RNA-Seq Reveals Hawthorn Tree as a New Natural Host for Apple Necrotic Mosaic Virus, Possibly Associated with Hawthorn Mosaic Disease

Apple mosaic disease is widespread in the major apple-producing areas in China and is frequently associated with the presence of the newly identified Apple necrotic mosaic virus (ApNMV), belonging to subgroup 3 of Ilarvirus genus in the family of Bromoviridae. Mosaic symptoms were also observed in a hawthorn tree. Deep sequencing revealed the hawthorn tree with mosaic symptom was infected by ApNMV, which was confirmed by RT-PCR. The complete nucleotide sequences of RNA1 (3,378 nt), RNA2 (2,778 nt), and RNA3 (1,917 nt) of ApNMV from the hawthorn were obtained, sharing 93.8 to 96.8%, 89.7 to 96.1%, and 89.8 to 94.6% nucleotide identities with those from apples and crabapples, respectively. Two hypervariable regions were found, which showed 59.2 to 85.7% and 64.0 to 89.3% sequence identities at position 142 to 198 aa and at position 780 to 864 aa in the POL protein, respectively, between the hawthorn isolate and other isolates (apple, crabapple). A grafting test demonstrated that ApNMV was easily transmissible from hawthorns to apple trees, with severe chlorosis, yellowing, mosaic, curling, and necrosis. In addition, a total of 11,685 hawthorn trees were surveyed for the incidence of mosaic disease from five provinces in China, and only six were found showing typical mosaic symptoms. A total of 145 individual trees (six symptomatic, 68 asymptomatic, and 71 other symptoms) were tested for the presence or absence of ApNMV by RT-PCR. Among them, six symptomatic, four asymptomatic, and 10 other symptomatic trees tested positive for ApNMV. Taken together, these results demonstrated that the hawthorn tree was identified as a new natural host for ApNMV with a relatively low frequency (13.8%, 20 out of 145) in the main producing areas, and it was likely to be the causal pathogen of hawthorn mosaic disease.

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Incidence and Molecular Identification of Apple Necrotic Mosaic Virus (ApNMV) in Southwest China

Plants ◽

10.3390/plants9040415 ◽

2020 ◽

Vol 9 (4) ◽

pp. 415

Author(s):

Wensen Shi ◽

Rundong Yao ◽

Runze Sunwu ◽

Kui Huang ◽

Zhibin Liu ◽

...

Keyword(s):

Mosaic Virus ◽

Southwest China ◽

Great Influence ◽

Mosaic Disease ◽

Pcr Analysis ◽

Rt Pcr ◽

Apple Trees ◽

Apple Leaves ◽

Prunus Necrotic Ringspot Virus ◽

Apple Production

Apple mosaic disease has a great influence on apple production. In this study, an investigation into the incidence of apple mosaic disease in southwest China was performed, and the pathogen associated with the disease was detected. The results show that 2869 apple trees with mosaic disease were found in the Sichuan, Yunnan, and Guizhou Provinces, with an average incidence of 9.6%. Although apple mosaic virus (ApMV) is widespread in apples worldwide, the diseased samples were negative when tested for ApMV. However, a novel ilarvirus (apple necrotic mosaic virus, ApNMV) was identified in mosaic apple leaves which tested negative for ApMV. RT-PCR analysis indicated that ApNMV was detected in 322 out of 357 samples with mosaic symptoms. Phylogenetic analysis of coat protein (CP) sequences of ApNMV isolates suggested that, compared with ApMV, ApNMV was closer to prunus necrotic ringspot virus (PNRSV). The CP sequences of the isolates showed the diversity of ApNMV, which may enable the virus to adapt to the changeable environments. In addition, the pathology of mosaic disease was observed by microscope, and the result showed that the arrangement of the tissue and the shape of the cell, including the organelle, were seriously destroyed or drastically changed.

