Analysis and Identification of Endogenous Viral Elements in Solanaceous Crop Genome

doi:10.16420/j.issn.0513-353x.2022-1197

Acta Horticulturae Sinica ›› 2024, Vol. 51 ›› Issue (1): 190-202.doi: 10.16420/j.issn.0513-353x.2022-1197

• Plant Protection • Previous Articles Next Articles

Analysis and Identification of Endogenous Viral Elements in Solanaceous Crop Genome

CHEN Ruhao¹, MENG Fanye¹, YANG Manhua¹, CHEN Jiaru¹, ZOU Ying², SONG Botao¹, MA Hui³, NIE Bihua¹^,^*()

¹ National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops/Key Laboratory of Potato Biology and Biotechnology，Ministry of Agriculture and Rural Affairs/College of Horticulture and Forestry，Huazhong Agricultural University，Wuhan 430070，China
² Enshi Tujia and Miao Autonomous Prefecture Academy of Agricultural Sciences/Southern China Potato Research Center in Enshi of Hubei，Enshi，Hubei 445000，China
³ Zhangjiakou Academy of Agriculture Sciences，Zhangjiakou，Hebei 075000，China

Received:2023-03-03 Revised:2023-10-23 Online:2024-01-25 Published:2024-01-16
Contact: * （E-mail：nbihua@mail.hzau.edu.cn）

Abstract

Abstract:

In this study，an analysis of endogenous virus elements（EVEs）were conducted from 35 open genome data sequences of six Solanaceae species，resulting in the identification of 17 suspected plant EVEs primarily from Caulmoviridae. The analysis revealed that TVCV sequences were present as large fragments in nearly all sampled Solanaceae genomes，with a content ranging from 0.01% to 0.32%，an average length of 500 bp to 2 300 bp and a total number of sequences ranging from 200 to 5 000. Additionally，the distribution and composition of endogenous TVCV sequences were investigated in the potato DM1-3 genome. The results found they were dispersed across 12 chromosomes with an average of 57 sequences on each chromosome. These endogenous sequences were compared with the TVCV genome，and although they did not cover the complete genome sequence of TVCV，they covered the complete coding region. Furthermore，the presence and distribution of TVCV were comfirmed in potato materials by RT-PCR followed by in situ hybridization.

Key words: Solanaceous, potato, genomes, endogenous viral element, tobacco vein clearing virus

CHEN Ruhao, MENG Fanye, YANG Manhua, CHEN Jiaru, ZOU Ying, SONG Botao, MA Hui, NIE Bihua. Analysis and Identification of Endogenous Viral Elements in Solanaceous Crop Genome[J]. Acta Horticulturae Sinica, 2024, 51(1): 190-202.

Figures/Tables 7

References 46

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引物名称 Primer name	引物序列 Primer sequences	大小/bp Size	引物类型 Primer type	特异性前引物 + 特异性后引物 Forward + reverse
TVCV-1F	CACACTGGTGGTTCACAACACCATG	396	基因内引物 Inner primers	TVCV + TVCV
TVCV-1R	GGGCTTGTATGCTTACTATTGC	396	基因内引物 Inner primers	TVCV + TVCV
TVCV-2F	CACCAATGATAGATACGGGAGC	506	基因内引物 Inner primers	TVCV + TVCV
TVCV-2R	CCCATCCTTGTAAAGGATCTTCAC	506	基因内引物 Inner primers	TVCV + TVCV
TVCV-3F	CACCAATGATAGATACGGGAGC	294	基因内引物 Inner primers	TVCV + TVCV
TVCV-3R	CATGGTGTTGTGAACCACCAGTGTG	294	基因内引物 Inner primers	TVCV + TVCV
TVCV-UF	ATGCTCTTGTCGTAGGTCG	1 014	跨基因引物 Gene-spanning primers	TVCV上游基因 + TVCV Gene-specific primers upstream of TVCV + TVCV
TVCV-UR	GTGGACAGTATGGACAATGAGATAC	1 014	跨基因引物 Gene-spanning primers
TVCV-DF	AGTGGATAGTATGGACAACG	716	跨基因引物 Gene-spanning primers	TVCV + TVCV下游基因 Gene-specific primers upstream of TVCV + TVCV specific primers
TVCV-DR	TCTTTACAACTTGTATCGGAGG	716	跨基因引物 Gene-spanning primers

