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Abstract

The present report describes the new occurrence of Tomato mosaic virus (ToMV) in cabbage, bean and Malva neglecta plants in Iran. In this study, sequence analyses of a partial RNA dependent RNA polymerases (RdRp) and complete movement protein (MP) and the coat protein (CP) nucleotide sequences of three new ToMV isolates collected from major crop fields in Iran revealed low genetic variation of RdRp gene compared to the CP and MP genes. The different topologies of the phylogenetic trees constructed, using available open reading frame (ORF1), ORF2 and ORF3 sequences from ToMV isolates, indicated different evolutionary constraints in these genomic regions. Statistical analysis also revealed that with the exception of CP other tested ToMV genes were under negative selection and the RdRp gene was under the strongest constraints. According to the phylogenetic tree it can be inferred from the nucleotide sequences of the complete CP and MP genes, that isolates from Iran and Egypt formed separate groups, irrespective of host origin. However, isolates clustered into groups with correlation to geographic origin but not the host. Analysis of the Ks *, Z* and Snn values also indicated genetic differentiation between ToMV populations. The Tajima’s D, Fu and Li’s statistical values were significantly negative for the RdRp gene of the Asian population which suggests the sudden expansion of ToMV in Asia. Taken together, the results indicate that negative selection and genetic drift were important evolutionary factors driving the genetic diversification of ToMV.
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Abstract

Function of duck (Anas platyrhynchos) major histocompatibility complex class I (Anpl-MHC I) molecules in binding peptides is through the peptide binding groove (PBG), which is thought to be influenced by the high polymorphism of α1 and α2 domains. However, little is known about the polymorphism of Anpl-MHC I peptide binding domain (PBD), especially in the domestic duck. Here, we analyzed the polymorphism of forty-eight Anpl-MHC I α1 and α2 domains from domestic duck breeds previously reported. All sequences were analyzed through multiple sequence alignment and a phylogenetic tree was constructed. The coefficient of variance of the peptide binding domains (PBDs) from WS, CV, JD, and SX duck breeds was estimated based on the Wu-Kabat variability index, followed by the location of the highly variable sites (HVSs) on reported crystal structure models. Analysis of α1 and α2 domains showed common features of classical MHC class I and high polymorphism, especially in α1 domain. The constructed phylogenetic tree showed that PBDs of domestic ducks did not segregate based on breeds and had a close phylogenetic relationship, even with wild ducks. In each breed, HVSs were mostly located in the PBG, suggesting that they might determine peptide-binding characteristics and subsequently influence peptide presentation and recognition. The combined results of sequence data and crystal structure provide novel valuable insights into the polymorphism and diversity of Anpl-MHC I PBDs that will facilitate further studies on disease resistance differences between duck breeds and the development of cytotoxic T-lymphocyte (CTL) epitope vaccines suited for preventing diseases in domestic ducks.
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