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Characterization of a highly divergent Sugarcane mosaic virus from Canna indica L. by deep sequencing

BMC Microbiology ◽

10.1186/s12866-019-1636-y ◽

2019 ◽

Vol 19 (1) ◽

Cited By ~ 1

Author(s):

Yongqiang Li ◽

Fei Xia ◽

Yixuan Wang ◽

Chenge Yan ◽

Anning Jia ◽

...

Keyword(s):

Mosaic Virus ◽

Deep Sequencing ◽

Viral Disease ◽

Mosaic Disease ◽

Sugarcane Mosaic Virus ◽

Full Genome Sequence ◽

Mosaic Symptom ◽

Cdna Clones ◽

Pathogenicity Test ◽

Sequence Identities

Abstract Background Cannas are popular ornamental plants and widely planted for the beautiful foliage and flower. Viral disease is a major threaten to canna horticulture industry. In the city of Beijing, mosaic disease in canna was frequently observed, but the associated causal agent and its biological characterization is still unknown. Results After small RNA deep sequencing, 36,776 contigs were assembled and 16 of them shared high sequence identities with the different proteins of Sugarcane mosaic virus (SCMV) of the size ranging from 86 to 1911 nt. The complete genome of SCMV isolate (canna) was reconstructed by sequencing all cDNA clones obtained from RT-PCR and 5′\3′ RACE amplifications. SCMV-canna isolate showed to have a full RNA genome of 9579 nt in length and to share 78% nt and 85% aa sequence identities with SCMV isolates from other hosts. The phylogenetic tree constructed based on the full genome sequence of SCMV isolates allocated separately the canna-isolate in a distinct clade, indicating a new strain. Recombination analyses demonstrated that SCMV-canna isolate was a recombinant originating from a sugarcane-infecting isolate (major parent, acc. no. AJ310103) and a maize-infecting isolate (minor parent, acc. no. AJ297628). Pathogenicity test showed SCMV-canna could cause typical symptoms of mosaic and necrosis in some tested plants with varying levels of severity but was less virulent than the isolate SCMV-BJ. Field survey showed that the virus was widely distributed. Conclusions This study identified SCMV as the major agent causing the prevalent mosaic symptom in canna plants in Beijing and its genomic and biological characterizations were further explored. All these data enriched the knowledge of the viruses infecting canna and would be helpful in effective disease management in canna.

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Genetic Diversity Among Viruses Associated with Sugarcane Mosaic Disease in Tucumán, Argentina

Phytopathology ◽

10.1094/phyto-99-1-0038 ◽

2009 ◽

Vol 99 (1) ◽

pp. 38-49 ◽

Cited By ~ 19

Author(s):

M. F. Perera ◽

M. P. Filippone ◽

C. J. Ramallo ◽

M. I. Cuenya ◽

M. L. García ◽

...

Keyword(s):

Genetic Diversity ◽

Mosaic Virus ◽

Fragment Length Polymorphism ◽

Rflp Analysis ◽

Mosaic Disease ◽

Rt Pcr ◽

Rflp Profile ◽

Pcr Rflp ◽

Polymerase Chain ◽

Sugarcane Mosaic Disease

Sugarcane leaves with mosaic symptoms were collected in 2006–07 in Tucumán (Argentina) and analyzed by reverse-transcriptase polymerase chain reaction (RT-PCR) restriction fragment length polymorphism (RFLP) and sequencing of a fragment of the Sugarcane mosaic virus (SCMV) and Sorghum mosaic virus (SrMV) coat protein (CP) genes. SCMV was detected in 96.6% of samples, with 41% showing the RFLP profile consistent with strain E. The remaining samples produced eight different profiles that did not match other known strains. SCMV distribution seemed to be more related to sugarcane genotype than to geographical origin, and sequence analyses of CP genes showed a greater genetic diversity compared with other studies. SrMV was detected in 63.2% of samples and most of these were also infected by SCMV, indicating that, unlike other countries and other Argentinean provinces, where high levels of co-infection are infrequent, co-existence is common in Tucumán. RFLP analysis showed the presence of SrMV strains M (68%) and I (14%), while co-infection between M and H strains was present in 18% of samples. Other SCMV subgroup members and the Sugarcane streak mosaic virus (SCSMV) were not detected. Our results also showed that sequencing is currently the only reliable method to assess SCMV and SrMV genetic diversity, because RT-PCR-RFLP may not be sufficiently discriminating.

