scholarly journals Double-Stranded RNA High-Throughput Sequencing Reveals a New Cytorhabdovirus in a Bean Golden Mosaic Virus-Resistant Common Bean Transgenic Line

Viruses ◽  
2019 ◽  
Vol 11 (1) ◽  
pp. 90 ◽  
Author(s):  
Dione M. T. Alves-Freitas ◽  
Bruna Pinheiro-Lima ◽  
Josias C. Faria ◽  
Cristiano Lacorte ◽  
Simone G. Ribeiro ◽  
...  
Keyword(s):  
Phaseolus Vulgaris ◽  
Common Bean ◽  
Mosaic Virus ◽  
High Throughput ◽  
Transgenic Line ◽  
High Throughput Sequencing ◽  
Open Reading Frames ◽  
Virus Species ◽  
Homologous Proteins ◽  
Bean Golden Mosaic Virus

Using double-strand RNA (dsRNA) high-throughput sequencing, we identified five RNA viruses in a bean golden mosaic virus (BGMV)-resistant common bean transgenic line with symptoms of viral infection. Four of the identified viruses had already been described as infecting common bean (cowpea mild mottle virus, bean rugose mosaic virus, Phaseolus vulgaris alphaendornavirus 1, and Phaseolus vulgaris alphaendornavirus 2) and one is a putative new plant rhabdovirus (genus Cytorhabdovirus), tentatively named bean-associated cytorhabdovirus (BaCV). The BaCV genome presented all five open reading frames (ORFs) found in most rhabdoviruses: nucleoprotein (N) (ORF1) (451 amino acids, aa), phosphoprotein (P) (ORF2) (445 aa), matrix (M) (ORF4) (287 aa), glycoprotein (G) (ORF5) (520 aa), and an RNA-dependent RNA polymerase (L) (ORF6) (114 aa), as well as a putative movement protein (P3) (ORF3) (189 aa) and the hypothetical small protein P4. The predicted BaCV proteins were compared to homologous proteins from the closest cytorhabdoviruses, and a low level of sequence identity (15–39%) was observed. The phylogenetic analysis shows that BaCV clustered with yerba mate chlorosis-associated virus (YmCaV) and rice stripe mosaic virus (RSMV). Overall, our results provide strong evidence that BaCV is indeed a new virus species in the genus Cytorhabdovirus (family Rhabdoviridae), the first rhabdovirus to be identified infecting common bean.

scholarly journals Partial resistance to Bean golden mosaic virus in a transgenic common bean (Phaseolus vulgaris L.) line expressing a mutated rep gene

Plant Science ◽  
2006 ◽  
Vol 171 (5) ◽  
pp. 565-571 ◽  
Author(s):  
Josias C. Faria ◽  
Margareth M.C. Albino ◽  
Bárbara B.A. Dias ◽  
Letícia J. Cançado ◽  
Nicolau B. da Cunha ◽  
...  
Keyword(s):  
Phaseolus Vulgaris ◽  
Common Bean ◽  
Mosaic Virus ◽  
Partial Resistance ◽  
Phaseolus Vulgaris L ◽  
Bean Golden Mosaic Virus ◽  
Transgenic Common Bean

scholarly journals Molecular Characterization of a New Virus Species Identified in Yam (Dioscorea spp.) by High-Throughput Sequencing

Plants ◽  
2019 ◽  
Vol 8 (6) ◽  
pp. 167 ◽  
Author(s):  
Gonçalo Silva ◽  
Moritz Bömer ◽  
Ajith I. Rathnayake ◽  
Steven O. Sewe ◽  
Paul Visendi ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Triple Gene Block ◽  
Open Reading Frames ◽  
Virus Species ◽  
Gene Block ◽  
Full Diversity ◽  
Putative Coat Protein ◽  
The Family ◽  
International Distribution

To date, several viruses of different genera have been reported to infect yam (Dioscorea spp.). The full diversity of viruses infecting yam, however, remains to be explored. High-throughput sequencing (HTS) methods are increasingly being used in the discovery of new plant viral genomes. In this study, we employed HTS on yam to determine whether any undiscovered viruses were present that would restrict the international distribution of yam germplasm. We discovered a new virus sequence present in 31 yam samples tested and have tentatively named this virus “yam virus Y” (YVY). Twenty-three of the samples in which YVY was detected showed mosaic and chlorotic leaf symptoms, but Yam mosaic virus was also detected in these samples. Complete genome sequences of two YVY viral isolates were assembled and found to contain five open reading frames (ORFs). ORF1 encodes a large replication-associated protein, ORF2, ORF3 and ORF4 constitute the putative triple gene block proteins, and ORF5 encodes a putative coat protein. Considering the species demarcation criteria of the family Betaflexiviridae, YVY should be considered as a novel virus species in the family Betaflexiviridae. Further work is needed to understand the association of this new virus with any symptoms and yield loss and its implication on virus-free seed yam production.

