Identification and Diversity Analysis of Mycoviruses from the Phytopathogenic Fungus Colletotrichum spp. of Walnut

doi:10.13560/j.cnki.biotech.bull.1985.2022-0732

Abstract

Abstract:

Colletotrichum spp. are the pathogens of walnut anthracnose, a major disease of walnuts, but little has been known about the types and their genomic sequence information of viruses carried by phytopathogenic fungus Colletotrichum spp. of walnut. In this study, 25 strains isolated from walnut fruits suffering walnut anthracnose in three different provinces of China were mined，identified and classified via meta-transcriptomic approach. After homologous alignment analysis, 22 kinds of viral genome sequences were obtained, 19 of them were novel. Among the 22 mycoviruses, 21 were positive single-stranded RNA viruses and one was dsRNA virus. The positive single-stranded RNAs belonged to family Narnaviridae, Mitoviridae and Botourmiaviridae, respectively, while the dsRNA belonged to Alternaviridae family. The RT-PCR validation results showed that all 22 mycoviruses were detected in our Colletotrichum spp. strains, and the virus carriage rate of 25 strains was 100%, with each strain being infected by at least 1 to 11 viruses. The results enriched the genomic information of viruses carried by Colletotrichum spp. and laid the foundation for the subsequent in-depth analysis of the diversity and molecular characteristics of mycoviruses from Colletotrichum.

Key words: mycovirus, pathogen of walnut anthracnose（Colletotrichum spp.）, meta-transcriptomic sequencing, diversity

XU Xiao-wen, LI Jin-cang, HAI Du, ZHA Yu-ping, SONG Fei, WANG Yi-xun. Identification and Diversity Analysis of Mycoviruses from the Phytopathogenic Fungus Colletotrichum spp. of Walnut[J]. Biotechnology Bulletin, 2023, 39(3): 278-289.

Figures/Tables 6

References 42

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种名Species	菌株编号Strain No.	采集地点Collecting location	种名Species	菌株编号Strain No.	采集地点Collecting location
C. gloeosporioides	SZ2-3	Shangzhou, Shanxi, China	C. siamense	YX1-5	Yunxi, Hubei, China
C. gloeosporioides	DJ1-1	Danjiang, Hubei, China	C. fioriniae	BK3-5	Baokang, Hubei, China
C. gloeosporioides	DJ2-1	Danjiang, Hubei, China	C. fioriniae	CX3	Chengxian, Gansu, China
C. gloeosporioides	DJ2-4	Danjiang, Hubei, China	C. fioriniae	BK2-3	Baokang, Hubei, China
C. gloeosporioides	YY1-11	Yunyang, Hubei, China	C. fioriniae	CX1	Chengxian, Gansu, China
C. fructicola	XS6	Xingshan, Hubei, China	C. fioriniae	CX7	Chengxian, Gansu, China
C. fructicola	FX1-3	Fengxiang, Shanxi, China	C. nymphaeae	ZS3-13	Zhushan, Hubei, China
C. fructicola	CX6	Chengxian, Gansu, China	C. nymphaeae	ZS3-8	Zhushan, Hubei, China
C. fructicola	YY1-28	Yunyang, Hubei, China	C. nymphaeae	BK1-11	Baokang, Hubei, China
C. fructicola	BK2-1	Baokang, Hubei, China	C. nymphaeae	ZS2-6	Zhushan, Hubei, China
C. siamense	YX1-7	Yunxi, Hubei, China	C. nymphaeae	XS5	Xingshan, Hubei, China
C. siamense	ZS2-9	Zhushan, Hubei, China	C. nymphaeae	BK4-4	Baokang, Hubei, China
C. siamense	DJ3-5	Danjiang, Hubei, China

