Abstract
Abstract Reverse Transcription Polymerase Chain Reaction (RT-PCR) using new designed primers pair for Heat Shock Protein70 homologue (HSP70h) of Olive leaf yellowing-associated virus revealed 667 amplified product of 10 olive accessions collected from various olive-growing regions in Tunisia. Amplicons were cloned and sequenced. The sequences were deposited in the international databases. Pairwise sequence comparisons among 10 Tunisian isolates along with a reference sequence (AJ440010) extracted from GenBank revealed a nucleotide identity of 86.06-99.40 and an amino acid similarity of 91.89-99.55. Sequence multiple alignments were searched for evidence of recombination using three methods, ie. Differences of Sums of Squares (DSS) implemented in TOPALi v2.5 software and Single Breakpoint (SBP) along with GARD, a genetic algorithm, both incorporated in HyPhy package. All used methods pointed out the presence of putative breaking points in partially sequenced HSP70h-coding gene. Since failing to account for recombination can mislead the phylogeny inference and can elevate the false positive error rate in positive selection assessment, the use of GARD resulted in the reconstruction of different phylogenies on the left as well as on the right sides of putative recombination breaking points, and the 11 accessions were distributed into at least three clusters compared to MEGA6 software which delineated only two clades. Nonetheless, by dividing the aligned sequences at breakpoints into separate sequence sets, MEGA6 delineated a clustering pattern different from the former two. As a result, recombination reshuffled the affiliation of the different accessions to the clusters. Analysis of selection pressures exerted on HSP70h encoded protein using different models (SLAC, IFEL, FEL, REL, PARRIS, FUBAR, MEME, GA Branch, and PRIME) taking into account recombination, and implemented in HyPhy package, revealed that it underwent predominantly purifying selection as confirmed by Tajima’s D, Fu and Li’s D and F tests, and SNAP algorithm. However, a few sites were also under positive selection as assessed by various models such as FEL, IFEL, REL, MEME, and PRIME.
Highlights
Viruses represent an important threat to plant production worldwide
Differences of Sums of Squares (DSS) implemented in TOPALi v2.5 software and Single Breakpoint (SBP) along with GARD, a genetic algorithm, both incorporated in HyPhy package
Viral populations would respond to changing selection pressure, and the evolution of high mutation rates would have an adaptive behaviour, allowing the virus to survive in changing environments
Summary
Viruses represent an important threat to plant production worldwide. In spite of numerous efforts for their elimination, the number of these viruses is still noticeably limited. A value of less than 1 indicates that a gene is under the influence of negative or purifying selection Recombination is another driving force of plant RNA virus evolution. In addition to increasing sequence variability, RNA recombination can be an efficient tool for viruses to repair viral genome, contributing to viral fitness [2] [3] [4] [5] [6] [7] It may play a role in the formation of subviral RNAs that include defecting interfering (DI) RNAs associated with many plant viruses, i.e. some members of the Tombusviridae [8]. DI-RNAs are mainly derived from the parent (helper) virus via sequence deletion The ease of their genetic manipulation has resulted in rapid discoveries on cisacting RNA replication elements required for replication and recombination [4]. They could trigger potent gene silencing response against the helper virus without hurting themselves from the same response [9]
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