scholarly journals Patterns of recombination in turnip mosaic virus genomic sequences indicate hotspots of recombination

2007 ◽  
Vol 88 (1) ◽  
pp. 298-315 ◽  
Author(s):  
Kazusato Ohshima ◽  
Yasuhiro Tomitaka ◽  
Jeffery T. Wood ◽  
Yoshiteru Minematsu ◽  
Hiromi Kajiyama ◽  
...  

Potyviruses have variable single-stranded RNA genomes and many show clear evidence of recombination. This report studied the distribution of recombination sites in the genomes of 92 isolates of the potyvirus Turnip mosaic virus (TuMV); 42 came from the international gene sequence databases and an additional 50 complete genomic sequences were generated from field samples collected in Europe and Asia. The sequences were examined for evidence of recombination using seven different sequence comparison methods and the exact position of each site was confirmed by sequence composition analysis. Recombination sites were found throughout the genomes, except in the small 6K1 protein gene, and only 24 of the genomes (26 %) showed no evidence of recombination. Statistically significant clusters of recombination sites were found in the P1 gene and in the CI/6K2/VPg gene region. Most recombination sites were bordered by an upstream (5′) region of GC-rich and downstream (3′) region of AU-rich sequence of a similar length. Correlations between the presence and type of recombination site and provenance, host type and phylogenetic relationships are discussed, as is the role of recombination in TuMV evolution.

Viruses ◽  
2018 ◽  
Vol 10 (8) ◽  
pp. 430 ◽  
Author(s):  
Miroslav Glasa ◽  
Katarína Šoltys ◽  
Lukáš Predajňa ◽  
Nina Sihelská ◽  
Slavomíra Nováková ◽  
...  

In recent years, the accumulated molecular data of Turnip mosaic virus (TuMV) isolates from various hosts originating from different parts of the world considerably helped to understand the genetic complexity and evolutionary history of the virus. In this work, four complete TuMV genomes (HC9, PK1, MS04, MS15) were characterised from naturally infected cultivated and wild-growing Papaver spp., hosts from which only very scarce data were available previously. Phylogenetic analyses showed the affiliation of Slovak Papaver isolates to the world-B and basal-B groups. The PK1 isolate showed a novel intra-lineage recombination pattern, further confirming the important role of recombination in the shaping of TuMV genetic diversity. Biological assays indicated that the intensity of symptoms in experimentally inoculated oilseed poppy are correlated to TuMV accumulation level in leaves. This is the first report of TuMV in poppy plants in Slovakia.


2003 ◽  
Vol 16 (9) ◽  
pp. 777-784 ◽  
Author(s):  
Carol E. Jenner ◽  
Xiaowu Wang ◽  
Kenta Tomimura ◽  
Kazusato Ohshima ◽  
Fernando Ponz ◽  
...  

Two isolates of the potyvirus Turnip mosaic virus (TuMV), UK 1 and CDN 1, differ both in their general symptoms on the susceptible propagation host Brassica juncea and in their ability to infect B. napus lines possessing a variety of dominant resistance genes. The isolate CDN 1 produces a more extreme mosaic in infected brassica leaves than UK 1 and is able to overcome the resistance genes TuRB01, TuRB04, and TuRB05. The resistance gene TuRB03, in the B. napus line 22S, is effective against CDN 1 but not UK 1. The nucleic acid sequences of the UK 1 and CDN 1 isolates were 90% identical. The C-terminal half of the P3 protein was identified as being responsible for the differences in symptoms in B. juncea. A single amino acid in the P3 protein was found to be the avirulence determinant for TuRB03. Previous work already has identified the P3 as an avirulence determinant for TuRB04. Our results increase the understanding of the basis of plant-virus recognition, show the importance of the potyviral P3 gene as a symptom determinant, and provide a role in planta for the poorly understood P3 protein in a normal infection cycle.


2011 ◽  
Vol 30 (2) ◽  
pp. 309-318 ◽  
Author(s):  
Lei Zhu ◽  
Yanman Li ◽  
Neelam Ara ◽  
Jinghua Yang ◽  
Mingfang Zhang

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Rebeca Cuesta ◽  
Carmen Yuste-Calvo ◽  
David Gil-Cartón ◽  
Flora Sánchez ◽  
Fernando Ponz ◽  
...  