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First Report of the Occurrence of African cassava mosaic virus in a Mosaic Disease of Soybean in Nigeria

Plant Disease ◽

10.1094/pdis-92-12-1709b ◽

2008 ◽

Vol 92 (12) ◽

pp. 1709-1709 ◽

Cited By ~ 5

Author(s):

J. U. Mgbechi-Ezeri ◽

O. J. Alabi ◽

R. A. Naidu ◽

P. Lava Kumar

Keyword(s):

Nucleotide Sequence ◽

Host Range ◽

Mosaic Virus ◽

Plant Viruses ◽

Mosaic Disease ◽

Natural Host ◽

Mottle Virus ◽

African Cassava Mosaic Virus ◽

First Report ◽

Cassava Mosaic Virus

African cassava mosaic virus (ACMV; genus Begomovirus, family Geminiviridae) is one of six viruses documented in cassava (Manihot esculenta Crantz.) plants showing cassava mosaic disease in sub-Saharan Africa (SSA). In addition to cassava, the natural host range of ACMV includes a few wild Manihot species, Jatropha multifida, and Ricinus communis L. in Euphorbiaceae, and Hewittia sublobata in Convolvulaceae. The experimental host range of ACMV includes Nicotiana sp. and Datura sp. in the Solanaceae (2). Recently, natural occurrence of ACMV was reported in Combretum confertum (Benth.), Leucana leucocephala (Lam.) De Witt, and Senna occidentalis (L.) Link belonging to Leguminasae from Nigeria (1,3). During reconnaissance studies conducted on soybean (Glycine max L. Merr.) in September and October of 2007 in the Ibadan (N = 19) and Benue (N = 23) regions and in February of 2008 in Ibadan (N = 16), we observed soybean showing yellow mosaic and mottling symptoms. Samples from these plants (N = 58) were tested by indirect ELISA and symptomatic leaves tested negative to Cucumber mosaic virus, Cowpea mottle virus, Southern bean mosaic virus, Tobacco ringspot virus, Soybean dwarf virus, Cowpea aphid-borne mosaic virus, Blackeye cowpea mosaic virus, Peanut mottle virus, and Broad bean mosaic virus, which have been documented in soybean in SSA. However, 8.6% of these samples (5 of 58) (one each from Ibadan and Benue in the 2007 survey and three from Ibadan in the 2008 survey) tested positive in triple-antibody sandwich-ELISA with a monoclonal antibody (SCR33) to ACMV. ELISA results were further confirmed by PCR with ACMV specific primers AL1/F and AR0/R that amplified a 987-bp DNA fragment corresponding to the intergenic region, AC-4 and AC-1 genes of DNA-A segment (4). The PCR product was cloned into pCR2.1 (Invitrogen, Carlsbad, CA) and three independent clones were sequenced in both orientations. Pairwise comparison of the derived consensus sequence (GenBank Accession No. EU367500) with corresponding ACMV sequence of ACMV isolate from Nigeria (GenBank Accession No. X17095) showed 98% identity at the nucleotide level. To further confirm the virus identity, complete nucleotide sequence of the DNA-A segment was determined by PCR amplification of viral DNA with four primers, cloning of overlapping products into pCR2.1 vector and sequencing. The derived sequence (2,781 nucleotides; GenBank Accession No. EU685385) was compared with the DNA sequences available at NCBI database using BLAST. This revealed 97% nucleotide sequence identity with ACMV-[NG:Ogo:90] (Accession No. AJ427910) and ACMV-[NG] (Accession No. X17095) from Nigeria. These results confirm the presence of ACMV in symptomatic soybean leaves. To our knowledge, this is the first report of soybean as a natural host of ACMV in SSA. On the basis of previous reports (1) and the results currently presented it seems that ACMV has a wide host range. References: (1) O. J. Alabi et al. Phytopathology (Abstr.) 97(suppl.):S3, 2007. (2) A. A. Brunt et al., eds. Plant viruses online: Descriptions and lists from the VIDE database. Version 20. Online publication, 1996. (3) F. O. Ogbe et al. Plant Dis. 90:548, 2006; (4) X. Zhou et al. J. Gen. Virol. 78:2101, 1997.