种名Species	菌株编号Strain No.	采集地点Collecting location	种名Species	菌株编号Strain No.	采集地点Collecting location
C. gloeosporioides	SZ2-3	Shangzhou, Shanxi, China	C. siamense	YX1-5	Yunxi, Hubei, China
C. gloeosporioides	DJ1-1	Danjiang, Hubei, China	C. fioriniae	BK3-5	Baokang, Hubei, China
C. gloeosporioides	DJ2-1	Danjiang, Hubei, China	C. fioriniae	CX3	Chengxian, Gansu, China
C. gloeosporioides	DJ2-4	Danjiang, Hubei, China	C. fioriniae	BK2-3	Baokang, Hubei, China
C. gloeosporioides	YY1-11	Yunyang, Hubei, China	C. fioriniae	CX1	Chengxian, Gansu, China
C. fructicola	XS6	Xingshan, Hubei, China	C. fioriniae	CX7	Chengxian, Gansu, China
C. fructicola	FX1-3	Fengxiang, Shanxi, China	C. nymphaeae	ZS3-13	Zhushan, Hubei, China
C. fructicola	CX6	Chengxian, Gansu, China	C. nymphaeae	ZS3-8	Zhushan, Hubei, China
C. fructicola	YY1-28	Yunyang, Hubei, China	C. nymphaeae	BK1-11	Baokang, Hubei, China
C. fructicola	BK2-1	Baokang, Hubei, China	C. nymphaeae	ZS2-6	Zhushan, Hubei, China
C. siamense	YX1-7	Yunxi, Hubei, China	C. nymphaeae	XS5	Xingshan, Hubei, China
C. siamense	ZS2-9	Zhushan, Hubei, China	C. nymphaeae	BK4-4	Baokang, Hubei, China
C. siamense	DJ3-5	Danjiang, Hubei, China