scholarly journals RNAi-Mediated Resistance to Bean golden mosaic virus in Genetically Engineered Common Bean (Phaseolus vulgaris)

2007 ◽  
Vol 20 (6) ◽  
pp. 717-726 ◽  
Author(s):  
Kenny Bonfim ◽  
Josias C. Faria ◽  
Elsa O. P. L. Nogueira ◽  
Érica A. Mendes ◽  
Francisco J. L. Aragão
Keyword(s):  
Phaseolus Vulgaris ◽  
Transgenic Plants ◽  
Common Bean ◽  
Mosaic Virus ◽  
Early Stage ◽  
Transcriptional Gene Silencing ◽  
Viral Gene ◽  
Small Interfering Rnas ◽  
Bean Golden Mosaic Virus ◽  
Transgenic Common Bean

Bean golden mosaic virus (BGMV) is transmitted by the whitefly Bemisia tabaci in a persistent, circulative manner, causing the golden mosaic of common bean (Phaseolus vulgaris L.). The characteristic symptoms are yellow-green mosaic of leaves, stunted growth, or distorted pods. The disease is the largest constraint to bean production in Latin America and causes severe yield losses (40 to 100%). Here, we explored the concept of using an RNA interference construct to silence the sequence region of the AC1 viral gene and generate highly resistant transgenic common bean plants. Eighteen transgenic common bean lines were obtained with an intron-hairpin construction to induce post-transcriptional gene silencing against the AC1 gene. One line (named 5.1) presented high resistance (approximately 93% of the plants were free of symptoms) upon inoculation at high pressure (more than 300 viruliferous whiteflies per plant during the whole plant life cycle) and at a very early stage of plant development. Transgene-specific small interfering RNAs were detected in both inoculated and non-inoculated transgenic plants. A semiquantitative polymerase chain reaction analysis revealed the presence of viral DNA in transgenic plants exposed to viruliferous whiteflies for a period of 6 days. However, when insects were removed, no virus DNA could be detected after an additional period of 6 days.

scholarly journals Seleção de progênies de feijoeiro F4 resistentes ao Bean golden mosaic virus

2005 ◽  
Vol 30 (3) ◽  
pp. 279-285 ◽  
Author(s):  
Fernando C. Juliatti ◽  
Simone A. Moraes ◽  
Heyder D. Silva ◽  
Márcio H. C. Borges
Keyword(s):  
Phaseolus Vulgaris ◽  
Mosaic Virus ◽  
Bean Golden Mosaic Virus

O objetivo deste trabalho foi identificar progênies de feijoeiro (Phaseolus vulgaris) na geração F4 provenientes do cruzamento entre cultivares resistentes ao Bean golden mosaic virus (BGMV). Os parentais foram as cultivares Carioca-MG (suscetível) e IAPAR-57, IAPAR-72 e IAPAR-65 (resistentes). A população de 480 progênies foi obtida pelo modelo dialélico completo. Estas foram semeadas em campo sob inoculação natural e estudada ao nível de plantas individuais para cálculo do índice de doença de BGMV (I.D.) Em relação ao I.D. médio, as progênies foram mais resistentes do que seus parentais (2,62 e 2,87), respectivamente. O processo de seleção foi realizado pelo I.D. (sigmag² = 0,2729 e h a² = 0,3953), onde foram obtidas famílias com grãos do tipo carioca e com I.D. inferior aos parentais resistentes. Segundo o GS% estimado, não serão necessárias muitas progênies ou famílias para se obter progresso com seleção para BGMV. O genótipo IAPAR-72 foi o parental superior na obtenção de progênies de maior resistência (menores I.D.). Possivelmente o mecanismo de resistência é do tipo resistência parcial.

scholarly journals Millet Could Be both a Weed and Serve as a Virus Reservoir in Crop Fields

Plants ◽  
2020 ◽  
Vol 9 (8) ◽  
pp. 954
Author(s):  
György Pasztor ◽  
Zsuzsanna Galbacs N. ◽  
Tamas Kossuth ◽  
Emese Demian ◽  
Erzsebet Nadasy ◽  
...  
Keyword(s):  
Mosaic Virus ◽  
Seed Dormancy ◽  
High Throughput ◽  
Small Rna ◽  
Diagnostic Method ◽  
High Throughput Sequencing ◽  
Infection Risk ◽  
Viral Diseases ◽  
Crop Fields ◽  
Special Control

