Analysis of the genetic diversity of genome sequences of variants of apple hammerhead viroid

Abstract

A dataset of approximately 85 apple hammerhead viroid (AHVd) genome sequences was analysed to determine genetic diversity. Sequences analysed included 18 new AHVd variants detected in a 2017/2018 survey, as well as suitable sequences deposited in GenBank. Two phylogenetically distinct clades were observed. A range of indel events was identified with most AHVd sequences ranging in size from 433 to 435 nt. None of these events appear to affect the predicted secondary structure of AHVd, which was well supported by a prevalence of unambiguous covariation events and or substitutions resulting in the conversion of canonical to wobble sequences, or vice versa. All AHVd variants analysed possess the 13 nt that are conserved in most hammerheads of viroids and viroid-like satellite RNA, except at positions 146 and 149. No significant recombination event was identified.