Genetic variability in coat protein gene of sugarcane mosaic virus in Pakistan and its relationship to other strains (original) (raw)
Related papers
2011
Leaf samples of sugarcane were collected from symptomatic and non-symptomatic plants. Total RNA was extracted and purified from sugarcane leaves samples. Presence of mosaic virus was confirmed by RT-PCR amplification using primers designed to the conserved regions of the coat protein genes of Sugarcane Mosaic Virus (SCMV). An amplification product of expected size (approx. 900 bp) was achieved from symptomatic samples but no amplification was detected from non-symptomatic plant samples. RT-PCR amplified DNA fragments were cloned and sequenced in both directions. DNA sequence from two virus isolates from sugarcane cultivars CSSG676 and CSSG668 showed highest level of sequence identity (97% and 96%, respectively) to SCMV (Bundaberg isolate), indicating that the virus isolates infecting sugarcane varieties are variants of SCMV in Pakistan.
Acta virologica, 2017
Sugarcane streak mosaic virus (SCSMV; the genus Poacevirus, the family Potyviridae) is an economically important causal agent of sugarcane mosaic disease in Asia. In this study, for the fi rst time, we determined the complete genomic sequences of two Iranian SCSMV isolates, IR-Khuz6 and IR-Khuz57 from sugarcane. Th e sequences of both isolates were 9,782 nucleotides (nt) long, excluding the 3' poly(A) tail. Both of them contained a 5'-untranslated region (UTR) of 199 nt, an open reading frame of 9,393 nt encoding a polyprotein of 3,130 amino acids (aa), and 3'-UTR of 190 nt. SCSMV-IR-Khuz6 and IR-Khuz57 genome nucleotide sequences were in 97.7% identical and shared identities of 81-92.4% with 10 other SCSMV isolates available in the GenBank. Th e highest identity was shared with the isolate PAK (NC_014037) from Pakistan. When separate genes were compared, most of the genes shared the highest identities with Pakistani isolate. Phylogenetic analysis of the complete genomic nucleotide and polyprotein amino acid sequences reveals that all SCSMV isolates clustered into two main groups. Both IR-Khuz6 and IR-Khuz57 clustered with isolates from Pakistan (PAK) and India (IND671) in group II but formed a separate subgroup. Population genetic analysis revealed greater between-group than within-group evolutionary divergence values, further supporting the results of the phylogenetic analysis. Th e results indicate that gene fl ow and selection pressure are important evolutionary factors shaping the genetic structure of SCSMV populations with implications for global exchange of sugarcane germplasm.
Modern Applied Science, 2016
Sugarcane leaves showing yellow streak mosaic symptoms were observed in farmers' fields in Kamphaeng Saen, Nakhon Pathom province, during disease surveys conducted in 2010. Diagnosis of symptomatic leaf samples by RT-PCR for Sugarcane mosaic potyvirus failed, but it revealed the presence of Sugarcane streak mosaic virus (SCSMV). SCSMV-infected sugarcane, designated as THA-NP3, was subjected to RNA extraction and RT-PCR-based viral gene cloning and sequencing. The complete genome of THA-NP3 (JN163911) contained 9,781 nucleotides, excluding 3′ poly (A) tail which encoded a polyprotein of 3,130 amino acid residues. Protein sequence analysis indicated nine putative cleavage sites that yielded ten functional proteins namely P1, HC-Pro, P3, 6K1, CI, 6K2, NIa-VPg, NIa-Pro, NIb and CP, and an additional frameshifted PIPO protein. Sequence alignment revealed that THA-NP3 shared 97.84% nucleotide identity with JP2 from China and 81.39-97.78% identities to other recorded SCSMV sequences. Surveys for streak mosaic disease were conducted from 2010 to 2014 at major sugarcane growing areas in five provinces, Nakhon Pathom, Kanchanaburi, Nakhon Ratchasima, Khon Kaen and Udon Thani, and among germplasm collections. The percentages of the infected samples ranged from 43.48-90.91% and 54.17-100% in collected farmers and germplasm fields, respectively. Genetic diversity based on coat protein (CP) coding sequences of 58 Thai SCSMV isolates showed 86.17-100% nucleotide identities among them and 85.70-99.29% identities to isolates from other countries. Phylogenetic analysis of CP sequences indicated two major clusters of virus variants, one in cropping fields and another in germplasm fields. Genetic variations of SCSMV isolates were consistently indicated according to recombination events detected in CP coding regions. These findings represent essential knowledge and should be utilized to improve the SCSMV resistance of sugarcane varieties.
Distribution of Sugarcane mosaic virus in sugarcane plants
Australasian Plant Pathology, 2003
Variation in the concentration of virus in different parts of the plant has implications for virus-indexing programs. To allow more reliable detection of Sugarcane mosaic virus (SCMV), the distribution of the virus in sugarcane plants after artificial inoculation was studied using a reverse transcription polymerase chain reaction (RT-PCR) assay. Leaves of susceptible and moderately resistant sugarcane were mechanically inoculated with SCMV 6 weeks after planting. Weekly for 8 weeks after inoculation, plants were examined for mosaic symptoms and samples of leaves, roots and tillers were tested by RT-PCR to detect virus. SCMV moved from the point of inoculation to younger leaves, roots and tillers and eventually to leaves that emerged prior to inoculation. The pattern of SCMV distribution in moderately resistant and susceptible cultivars was not substantially different. However, the virus moved more slowly in the moderately resistant than in the susceptible cultivar. Young leaves proved to be the most suitable tissue for testing.