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First Report of Cucumber mosaic virus on Vigna marina in Taiwan

Plant Disease ◽

10.1094/pdis-06-10-0459 ◽

2010 ◽

Vol 94 (10) ◽

pp. 1267-1267 ◽

Cited By ~ 1

Author(s):

T.-C. Deng ◽

C.-H. Tsai ◽

H.-L. Tsai ◽

J.-Y. Liao ◽

W.-C. Huang

Keyword(s):

Cucumber Mosaic Virus ◽

Mosaic Virus ◽

Broad Bean ◽

Solomon Islands ◽

Natural Host ◽

Vector System ◽

Rt Pcr ◽

First Report ◽

Wilt Virus ◽

Broad Bean Wilt Virus

Vigna marina (Burm.) Merr., the dune bean or notched cowpea, is a tropical creeping vine that grows on sand dunes along the coastal regions of Taiwan. Although V. marina is a weed, some varieties are also grown for fodder and food. This legume is a natural host of Bean common mosaic virus in the Solomon Islands (1) and Alfalfa mosaic virus or Beet western yellows virus in Australia (2). In April 2009, plants of V. marina showing severe mosaic and chlorotic ringspots on the foliage were found in the coastal region of Hualien County in eastern Taiwan. Indirect ELISA on a single diseased plant showed positive results with antibodies against the cucumber isolate of Cucumber mosaic virus (CMV) but negative to Broad bean wilt virus-1, Broad bean wilt virus-2, and some potyviruses (Agdia Inc., Elkhart, IN). A pure isolate of CMV was obtained from V. marina through three successive passages of single lesion isolation in sap-inoculated Chenopodium quinoa. Results of mechanical inoculations showed that the CMV-V. marina isolate was successfully transmitted to C. amaranticolor, C. murale, C. quinoa, Chrysanthemum coronarium, Gomphrena globosa, Nicotiana benthamiana, N. tabacum cv. Vam-Hicks, Phaseolus limensis, P. lunatus, P. vulgaris, Tetragonia tetragonioides, V. marina, V. radiata, and V. unguiculata subsp. sesquipedalis. These results of artificial inoculations were confirmed by ELISA. Homologous reactions of the CMV-V. marina isolate with a stock polyclonal antiserum against the CMV-cucumber isolate (4) were observed in sodium dodecyl sulfate-immunodiffusion. To determine the specific CMV subgroup, total RNA was extracted from inoculated leaves of C. quinoa using the Total Plant RNA Extraction Miniprep System (Viogene, Sunnyvale, CA). A DNA fragment of 940 bp covering the 3′ end of the coat protein gene and C-terminal noncoding region of RNA-3 was amplified using the Cucumovirus-specific primers (3) after reverse transcription (RT)-PCR with AccuPower RT/PCR PreMix Kit (Bioneer, Daejeon, Korea). The product was gel purified by Micro-Elute DNA/Clean Extraction Kit (GeneMark Technology Co., Tainan, Taiwan) and cloned in yT&A Cloning Vector System (Yeastern Biotech Co., Taipei, Taiwan) for sequencing (Mission Biotech Co., Taipei, Taiwan) and the sequence was submitted to GenBank (No. HM015286). Pairwise comparisons of the sequence of CMV-V. marina isolate with corresponding sequences of other CMV isolates revealed the maximum (95 to 96%) nucleotide identities with CMV subgroup IB isolates (strains Nt9 and Tfn) compared with 94 to 95% identities with subgroup IA isolates (strains Y and Fny) or 77 to 78% identities with subgroup II (strains LS and Q). These results suggest that CMV is the causal agent for the mosaic disease of V. marina in Taiwan and the isolate belongs to subgroup I. To our knowledge, this is the first report of V. marina as a natural host of CMV. This strain of CMV with specific pathogenicity could threaten crop production in the coastal zones. In addition, V. marina associated with native coastal vegetation was injured by CMV infection, which might lead to ecological impacts on shoreline fading. References: (1) A. A. Brunt. Surveys for Plant Viruses and Virus Diseases in Solomon Islands. FAO, Rome, 1987. (2) C. Büchen-Osmond, ed. Viruses of Plants in Australia. Retrieved from http://www.ictvdb.rothamsted.ac.uk/Aussi/aussi.htm . September, 2002. (3) S. K. Choi et al. J. Virol. Methods 83:67, 1999. (4) S. H. Hseu et al. Plant Prot. Bull. (Taiwan) 29:233, 1987.

