Abstract
Botryosphaeria dothidea is a widespread and economically important pathogen on various fruit trees, and it often causes die-back and canker on limbs and fruit rot. In characterizing intraspecies genetic variation within this fungus, group I introns, rich in rDNA of fungi, may provide a productive region for exploration. In this research, we analysed complete small subunit (SSU) ribosomal DNA (rDNA) sequences of 37 B. dothidea strains, and found four insertions, designated Bdo.S943, Bdo.S1199-A, Bdo.S1199-B and Bdo.S1506, at three positions. Sequence analysis and structure prediction revealed that both Bdo.S943 and Bdo.S1506 belonged to subgroup IC1 of group I introns, whereas Bdo.S1199-A and Bdo.S1199-B corresponded to group IE introns. Moreover, Bdo.S1199-A was found to host an open reading frame (ORF) for encoding the homing endonuclease (HE), whereas Bdo.S1199-B, an evolutionary descendant of Bdo.S1199-A, included a degenerate HE. The above four introns were novel, and were the first group I introns observed and characterized in this species. Differential distribution of these introns revealed that all strains could be separated into four genotypes. Genotype III (no intron) and genotype IV (Bdo.S1199-B) were each found in only one strain, whereas genotype I (Bdo.S1199-A) and genotype II (Bdo.S943 and Bdo.S1506) occurred in 95% of the strains. There is a correlation between B. dothidea genotypes and hosts or geographic locations. Thus, these newly discovered group I introns can help to advance understanding of genetic differentiation within B. dothidea.
Highlights
Group I introns, a class of RNAs with autocatalytic activity that was initially discovered in Tetrahymena, are known as ribozymes [1]
Four types of insertions were found at three different sites of the nuclear small subunit (SSU) ribosomal DNA (rDNA) in Botryosphaeria dothidea
Distribution of these introns among the 37 B. dothidea strains provided clear evidence of genetic diversity within this species. Both Bdo.S943 and Bdo.S1506 were found to belong to subgroup IC1 with the typical characteristics of group I intron, namely, size ranging from 250–500 nt and approximately ten paired elements [36]
Summary
Group I introns, a class of RNAs with autocatalytic activity that was initially discovered in Tetrahymena, are known as ribozymes [1] Their characteristic RNA folds consist generally of 10 conserved paired elements (P1 to P10) that can help catalyze a two-step, self-splicing transesterification reaction resulting in intron release and ligation of the exons [2]. & De Not. was designated as the type species by Barr [8] and Slippers et al [9] Ubiquitous and cosmopolitan, it has been found in most tropical and warm temperate regions as a pathogen on dozens of economically important shrub and tree fruit crops including apple, pistachio, peach, grape and blueberry, causing symptoms such as die-back, stem and shoot blight, gummosis, canker and fruit rot [10,11,12,13,14]. Peng et al [16] separated the isolates causing apple ring rot into two distinct groups by ITS sequence and ISSR diversity analysis
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