Contig 编号 Contig code	病毒名称 Name of putative viruses	病毒名称缩写 Name abbreviation	长度 Length	序列相似度 Acid similarity/%	E值 E-value	最佳匹配 Best match	基因组类型 Genome type	病毒科 Family	Contig 计数 Contig counts
Contig 22546	Colletotrichum fioriniae alternavirus 1	CfAV1 dsRNA2	2 463 bp	70.4	3.50E-303	Fusarium graminearum alternavirus 1（YP_009449446.1）	dsRNA	Alternaviridae	1
Contig11036	Colletotrichum fioriniae alternavirus 1	CfAV1 dsRNA1	3 534 bp	73.3	0.00E+00	Fusarium graminearum alternavirus 1（YP_009449439.1）	dsRNA	Alternaviridae	1
Contig22686	Colletotrichum fioriniae alternavirus 1	CfAV1 dsRNA3	2 454 bp	72	3.00E-307	Fusarium graminearum alternavirus 1（AUI80777.1）	dsRNA	Alternaviridae	1
Contig51809	Colletotrichum fioriniae narnavirus 1	CfNV1	1 136 nt	59.28	3.00E-76	Sclerotinia sclerotiorum narnavirus 2（QZE12028.1）	+ssRNA	Narnaviridae	1
Contig26097	Colletotrichum siamense narnavirus 1	CsNV1	2 239 nt	65.3	0.00E+00	Sclerotinia sclerotiorum narnavirus 2（QZE12027.1）	+ssRNA	Narnaviridae	1
Contig20122	Colletotrichum siamense narnavirus 2	CsNV2	2 420 nt	33.2	8.00E-88	Oidiodendron maius splipalmivirus 1（QNN89180.1）	+ssRNA	Narnaviridae	1
Contig11676	Colletotrichum nymphaeae narnavirus 1	CnNV1	3 090 nt	65	0.00E+00	Botryosphaeria dothidea narnavirus 3（QQD86177.1）	+ssRNA	Narnaviridae	5
Contig10410	Colletotrichum fioriniae narnavirus 2	CfNV2	3 619 nt	55.3	0.00E+00	Erysiphe necator associated narnavirus 15（QJT93747.1）	+ssRNA	Narnaviridae	1
Contig19559	Colletotrichum nymphaeae narnavirus 2	CnNV2	2 455 nt	62.2	1.00E-278	Erysiphe necator associated narnavirus 4（QHD64827.1）	+ssRNA	Narnaviridae	2
Contig4718	Colletotrichum gloeosporioides narnavirus 1	CgNV1	4 200 nt	51.8	1.60E-300	Monilinia narnavirus H （QED42934.1）	+ssRNA	Narnaviridae	3
Contig35776	Colletotrichum fructicola narnavirus 1	CfrNV1	1 689 nt	60	1.00E-27	Aspergillus lentulus narnavirus 1（BCH36644.1）	+ssRNA	Narnaviridae	2
Contig19474	Colletotrichum fructicola botourmiavirus 1	CfBV1	2 460 nt	55.1	1.60E-178	Pestalotiopsis botourmiavirus 3（QTH80197.1）	+ssRNA	Botourmiaviridae	2
Contig22684	Colletotrichum fioriniae mitovirus 1	CfMV1	2 455 nt	51.7	4.00E-158	Grapevine-associated mitovirus 10（QXN75363.1）	+ssRNA	Mitoviridae	2
Contig41113	Colletotrichum fioriniae mitovirus 2	CfMV2	1 493 nt	78	9.10E-113	Rhizoctonia solani mitovirus 33（QDW65423.1）	+ssRNA	Mitoviridae	1
Contig55502	Colletotrichum fioriniae mitovirus 3	CfMV3	1 012 nt	68.2	1.50E-29	Rhizoctonia solani mitovirus 33（QDW65423.1）	+ssRNA	Mitoviridae	1
Contig3026	Colletotrichum gloeosporioides mitovirus 1	CgMV1	4 742 nt	91.4	4.20E-236	Colletotrichum fructicola mitovirus 1（BBN51032.1）	+ssRNA	Mitoviridae	1
Contig18460	Colletotrichum fructicola mitovirus 1	CfrMV1	2 520 nt	94.5	0.00E+00	Colletotrichum fructicola mitovirus 1（BBN51032.1）	+ssRNA	Mitoviridae	4
Contig42866	Colletotrichum siamense mitovirus 3	CsMV3	1 462 nt	93.1	4.20E-211	Colletotrichum fructicola mitovirus 1（BBN51032.1）	+ssRNA	Mitoviridae	5
Contig46248	Colletotrichum fioriniae mitovirus 5	CfMV4	1 337 nt	89.4	2.90E-227	Colletotrichum fructicola mitovirus 1（BBN51032.1）	+ssRNA	Mitoviridae	5
Contig46871	Colletotrichum gloeosporioides mitovirus 2	CgMV2	1 313 nt	92.4	1.30E-75	Colletotrichum fructicola mitovirus 1（BBN51032.1）	+ssRNA	Mitoviridae	5
Contig50030	Colletotrichum nymphaeae mitovirus 1	CnMV1	1 197 nt	94.9	3.90E-66	Colletotrichum fructicola mitovirus 1（BBN51032.1）	+ssRNA	Mitoviridae	5
Contig23629	Colletotrichum fioriniae mitovirus 6	CfMV5	2 393 nt	67.2	2.30E-259	Colletotrichum falcatum mitovirus 1（AZT88621.1）	+ssRNA	Mitoviridae	1
Contig21451	Colletotrichum siamense mitovirus 2	CsMV2	2 539 nt	65.2	1.20E-258	Sclerotinia sclerotiorum mitovirus 32（AWY10990.1）	+ssRNA	Mitoviridae	2
Contig21504	Colletotrichum siamense mitovirus 1	CsMV1	2 536 nt	65.5	1.5E-208	Sclerotinia sclerotiorum mitovirus 6（QGY72611.1）	+ssRNA	Mitoviridae	1