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Genetic Diversity of Cucumber Mosaic Virus from Catharanthus roseus, Jasminum sambac, Patchouly, Cubeb and Java-tea

Buletin Penelitian Tanaman Rempah dan Obat ◽

10.21082/bullittro.v31n2.2020.59-66 ◽

2020 ◽

Vol 31 (2) ◽

pp. 59

Author(s):

NFN Miftakhurohmah ◽

Rita Noveriza ◽

Maya Mariana

Keyword(s):

Nucleotide Sequence ◽

Cucumber Mosaic Virus ◽

Mosaic Virus ◽

Catharanthus Roseus ◽

Mosaic Symptom ◽

Rt Pcr ◽

Pcr Assay ◽

Pogostemon Cablin ◽

Polymerase Chain ◽

Jasminum Sambac

Cucumber mosaic virus (CMV) symptoms are found in Catharanthus roseus, patchouly (Pogostemon cablin), cubeb (Piper chaba), Jasminum sambac and Java-tea (Orthosiphon aristatus); however, their genetic characterization has not been studied. The study aimed to molecularly characterize the CMV isolates from Catharanthus roseus, patchouly, cubeb, Jasminum sambac and Java-tea. Disease plant samples showing mosaic and yellow mosaic symptoms were collected from Petak Pamer Garden, ISMCRI, Bogor. Molecular characterization was carried out by reverse transcription-polymerase chain reaction (RT-PCR) assay using a specific primer of CMV coat protein gene and DNA sequenced. Sequence analysis was performed using the BLAST, Bioedit, Genedoc, Mega 5 programs. The RT-PCR technique succeeded in amplifying a DNA band measuring 650 bp, according to the prediction of the primary design. BLAST analyses revealed that all of these CMV isolates belonged to subgroup IB. Nucleotide sequence homology of CMV from C. roseus, patchouly, P. chaba, and J. sambac, were more than 95.00%. Based on the phylogenetic tree, these four isolates were closely related to CMV isolate from Japan (AB070622). Homology of the nucleotide sequence of CMV from Java-tea with the other four isolates was below 95.00%. This isolate clustered with CMV isolate from Indonesia (AB042294) and was separated with another four isolates according to the phylogeny tree. In the amino acid sequence alignment, Java-tea isolates had five different amino acids compared to the other four isolates. This result indicates the possibility of CMV transmission between patchouly, Java-tea, C. roseus and J. sambac, so it must be anticipated to prevent its spread.

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First Report of Watermelon mosaic virus causing a Mosaic Disease on Cucumis metuliferus in China

Plant Disease ◽

10.1094/pdis-12-20-2744-pdn ◽

2021 ◽

Author(s):

Qiang Gao ◽

Hai-long Ren ◽

Wanyu Xiao ◽

Yan Zhang ◽

Bo Zhou ◽

...

