Peach latent mosaic viroid (PLMVd) is a circular RNA pathogen that replicates in a DNA-independent fashion via a rolling circle mechanism. PLMVd has been shown to self-ligate in vitro primarily via the formation of 2,5-phosphodiester bonds; however, in vivo the occurrence and necessity of this nonenzymatic mechanism are not evident. Here, we unequivocally report the presence of 2,5-phosphodiester bonds at the ligation site of circular PLMVd strands isolated from infected peach leaves. These bonds serve to close the linear conformers (i.e., intermediates), yielding circular ones. Furthermore, these bonds are shown to stabilize the replicational circular templates, resulting in a significant advantage in terms of viroid viability. Although the mechanism responsible for the formation of these 2,5-phosphodiester bonds remains to be elucidated, a hypothesis describing in vivo nonenzymatic self-ligation is proposed. Most significantly, our results clearly show that 2,5-phosphodiester bonds are still present in nature and that they are of biological importance.Viroids are the smallest nucleic acid-based pathogens known to date (see references 15 and 33 for reviews). They are small (ϳ300 nucleotides [nt]), single-stranded, circular RNAs that infect higher plants and cause significant losses in agriculture. Viroids have been classified into two groups (A and B) based primarily on whether or not they possess the five typical structural domains found in the group B viroids. Further division among the 27 group B members depends on the sequence and length of the conserved central regions (7,14,33). Viroids that do not possess any kind of sequence or structural similarity with group B viroids have been classified as belonging to group A. The latter group includes the avocado sunblotch viroid, the peach latent mosaic viroid (PLMVd), and the chrysanthenum chlorotic mottle viroid (7, 15). All group A viroids possess hammerhead self-cleaving motifs and are proposed to replicate in chloroplasts (8,11,23). This localization has received recent support from the identification of a chloroplastic RNA polymerase that has the ability to replicate avocado sunblotch viroid (26). In contrast, group B viroids are localized in the nucleus, and RNA polymerase II appears to be responsible for their replication (4,18,30).In infected cells, viroids replicate in a DNA-independent manner via a rolling circle mechanism that follows either a symmetric or an asymmetric mode (6,8,33,36). The replicational intermediates of PLMVd, a 338-nt group A viroid that is the causal agent of peach latent mosaic disease (19), were recently studied by Northern blot analysis (8). PLMVd has been shown to replicate in a symmetric mode involving the accumulation of both circular and linear monomeric strands of both polarities (see Fig. 1). No multimeric conformer (i.e., intermediate) has been detected, indicating that both strands self-cleave efficiently via their hammerhead sequences. Moreover, it has been observed that monomeric linear RNAs accumulate at a high level...