A Diverse Population of Introns in the Nuclear Ribosomal Genes of Ericoid Mycorrhizal Fungi Includes Elements with Sequence Similarity to Endonuclease-Coding Genes

Molecular Biology and Evolution, Jan 2000

Ericoid mycorrhizal fungi form symbioses with the roots of members of the Ericales. Although only two genera have been identified in culture, the taxonomic diversity of ericoid symbionts is certainly wider. Genetic variation among 40 ericoid fungal isolates was investigated in this study. PCR amplification of the nuclear small-subunit ribosomal DNA (SSU rDNA) and of the internal transcribed spacer (ITS), followed by sequencing, led to the discovery of DNA insertions of various sizes in the SSU rDNA of most isolates. They reached sizes of almost 1,800 bp and occurred in up to five different insertion sites. Their positions and sizes were generally correlated with morphological and ITS-RFLP grouping of the isolates, although some insertions were found to be optional among isolates of the same species, and insertions were not always present in all SSU rDNA repeats within an isolate. Most insertions were identified as typical group I introns, possessing the conserved motifs characteristic of this group. However, other insertions lack these motifs and form a distinct group that includes other fungal ribosomal introns. Alignments with almost 70 additional sequences from fungal nuclear SSU rDNA introns indicate that introns inserted at the same site along the rDNA gene are generally homologous, but they also suggest the possibility of some horizontal transfers. Two of the ericoid fungal introns showed strong homology with a conserved motif found in endonuclease genes from nuclear rDNA introns.

A PDF file should load here. If you do not see its contents the file may be temporarily unavailable at the journal website or you do not have a PDF plug-in installed and enabled in your browser.

Alternatively, you can download the file locally and open with any standalone PDF reader:

https://mbe.oxfordjournals.org/content/17/1/44.full.pdf

A Diverse Population of Introns in the Nuclear Ribosomal Genes of Ericoid Mycorrhizal Fungi Includes Elements with Sequence Similarity to Endonuclease-Coding Genes

Silvia Perotto 2 Paola Nepote-Fus 0 Laura Saletta 2 Claudio Bandi 1 J. Peter W. Young 3 0 Dipartimento di Biologia Vegetale dell'Universita` , Turin , Italy 1 Istituto di Patologia Generale Veterinaria , Milan , Italy 2 Centro Studio Micologia del Terreno-CNR 3 Department of Biology, University of York , York, England Ericoid mycorrhizal fungi form symbioses with the roots of members of the Ericales. Although only two genera have been identified in culture, the taxonomic diversity of ericoid symbionts is certainly wider. Genetic variation among 40 ericoid fungal isolates was investigated in this study. PCR amplification of the nuclear small-subunit ribosomal DNA (SSU rDNA) and of the internal transcribed spacer (ITS), followed by sequencing, led to the discovery of DNA insertions of various sizes in the SSU rDNA of most isolates. They reached sizes of almost 1,800 bp and occurred in up to five different insertion sites. Their positions and sizes were generally correlated with morphological and ITS-RFLP grouping of the isolates, although some insertions were found to be optional among isolates of the same species, and insertions were not always present in all SSU rDNA repeats within an isolate. Most insertions were identified as typical group I introns, possessing the conserved motifs characteristic of this group. However, other insertions lack these motifs and form a distinct group that includes other fungal ribosomal introns. Alignments with almost 70 additional sequences from fungal nuclear SSU rDNA introns indicate that introns inserted at the same site along the rDNA gene are generally homologous, but they also suggest the possibility of some horizontal transfers. Two of the ericoid fungal introns showed strong homology with a conserved motif found in endonuclease genes from nuclear rDNA introns. Introduction Ericoid mycorrhizal fungi are a diverse group of fungi that form symbiotic associations with plants in the Ericales (Perotto et al. 1995; Read 1996; Straker 1996). The fine roots of these plants are colonized in nature by both Ascomycetes and Basidiomycetes (Bonfante 1980; Peterson, Mueller, and Englander 1980), but taxonomic identification is confined to the Ascomycetes, as Basidiomycetes symbionts have not yet been isolated in pure culture. Species from two genera are reported as mycorrhizal partners of ericaceous plants: Hymenoscyphus ericae (Read) Korf and Kernan (Read 1974), with its anamorph Scytalidium vaccinii Dalpe, Litten, and Siegler (Egger and Siegler 1993), and Oidiodendron spp. (Couture, Fortin, and Dalpe 1983; Dalpe 1986), with their teleomorphs in the Gymnoascaceae and Mixothricaceae (Dalpe 1989; Hambleton et al. 1998). Sterile mycelia with different colony morphologies have also been described as common symbionts of ericoid roots in North America (Stoyke, Egger, and Currah 1992; Hambleton and Currah 1997), Europe (Duclos and Fortin 1983; Perotto et al. 1990, 1996), South Africa (Straker and Mitchell 1985), and Australia (Hutton, Dixon, and Sivasithamparam 1994; Liu, Chambers, and Cairney 1998), where they often form the majority of mycorrhizal isolates. Their taxonomic position, however, is unknown because they lack the morphological structures that could be used for identification. The nuclear ribosomal genes have been extensively used for taxonomic purposes in fungi (e.g., Berbee and Taylor 1993; Gargas et al. 1995). Therefore, we have begun to sequence these genes to determine the genetic diversity of ericoid mycelia collected worldwide, focusing on the nuclear small subunit (SSU) rDNA genes and the internal transcribed sequences (ITSs). While sequencing the SSU rDNA, we have discovered introns in most of the ericoid isolates. The presence and sequence of an intron in the SSU rDNA of one H. ericae isolate has already been reported by Egger, Osmond, and Goodier (1995). In this paper, we analyzed the entire SSU rDNA of several isolates of H. ericae and of Oidiodendron spp., as well as representatives of 16 groups of sterile mycelia. The sites of intron insertion have been mapped in all isolates and shown to occur at five different positions, including sites rarely described in fungi. Sequence analysis demonstrates that many of these introns belong to group I. Group I introns are a structural and functional group with a widespread but irregular distribution (Dujon 1989) and are frequently found in lower eukaryotes, especially algae and fungi (Dujon 1989; Johansen, Muscarella, and Vogt 1996). They occur at several locations along the chloroplast and mitochondrial genome, including protein coding genes, but in the nuclear genome they seem to be restricted to the rDNA genes. Several have been shown to splice both in vitro and in vivo due to the autocatalytic properties of the intron RNA. Insertion in intronless copies of the same gene, a process called homing (Cech 1990), is usually catalyzed by an intron-encoded DNA endonuclease (Belfort and Roberts 1997), although alternative (...truncated)


This is a preview of a remote PDF: https://mbe.oxfordjournals.org/content/17/1/44.full.pdf

Silvia Perotto, Paola Nepote-Fus, Laura Saletta, Claudio Bandi, J. Peter W. Young. A Diverse Population of Introns in the Nuclear Ribosomal Genes of Ericoid Mycorrhizal Fungi Includes Elements with Sequence Similarity to Endonuclease-Coding Genes, Molecular Biology and Evolution, 2000, pp. 44-59, 17/1,