Contig 编号 Contig code	病毒名称 Name of putative viruses	病毒名称缩写 Name abbreviation	长度 Length	序列相似度 Acid similarity/%	E值 E-value	最佳匹配 Best match	基因组类型 Genome type	病毒科 Family	Contig 计数 Contig counts
Contig 22546	Colletotrichum fioriniae alternavirus 1	CfAV1 dsRNA2	2 463 bp	70.4	3.50E-303	Fusarium graminearum alternavirus 1（YP_009449446.1）	dsRNA	Alternaviridae	1
Contig11036	Colletotrichum fioriniae alternavirus 1	CfAV1 dsRNA1	3 534 bp	73.3	0.00E+00	Fusarium graminearum alternavirus 1（YP_009449439.1）	dsRNA	Alternaviridae	1
Contig22686	Colletotrichum fioriniae alternavirus 1	CfAV1 dsRNA3	2 454 bp	72	3.00E-307	Fusarium graminearum alternavirus 1（AUI80777.1）	dsRNA	Alternaviridae	1
Contig51809	Colletotrichum fioriniae narnavirus 1	CfNV1	1 136 nt	59.28	3.00E-76	Sclerotinia sclerotiorum narnavirus 2（QZE12028.1）	+ssRNA	Narnaviridae	1
Contig26097	Colletotrichum siamense narnavirus 1	CsNV1	2 239 nt	65.3	0.00E+00	Sclerotinia sclerotiorum narnavirus 2（QZE12027.1）	+ssRNA	Narnaviridae	1
Contig20122	Colletotrichum siamense narnavirus 2	CsNV2	2 420 nt	33.2	8.00E-88	Oidiodendron maius splipalmivirus 1（QNN89180.1）	+ssRNA	Narnaviridae	1
Contig11676	Colletotrichum nymphaeae narnavirus 1	CnNV1	3 090 nt	65	0.00E+00	Botryosphaeria dothidea narnavirus 3（QQD86177.1）	+ssRNA	Narnaviridae	5
Contig10410	Colletotrichum fioriniae narnavirus 2	CfNV2	3 619 nt	55.3	0.00E+00	Erysiphe necator associated narnavirus 15（QJT93747.1）	+ssRNA	Narnaviridae	1
Contig19559	Colletotrichum nymphaeae narnavirus 2	CnNV2	2 455 nt	62.2	1.00E-278	Erysiphe necator associated narnavirus 4（QHD64827.1）	+ssRNA	Narnaviridae	2
Contig4718	Colletotrichum gloeosporioides narnavirus 1	CgNV1	4 200 nt	51.8	1.60E-300	Monilinia narnavirus H （QED42934.1）	+ssRNA	Narnaviridae	3
Contig35776	Colletotrichum fructicola narnavirus 1	CfrNV1	1 689 nt	60	1.00E-27	Aspergillus lentulus narnavirus 1（BCH36644.1）	+ssRNA	Narnaviridae	2
Contig19474	Colletotrichum fructicola botourmiavirus 1	CfBV1	2 460 nt	55.1	1.60E-178	Pestalotiopsis botourmiavirus 3（QTH80197.1）	+ssRNA	Botourmiaviridae	2
Contig22684	Colletotrichum fioriniae mitovirus 1	CfMV1	2 455 nt	51.7	4.00E-158	Grapevine-associated mitovirus 10（QXN75363.1）	+ssRNA	Mitoviridae	2
Contig41113	Colletotrichum fioriniae mitovirus 2	CfMV2	1 493 nt	78	9.10E-113	Rhizoctonia solani mitovirus 33（QDW65423.1）	+ssRNA	Mitoviridae	1
Contig55502	Colletotrichum fioriniae mitovirus 3	CfMV3	1 012 nt	68.2	1.50E-29	Rhizoctonia solani mitovirus 33（QDW65423.1）	+ssRNA	Mitoviridae	1
Contig3026	Colletotrichum gloeosporioides mitovirus 1	CgMV1	4 742 nt	91.4	4.20E-236	Colletotrichum fructicola mitovirus 1（BBN51032.1）	+ssRNA	Mitoviridae	1
Contig18460	Colletotrichum fructicola mitovirus 1	CfrMV1	2 520 nt	94.5	0.00E+00	Colletotrichum fructicola mitovirus 1（BBN51032.1）	+ssRNA	Mitoviridae	4
Contig42866	Colletotrichum siamense mitovirus 3	CsMV3	1 462 nt	93.1	4.20E-211	Colletotrichum fructicola mitovirus 1（BBN51032.1）	+ssRNA	Mitoviridae	5
Contig46248	Colletotrichum fioriniae mitovirus 5	CfMV4	1 337 nt	89.4	2.90E-227	Colletotrichum fructicola mitovirus 1（BBN51032.1）	+ssRNA	Mitoviridae	5
Contig46871	Colletotrichum gloeosporioides mitovirus 2	CgMV2	1 313 nt	92.4	1.30E-75	Colletotrichum fructicola mitovirus 1（BBN51032.1）	+ssRNA	Mitoviridae	5
Contig50030	Colletotrichum nymphaeae mitovirus 1	CnMV1	1 197 nt	94.9	3.90E-66	Colletotrichum fructicola mitovirus 1（BBN51032.1）	+ssRNA	Mitoviridae	5
Contig23629	Colletotrichum fioriniae mitovirus 6	CfMV5	2 393 nt	67.2	2.30E-259	Colletotrichum falcatum mitovirus 1（AZT88621.1）	+ssRNA	Mitoviridae	1
Contig21451	Colletotrichum siamense mitovirus 2	CsMV2	2 539 nt	65.2	1.20E-258	Sclerotinia sclerotiorum mitovirus 32（AWY10990.1）	+ssRNA	Mitoviridae	2
Contig21504	Colletotrichum siamense mitovirus 1	CsMV1	2 536 nt	65.5	1.5E-208	Sclerotinia sclerotiorum mitovirus 6（QGY72611.1）	+ssRNA	Mitoviridae	1

