Deciphering the virome of Chunkung (Cnidium officinale) showing dwarfism-like symptoms via a high-throughput sequencing analysis

Belete, Mesele Tilahun; Kim, Se Eun; Gudeta, Workitu Firmosa; Igori, Davaajargal; Kwon, Jeong A.; Lee, Su-Heon; Moon, Jae Sun

doi:10.1186/s12985-024-02361-7

Virology Journal

Table 3 A list of viruses identified based on RNA sequencing data and their PCR/RT-PCR validation in the chunkugn samples collected from production fields in south Korea in 2021; where Bold font: viruses not confirmed via PCR/RT-PCR assay and viruses indicated with (^a): viruses known to infect chunkugn plant

From: Deciphering the virome of Chunkung (Cnidium officinale) showing dwarfism-like symptoms via a high-throughput sequencing analysis

Genome type	Family	Genus	Virus name	Abbreviation	Total reads	Abundance (%)	Identity (%)	Contig length
circular dsDNA,RT	Caulimoviridae	Badnavirus	Blackberry virus F	BVF	69	1.14	50–76	204–472
			Cacao Bacilliform SriLanka Virus	CBSLV	12	0.29	46	327
			Gulupa bacilliform virus A	GBVA	51	0.57	68–77	264–266
			Jujube mosaic-associated virus	JuMaV	59	0.29	41	569
			Pelargonium vein banding virus	PVBV	142	1.71	45–85	249–1051
			Taro bacilliform virus	TaBV	40	0.29	57	492
			Yacon necrotic mottle virus	YNMoV	17	0.29	79	341
			Dioscorea bacilliform TR virus	DVB9	42	0.29	81	408
		Caulimovirus	Angelica bushy stunt virus^a	AnBSV	22,898	9.71	40–100	201–8323
			Atractylodes mild mottle virus	AMMV	91	1.14	37–61	303–475
			Carnation etched ring virus	CERV	48	0.86	53–80	242–645
			Cauliflower mosaic virus	CaMV	1316	3.43	35–72	206–1518
			Plantago latent caulimovirus	PlLV	129	0.57	47–82	242–798
			Pueraria virus A	PVA	158	0.29	41	897
			Soybean Putnam virus	SPuV	6949	3.71	37–88	222–4275
			Strawberry vein banding virus	SVBV	436	0.86	41–66	445–1390
			Dahlia mosaic virus	DMV	10	0.29	72	272
			Horseradish latent virus	HRLV	7	0.29	42	209
			Lamium leaf distortion virus	LLDV	220	0.29	50	975
		Rosadnavirus	Rose yellow vein virus	RYVV	559	1.71	43–59	240–673
		Rosadnavirus	Viola yellow mottle virus	VYMoV	95	0.57	50–56	293–322
		Solendovirus	Tobacco vein clearing virus	TVCV	11	0.57	37–47	203–439
		Vaccinivirus	Blueberry fruit drop associated virus	BFDaV	19	0.29	64	341
circular ssDNA	Geminiviridae	Begomovirus	African cassava mosaic virus	ACMV	76	0.29	50	456
			Cucurbit leaf crumple virus	CuLCrV	12	0.29	45	209
			Merremia leaf curl virus	MerLCV	3	0.29	60	220
			Squash leaf curl virus	SLCV	50	0.57	65–82	269–289
			Tomato leaf curl Burkina Faso virus	TolCBFV	11	0.29	50	255
			Tomato leaf curl Pakistan virus	ToLCPaKV	22	0.29	54	243
			Tomato yellow leaf curl Thailand virus	TYLCTHV	82	0.29	48	852
			Tomato yellow leaf curl virus	TYLCV	33	0.57	51–52	202–43
			Yam yellow spot mosaic virus	YYSMV	61	0.29	49	338
			Ageratum yellow vein virus	AYVV	1	0.29	54	219
		Citlodavirus	Passion fruit chlorotic mottle virus	PCMoV	1515	0.57	44–45	2056–2978
		Unassigned	Tomato curly top virus	ToCTV	527	0.57	57–59	659–1490
linear dsRNA	Reoviridae	Fijivirus	Fiji disease virus	FDV	205,206	0.86	22–32	3759–4564
			Oat sterile dwarf virus	OSDV	104,808	0.57	22–23	1975–2018
