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Two TGA Transcription Factor Members from Hyper-Susceptible Soybean Exhibiting Significant Basal Resistance to Soybean mosaic virus

Hua Jiang, Shengyu Gu, Kai Li, Junyi Gai
2021 International Journal of Molecular Sciences  
In this study, 27 TGA genes were isolated from a SMV hyper-susceptible soybean NN1138-2, designated GmTGA1~GmTGA27, which were clustered into seven phylogenetic groups.  ...  than the others in inhibiting SMV multiplication.  ...  Abbreviations TF transcription factor SMV Soybean mosaic virus N. benthamiana Nicotiana benthamiana  ... 
doi:10.3390/ijms222111329 pmid:34768757 pmcid:PMC8583413 fatcat:puqlxmtsqvculdqkn4yytedhtu

Molecular variability and genetic structure of the population of Soybean mosaic virus based on the analysis of complete genome sequences

Jang-Kyun Seo, Kazusato Ohshima, Hyeok-Geun Lee, Moonil Son, Hong-Soo Choi, Su-Heon Lee, Seong-Han Sohn, Kook-Hyung Kim
2009 Virology  
Phylogenetic analyses revealed a significant correlation between phylogeny of the cylindrical inclusion (CI) gene of SMV and SMV resistance gene 3 (Rsv3)-relating pathogenicity of SMV, suggesting CI might  ...  Our finding suggests that recombination as well as mutation is an important evolutionary process in the genetic diversification of SMV population.  ...  To obtain a network structure for this phylogenetic incompatibility of the SMV population, we next performed a split decomposition analysis using the SplitsTree4 program.  ... 
doi:10.1016/j.virol.2009.07.007 pmid:19716150 fatcat:t5pi7hbi7zfudnfpyhwdue3gmy

Recombination analysis of Soybean mosaic virus sequences reveals evidence of RNA recombination between distinct pathotypes

Alla G Gagarinova, Mohan Babu, Martina V Strömvik, Aiming Wang
2008 Virology Journal  
The high incidence of SMV recombination suggests that recombination plays an important role in SMV evolution. Obtaining additional full-length sequences will help elucidate this role.  ...  The sequences were analyzed for possible recombination events using a variety of automatic and manual recombination detection and verification approaches.  ...  Phylogenetic relationships of SMV isolates to each other and to PPV as an outgroup.  ... 
doi:10.1186/1743-422x-5-143 pmid:19036160 pmcid:PMC2627826 fatcat:a6woxfjls5eyfgzxhucy7xe2fe

A Polyphasic Approach Reveals Novel Genotypes and Updates the Genetic Structure of the Banana Fusarium Wilt Pathogen

Diane Mostert, Emmanuel Wicker, Mignon M. de Jager, Saif M. Al Kaabi, Wayne T. O'Neill, Suzy Perry, Chunyu Li, Yi Ganyun, Kenneth G. Pegg, Lizel Mostert, Altus Viljoen
2022 Microorganisms  
Genetic relatedness between the undescribed and known Foc VCGs were determined using a multi-gene phylogeny and diversity array technology (DArT) sequencing.  ...  Clustering analysis of the DArT-seq data supported the separation of Foc isolates into eight distinct clusters, with the suite of SIX genes mostly conserved within these clusters.  ...  Phylogenetic Analysis Based on DArT-Seq Data Phylogenetic analysis was performed on the SNP data only, and the SNP data transformed using the gl2fasta function in dartR package.  ... 
doi:10.3390/microorganisms10020269 pmid:35208723 pmcid:PMC8876670 fatcat:lnt2vlcgpzd7pij2t6znmf6oie

Complete Genome Sequencing and Infectious cDNA Clone Construction of Soybean Mosaic Virus Isolated from Shanxi

Defu Wang, Liyan Cui, Li Zhang, Zhennan Ma, Yanbing Niu
2021 The Plant Pathology Journal  
A phylogenetic tree indicated that SMV-SX and SMV-XFQ018 were clustered together, sharing the closest relationship.  ...  techniques to carry out SMV full-length genome amplification from susceptible soybeans and constructed an infectious cDNA clone for SMV.  ...  Bioinformatics analysis of SMV-SX. The amplified sequences were spliced using SeqMan tool from the DNASTAR package (DNASTAR, Inc., Madison, WI, USA).  ... 
doi:10.5423/ppj.oa.11.2020.0209 pmid:33866758 pmcid:PMC8053849 fatcat:si4virjxgrg7lcybwka2xqdrva