Keyword(s):

Mosaic Virus ◽

Direct Sequencing ◽

Rna Extraction ◽

Viral Disease ◽

Complete Sequence ◽

Mosaic Disease ◽

Shanxi Province ◽

Watermelon Mosaic Virus ◽

Rt Pcr ◽

First Report

Cucumis metuliferus, also called horned cucumber or jelly melon, is considered as a wild species in the Cucumis genus and a potential material for nematodes- or viruses-resistant breeding (Provvidenti, et al. 1977; Sigüenza et al. 2005; Chen et al. 2020). This species, originating from Africa, has been cultivated as a fruit in China in recent years. In July 2020, a mosaic disease was observed on C. metuliferus growing in five fields (approximately 0.7 hectare) in Urumqi, Xijiang, China, where more than 85~100% of the field plants exhibited moderate to severe viral disease-like leaf mosaic and/or deformation symptoms. Delayed flowering and small and/or deformed fruits on the affected plants could result in yield loss of about 50%. To identify the causal pathogen, the symptomatic leaf samples were collected from the five fields (five plants/points for each field) and their total RNAs were extracted using a commercial RNA extraction kit. The universal potyviral primers (Ha et al. 2008) and specific primers for a number of frequently-occurring, cucurbit crop-infecting viruses including Papaya ringspot virus (PRSV) (Lin et al. 2013), Cucumber mosaic virus (CMV) and Watermelon mosaic virus (WMV) were designed and used for detection by RT-PCR. The result showed that only the WMV primers (forward: 5’-AAGTGTGACCAAGCTTGGACTGCA-3’ and reverse: 5’-CTCACCCATTGTGCCAAAGAACGT-3’) could amplify the corresponding target fragment from the total RNA templates, and direct sequencing of the RT-PCR products and GenBank BLAST confirmed the presence of WMV (genus Potyvirus) in the collected C. metuliferus samples. To complete Koch’s postulates, the infected C. metuliferus leaves were ground in the sodium phosphate buffer (0.01 M, pH 7.0) and the sap was mechanically inoculated onto 30 four-leaf-stage C. metuliferus seedlings (two leaves for each seedling were inoculated) kept in an insect-proof, temperature-controlled greenhouse at 25~28℃. Twenty-five of the inoculated plants were observed to have apparent leaf mosaic similar to the field symptoms two weeks after inoculation, and positive result was obtained in RT-PCR detection for the symptomatic leaves of inoculated plants using the WMV primers aforementioned, confirming the virus as the pathogen of C. metuliferus in Urumqi. To our knowledge, this is the first report of WMV naturally infecting C. metuliferus in China. We obtained the full-length sequence of the WMV Urumqi isolation (WMV-Urumqi) by sequencing the RT-PCR amplicons from seven pairs of primers spanning the viral genome and the 5’RACE and 3’RACE products. The complete sequence of WMV-Urumqi (GenBank accession no. MW345911) is 10046 nucleotides (nt) long and contains an open reading frame that encodes a polyprotein of 3220 amino acids (aa). WMV-Urumqi shares the highest nt identity (95.9%) and aa identity (98.0%) with the Cucurbita pepo-infecting isolation (KX664483) from Shanxi province, China. Our findings provide a better understanding of the host range and genetic diversity of WMV, and a useful reference for virus-resistant breeding involving C. metuliferus.

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First Report of the Natural Infection of Robinia pseudoacacia with Alfalfa mosaic virus

Plant Disease ◽

10.1094/pdis-12-12-1136-pdn ◽

2013 ◽

Vol 97 (6) ◽

pp. 851-851 ◽

Cited By ~ 2

Author(s):

G. Delibašić ◽

B. Tanović ◽

J. Hrustic ◽

I. Stanković ◽

A. Bulajić ◽

...

