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Rodrigo A Valverde - One of the best experts on this subject based on the ideXlab platform.
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Identification of a novel Endornavirus in Geranium carolinianum and occurrence within three agroecosystems.
Virus research, 2020Co-Authors: Rachel Herschlag, Ryo Okada, Ricardo I. Alcalá-briseño, Eliezer Rodrigues De Souto, Rodrigo A ValverdeAbstract:Abstract A putative Endornavirus was detected in Carolina geranium (Geranium carolinianum) in Louisiana, USA. The virus was provisionally named Geranium carolinianum Endornavirus 1 (GcEV1). The viral RNA was sequenced, and it consisted of 14,625 nt containing a single ORF coding a putative polyprotein of 4815 aa with conserved domains for a helicase 1, peptidase C97, glycosyl transferase GTB-type, and RNA-dependent RNA polymerase 2. The 5′end consisted of 130 nt while the 3′end consisted of 54 nt ending in nine cytosine residues. The closest relative to GcEV1 was Phaseolus vulgaris Endornavirus 3. In phylogenetic analyses, GcEV1 clustered with members of the genus AlphaEndornavirus. GcEV1 was detected in 57 of 60 G. carolinianum plants collected from three distinct agroecosystems. The virus was not detected in eight other species of the genus Geranium. There was no association of a particular phenotypic trait of the host with the presence or absence of the virus. GcEV1 was transmitted at a rate of 100% in seeds of a self-pollinated G. carolinianum plant.
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Ultrastructural Analysis of Cells From Bell Pepper (Capsicum annuum) Infected With Bell Pepper Endornavirus.
Frontiers in plant science, 2020Co-Authors: Katarzyna Otulak-kozieł, Cesar Escalante, Edmund Kozieł, Rodrigo A ValverdeAbstract:Endornaviruses include viruses that infect fungi, oomycetes, and plants. The genome of plant Endornaviruses consists of linear ssRNA ranging in size from approximately 13-18 kb and lacking capsid protein and cell-to-cell movement capability. Although, plant Endornaviruses have not been shown to cause detectable changes in the plant phenotype, they have been associated with alterations of the host physiology. Except for the association of cytoplasmic vesicles with infections by Vicia faba Endornavirus, effects on the plant cell ultrastructure caused by Endornaviruses have not been reported. Bell pepper Endornavirus (BPEV) has been identified in several pepper (Capsicum spp.) species. We conducted ultrastructural analyses of cells from two near-isogenic lines of the bell pepper (C. annuum) cv. Marengo, one infected with BPEV and the other BPEV-free, and found cellular alterations associated with BPEV-infections. Some cells of plants infected with BPEV exhibited alterations of organelles and other cell components. Affected cells were located mainly in the mesophyll and phloem tissues. Altered organelles included mitochondrion, chloroplast, and nucleus. The mitochondria from BPEV-infected plants exhibited low number of cristae and electron-lucent regions. Chloroplasts contained plastoglobules and small vesicles in the surrounding cytoplasm. Translucent regions in thylakoids were observed, as well as hypertrophy of the chloroplast structure. Many membranous vesicles were observed in the stroma along the envelope. The nuclei revealed a dilation of the nuclear envelope with vesicles and perinuclear areas. The organelle changes were accompanied by membranous structure rearrangements, such as paramural bodies and multivesicular bodies. These alterations were not observed in cells from plants of the BPEV-free line. Overall, the observed ultrastructural cell alterations associated with BPEV are similar to those caused by plant viruses and viroids and suggest some degree of parasitic interaction between BPEV and the plant host.
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Effect of two digestive enzymes and pH on the dsRNA of Endornaviruses of bell pepper and melon under in vitro conditions
Annals of Microbiology, 2019Co-Authors: Adair Mccanless, Cesar Escalante, Allison Hultgren, Alyssa Ardt, Rodrigo A ValverdeAbstract:Purpose The objective of this investigation was to determine the in vitro effect of two common digestive enzymes, amylase and pepsin, and pH on the integrity of the RI dsRNA of bell pepper Endornavirus (BPEV) and Cucumis melo Endornavirus (CmEV) evaluated by gel electrophoresis and reverse-transcription PCR (RT-PCR). Methods We conducted experiments on the in vitro effect of two common digestive enzymes, amylase and pepsin, and pH on the structural integrity of the replicative intermediate (RI) dsRNA of bell pepper Endornavirus (BPEV) and Cucumis melo Endornavirus (CmEV), evaluated by gel electrophoresis and reverse-transcription polymerase chain reaction. Result The effect of the amylase, pepsin, and pH treatments on the dsRNA of both viruses was similar. Amylase did not appear to affect the structural integrity of the dsRNA. In contrast, gel electrophoresis analysis of pepsin-treated dsRNA samples showed an abnormal electrophoretic migration and evidence of partial dsRNA degradation. DsRNAs from both fruits were partially degraded when exposed to a pH value of 2.0 and completely degraded at a pH value of 1.0. Conclusion The results of this investigation suggest that when exposed to pepsin and pH values lower than 2.0, the RI of BPEV and CmEV lose their structural integrity. Therefore, when consuming Endornavirus-infected bell pepper or melon, our digestive organs are exposed to both fragmented and full RI dsRNA of these two viruses.
