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Sequencing and phylogenetic analysis

FE Fereshteh Esmaeilzadeh
AG Abozar Ghorbani
DK Davoud Koolivand
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We purified and directly sequenced 45 PCR products corresponding to the four RNA segments (RNA1-RNA4) of the TPNRBV genome for each of the nine isolates, as well as the MP gene of the same isolates. Sequencing was performed using the Sanger sequencing method (BGI Tech. Solutions, Shenzhen, China). The obtained sequences were edited and analyzed using BLASTn and were deposited in GenBank as novel TPNRBV sequences from Iran. Sequence alignment was carried out using ClustalW in MEGA 11 (Table ​(Table22)20. The best nucleotide substitution model for phylogenetic analysis was selected using MEGA 11, and phylogenetic trees were constructed using the Maximum Likelihood method with the GTR + G + I model and 1000 bootstrap replicates in MEGA 11 for RNA segments and MP sequences. Bootstrap values below 50% were omitted from the trees.

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