菌株Strain	种名Species	携带病毒名称Contained mycoviruses
BK1-11	C. nymphaeae	CfMV4,CnNV2,CsNV1, CfAV1,CfMV1,CfMV2,CnMV1
BK2-1	C. fructicola	CfMV4,CsNV1,CfBV1,CfMV1,CfMV2
BK2-3	C. fioriniae	CfMV2,CfMV3,CfMV4,CfMV5,CfNV1,CfMV1
BK3-5	C. fioriniae	CfMV2,CfMV3,CfNV2,CfBV1
BK4-4	C. nymphaeae	CfMV2,CsMV3,CgMV2,CfAV1,CnNV1,CfMV1
CX1	C. fioriniae	CfMV2
CX3	C. fioriniae	CfMV2,CfMV4,CnNV1,CfMV1
CX6	C. fructicola	CfrMV1,CfMV4,CsMV2,CnNV1,CfBV1,CfMV1,CsNV1
CX7	C. fioriniae	CfAV1,CfMV1,CfMV3,CfMV2
DJ1-1	C. gloeosporioides	CfMV2,CfMV3
DJ2-1	C. gloeosporioide	CfrMV1,CgNV1,CsNV1,CnNV1,CfBV1,CfMV1,CfMV3,CfMV2
DJ2-4	C. gloeosporioide	CgMV1,CfrMV1,CfMV4,CfMV1,CfMV3,CfMV2,CfNV1
DJ3-5	C. siamense	CsMV3,CfMV4,CfMV5,CsMV2,CsNV1,CfNV1,CfMV1,CfMV3,CfMV2
FX1-3	C. fructicola	CsMV3,CfMV4,CfMV5,CsMV2,CfMV3,CfNV2,CsNV1,CfNV1,CfAV1,CfMV1,CfMV2
SZ2-3	C. gloeosporioides	CgMV2,CsMV2,CgNV1,CsNV1,CfNV1,CnNV1,CfMV1,CfMV2
XS5	C. nymphaeae	CsMV3,CfMV1,CfrMV1,CsMV1,CfrNV1,CfMV2
XS6	C. fructicola	CsMV3,CfNV2,CfrNV1,CsNV1,CnNV1,CfMV1,CfMV2
YX1-5	C. siamense	CfMV2,CgMV1,CfrMV1,CfMV4,CfMV5,CsMV2,CfNV1,CnNV1,CfBV1,CfMV1
YX1-7	C. siamense	CfMV2,CfrMV1,CfMV4,CfrNV1,CsNV2,CsNV1,CfAV1,CnNV1,CfMV1,CfBV1
YY1-11	C. gloeosporioides	CfMV3,CfMV2,CfrMV1,CfMV4,CgMV2,CfMV5,CsMV1,CnNV2,CsNV1,CnNV1,CfMV1
YY1-28	C. fructicola	CfrMV1,CfMV1,CfMV3,CfMV2
ZS3-8	C. nymphaeae	CfrNV1,CfMV1,CfMV2
ZS2-6	C. nymphaeae	CgMV2,CsMV2,CnNV2,CfrNV1,CsNV1,CfMV2
ZS2-9	C. siamense	CgMV1,CfMV4,CsMV2,CsMV1,CnNV2,CsNV2,CfAV1,CnNV1,CfBV1,CfMV1
ZS3-13	C. nymphaeae	CsNV1,CfMV2