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Effect of two digestive enzymes and pH on the dsRNA of Endornaviruses of bell pepper and melon under in vitro conditions
Annals of Microbiology, 2019Co-Authors: Adair Mccanless, Cesar Escalante, Allison Hultgren, Alyssa Ardt, Rodrigo A ValverdeAbstract:The objective of this investigation was to determine the in vitro effect of two common digestive enzymes, amylase and pepsin, and pH on the integrity of the RI dsRNA of bell pepper Endornavirus (BPEV) and Cucumis melo Endornavirus (CmEV) evaluated by gel electrophoresis and reverse-transcription PCR (RT-PCR). We conducted experiments on the in vitro effect of two common digestive enzymes, amylase and pepsin, and pH on the structural integrity of the replicative intermediate (RI) dsRNA of bell pepper Endornavirus (BPEV) and Cucumis melo Endornavirus (CmEV), evaluated by gel electrophoresis and reverse-transcription polymerase chain reaction. The effect of the amylase, pepsin, and pH treatments on the dsRNA of both viruses was similar. Amylase did not appear to affect the structural integrity of the dsRNA. In contrast, gel electrophoresis analysis of pepsin-treated dsRNA samples showed an abnormal electrophoretic migration and evidence of partial dsRNA degradation. DsRNAs from both fruits were partially degraded when exposed to a pH value of 2.0 and completely degraded at a pH value of 1.0. The results of this investigation suggest that when exposed to pepsin and pH values lower than 2.0, the RI of BPEV and CmEV lose their structural integrity. Therefore, when consuming Endornavirus-infected bell pepper or melon, our digestive organs are exposed to both fragmented and full RI dsRNA of these two viruses.
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Occurrence of putative Endornaviruses in non-cultivated plant species in South Louisiana.
Archives of Virology, 2019Co-Authors: Rachel Herschlag, Cesar Escalante, Surasak Khankhum, Ryo Okada, Eliezer R. Souto, Rodrigo A ValverdeAbstract:: Extraction and electrophoretic analysis of viral dsRNA from plants has been used successfully to detect infections by RNA viruses. We used this approach as an initial tool to test non-cultivated plant species for the presence of Endornaviruses. Foliar samples were collected from symptomless plants in various locations within East Baton Rouge Parish, Louisiana, USA, and tested for viral dsRNA. After testing 208 plant species belonging to 74 families, five (Geranium carolinianum, Hydrocotyle umbellata, H. prolifera, Sorghum halepense, and Sisyrinchium atlanticum) yielded dsRNAs similar in size to the dsRNAs of members of the family Endornaviridae. The Endornavirus nature of the dsRNAs was confirmed by reverse-transcription PCR (RT-PCR) and sequencing the RT-PCR products. Sequence data were used to determine relationships of the putative Endornaviruses to members of the family Endornaviridae. The putative Endornaviruses were detected in both native and introduced plants species. This is the first survey on the occurrence of Endornaviruses in non-cultivated plant species.
Renato Oliveira Resende - One of the best experts on this subject based on the ideXlab platform.