			Rice black streaked dwarf virus	RBSDV	95,274	0.29	32	4570
			Southern rice black-streaked dwarf virus	SRBSDV	323,936	1.14	21–23	3576–3610
		Unassigned	Grapevine Cabernet Sauvignon reovirus	GCSV	414	0.86	22–36	794–1386
		Unassigned	Raspberry latent virus	RpLV	479	1.71	27–53	401–1738
	Partitiviridae	Unassigned	Panax cryptic virus 4	PCV4	6	0.29	52	262
	Picobirnaviridae	Unassigned	Lysoka partiti-like virus	LPLV	9	0.29	54	222
	Spinareoviridae	Oryzavirus	Rice ragged stunt virus	RRSV	34	0.86	39–46	317–386
ssRNA (-)	Rhabdoviridae	Betanucleorhabdovirus	Cnidium virus 1^a	CnV1	67,823	2	77–100	779–8725
		Cytorhabdovirus	Ivy vein banding virus	IVBV	15	0.29	90	285
			Black currant cytorhabdovirus 1	BCaRV	45	0.57	58–60	239–492
			Lettuce yellow mottle virus	LYMoV	30	0.29	60	426
			Raspberry vein chlorosis virus	RVCV	21	0.57	58–64	225–237
			Strawberry virus 2	SV2	406	4	51–89	204–998
			Alfalfa dwarf virus	ADV	3	0.29	51	218
			Sambucus virus1	SaV1	50,191	3.43	60–92	258–13,564
			Trichosanthes associated rhabdovirus 1	TrARV1	3384	1.71	63–91	275–3010
		Unassigned	Bacopa monnieri virus 3	BmV3	125	0.57	36–40	539–610
			Cynara cardunculus rhabdovirus	CyRV	10	0.29	93	248
			Glehnia littoralis virus 1	GlLV1	4697	8.57	48–98	205–2498
		Varicosavirus	Aponogeton virus 1	ApoV1	3903	0.57	40–74	1789–1829
ssRNA( +)	Tombusviridae	Betacarmovirus	Japanese iris necrotic ring virus	JINRV	12	1.14	88–95	214–421
	Betaflexiviridae	Betaflexivirus	Iris domestica betaflexivirus 1	IDBV	47,633	0.57	85–86	5023–5024
		Capillovirus	Apple stem grooving virus^a	ASGV	76,642	2.86	95–100	243–6507
		Chordovirus	Carrot Ch virus 1	CChV1	760	3.43	60–95	232–1879
		Chordovirus	Hogweed virus 4	HV4	15	0.29	88	591
	Bromoviridae	Cucumovirus	Cucumber mosaic virus^a	CMV	17,428,208	8.86	87–100	205–3380
	Bromoviridae	Cucumovirus	Hydrocharis dubia cucumovirus	HDCV	159	0.29	97	422
	Solemoviridae	Enamovirus	Arracacha latent virus E associated RNA	ALVE	4,238,694	1.71	49–85	1078–2923
		Polerovirus	Cnidium polerovirus 1^a	CnPV1	578,766	0.57	96–98	343–6094
			Pepper vein yellows virus	PeVYV	40	0.29	94	547
			Pepper yellow leaf curl Thailand virus	PepYLCTHV	12	0.29	67	238
	Alphaflexivirida	Potexvirus	Cnidium virus X^a	CnVX	120,246	5.71	79–100	204–5422
	Alphaflexivirida	Potexvirus	Potato virus X	PVX	43,104	0.57	33	2127–2155
	Unclassified	Satellite RNAs	Cucumber mosaic virus satellite RNA	CMVsat	7553	0.57	93–97	363–711
	Unclassified	Satellite RNAs	Peony yellowing associated secovirus satellite RNA	PYSV	555,062	0.57	67	1016–1017
	Secoviridae	Stralarivirus	Lychnis mottle virus^a	LyMoV	289,682	0.57	96–97	3685–3710
		Stralarivirus	Strawberry latent ringspot virus	SLRV	5289	1.43	82–98	394–517
		Unassigned	Cnidium vein yellowing virus 1^a	CnVYV1	350,522	0.86	91–100	1476–6914
		Unassigned	Cnidium vein yellowing virus 2^a	CnVYV2	143,789	4.29	94–100	216–2530
	Virgaviridae	Tobamovirus	Opuntia virus 2	OpV2	97	0.29	85	672
	Virgaviridae	Tobamovirus	Rubber tree latent virus 1	RTLV1	43,403	0.57	36	8256–8315

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ISSN: 1743-422X

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