引物名称 Primer name	引物序列 Primer sequences	大小/bp Size	引物类型 Primer type	特异性前引物 + 特异性后引物 Forward + reverse
TVCV-1F	CACACTGGTGGTTCACAACACCATG	396	基因内引物 Inner primers	TVCV + TVCV
TVCV-1R	GGGCTTGTATGCTTACTATTGC	396	基因内引物 Inner primers	TVCV + TVCV
TVCV-2F	CACCAATGATAGATACGGGAGC	506	基因内引物 Inner primers	TVCV + TVCV
TVCV-2R	CCCATCCTTGTAAAGGATCTTCAC	506	基因内引物 Inner primers	TVCV + TVCV
TVCV-3F	CACCAATGATAGATACGGGAGC	294	基因内引物 Inner primers	TVCV + TVCV
TVCV-3R	CATGGTGTTGTGAACCACCAGTGTG	294	基因内引物 Inner primers	TVCV + TVCV
TVCV-UF	ATGCTCTTGTCGTAGGTCG	1 014	跨基因引物 Gene-spanning primers	TVCV上游基因 + TVCV Gene-specific primers upstream of TVCV + TVCV
TVCV-UR	GTGGACAGTATGGACAATGAGATAC	1 014	跨基因引物 Gene-spanning primers
TVCV-DF	AGTGGATAGTATGGACAACG	716	跨基因引物 Gene-spanning primers	TVCV + TVCV下游基因 Gene-specific primers upstream of TVCV + TVCV specific primers
TVCV-DR	TCTTTACAACTTGTATCGGAGG	716	跨基因引物 Gene-spanning primers