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Identification and genome analysis of tomato chlorotic spot virus and dsRNA viruses from coinfected vegetables in the Dominican Republic by high-throughput sequencing
Virology Journal, 2018Co-Authors: Reina Teresa Martínez, Mariana Martins Severo De Almeida, Rosalba Rodriguez, Athos Silva De Oliveira, Fernando Lucas Melo, Renato Oliveira ResendeAbstract:The Tomato chlorotic spot virus (TCSV) was first reported in the 1980s, having its occurrence limited to Brazil and Argentina. Due to an apparent mild severity in the past, molecular studies concerning TCSV were neglected. However, TCSV has disseminated over the USA and Caribbean countries. In Dominican Republic TCSV has been recently reported on important cultivated crops such as pepper and beans. In this work, we provide the first complete genome of a TCSV isolate from symptomatic plants in Dominican Republic, which was obtained by high-throughput sequencing. In addition, three dsRNA viruses from different virus families were identified coinfecting these plants Bell pepper Endornavirus (BPEV), Southern tomato virus (STV) and Pepper cryptic virus 2 (PCV-2). Phylogenetic analysis showed that the Dominican Republic TCSV isolate has a close relationship with other TCSV isolates and a reassortant isolate between TCSV and Groundnut ringspot virus (GRSV), all found in USA. BPEV, STV and PCV-2 isolates from Dominican Republic were close related to corresponding American isolates. The possible biological implications of these virus-mixed infections are discussed.
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Identification and genome analysis of tomato chlorotic spot virus and dsRNA viruses from coinfected vegetables in the Dominican Republic by high-throughput sequencing.
Virology journal, 2018Co-Authors: Reina Teresa Martínez, Mariana Martins Severo De Almeida, Rosalba Rodriguez, Athos Silva De Oliveira, Fernando Lucas Melo, Renato Oliveira ResendeAbstract:The Tomato chlorotic spot virus (TCSV) was first reported in the 1980s, having its occurrence limited to Brazil and Argentina. Due to an apparent mild severity in the past, molecular studies concerning TCSV were neglected. However, TCSV has disseminated over the USA and Caribbean countries. In Dominican Republic TCSV has been recently reported on important cultivated crops such as pepper and beans. In this work, we provide the first complete genome of a TCSV isolate from symptomatic plants in Dominican Republic, which was obtained by high-throughput sequencing. In addition, three dsRNA viruses from different virus families were identified coinfecting these plants Bell pepper Endornavirus (BPEV), Southern tomato virus (STV) and Pepper cryptic virus 2 (PCV-2). Phylogenetic analysis showed that the Dominican Republic TCSV isolate has a close relationship with other TCSV isolates and a reassortant isolate between TCSV and Groundnut ringspot virus (GRSV), all found in USA. BPEV, STV and PCV-2 isolates from Dominican Republic were close related to corresponding American isolates. The possible biological implications of these virus-mixed infections are discussed.
Surasak Khankhum - One of the best experts on this subject based on the ideXlab platform.
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Occurrence of putative Endornaviruses in non-cultivated plant species in South Louisiana.
Archives of Virology, 2019Co-Authors: Rachel Herschlag, Cesar Escalante, Surasak Khankhum, Ryo Okada, Eliezer R. Souto, Rodrigo A ValverdeAbstract:: Extraction and electrophoretic analysis of viral dsRNA from plants has been used successfully to detect infections by RNA viruses. We used this approach as an initial tool to test non-cultivated plant species for the presence of Endornaviruses. Foliar samples were collected from symptomless plants in various locations within East Baton Rouge Parish, Louisiana, USA, and tested for viral dsRNA. After testing 208 plant species belonging to 74 families, five (Geranium carolinianum, Hydrocotyle umbellata, H. prolifera, Sorghum halepense, and Sisyrinchium atlanticum) yielded dsRNAs similar in size to the dsRNAs of members of the family Endornaviridae. The Endornavirus nature of the dsRNAs was confirmed by reverse-transcription PCR (RT-PCR) and sequencing the RT-PCR products. Sequence data were used to determine relationships of the putative Endornaviruses to members of the family Endornaviridae. The putative Endornaviruses were detected in both native and introduced plants species. This is the first survey on the occurrence of Endornaviruses in non-cultivated plant species.
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Physiological traits of Endornavirus-infected and Endornavirus-free common bean (Phaseolus vulgaris) cv Black Turtle Soup
Archives of Virology, 2018Co-Authors: Surasak Khankhum, R. A. ValverdeAbstract:This study evaluated the physiological traits of eight lines of common bean ( Phaseolus vulgaris ) cv. Black Turtle Soup, four of which were double-infected with Phaseolus vulgaris Endornavirus 1 and Phaseolus vulgaris Endornavirus 2, and four of which were Endornavirus-free. Plants from all eight lines were morphologically similar and did not show statistically significant differences in plant height, wet weight, number of days to flowering and pod formation, pods per plant, pod thickness, seed size, number of seeds per pod, and anthocyanin content. However, the Endornavirus-infected lines had faster seed germination, longer radicle, lower chlorophyll content, higher carotene content, longer pods, and higher weight of 100 seeds, all of which were statistically significant. The Endornaviruses were not associated with visible pathogenic effects.