Millet is a dangerous weed in crop fields. A lack of seed dormancy helps it to spread easily and be present in maize, wheat, and other crop fields. Our previous report revealed the possibility that millet can also play a role as a virus reservoir. In that study, we focused on visual symptoms and detected the presence of several viruses in millet using serological methods, which can only detect the presence of the investigated pathogen. In this current work, we used small RNA high-throughput sequencing as an unbiased virus diagnostic method to uncover presenting viruses in randomly sampled millet grown as a volunteer weed in two maize fields, showing stunting, chlorosis, and striped leaves. Our results confirmed the widespread presence of wheat streak mosaic virus at both locations. Moreover, barley yellow striate mosaic virus and barley virus G, neither of which had been previously described in Hungary, were also identified. As these viruses can cause severe diseases in wheat and other cereals, their presence in a weed implies a potential infection risk. Our study indicates that the presence of millet in fields requires special control to prevent the emergence of new viral diseases in crop fields.

scholarly journals High-Throughput Sequencing Facilitates Discovery of New Plant Viruses in Poland

Plants ◽  
2020 ◽  
Vol 9 (7) ◽  
pp. 820
Author(s):  
Julia Minicka ◽  
Aleksandra Zarzyńska-Nowak ◽  
Daria Budzyńska ◽  
Natasza Borodynko-Filas ◽  
Beata Hasiów-Jaroszewska
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Plant Viruses ◽  
Yellow Mosaic Virus ◽  
Virus Species ◽  
Phylogenetic Groups ◽  
Accurate Identification ◽  
Detection And Identification ◽  
New Finding ◽  
Recent Occurrence

Viruses cause epidemics on all major crops of agronomic importance, and a timely and accurate identification is essential for control. High throughput sequencing (HTS) is a technology that allows the identification of all viruses without prior knowledge on the targeted pathogens. In this paper, we used HTS technique for the detection and identification of different viral species occurring in single and mixed infections in plants in Poland. We analysed various host plants representing different families. Within the 20 tested samples, we identified a total of 13 different virus species, including those whose presence has not been reported in Poland before: clover yellow mosaic virus (ClYMV) and melandrium yellow fleck virus (MYFV). Due to this new finding, the obtained sequences were compared with others retrieved from GenBank. In addition, cucurbit aphid-borne yellows virus (CABYV) was also detected, and due to the recent occurrence of this virus in Poland, a phylogenetic analysis of these new isolates was performed. The analysis revealed that CABYV population is highly diverse and the Polish isolates of CABYV belong to two different phylogenetic groups. Our results showed that HTS-based technology is a valuable diagnostic tool for the identification of different virus species originating from variable hosts, and can provide rapid information about the spectrum of plant viruses previously not detected in a region.

scholarly journals Recessive Resistance to Bean common mosaic virus Conferred by the bc-1 and bc-2 Genes in Common Bean (Phaseolus vulgaris) Affects Long-Distance Movement of the Virus

2018 ◽  
Vol 108 (8) ◽  
pp. 1011-1018 ◽  
Author(s):  
Xue Feng ◽  
Gardenia E. Orellana ◽  
James R. Myers ◽  
Alexander V. Karasev
Keyword(s):  
Phaseolus Vulgaris ◽  
Common Bean ◽  
Mosaic Virus ◽  
Bean Common Mosaic Virus ◽  
Translation Initiation Factor ◽  
Initiation Factor ◽  
Recessive Resistance ◽  
Long Distance ◽  
Systemic Spread ◽  
Long Distance Movement

Recessive resistance to Bean common mosaic virus (BCMV) in common bean (Phaseolus vulgaris) is governed by four genes that include one strain-nonspecific helper gene bc-u, and three strain-specific genes bc-1, bc-2, and bc-3. The bc-3 gene was identified as an eIF4E translation initiation factor gene mediating resistance through disruption of the interaction between this protein and the VPg protein of the virus. The mode of action of bc-1 and bc-2 in expression of BCMV resistance is unknown, although bc-1 gene was found to affect systemic spread of a related potyvirus, Bean common mosaic necrosis virus. To investigate the possible role of both bc-1 and bc-2 genes in replication, cell-to-cell, and long-distance movement of BCMV in P. vulgaris, we tested virus spread of eight BCMV isolates representing pathogroups I, IV, VI, VII, and VIII in a set of bean differentials expressing different combinations of six resistance alleles including bc-u, bc-1, bc-12, bc-2, bc-22, and bc-3. All studied BCMV isolates were able to replicate and spread in inoculated leaves of bean cultivars harboring bc-u, bc-1, bc-12, bc-2, and bc-22 alleles and their combinations, while no BCMV replication was found in inoculated leaves of cultivar IVT7214 carrying the bc-u, bc-2, and bc-3 genes, except for isolate 1755a, which was capable of overcoming the resistance conferred by bc-2 and bc-3. In contrast, the systemic spread of all BCMV isolates from pathogroups I, IV, VI, VII, and VIII was impaired in common bean cultivars carrying bc-1, bc-12, bc-2, and bc-22 alleles. The data suggest that bc-1 and bc-2 recessive resistance genes have no effect on the replication and cell-to-cell movement of BCMV, but affect systemic spread of BCMV in common bean. The BCMV resistance conferred by bc-1 and bc-2 and affecting systemic spread was found only partially effective when these two genes were expressed singly. The efficiency of the restriction of the systemic spread of the virus was greatly enhanced when the alleles of bc-1 and bc-2 genes were combined together.