病毒名称 Virus name	病毒ID Virus ID	科 Family	属 Genus	检出率/ Detec- tion rate	总数 Total number	总长/bp Total length	平均长/bp Average length	检出基因组 Genome containing the virus
烟草脉明病毒 Tobacco vein clearing virus	NC_003378.1	花椰菜病毒科 Caulimoviridae	木薯脉花叶病毒属Cavemovirus	94.3 (33/35)	45 733	57 538 756	1 258	几乎所有基因组 Almost all genomes
花生褪绿条纹病毒 Peanut chlorotic streak virus	NC_001634.1	花椰菜病毒科 Caulimoviridae	大豆褪绿斑驳病毒属Soymovirus	2.8 (1/35)	5	4 220	844	本氏烟草 Nicotiana benthamiana
金黄球藻病毒 Chrysochromulina ericina virus	NC_028094.1	藻类DNA病毒科 Phycodnaviridae	未分类 Unclassified	48.6 (17/35)	48	35 546	741	烟草、茄子、矮牵牛 Tobacco，eggplant，petunia
矮牵牛清脉病毒 Petunia vein clearing virus	NC_001839.2	花椰菜病毒科 Caulimoviridae	碧冬茄病毒属 Petuvirus	40.0 (14/35)	892	550 159	617	烟草、矮牵牛 Tobacco，petunia
木薯脉花叶病毒 Cassava vein mosaic virus	NC_001648.1	花椰菜病毒科 Caulimoviridae	木薯脉花叶病毒属Cavemovirus	28.6 (10/35)	63	22 235	353	马铃薯、番茄、辣椒、茄子Potato，tomato，pepper，eggplant
甘薯清脉病毒 Sweet potato vein clearing virus	NC_015228.1	花椰菜病毒科 Caulimoviridae	索伦病毒属Solendovirus	25.7 (9/35)	112	26 347	235	番茄、烟草 Tomato，tobacco
棉花曲叶木尔坦病毒 Cotton leaf curl Multan virus	NC_007721.1	双生病毒科 Geminiviridae	菜豆金色花叶病毒Begomovirus	22.9 (8/35)	1 590	351 770	221	烟草 Tobacco
尤卡坦黄斑病毒 Capraria yellow spot Yucatan virus	NC_022007.1	双生病毒科 Geminiviridae	菜豆金色花叶病毒Begomovirus	11.4 (4/35)	20	4 308	215	普通烟草 Nicotiana tabacum
甘薯茎状病毒 Sweet potato caulimo- Like virus	NC_015328.1	花椰菜病毒科 Caulimoviridae	木薯脉花叶病毒属Cavemovirus	14.3 (5/35)	113	20 335	180	茄子、辣椒、马铃薯 Eggplant，pepper，potato
棉皱叶病毒 Cotton leaf crumple virus	NC_004580.1	双生病毒科 Geminiviridae	菜豆金色花叶病毒Begomovirus	11.4 (4/35)	34	4 700	138	普通烟草 Nicotiana tabacum
马铃薯卷叶病毒 Potato leafroll virus	NC_001747.1	黄症病毒科 Luteoviridae	马铃薯卷叶病毒属Polerovirus	48.6 (17/35)	155	16 283	105	辣椒、烟草、矮牵牛 Pepper，tobacco， petunia
香蕉条纹ca病毒 Banana streak ca Virus	NC_015506.1	花椰菜病毒科 Caulimoviridae	杆状DNA病毒属Badnavirus	11.4 (4/35)	18	831	46	辣椒、矮牵牛 Pepper，petunia
柑橘内源副逆转录病毒citrus endogenous Pararetrovirus	NC_023153.1	逆转录病毒科 Retroviridae	未知 Unknown	54.3 (19/35)	444	19 616	44	烟草、矮牵牛、番茄 Tobacco，petunia， Tomato
大丽花花叶病毒 Dahlia mosaic virus	NC_018616.1	花椰菜病毒科 Caulimoviridae	花椰菜花叶病毒属Caulimovirus	22.9 (8/35)	45	1 799	40	辣椒、矮牵牛、马铃薯Pepper，petunia， potato
香蕉条纹糠秕病毒 Banana streak Mysore virus	NC_006955.1	花椰菜病毒科 Caulimoviridae	杆状DNA病毒属Badnavirus	2.8 (1/35)	4	139	35	马铃薯品种 Solanum tuberosum commersonii
天竺葵脉带病毒 Pelargonium vein Banding virus	NC_013262.1	花椰菜病毒科 Caulimoviridae	杆状DNA病毒属Badnavirus	5.7 (2/35)	4	144	36	醋栗番茄 Solanum pimpinellifolium
水稻东格鲁杆状病毒 Rice tungro bacilliform virus	NC_001914.1	花椰菜病毒科 Caulimoviridae	东格鲁病毒属 Tungrovirus	11.4 (4/35)	15	495	33	烟草Tobacco