Abstract Turnip mosaic virus (TuMV), a potyvirus, is a flexible filamentous plant virus that displays a helical arrangement of coat protein copies (CPs) bound to the ssRNA genome. TuMV is a bona fide representative of the Potyvirus genus, one of most abundant groups of plant viruses, which displays a very wide host range. We have studied by cryoEM the structure of TuMV virions and its viral-like particles (VLPs) to explore the role of the interactions between proteins and RNA in the assembly of the virions. The results show that the CP-RNA interaction is needed for the correct orientation of the CP N-terminal arm, a region that plays as a molecular staple between CP subunits in the fully assembled virion.


Virus Genes ◽  
2009 ◽  
Vol 38 (3) ◽  
pp. 421-428 ◽  
Author(s):  
Hong-Yan Wang ◽  
Jin-Liang Liu ◽  
Rui Gao ◽  
Jia Chen ◽  
Yun-Hua Shao ◽  
...  

Plant Disease ◽  
2014 ◽  
Vol 98 (10) ◽  
pp. 1450-1450 ◽  
Author(s):  
D. P. Di ◽  
Y. L. Zhang ◽  
C. Yan ◽  
T. Yan ◽  
A. H. Zhang ◽  
...  

In the spring of 2014, a survey of viral diseases on wheat (Triticum aestivum L.) was carried out in Hebei Province, China. The samples with virus-like symptoms of dwarfing and flag leaf yellowing were collected in Zhaoxian, Quyang, Anxin, and Luannan. To reproduce the viral symptoms and confirm whether the unknown virus was transmitted by insect vectors, the nymphs of aviruliferous planthopper (Laodelphax striatellus Fallen, Homoptera: Delphacidae) were transferred onto diseased wheat from the field for a 3-day acquisition access period and a 10-day incubation on fresh wheat seedlings, and then were exposed to 2- to 3-leaf stage wheat seedlings of wheat variety Shixin828 for a 3-day inoculation access period. The infected wheat plants developed mosaic symptoms on the young leaves at 7 days post inoculation (dpi), and followed with severe symptoms including stunting, chlorotic spots, and striation along the veins of leaves at around 14 dpi. The infection symptoms were same as in the field but distinct from wheat infected with Rice black streaked dwarf virus (RBSDV) or Northern cereal mosaic virus (NCMV). For further confirmation, total RNA was extracted from the symptomatic wheat leaves, and NCMV specific primers, NCMV-PF/NCMV-PR (5′-ATGGATAAGAAAGCAAGTGGA-3′/5′-TTAAAAGTCGGCATACGGGTC-3′) and RBSDV specific primers, S10-F/S10-R (5′-TTACCCAACATCACGCAACT-3′/5′-GAGCAGGAACTTCACGACAAC-3′) were used for amplification of sequences of phosphoprotein and coat protein genes, respectively. Neither RBSDV nor NCMV were present in the symptomatic tissue according to the RT-PCR assay (4). Tissues derived from symptomatic wheat leaves were fixed and embedded in Spurr's resin and used for ultra-thin sectioning and transmission electron microscopy observations, revealing large amounts of Rhabdovirus-like particles in the cytoplasm. The identified particles were about 315 to 353 × 46 to 57 nm, similar in size to Barley yellow striate mosaic virus (BYSMV), a member of the genus Cytorhabdovirus reported from Italy (2). The specific primer pair (5′-ACTAAGGGGGTACTCCGACC-3′ and 5′-CTGATCTGCTTTGAGGGGCA-3′) was designed based on the reported polymerase (L) gene sequence of BYSMV isolate Zanjan-1 (GenBank Accession No. FJ665628) (1), and used for the BYSMV detection by RT-PCR. A single bright band of the expected size (~500 bp) was obtained from total RNA extracted from the plants exhibiting symptoms in the greenhouse. No such band was amplified from asymptomatic plants, while 15 out of 23 field samples also produced the same 500-bp products in RT-PCR. PCR products from three virus-positive field samples were sequenced directly and the sequences were submitted to GenBank (KM052176, KM052177, and KM052178). BLAST search showed that the sequences shared 96 to 97% nucleotide identity with the polymerase L gene sequence of BYSMV isolate Zanjan-1, whereas only 73 to 75% identity with NCMV (AB030277 and GU985153) (1,3,5). To our knowledge, this is the first report of BYSMV occurrence on wheat in China. References: (1) R. Almasi et al. J. Phytopathol. 158:351, 2010. (2) A. Appiano et al. Cytol. 6:105, 1974. (3) H. C. Chen et al. Sci. Agric. Sinica 3:64, 1980. (4) X. F. Duan et al. Acta Phytopathol. Sinica 40:337, 2010. (5) F. Tanno et al. Arch. Virol. 145:1373, 2000.