Keyword(s):

Mosaic Virus ◽

Black Locust ◽

Natural Infection ◽

Robinia Pseudoacacia ◽

Alfalfa Mosaic Virus ◽

Natural Host ◽

Post Inoculation ◽

Rt Pcr ◽

First Report ◽

Negative Controls

Robinia pseudoacacia L. (family Fabaceae), commonly known as black locust, is native to the southeastern United States, but has been widely planted and naturalized in temperate regions worldwide. In Europe it is often planted alongside streets and in parks, not only because of the dense canopy and impressive flower clusters in spring, but also because it tolerates air pollution well. In June 2012, several black locust trees exhibiting yellow leaf spots accompanied by mottling and leaf deformation were observed in a park in Backa Topola, North Backa District, Serbia. Numerous aphid colonies were found colonizing symptomatic trees. Leaves collected from nine symptomatic and 10 asymptomatic trees were tested for the presence of three common aphid-transmitted viruses, Alfalfa mosaic virus (AMV), Cucumber mosaic virus, and Potato virus Y, using double-antibody sandwich (DAS)-ELISA with commercial polyclonal antibody (Bioreba AG, Reinach, Switzerland). Commercial positive and negative controls and extracts from healthy black locust leaves were included in each assay. AMV was serologically detected in all symptomatic and also in four of the asymptomatic trees, while no other tested viruses were found. Sap from affected leaves of a ELISA-positive sample (373-12) was mechanically inoculated onto five plants each of Chenopodium quinoa and Nicotiana benthamiana using 0.01 M phosphate buffer (pH 7). Symptoms including local chlorotic leaf lesions followed by mosaic on C. quinoa and a bright yellow mosaic on N. benthamiana were observed on all inoculated plants 5 and 10 days post-inoculation, respectively. The identity of the virus was confirmed using reverse transcription (RT)-PCR analysis. Total RNAs from all naturally and mechanically infected plants were isolated using RNeasy Plant Mini Kit (Qiagen, Hilden, Germany). RT-PCR was carried out using the One-Step RT-PCR Kit (Qiagen) with primer pair CP AMV1 and CP AMV2 specific to the partial CP gene and 3′-UTR of AMV RNA 3 (1). Total RNAs from Serbian AMV isolate from alfalfa (GenBank Accession No. FJ527748) and RNA extract from healthy leaves of R. pseudoacacia were used as positive and negative controls, respectively. All tested plants, as well as the positive control, yielded an amplicon of the correct predicted size (751 bp), while no amplicon was recorded in the healthy control. The amplified product of isolate 373-12 was purified with QIAquick PCR Purification Kit (Qiagen) and sequenced on ABI PRISM 3700 DNA analyzer (Macrogen, South Korea) in both directions (KC288155). Pairwise comparison of the 373-12 isolate CP sequence with those available in GenBank, conducted with MEGA5 software (4), revealed the maximum nucleotide identity of 99% (99% amino acid identity) with the soybean isolate (HQ185569) from Tennessee. AMV has a worldwide distribution and its natural host range includes over 150 plant species, including many herbaceous and several woody plants (2). To our knowledge, this is the first report of R. pseudoacacia as a natural host of AMV worldwide. This finding has potentially significant implications for the successful production of susceptible crops, considering that black locust could act as an important link in the epidemiology of AMV as it may serve as a virus reservoir (3). References: (1) M. M. Finetti-Sialer et al. J. Plant Pathol. 79:115, 1997. (2) R. Hull. Comparative Plant Virology. 2nd ed. Elsevier Academic Press, Burlington, MA, 2009. (3) E. E. Muller et al. Plant Dis. 96:506, 2012. (4) K. Tamura et al. Mol. Biol. Evol. 28:2731, 2011.

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Molecular characterization of Mosaic Virus from the cocoa trees showing mosaic symptoms in Yogyakarta, Indonesia

Biodiversitas Journal of Biological Diversity ◽

10.13057/biodiv/d201232 ◽

2019 ◽

Vol 20 (12) ◽

Author(s):

Wiwit Probowati ◽

SUSAMTO SOMOWIYARJO ◽

SEDYO HARTONO

Keyword(s):