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RNAseq Analysis of Endornavirus-Infected vs. Endornavirus-Free Common Bean (Phaseolus vulgaris) Cultivar Black Turtle Soup
Frontiers in microbiology, 2016Co-Authors: Surasak Khankhum, Juan M. Osorno, Noa Sela, Rodrigo A ValverdeAbstract:Common bean (Phaseolus vulgaris L.) is the most important grain legume for direct human consumption worldwide and represents a rich source of protein, vitamins, minerals, and fiber (Broughton et al., 2003). The recent sequencing of the common bean genome, together with the availability of genomic and transcriptomic data have provided useful information to common bean breeders that will help in the development of genotypes with desirable characteristics (Schmutz et al., 2014; Vlasova et al., 2016). Endornaviruses are persistent viruses with a non-encapsidated RNA genome that ranges from 9.8 to 17.6 kb, infect plants, fungi, and oomycetes, are transmitted only via gametes, and do not cause apparent symptoms (Stielow et al., 2011; Fukuhara and Gibbs, 2012). Although Endornaviruses have been reported in several economically important plant species, little is known about the effect they have on their hosts. One of the major obstacles to study their effect to the host is the lack of a transmission method. In plants, Endornaviruses do not move from cell to cell and spread only during cell division. Recently, Khankhum et al. (2015) reported that most common bean genotypes of Mesoamerican origin are double-infected with Phaseolus vulgaris Endornavirus 1 (PvEV1) and Phaseolus Endornavirus 2 (PvEV2); in contrast, genotypes of Andean origin are often Endornavirus-free. Black Turtle Soup (BTS), a cultivar of Mesoamerican origin has been reported to be double-infected by these two Endornaviruses (Okada et al., 2013). A BTS Endornavirus-free selection (BTS−), obtained from an Endornavirus-infected BTS (BTS+) seed lot has been reported by Okada et al. (2013). To establish the bases for future research on the role that Endornaviruses play in the common bean plant, and the effect these viruses have on the host gene expression, we conducted RNAseq on two BTS lines: one Endornavirus-infected and the other Endornavirus-free.
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Two Endornaviruses show differential infection patterns between gene pools of Phaseolus vulgaris
Archives of virology, 2015Co-Authors: Surasak Khankhum, Rodrigo A Valverde, Marcial A. Pastor-corrales, Juan M. Osorno, Sead SabanadzovicAbstract:We investigated the occurrence of two plant Endornaviruses, Phaseolus vulgaris Endornavirus 1 and Phaseolus vulgaris Endornavirus 2, in breeding lines, cultivars, landraces, and wild genotypes of common bean (Phaseolus vulgaris) collected from the two centers of common bean domestication: Mesoamerica and the Andes. The two Endornaviruses were detected in many genotypes of Mesoamerican origin but rarely in genotypes of Andean origin. The results suggest that these two Endornaviruses were introduced into the Mesoamerican modern genotypes during common bean domestication and provide more evidence for the existence of two divergent gene pools of common bean.
Huaigu Chen - One of the best experts on this subject based on the ideXlab platform.
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Genome structure and diversity of novel Endornaviruses from wheat sharp eyespot pathogen Rhizoctonia cerealis.
Virus research, 2021Co-Authors: Haotian Zhang, Aixiang Zhang, Yan Shu, Cao Shulin, Sun Haiyan, Huaigu ChenAbstract:Rhizoctonia cerealis (teleomorph Ceratobasidium cereale) is a soil-borne plant pathogenic fungus that can cause sharp eyespot in wheat or yellow patch in grasses. In this study, 21 new Endornavirus genomes were obtained from five R. cerealis strains through the high-throughput sequencing of viral double-stranded RNA. Eighteen viruses were identified as AlphaEndornavirus, and three viruses were identified as new species of BetaEndornavirus on the basis of the phylogenetic analysis of the deduced amino acid sequences of RNA-dependent RNA polymerase. Notably, 12 of the new alphaEndornaviruses could encode two open reading frames (ORFs), which were a rare feature of Endornaviridae. The amino acid sequences encoded by ORF2 from different Endornaviruses had very low identity, and their functions and evolution origins remained unclear. Different Endornavirus species with remarkably different genome structures could be found in the same R. cerealis strain. This study indicated that Endornaviruses are common in R. cerealis and display wide diversity. BetaEndornaviruses were found in R. cerealis, and a new species was proposed. This study is the first to report that the Endornaviruses from R. cerealis can encode two ORFs and enhances our understanding of the viruses in the Endornaviridae family.