病毒名称 Virus name	病毒ID Virus ID	科 Family	属 Genus	检出率/ Detec- tion rate	总数 Total number	总长/bp Total length	平均长/bp Average length	检出基因组 Genome containing the virus
烟草脉明病毒 Tobacco vein clearing virus	NC_003378.1	花椰菜病毒科 Caulimoviridae	木薯脉花叶病毒属Cavemovirus	94.3 (33/35)	45 733	57 538 756	1 258	几乎所有基因组 Almost all genomes
花生褪绿条纹病毒 Peanut chlorotic streak virus	NC_001634.1	花椰菜病毒科 Caulimoviridae	大豆褪绿斑驳病毒属Soymovirus	2.8 (1/35)	5	4 220	844	本氏烟草 Nicotiana benthamiana
金黄球藻病毒 Chrysochromulina ericina virus	NC_028094.1	藻类DNA病毒科 Phycodnaviridae	未分类 Unclassified	48.6 (17/35)	48	35 546	741	烟草、茄子、矮牵牛 Tobacco，eggplant，petunia
矮牵牛清脉病毒 Petunia vein clearing virus	NC_001839.2	花椰菜病毒科 Caulimoviridae	碧冬茄病毒属 Petuvirus	40.0 (14/35)	892	550 159	617	烟草、矮牵牛 Tobacco，petunia
木薯脉花叶病毒 Cassava vein mosaic virus	NC_001648.1	花椰菜病毒科 Caulimoviridae	木薯脉花叶病毒属Cavemovirus	28.6 (10/35)	63	22 235	353	马铃薯、番茄、辣椒、茄子Potato，tomato，pepper，eggplant
甘薯清脉病毒 Sweet potato vein clearing virus	NC_015228.1	花椰菜病毒科 Caulimoviridae	索伦病毒属Solendovirus	25.7 (9/35)	112	26 347	235	番茄、烟草 Tomato，tobacco
棉花曲叶木尔坦病毒 Cotton leaf curl Multan virus	NC_007721.1	双生病毒科 Geminiviridae	菜豆金色花叶病毒Begomovirus	22.9 (8/35)	1 590	351 770	221	烟草 Tobacco
尤卡坦黄斑病毒 Capraria yellow spot Yucatan virus	NC_022007.1	双生病毒科 Geminiviridae	菜豆金色花叶病毒Begomovirus	11.4 (4/35)	20	4 308	215	普通烟草 Nicotiana tabacum
甘薯茎状病毒 Sweet potato caulimo- Like virus	NC_015328.1	花椰菜病毒科 Caulimoviridae	木薯脉花叶病毒属Cavemovirus	14.3 (5/35)	113	20 335	180	茄子、辣椒、马铃薯 Eggplant，pepper，potato
棉皱叶病毒 Cotton leaf crumple virus	NC_004580.1	双生病毒科 Geminiviridae	菜豆金色花叶病毒Begomovirus	11.4 (4/35)	34	4 700	138	普通烟草 Nicotiana tabacum
马铃薯卷叶病毒 Potato leafroll virus	NC_001747.1	黄症病毒科 Luteoviridae	马铃薯卷叶病毒属Polerovirus	48.6 (17/35)	155	16 283	105	辣椒、烟草、矮牵牛 Pepper，tobacco， petunia
香蕉条纹ca病毒 Banana streak ca Virus	NC_015506.1	花椰菜病毒科 Caulimoviridae	杆状DNA病毒属Badnavirus	11.4 (4/35)	18	831	46	辣椒、矮牵牛 Pepper，petunia
柑橘内源副逆转录病毒citrus endogenous Pararetrovirus	NC_023153.1	逆转录病毒科 Retroviridae	未知 Unknown	54.3 (19/35)	444	19 616	44	烟草、矮牵牛、番茄 Tobacco，petunia， Tomato
大丽花花叶病毒 Dahlia mosaic virus	NC_018616.1	花椰菜病毒科 Caulimoviridae	花椰菜花叶病毒属Caulimovirus	22.9 (8/35)	45	1 799	40	辣椒、矮牵牛、马铃薯Pepper，petunia， potato
香蕉条纹糠秕病毒 Banana streak Mysore virus	NC_006955.1	花椰菜病毒科 Caulimoviridae	杆状DNA病毒属Badnavirus	2.8 (1/35)	4	139	35	马铃薯品种 Solanum tuberosum commersonii
天竺葵脉带病毒 Pelargonium vein Banding virus	NC_013262.1	花椰菜病毒科 Caulimoviridae	杆状DNA病毒属Badnavirus	5.7 (2/35)	4	144	36	醋栗番茄 Solanum pimpinellifolium
水稻东格鲁杆状病毒 Rice tungro bacilliform virus	NC_001914.1	花椰菜病毒科 Caulimoviridae	东格鲁病毒属 Tungrovirus	11.4 (4/35)	15	495	33	烟草Tobacco