MOLECULAR AND BIOLOGICAL PROPERTIES OF SOYBEAN MOSAIC VIRUS AND ITS INFLUENCE ON THE YIELD AND QUALITY OF SOYBEAN UNDER CLIMATE CHANGE CONDITIONS

Lidiya MISHCHENKO, Alina DUNICH, Ivan MISHCHENKO, Olga MOLODCHENKOVA
2018 Poljoprivreda i Šumarstvo  
The analysis of the nucleotide and amino acid sequences of the SKP-16 capsid protein gene revealed the highest percentage of identity (97.9% and 97.2% respectively) with the isolates UA1Gr, Ar33, Lo3,  ...  The low HTC provided a significant number of aphids -vectors of SMV. We have studied in detail the SMV isolate SKP-16 from soybean variety Kophy (GenBank Accession No MG940990).  ...  Phylogenetic trees for the part of SMV coat protein gene were constructed by the maximum-likelihood method (ML) (Huelsenbeck JP, Rannala, 1997) using the best-fitting evolutionary models.  ... 
doi:10.17707/agricultforest.64.4.05 fatcat:ehkkor57rbb2ramv473jmdnwca

Discovery and genetic characterization of diverse smacoviruses in Zambian non-human primates

Paulina D. Anindita, Michihito Sasaki, Gabriel Gonzalez, Wallaya Phongphaew, Michael Carr, Bernard M. Hang'ombe, Aaron S. Mweene, Kimihito Ito, Yasuko Orba, Hirofumi Sawa
2019 Scientific Reports  
An increasing number of smacovirus genomes have been identified exclusively in faecal matter of various vertebrate species and from insect body parts.  ...  Moreover, phylogenetic and recombination analyses provided evidence for recombination events encompassing the 3'-end of the Rep ORF in the unclassified CRESS DNA virus.  ...  The pairwise identity among sequences was calculated with Sequence Demarcation Tool (SDT) v1.2 36 . phylogenetic analysis.  ... 
doi:10.1038/s41598-019-41358-z pmid:30962460 pmcid:PMC6453971 fatcat:x52j3q6jrjf6bf4celuucbz3d4

The Rsv3 Locus Conferring Resistance to Soybean Mosaic Virus is Associated with a Cluster of Coiled-Coil Nucleotide-Binding Leucine-Rich Repeat Genes

Su Jeoung Suh, Brian C. Bowman, Namhee Jeong, Kiwoung Yang, Christin Kastl, Sue A. Tolin, M.A. Saghai Maroof, Soon-Chun Jeong
2011 The Plant Genome  
Phylogenetic analysis of fi ve CC-NB-LRR genes including a pseudogene showed they were highly similar to each other and formed a subclade within a CC-NB-LRR gene clade with representatives from several  ...  The Soybean mosaic virus (SMV) resistance locus, Rsv3, previously mapped between markers A519F/R and M3Satt in the soybean molecular linkage group B2 (chromosome 14), has been characterized by examination  ...  We thank two anonymous reviewers for their constructive comments on an earlier version of the manuscript.  ... 
doi:10.3835/plantgenome2010.11.0024 fatcat:b3ewfsveofbd3aiztvfyunyy2m

Wisteria Vein Mosaic Virus Detected for the First Time in Iran from an Unknown Host by Analysis of Aphid Vectors

Hajar Valouzi, Seyedeh-Shahrzad Hashemi, Stephen J Wylie, Ali Ahadiyat, Alireza Golnaraghi
2020 The Plant Pathology Journal  
Sequence analysis of the amplicon confirmed the presence of an isolate of Wisteria vein mosaic virus (WVMV), a virus species not previously identified from Western Asia.  ...  We used an alternative approach which utilized aphid vectors and indicator plants to identify potyviruses capable of infecting common bean (Phaseolus vulgaris).  ...  Phylogenetic analysis was performed by Mega 6.0 software using the SMV sequence as the outgroup, as described above, except that the best nucleotide substitution models used for ML analysis were Tamura  ... 
doi:10.5423/ppj.oa.10.2019.0268 pmid:32089664 pmcid:PMC7012578 fatcat:qq66r4rf4felnmleiomk4xidse