Mosaic Virus ◽

Molecular Characterization ◽

National Income ◽

Mosaic Disease ◽

Mosaic Symptom ◽

Pcr Analysis ◽

Sequencing Analysis ◽

Cacao Swollen Shoot Virus ◽

Molecular Characters

Abstact. Probowati W, Somowiyarjo S, Hartono S. 2019. Molecular characterization of Mosaic Virus From the cocoa trees showing mosaic symptoms in Yogyakarta, Indonesia. Biodiversitas 20: 3698-3704. Indonesia is the world's second-biggest producer of cacao after Ivory Coast with its cacao plantations spreads over 1,652 million hectares and mostly managed by smallholders. Cacao as a beneficial commodity can provide job opportunities for over 1.64 million people, with its contribution of more than US-$ 1.6 billion/year to national income. However, pest and disease infections are inevitably common constraints for the cacao cultivators. One current disease is caused by Cacao Swollen Shoot Virus (CSSV). Despite its noticeable symptoms on the cacao trees suffering from the disease, the knowledge on both the virus existence and the prevention steps in dealing with it is lacking. The information on the diversity of mosaic virus will help us to comprehend its epidemiologic development and the needed countermeasures, as well as its evolution. This research is intended to study the mosaic disease virus molecularly, the virus was obtained from DR1 clones from Kalibawang cacao plantation in Kulon Progo, Yogyakarta. The virus morphology was observed using a transmission electron microscope applying quick dipping method. The PCR analysis with conserved region ORF1 primers was conducted to detect the viral existence in the infected trees. The identification of CSSV molecular characters was undertaken using PCR sequencing analysis which was then examined using BioEdit and Mega5 programs to initiate a relationship dendrogram. The result showed that the DR1 cacao tree clones from Kalibawang were infected by mosaic virus with mild visual severity of leaf typical symptom. From the electronic microscope observation, a ±100 nm rod-shaped viral particle with a diameter of 15.3 mm was found. On the molecular level, the cause of mosaic symptom has CSSV amplified at conserved regions with size 375 bp. The results are the first report confirming that the molecular cause of cacao mosaic disease in Indonesia is CSSV. The molecular characters of CSSV in Yogyakarta are very different from those found abroad.

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Complete Genomic Sequence of Noni mosaic virus (NoMV), a Novel Potyvirus Associated with a Mosaic Disease in Morinda citrifolia L.

10.20944/preprints201910.0156.v1 ◽

2019 ◽

Author(s):

Nai-Tong Yu ◽

Zhi-Ying Cai ◽

Zhongguo Xiong ◽

Yan Yang ◽

Zhi-Xin Liu

Keyword(s):

Amino Acid ◽

Mosaic Virus ◽

Complete Genome ◽

De Novo ◽

Genomic Sequence ◽

Mosaic Disease ◽

Amino Acid Sequences ◽

Morinda Citrifolia ◽

Mosaic Symptom ◽

Amino Acid Sequence Similarity

An outbreak of a virus-like disease has caused severe damage to noni plants (Morinda citrifolia L.) in Xishuangbanna area of China's southwestern Yunnan province since 2015. The diseased plants displayed typical mosaic symptom with light and dark green patches on leaves. Flexuous filamentous virus particles of about 800 nm in length were observed from the leaf saps by transmission electron microscope. Illumina transcriptomic sequencing further revealed the presence of a potyvirus and its near complete genome was obtained from de novo assembly. The complete genome of 9,659 nts was obtained by Sanger sequencing of eight amplicons generate by RT-PCR and 5’ and 3’ RACE. BLASTp analysis of the polyprotein sequence showed that the virus was most closely related to Tobacco vein banding mosaic virus (TVBMV), but these two viruses only shared 50.7% amino acid sequence similarity. Both phylogenetic analyses of the polyprotein and CP amino acid sequences indicated that this virus is a member of genus Potyvirus. However, the low sequence homology with all known potyviruses established this virus as a new species in the genus, tentatively named as Noni mosaic virus (NoMV). Our field surveys showed that 100% of the symptomatic samples and 28.57% of the asymptomatic samples were infected with this novel potyvirus. Aphids collected from diseased leaves were also detected carrying the virus. In summary, our data indicated that a novel species of potyvirus, NoMV, is prevalent in Yunnan, China and is associated with an emerging mosaic disease on M. citrifolia.

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