Indian phytopathology, 1998
Sixteen potyvirus isolates from sugarcane, maize, sorghum and jowar plants showing typical mosaic symptoms under natural field conditions in different locations of India were compared for biological and serological properties. Results based on different hosts reaction and serological assays (DAC-ELISA, ISEM and Western blotting tests) indicated that potyvirus isolates belonged to two distinct species, viz., sugarcane mosaic virus (SCMV) and maize dwarf mosaic virus (MDMV). SCMV was recorded on sugarcane, maize, sorghum and jowar, and MDMV was only on maize and sorghum.
Archives of Virology, 1999
A virus isolate causing mosaic disease of commercial sugarcane was purified to homogeneity. Electron microscopy revealed flexuous filamentous virus particles of ca 890 × 15 nm. The virus isolate reacted positively with heterologous antiserum to narcissus latent virus form UK, but failed to react with potyvirus group specific antiserum. N-terminal sequencing of the intact coat protein (CP) and the tryptic peptides indicated that the virus was probably a potyvirus but distinct from several reported potyviruses. Comparison of the 3-terminal 1084 nucleotide sequence of the RNA genome of this virus revealed 93.6% sequence identity in the coat protein coding region with the recently described sugarcane streak mosaic virus (Pakistani isolate). The molecular weight of the coat protein (40 kDa) was higher than that deduced from the amino acid sequence (34 kDa). The apparent increase in size was shown to be due to glycosylation of the coat protein which has not been reported thus far in the family, Potyviridae. This is the first report on the molecular characterization of a virus causing mosaic disease of sugarcane in India and the results demonstrate that the virus is a strain of sugarcane streak mosaic virus, a member of the Tritimovirus genus of the Potyviridae. We have named it sugarcane streak mosaic virus-Andhra Pradesh isolate (SCSMV-AP).
Agronomy, 2017
Sugarcane mosaic virus (SCMV) is one among many viruses that infect sugarcane, cause yield loss, and become serious disease agents on sugarcane plantations. Since the morphological symptoms of SCMV are similar to other symptoms caused by Sugarcane streak mosaic virus (SCSMV) or nitrogen deficiency, the detection of SCMV is important through accurate diagnostic-like ELISA or RT-PCR. This research aimed to study the causative mosaic pathogen of SCMV in East Java, Indonesia, including mosaic development. The results showed that the mosaic symptom is present in all sugarcane plantations with 78% and 65% disease incidence and severity, respectively. Moreover, the detection procedure based on an amplification of cDNA of the coat protein gene sequence confirmed that SCMV was the causative agent of mosaic disease on sugarcane. Re-inoculation of healthy sugarcane plants with plant sap from a symptomatic leaf from the field showed similar mosaic or yellowish chlorotic areas on the leaf blade, and appeared on the fourth leaves upward from the inoculation leaf, in addition to showing different levels of peroxidase but not total phenol. Mosaic also correlated with the amount of total chlorophyll. Although Sucrose phosphate synthase (SPS) protein accumulation and activity were at a lower level in infected leaves, sucrose accumulation was at a higher level in the same leaves.
Archives of Virology, 2006
Three isolates of sugarcane mosaic virus (SCMV) from sugarcane and maize in Thailand, were selected and used as viral sources for coat protein (CP) genes cloning by immunocapture reverse transcription polymerase chain reaction (IC-RT-PCR). The CP gene sequences and their deduced amino acids were determined. The sequences of three cloned CP genes, UT6TH-sgc and UD7TH-sgc from sugarcane, and SBC2TH-mz from maize were compared with other previously reported sequences of SCMV-CP gene and their phylogeny were studied. The analysis revealed that Thai SCMV CP gene contained 942 nucleotides encoded for coat protein MW of 33.65 kDa. The nucleotide sequence identity among cloned CPs from three isolates were 98–99% to each other. The N-terminus of the Thai SCMV CP contained a distinctive sequence, especially at nucleotide positions 28–46 of the N-terminal variable 70 amino acid residues which discriminated Thai SCMV from all previously reported SCMV isolates. Thai SCMV were placed in a separate branch of SCMV-MDB cluster which is closely related to most of SCMV isolates from maize, and distinct from the other cluster containing sugarcane-SCMV strains.
A Genetic Shift in the Virus Strains that Cause Mosaic in Louisiana Sugarcane
Plant Disease, 2007
Leaf samples from 693 sugarcane plants showing mosaic symptoms were collected in 2001, 2002, and 2003 at 12 locations within the Louisiana sugarcane industry. Virus isolates associated with the diseased plants were identified using reverse-transcriptase polymerase chain reaction (RT-PCR) to distinguish between Sugarcane mosaic virus (SCMV) and Sorghum mosaic virus (SrMV). No SCMV strain was associated with any diseased plant collected during the survey. RT-PCR-based restriction fragment length polymorphism (RFLP) analysis showed that SrMV strains I, H, and M were associated with 67, 10, and 2% of the plants with mosaic symptoms, respectively. In previous surveys conducted between 1978 and 1995, over 90% of the plants sampled were infected with SrMV strain H. The remaining plants mostly were infected with SrMV strain I, except for an occasional sample with SrMV strain M. RT-PCR showed that approximately 13% of the samples collected between 2001 and 2003 were infected with SrMV, but t...