The Current Status of the Soybean-Soybean Mosaic Virus (SMV) Pathosystem

Jian-Zhong Liu, Yuan Fang, Hongxi Pang
2016 Frontiers in Microbiology  
In addition, we review the progress in dissecting the SMV resistant signaling pathways in soybean, with a special focus on the studies using virus-induced gene silencing.  ...  With these resources available together with the newly developed genome editing tools, and more efficient soybean transformation system, cloning SMV resistant genes, and ultimately generating cultivars  ...  A haplotype phylogenetic analysis of this region suggests that the Rsv4 locus in G. max is recently introgressed from G. soja (Ilut et al., 2016) .  ... 
doi:10.3389/fmicb.2016.01906 pmid:27965641 pmcid:PMC5127794 fatcat:7nqpjqlsdrhf7opzd4of7xekf4

Wisteria Vein Mosaic Virus Detected for the First Time in Iran from an Unknown Host by Analysis of Aphid Vectors

Hajar Valouzi, Seyedeh-Shahrzad Hashemi, Stephen J. Wylie, Ali Ahadiyat, Alireza Golnaraghi
2020 The Plant Pathology Journal  
Sequence analysis of the amplicon confirmed the presence of an isolate of Wisteria vein mosaic virus (WVMV), a virus species not previously identified from Western Asia.  ...  We used an alternative approach which utilized aphid vectors and indicator plants to identify potyviruses capable of infecting common bean (Phaseolus vulgaris).  ...  Phylogenetic analysis was performed by Mega 6.0 software using the SMV sequence as the outgroup, as described above, except that the best nucleotide substitution models used for ML analysis were Tamura  ... 
doi:10.5423/ppj.oa.10.2019.0268 fatcat:i6xcef77inf6vo273msbp3qnye

Degenerate Primers Facilitate the Detection and Identification of Potyviruses From the Northwest Region of Iran

Nemat Sokhandan-Bashir, Aisan Ghasemzadeh, Nahid Masoudi, Reza Khakvar, Davoud Farajzadeh
2013 Iranian Journal of Biotechnology  
PCR products resulting from the use of NIb2F/NIb3R were subjected for cloning and sequencing.  ...  Amplification was achieved from 7 samples when Sprimer and M4 were used, but non-specific fragments were also amplified.  ...  Phylogenetic analysis was performed to reconfirm the potyvirus affiliation of the newly identified isolates.  ... 
doi:10.5812/ijb.11213 fatcat:vtame3oyrzdgxg2bazpw7zubme

Engineering a Decoy Substrate in Soybean to Enable Recognition of the Soybean Mosaic Virus NIa Protease

Matthew Helm, Mingsheng Qi, Shayan Sarkar, Haiyue Yu, Steven A. Whitham, Roger W Innes
2019 Molecular Plant-Microbe Interactions  
protease, indicating that the PBS1 decoy approach will work in soybean, using endogenous PBS1 genes.  ...  AvrPphB also activates defense responses in soybean (Glycine max), suggesting that soybean may contain an R protein analogous to RPS5.  ...  This research was funded, in part, by BASF Plant Sciences and we have filed for a patent on the use of soybean PBS1 genes to engineer recognition of diverse pathogen proteases.  ... 
doi:10.1094/mpmi-12-18-0324-r fatcat:y37allttwbasfax3caylh7wz6q

Chimeric viruses blur the borders between the major groups of eukaryotic single-stranded DNA viruses

Simon Roux, François Enault, Gisèle Bronner, Daniel Vaulot, Patrick Forterre, Mart Krupovic
2013 Nature Communications  
Our results indicate a single event of capsid protein (CP) gene capture from an RNA virus in the history of this virus group.  ...  The domestication of the CP gene was followed by an unprecedented recurrent replacement of the Rep genes in CHIVs with distant counterparts from diverse ssDNA viruses.  ...  Positions (560 and 289) were selected from the CP and RC-Rep alignments, respectively, and were used for subsequent phylogenetic analysis.  ... 
doi:10.1038/ncomms3700 pmid:24193254 fatcat:u4wwk3suhvbg7j7u4xb4gplx3a

Reducing Dimensionality in Remote Homology Detection

S. Dinesh
2021 International Journal for Research in Applied Science and Engineering Technology  
Different type of methods is used for Homology detection.  ...  Here we extract the information from protein sequences and then uses the various algorithm to predict the similarity between protein families.  ...  The profile-profile comparison tools contain: COMPASS, PROF_SIM, COACH, HH search, FORTE, HMAP, and SP3. 3) Phylogenetic Analysis: Phylogenetic analysis and sequence alignment are closely related with  ... 
doi:10.22214/ijraset.2021.39417 fatcat:7kav4suxavbb3jrvjxv3e7aq6q
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