The Major Sources of Genetic Differentiation Among Apricot Latent Virus (ApLV) Isolates

Authors

  • Reza Pourrahim Plant Virus Research Department, Iranian Research Institute of Plant Protection (IRIPP), Agricultural Research, Education, and Extension Organization (AREEO), P.O.Box 19395-1454. Tehran, Iran.
  • Shirin Farzadfar Plant Virus Research Department, Iranian Research Institute of Plant Protection (IRIPP), Agricultural Research, Education, and Extension Organization (AREEO), P.O.Box 19395-1454. Tehran, Iran.
Abstract:

Background and Aims: Apricot latent virus (ApLV) is a species within Foveavirus genus (Betaflexiviridae family, Tymovirales order). Phylogenetic analyses using different ORFs nucleotide sequences divided most ApLV isolates into two clusters. However, there is little data about the sources of genetic differentiation among ApLV isolates. Materials and Methods: Partial coat protein (CP) sequences of two Iranian ApLV isolates were determined. The complete or partial CP sequences of ApLV isolates available in the GenBank with two partial CP sequences of Iranian isolates were used for phylogenetic analyses. Also, non-overlapping regions of ORFs were considered for molecular analysis using PATRISTIC, MEGAX, and Phylip 3.67 softwares. Results: High nucleotide diversity 0.0 to 39.2 % was indicated for TGB2 gene, followed by CP 0.0 to 30.9 %, RdRp 0.0 to 30.3% and TGB1 0.0 to 25.9 % genes. Although Caserta12 and SB12452 isolates showed the low nucleotide diversity in RdRp, TGB1 and TGB2 genes, but high nucleotide diversity was indicated for them in CP gene (26.7 to 30.9 %). Alignment of CP indicated insertion/deletion may affect the phylogenetic differentiation of ApLV isolates. Comparision of nucleotide diversity within and between groups showing that founder effect may affect the variation of ApLV isolates. The values of FST between ApLV phylogenetic groups were < 0.33 indicating a relative rate of dissociation. Recombination breakpoints were detected in the different ORFs especially in Caserta12 isolate from Italy. The ω ratios (dNS/dS) in various proteins were conserved from 0.035 to 0.073. The ENC plot analysis indicated that the codon usage is affected by selection instead of mutation pressure for all genes except TGB2 gene. In addition, the results of mean CAI values indicated the TGB2 gene as a high expression gene. The genetic exchanges by recombination were also correlated with the appearance of new ApLV strains. ENC-Plot and mean CAI analysis are evaluated for the first time in this study to better explains the evolutionary process and fitness of ApLV. Conclusion: Altogether, our analysis indicated that recombination, mutation and selection pressure are the major sources of genetic differentiation among ApLV isolates.

Upgrade to premium to download articles

Sign up to access the full text

Already have an account?login

similar resources

Differentiation of Virulent and Non-Virulent Newcastle Disease Virus Isolates Using RT-PCR

Newcastle disease is one of the main concerns of poultry farmers. Detection of virulent strains of Newcastle disease virus (NDV) has a great impact on control measures against the disease. In this study RT-PCR was optimized in high sensitivity in order to differentiate the virulent from non-virulent NDV isolates directly in tissue homogenates. The vaccinal NDV strain and known field isolates we...

full text

Genetic Heterogeneity among Leishmania major Isolates in Iran Determined by Restriction Fragment Length Polymorphism (RFLP) and Multilocus Microsatellite Typing (MLMT)

Background & Aims: In recent years, molecular methods for characterizing genetic heterogeneity have found a major place in modern approaches. In this study, two different molecular techniques including Restriction Fragment Length Polymorphism (RFLP) and Multi Locus microsatellite typing (MLMT) were carried out in order to evaluate genetic heterogeneity among isolates of Leishmania major in Iran...

full text

the effect of using visual aids on the development of speech act of disagreement among iranian intermediate efl learners

abstract the present study tried to investigate the effect of visual aids (films) on the development of the speech act of disagreement among iranian efl intermediate learners. to this end, the researcher selected 40 homogeneous intermediate learners based on their scores on oxford placement test. .the subjects then divided into control group and experimental group. both classes were tested by ...

the speech act of advice and the introvert/extrovert distinction among iranian efl university students

the aim of this study is to examine the difference between the introverts and extroverts in preferred advice-giving style. furthermore, it explores the difference between l1 (persian) and l2 (english) regarding the giving of advice for the extroverts and introverts separately. it investigates whether an extrovert or introvert gives advice in the same manner in his l1 (persian) and l2 (english) ...

Deep Sequencing Analysis of Apple Infecting Viruses in Korea

Deep sequencing has generated 52 contigs derived from five viruses; Apple chlorotic leaf spot virus (ACLSV), Apple stem grooving virus (ASGV), Apple stem pitting virus (ASPV), Apple green crinkle associated virus (AGCaV), and Apricot latent virus (ApLV) were identified from eight apple samples showing small leaves and/or growth retardation. Nucleotide (nt) sequence identity of the assembled con...

full text

My Resources

Save resource for easier access later

Save to my library Already added to my library

{@ msg_add @}


Journal title

volume 15  issue None

pages  15- 25

publication date 2021-06

By following a journal you will be notified via email when a new issue of this journal is published.

Keywords

Hosted on Doprax cloud platform doprax.com

copyright © 2015-2023