scholarly journals Use of interracial hybridization in breeding the race Durango common bean

1993 ◽  
Vol 73 (3) ◽  
pp. 785-793 ◽  
Author(s):  
Shree P. Singh ◽  
Albeiro Molina ◽  
Carlos A. Urrea ◽  
J. Ariel Gutiérrez
Keyword(s):  
Disease Resistance ◽  
Phaseolus Vulgaris ◽  
Common Bean ◽  
Mosaic Virus ◽  
Seed Yield ◽  
Block Design ◽  
Bean Common Mosaic Virus ◽  
Mass Selection ◽  
Plant Seed ◽  
High Level

Recently, interracial hybridization was used successfully in breeding common bean (Phaseolus vulgaris L.), but its use has not been adequately documented. Approximately 125 lines with medium-sized seed were selected in the first cycle, mostly from race Durango × race Mesoamerica (both from the Middle American domestication center) single- and multiple-cross populations, for disease resistance and race Durango characteristics. Fifteen of these improved lines, three race Durango control cultivars, and one control cultivar each from races Jalisco and Mesoamerica were evaluated for 3 yr (1989–1991) at three locations in Colombia. A randomized complete block design with three replications was used. Lines were developed using visual mass selection for seed yield and/or resistance to diseases in F2 and F3, followed by single plant harvests in F4 or F5 and seed increases in F6 or F7. Lines resistant to bean common mosaic virus and possessing other desirable traits were yield-tested in F7 or F8. All but two lines outyielded Alteño and Flor de Mayo, the highest yielding control cultivars from races Durango and Jalisco, respectively. Two lines also outyielded Carioca, the race Mesoamerica control cultivar. Improved lines tended to possess higher yield per day. All lines were resistant to bean common mosaic virus and most lines also carried a high level of resistance to anthracnose. Plant, seed, and maturity characteristics of most improved lines were similar to those of race Durango control cultivars. These results support the use of interracial hybridization in improving race Durango common bean. Key words: Common bean, Phaseolus vulgaris, race Durango, interracial populations, seed yield, disease resistance

scholarly journals Intrinsic and regulated properties of minimally edited trypanosome mRNAs

2019 ◽  
Vol 47 (7) ◽  
pp. 3640-3657 ◽  
Author(s):  
Brianna L Tylec ◽  
Rachel M Simpson ◽  
Laura E Kirby ◽  
Runpu Chen ◽  
Yijun Sun ◽  
...  
Keyword(s):  
Rna Editing ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Substrate Binding ◽  
Open Reading Frames ◽  
Mrna Editing ◽  
Accessory Factors ◽  
Reading Frames ◽  
Complex Components

Abstract Most mitochondrial mRNAs in kinetoplastids require extensive uridine insertion/deletion editing to generate translatable open reading frames. Editing is specified by trans-acting gRNAs and involves a complex machinery including basal and accessory factors. Here, we utilize high-throughput sequencing to analyze editing progression in two minimally edited mRNAs that provide a simplified system due their requiring only two gRNAs each for complete editing. We show that CYb and MURF2 mRNAs exhibit barriers to editing progression that differ from those previously identified for pan-edited mRNAs, primarily at initial gRNA usage and gRNA exchange. We demonstrate that mis-edited junctions arise through multiple pathways including mis-alignment of cognate gRNA, incorrect and sometimes promiscuous gRNA utilization and inefficient gRNA anchoring. We then examined the roles of accessory factors RBP16 and MRP1/2 in maintaining edited CYb and MURF2 populations. RBP16 is essential for initiation of CYb and MURF2 editing, as well as MURF2 editing progression. In contrast, MRP1/2 stabilizes both edited mRNA populations, while further promoting progression of MURF2 mRNA editing. We also analyzed the effects of RNA Editing Substrate Binding Complex components, TbRGG2 and GAP1, and show that both proteins modestly impact progression of editing on minimally edited mRNAs, suggesting a novel function for GAP1.

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