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Genome characterization of citrus yellow vein-clearing virus: limited heterogeneity of viral genomes in Mandarivirus-infecting different citrus species.

ABSTRACT: Citrus yellow vein-clearing virus (CYVCV) is a mandarivirus infecting citrus producing yellow vein-clearing symptoms. The leaf samples collected during surveys of different citrus-growing areas in India exhibited diverse symptoms and 40% of the plants were positive for CYVCV in RT-PCR, indicating the wide distribution of the virus in India. It was reported for first time that CYVCV infects kinnow mandarin and sweet oranges and produces chlorotic ringspots symptoms identical to Indian citrus ringspot virus (ICRSV). The complete genome sequences of CYVCV infecting four citrus cultivars have been deciphered through overlapping primers. All the four genomes comprise of 7531 nucleotides excluding the 3' poly (A) tail. The sequence identity of genomes of four CYVCV isolates in the present study ranged from 95.2 to 99.8% with genome sequences of 31 CYVCV isolates available in public domain and the mean genomic diversity was 0.017, indicating low level of heterogeneity. The phylogenetic analysis revealed that CYVCV isolates from India, Pakistan, and Turkey were clustered in the same clad apart from China isolates. The least normalized dN/dS mean value (0.092) indicated that RdRP region evolved under relatively stronger selection constraints than the other five coding regions of CYVCV. The four intragenic putative recombination events detected in RDP4 program occurred naturally in CYVCV genome, indicating the evolutionary progress of the virus. Tajima's and Fu and Li's D parameters were performed using genomic sequences in DnaSP v5 program and the retrieved negative values indicated the presence of limited genetic variability in CYVCV genomes. To the best of our knowledge, this is the first comprehensive report on molecular characterization of CYVCV from India. It will be helpful in understanding the evolutionary relationship of CYVCV and ICRSV.

SUBMITTER: Meena RP

PROVIDER: S-EPMC6717225 | biostudies-literature | 2019 Sep

REPOSITORIES: biostudies-literature

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Genome characterization of citrus yellow vein-clearing virus: limited heterogeneity of viral genomes in <i>Mandarivirus-</i>infecting different citrus species.

Meena Ram Prasnna RP Prabha K K Baranwal V K VK

3 Biotech 20190830 9

Citrus yellow vein-clearing virus (CYVCV) is a mandarivirus infecting citrus producing yellow vein-clearing symptoms. The leaf samples collected during surveys of different citrus-growing areas in India exhibited diverse symptoms and 40% of the plants were positive for CYVCV in RT-PCR, indicating the wide distribution of the virus in India. It was reported for first time that CYVCV infects kinnow mandarin and sweet oranges and produces chlorotic ringspots symptoms identical to Indian citrus ring ...[more]

PMID: 31497466

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Project description:The Citrus yellow vein clearing virus (CYVCV) causes a viral disease that has been reported in some citrus-growing regions in countries in Eurasia including Pakistan, India, Türkiye, Iran, China, and South Korea. Recently, CYVCV was detected in a localized urban area in a town in the middle of California's citrus-growing region and marks the first occurrence of the virus in North America. CYVCV has been reported to be spread by aphid and whitefly vectors and is graft and mechanically transmitted. Hence, it is an invasive pathogen that presents a significant threat to the California citrus industry, especially lemons, which are highly symptomatic to CYVCV. To elucidate the origin of the CYVCV California strain, we used long-read sequencing technology and obtained the complete genomes of three California CYVCV isolates, CA1, CA2, and CA3. The sequences of these isolates exhibited intergenomic similarities ranging from 95.4% to 97.4% to 54 publicly available CYVCV genome sequences, which indicated a relatively low level of heterogeneity. However, CYVCV CA isolates formed a distinct clade from the other isolates when aligned against other CYVCV genomes and coat protein gene sequences as shown by the neighbor network analysis. Based on the rooted Maximum Likelihood phylogenetic trees, CYVCV CA isolates shared the most recent common ancestor with isolates from India/South Asia. Bayesian evolutionary inferences resulted in a spatiotemporal reconstruction, suggesting that the CYVCV CA lineage diverged from the Indian lineage possibly around 1995. This analysis placed the origin of all CYVCV to around 1990, with South Asia and/or Middle East as the most plausible geographic source, which matches to the first discovery of CYVCV in Pakistan in 1988. Moreover, the spatiotemporal phylogenetic analysis indicated an additional virus diffusion pathway: one from South Asia to China and South Korea. Collectively, our phylogenetic inferences offer insights into the probable dynamics of global CYVCV dissemination, emphasizing the need for citrus industries and regulatory agencies to closely monitor citrus commodities crossing state and international borders.

Project description:Osteosarcoma is an aggressive malignancy characterized by high genomic complexity. Identification of few recurrent mutations in protein coding genes suggests that somatic copy-number aberrations (SCNA) are the genetic drivers of disease. Models around genomic instability conflict-it is unclear whether osteosarcomas result from pervasive ongoing clonal evolution with continuous optimization of the fitness landscape or an early catastrophic event followed by stable maintenance of an abnormal genome. We address this question by investigating SCNAs in >12,000 tumor cells obtained from human osteosarcomas using single-cell DNA sequencing, with a degree of precision and accuracy not possible when inferring single-cell states using bulk sequencing. Using the CHISEL algorithm, we inferred allele- and haplotype-specific SCNAs from this whole-genome single-cell DNA sequencing data. Surprisingly, despite extensive structural complexity, these tumors exhibit a high degree of cell-cell homogeneity with little subclonal diversification. Longitudinal analysis of patient samples obtained at distant therapeutic timepoints (diagnosis, relapse) demonstrated remarkable conservation of SCNA profiles over tumor evolution. Phylogenetic analysis suggests that the majority of SCNAs were acquired early in the oncogenic process, with relatively few structure-altering events arising in response to therapy or during adaptation to growth in metastatic tissues. These data further support the emerging hypothesis that early catastrophic events, rather than sustained genomic instability, give rise to structural complexity, which is then preserved over long periods of tumor developmental time.SignificanceChromosomally complex tumors are often described as genomically unstable. However, determining whether complexity arises from remote time-limited events that give rise to structural alterations or a progressive accumulation of structural events in persistently unstable tumors has implications for diagnosis, biomarker assessment, mechanisms of treatment resistance, and represents a conceptual advance in our understanding of intratumoral heterogeneity and tumor evolution.

Dataset Information

Genome characterization of citrus yellow vein-clearing virus: limited heterogeneity of viral genomes in Mandarivirus-infecting different citrus species.

Publications

Genome characterization of citrus yellow vein-clearing virus: limited heterogeneity of viral genomes in <i>Mandarivirus-</i>infecting different citrus species.

Similar Datasets

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