2018 ◽  
Vol 85 (2) ◽  
pp. 158-161 ◽  
Author(s):  
Satomi Abe ◽  
Yutaro Neriya ◽  
Kengo Noguchi ◽  
Sedyo Hartono ◽  
Sri Sulandari ◽  
...  

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4550 ◽  
Author(s):  
Fangluan Gao ◽  
Zhenguo Du ◽  
Jianguo Shen ◽  
Hongkai Yang ◽  
Furong Liao

Ornithogalum mosaic virus (OrMV) has a wide host range and affects the production of a variety of ornamentals. In this study, the coat protein (CP) gene of OrMVwas used to investigate the molecular mechanisms underlying the evolution of this virus. The 36 OrMV isolates fell into two groups which have significant subpopulation differentiation with an FST value of 0.470. One isolate was identified as a recombinant and the other 35 recombination-free isolates could be divided into two major clades under different evolutionary constraints with dN/dS values of 0.055 and 0.028, respectively, indicating a role of purifying selection in the differentiation of OrMV. In addition, the results from analysis of molecular variance (AMOVA) indicated that the effect of host species on the genetic divergence of OrMV is greater than that of geography. Furthermore, OrMV isolates from the genera Ornithogalum, Lachenalia and Diuri tended to group together, indicating that OrMV diversification was maintained, in part, by host-driven adaptation.


2004 ◽  
Vol 85 (9) ◽  
pp. 2683-2696 ◽  
Author(s):  
Zhongyang Tan ◽  
Yasuhiko Wada ◽  
Jishuang Chen ◽  
Kazusato Ohshima

A recombination map of the genome of Turnip mosaic virus (TuMV) was assembled using data from 19 complete genomic sequences, previously reported, and a composite sample of three regions of the genome, one-third in total, of a representative Asia-wide collection of 70 isolates. Thus, a total of 89 isolates of worldwide origin was analysed for recombinants. Eighteen recombination sites were found spaced throughout the 5′ two-thirds of the genome, but there were only two in the 3′ one-third; thus, 24 and 35 % of the P1 and NIa-VPg gene sequences examined were recombinants, whereas only 1 % of the corresponding NIa-Pro and CP gene sequences were recombinants. Recombinants with parents from the same or from different lineages were found, and some recombination sites characterized particular lineages. Most of the strain BR recombinants belonged to the Asian-BR group, as defined previously, and it was concluded that this lineage resulted from a recent migration, whereas many of the strain B recombinants from Asia fell into the world-B group. Again, a large proportion of isolates in this group were recombinants. Some recombination sites were found only in particular lineages, and hence seemed more likely to be the surviving progeny from single recombinational events, rather than the progeny of multiple events occurring at recombination hotspots. It seems that the presence of recombination sites, as well as sequence similarities, may be used to trace the migration and evolution of TuMV.


2021 ◽  
Vol 12 ◽  
Author(s):  
Silvia López-González ◽  
Concepción Gómez-Mena ◽  
Flora Sánchez ◽  
Mathias Schuetz ◽  
A. Lacey Samuels ◽  
...  

Two isolates of Turnip mosaic virus (UK 1 and JPN 1), representative of two different viral strains, induced differential alterations on secondary cell wall (SCW) development in Arabidopsis thaliana, suggesting cell-type specific effects of these viral infections. These potential effects were analyzed in inflorescence stems and flowers of infected plants, together with other possible cellular effects of the infections. Results obtained from macroscopic and histochemical analyses showed that infection with either virus significantly narrowed stem area, but defects in SCW were only found in JPN 1 infections. In flowers, reduced endothecium lignification was also found for JPN 1, while UK 1 infections induced severe floral cell and organ development alterations. A transcriptomic analysis focused on genes controlling and regulating SCW formation also showed notable differences between both viral isolates. UK 1 infections induced a general transcriptional decrease of most regulatory genes, whereas a more complex pattern of alterations was found in JPN 1 infections. The role of the previously identified viral determinant of most developmental alterations, the P3 protein, was also studied through the use of viral chimeras. No SCW alterations or creeping habit growth were found in infections by the chimeras, indicating that if the P3 viral protein is involved in the determination of these symptoms, it is not the only determinant. Finally, considerations as to the possibility of a taxonomical reappraisal of these TuMV viral strains are provided.


Sign in / Sign up

Export Citation Format

Share Document