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Complete genome sequence of a novel Endornavirus in the wheat sharp eyespot pathogen Rhizoctonia cerealis.
Archives of virology, 2013Co-Authors: Tao Zhang, Haiyan Sun, Deng Yuanyu, Aixiang Zhang, Huaigu Chen, Kerong WangAbstract:We report here the presence of a novel double-stranded RNA (dsRNA) virus in an isolate (R0959) of the fungus Rhizoctonia cerealis, the causal agent of sharp eyespot of wheat in China. Sequence analysis showed that the dsRNA segment is 17,486 bp long and contains a single open reading frame (ORF) with the potential to encode a protein of 5,747 amino acids. The predicted protein contains conserved motifs of putative viral methyltransferase, helicase 1, and RNA-dependent RNA polymerase. Sequence similarity and phylogenetic analysis clearly place it in a distinct species within the genus Endornavirus, family Endornaviridae, and therefore we propose its name to Rhizoctonia cerealis Endornavirus 1 (RcEV1). This is the first report of the full-length genomic sequence of a dsRNA mycovirus in R. cerealis.
Reina Teresa Martínez - One of the best experts on this subject based on the ideXlab platform.
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Identification and genome analysis of tomato chlorotic spot virus and dsRNA viruses from coinfected vegetables in the Dominican Republic by high-throughput sequencing
Virology Journal, 2018Co-Authors: Reina Teresa Martínez, Mariana Martins Severo De Almeida, Rosalba Rodriguez, Athos Silva De Oliveira, Fernando Lucas Melo, Renato Oliveira ResendeAbstract:The Tomato chlorotic spot virus (TCSV) was first reported in the 1980s, having its occurrence limited to Brazil and Argentina. Due to an apparent mild severity in the past, molecular studies concerning TCSV were neglected. However, TCSV has disseminated over the USA and Caribbean countries. In Dominican Republic TCSV has been recently reported on important cultivated crops such as pepper and beans. In this work, we provide the first complete genome of a TCSV isolate from symptomatic plants in Dominican Republic, which was obtained by high-throughput sequencing. In addition, three dsRNA viruses from different virus families were identified coinfecting these plants Bell pepper Endornavirus (BPEV), Southern tomato virus (STV) and Pepper cryptic virus 2 (PCV-2). Phylogenetic analysis showed that the Dominican Republic TCSV isolate has a close relationship with other TCSV isolates and a reassortant isolate between TCSV and Groundnut ringspot virus (GRSV), all found in USA. BPEV, STV and PCV-2 isolates from Dominican Republic were close related to corresponding American isolates. The possible biological implications of these virus-mixed infections are discussed.
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Identification and genome analysis of tomato chlorotic spot virus and dsRNA viruses from coinfected vegetables in the Dominican Republic by high-throughput sequencing.
Virology journal, 2018Co-Authors: Reina Teresa Martínez, Mariana Martins Severo De Almeida, Rosalba Rodriguez, Athos Silva De Oliveira, Fernando Lucas Melo, Renato Oliveira ResendeAbstract:The Tomato chlorotic spot virus (TCSV) was first reported in the 1980s, having its occurrence limited to Brazil and Argentina. Due to an apparent mild severity in the past, molecular studies concerning TCSV were neglected. However, TCSV has disseminated over the USA and Caribbean countries. In Dominican Republic TCSV has been recently reported on important cultivated crops such as pepper and beans. In this work, we provide the first complete genome of a TCSV isolate from symptomatic plants in Dominican Republic, which was obtained by high-throughput sequencing. In addition, three dsRNA viruses from different virus families were identified coinfecting these plants Bell pepper Endornavirus (BPEV), Southern tomato virus (STV) and Pepper cryptic virus 2 (PCV-2). Phylogenetic analysis showed that the Dominican Republic TCSV isolate has a close relationship with other TCSV isolates and a reassortant isolate between TCSV and Groundnut ringspot virus (GRSV), all found in USA. BPEV, STV and PCV-2 isolates from Dominican Republic were close related to corresponding American isolates. The possible biological implications of these virus-mixed infections are discussed.