SUMMARY Hop stunt viroid (HSVd), genus Hostuviroid, family Pospiviroidae is a circular single-stranded RNA 294-303 nt in size, infecting a large number of woody hosts, such as grapevine, Citrus spp. and Prunus spp. In this study, we report the identification and molecular characteriza- tion of HSVd variants isolated in Turkey from different naturally infected Prunus sources, including apricot, plum and peach. We determined the nucleotide se- quences of eleven isolates and found five new sequence variants of 296 (3 variants) or 297 (2 variants) nt, com- parable in length to previously known HSVd isolates. Multiple alignments and phylogenetic analyses showed that one apricot isolate (HSVd.AP1) clustered with the recombinant P-H/cit3 group, whereas all the others (one apricot; HSVd.AP23, two plum; HSVd.PL49 and HSVd.PL278 and one peach, HSVd.PE73) clustered with the Hop group, confirming the molecular variabili- ty of HSVd isolates. The sequence variability seems to be more related to the geographical origin of the isolates than to their hosts. Key words: HSVd, detection, PCR, characterization, fruit trees, sequencing, viroid. INTRODUCTION Viroids are subviral pathogens whose genome con- sists of a small, circular RNA with a high degree of self- complementarity in its sequence (Diener, 1991). In some well characterized examples, viroid infection has been shown to cause plant diseases that adversely affect agronomic quality. Hop stunt viroid (HSVd) belongs to genus Hostuviroid, family Pospiviroidae and consists of 294-303 nucleotides. HSVd was first described as the causal agent of hop stunt disease in Japan and has since been found in several plant species, particularly in fruit Corresponding author: M. Gazel Fax: +90.326.2455832 E-mail: monagazel@hotmail.com trees such as citrus, pear, peach, apricot, plum and al- mond (Shikata, 1990; Astruc et al., 1996). In some hosts, such as grapevine (Shikata, 1990; Polivka et al., 1996) and apricot (Astruc et al., 1996), infection appears to be la- tent. Recently, HSVd was detected in degenerated apricot trees (Amari et al., 2007). In other hosts, specific disor- ders such as hop stunt (Shikata, 1990), dapple fruit of peach and plum (Sano et al., 1989; Ragozzino et al., 2002) and citrus cachexia (Semancik et al., 1988) have been as- sociated with infection by HSVd. Overall sequence ho- mologies (Shikata, 1990) and phylogenetic analyses (Hsu et al., 1994) indicate that HSVd isolates can be separated into three main groups. Since isolates of each group had only a few isolation hosts, the groups were named plum- type (peach, plum and grapevine isolates), hop-type (hop, grapevine, peach and pear isolates) and citrus-type (citrus and cucumber isolates) (Sano et al., 1989; Shikata, 1990). Recently, Kofalvi et al. (1997) characterized nine new HSVd variants from different Prunus sources, and the grouping of variants was redefined to include two new re- combinant minor groups: plum-citrus type and plum- hop-citrus type (Pallás et al., 2002). Different studies were done to detect HSVd infec- tion rates in different stone fruit species in Turkey. HSVd was detected with infection rates of 14.3%, 57.1%, and 66.6% in plum, peach and apricot, respec- tively (Torres et al., 2004). However, HSVd was not de- tected in sweet or sour cherry samples from eastern Anatolia (Sipahioglu et al., 1999). HSVd was also de- tected in an apricot sample from Turkey and its primary structure was determined (Amari et al., 2000). The studies conducted so far have been concerned with the western and eastern parts of Turkey and have not dealt with the molecular characterization of HSVd except for the apricot isolate (Amari et al., 2001). In this study, a survey was made of the incidence of HSVd in several stone fruit orchards in the eastern Mediter- ranean region, and sequences of variant HSVd isolates were determined. MATERIALS AND METHODS Plant material. A total of 335 samples were collected Journal of Plant Pathology (2008), 90 (1), 23-28 Edizioni ETS Pisa, 2008 23 SEQUENCE VARIABILITY OF HOP STUNT VIROID ISOLATES FROM STONE FRUITS IN TURKEY M. Gazel 1 , C. Ulubas Serce 1 , K. Caglayan 1 and F. Faggioli 2 1 Mustafa Kemal University, Plant Protection Department, 31034 Antakya-Hatay, Turkey 2 CRA, Centro di Ricerca per la Patologia Vegetale, 00156 Rome, Italy