451 × 10^-45 5.539 × 10^-46	2.963 × 10^-11
OQ658831	MT607622 OQ658829	待定Undetermined 1 998	1.256 × 10^-58 9.314 × 10^-73	3.861 × 10^-64 1.142 × 10^-32	6.943 × 10^-37 2.647 × 10^-39	5.926 × 10^-11
OQ658833	未知Unknown MT607622	4 084 待定Undetermined	1.174 × 10^-41 2.230 × 10^-36	3.444 × 10^-21 1.725 × 10^-18	5.191 × 10^-14 4.712 × 10^-32	2.963 × 10^-11
OQ658831	MT607622 未知Unknown	待定Undetermined 2 446	1.221 × 10^-30 3.455 × 10^-17	9.406 × 10^-27 9.470 × 10^-11	5.297 × 10^-12 2.231 × 10^-9	5.926 × 10^-11
MT607622	未知Unknown OQ658835	待定Undetermined 2 550	1.716 × 10^-13 8.543 × 10^-6	1.459 × 10^-12 2.437 × 10^-15	9.076 × 10^-12 3.670 × 10^-29	6.118 × 10^-23
OQ658835	OQ658834 MK929792	5 532 待定Undetermined	1.740 × 10^-22 1.291 × 10^-12	1.736 × 10^-22 —	1.244 × 10^-6 4.068 × 10^-11	5.926 × 10^-11

序列 Sequence	分离物 Isolate	寄主 Host	地理位置 Geographical region
OQ658829	Peony BJ2	牡丹Tree peony	中国China
OQ658831	Peony BJ4	牡丹Tree peony	中国China
OQ658832	Peony BJ5	牡丹Tree peony	中国China
OQ658833	Peony BJ6	牡丹Tree peony	中国China
OQ658834	Peony BJ7	牡丹Tree peony	中国China
OQ658835	Peony BJ8	牡丹Tree peony	中国China
MT607622	Peony BJ	牡丹Tree peony	中国China
MK929792	BR-Brael	苹果Apple	巴西Brazil

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