物种 Species	植物基因组大小/bp Assembly size of plant genome	内源性TVCV Endogenous TVCV				数据库 Data- base
物种 Species	植物基因组大小/bp Assembly size of plant genome	覆盖大小Coverage size	占植物基因组百分比 Percentagein plant genome	数量 Number	平均长度/bp The average length	数据库 Data- base
Capsicum annuum‘CM334’	2 753 501 891	8 829 122	0.320651	5 341	1 653	SOL
Capsicum annuum‘CM334’	3 106 362 892	9 863 964	0.317541	6 379	1 546	NCBI
Capsicum annuum‘Zunla-1’	3 420 028 601	6 640 658	0.194170	4 580	1 450	SOL
Capsicum annuum‘Zunla-1’	2 972 093 730	7 472 302	0.251415	5 139	1 454	NCBI
Capsicum annuum var. glabriusculum	3 586 841 310	3 990 309	0.111249	3 080	1 296	SOL
Capsicum annuum var. glabriusculum	2 803 123 110	4 678 985	0.166920	3 575	1 309	NCBI
Nicotiana benthamiana	3 020 841 706	4 409	0.000146	5	882	SOL
Nicotiana benthamiana	76 127 810	0	0	0	0	NCBI
Nicotiana otophora	2 749 613 483	278 606	0.010133	756	369	SOL
Nicotiana otophora	2 805 105 985	278 606	0.009932	756	369	NCBI
Nicotiana sylvestris	2 258 816 203	321 141	0.014217	564	569	SOL
Nicotiana sylvestris	2 280 242 707	321 141	0.014084	564	569	NCBI
Nicotiana tabacum Basma Xanthi	3 805 503 023	440 123	0.011565	928	474	SOL
Nicotiana tabacum Basma Xanthi	3 854 148 512	440 361	0.011426	931	473	NCBI
Nicotiana tabacum K326 (Flue-cured)	3 799 828 677	463 973	0.012210	991	468	SOL
Nicotiana tabacum K326 (Flue-cured)	3 840 635 360	464 426	0.012092	999	465	NCBI
Nicotiana tabacum TN90 (Burley)	3 772 618 817	624 141	0.016544	1 062	588	SOL
Nicotiana tabacum TN90 (Burley)	3 802 293 918	624 217	0.016417	1 063	587	NCBI
Nicotiana tomentosiformis	1 715 755 740	185 908	0.010835	516	360	SOL
	1 730 121 004	185 908	0.010745	516	360	NCBI
Petunia axillaris N	1 281 752 908	0	0	0	0	SOL
Petunia inflate S6	1 312 457 388	321	0.000024	6	54	SOL
Solanum arcanum LA2157	678 871 964	548 248	0.080759	350	1 566	NCBI
Solanum habrochaites LYC4	738 507 092	986 200	0.133540	554	1 780	NCBI
Solanum lycopersicum Heinz 1706	835 714 844	1 475 086	0.176506	710	2 078	SOL
	834 512 558	1 475 086	0.176760	710	2 078	NCBI
Solanum pennellii LA716	1 003 809 056	1 299 035	0.129411	559	2 324	SOL
Solanum pennellii LA716	938 007 464	1 238 991	0.132088	519	2 387	NCBI
Solanum pimpinellifolium LA1589	716 421 466	274 456	0.038309	481	571	SOL
Solanum pimpinellifolium LA1589	728 838 890	274 465	0.037658	481	571	NCBI
Solanum tuberosum DM1-3	735 374 925	697 015	0.094784	684	1 019	SOL
Solanum tuberosum DM1-3	716 822 822	852 693	0.118954	840	1 015	NCBI
Solanum commersonii	744 831 912	2 080 946	0.279385	1 652	1 260	NCBI
Solanum melongena	847 552 547	113 957	0.013445	221	516	SOL
Solanum melongena	846 607 191	113 957	0.013460	221	516	NCBI

Analysis and Identification of Endogenous Viral Elements in Solanaceous Crop Genome

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