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Canadian Food Inspection Agency, Ottawa Laboratory (Fallowfield), Centre for Plant Quarantine Pests, 3851 Fallowfield Road, Ottawa, Ontario, K2H 8P9 Canada
Mireille Prudhomme
Health Canada, Food Directorate, Building No. 7, Tunneys Pasture, P.L. 0700E1, Ottawa, Ontario, K1A 0L2 Canada
Allison J. Meldrum
Canadian Food Inspection Agency, Ottawa Laboratory (Fallowfield), Centre for Plant Quarantine Pests, 3851 Fallowfield Road, Ottawa, Ontario, K2H 8P9 Canada
Marie-Claude Tardif
Health Canada, Food Directorate, Building No. 7, Tunneys Pasture, P.L. 0700E1, Ottawa, Ontario, K1A 0L2 Canada
| ABSTRACT |
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A group I intron of 418 base pairs in the Monilinia fructicola ribosomal small-subunit sequence was characterized. The absence of such an intron in M. laxa and M. fructigena led to a PCR test for M. fructicola identification based on the presence of this intron. The failure to amplify a PCR fragment for some isolates of M. fructicola recently lead to speculation that the intron might not be present always in M. fructicola. In this study, we analyzed 13 isolates of M. fructicola and found that the intron was absent in four isolates and we determined from sequence analysis that there are several nucleotide variations that allow the M. fructicola ribosomal SSU intron to be grouped into 6 polymorphic types.
Key words: 18S rRNA, brown rot, group I intron sequences
| INTRODUCTION |
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Group I introns are recognized by a particular secondary structure and splicing pathway (Cech and Herschlag 1996
) and are common in rDNA sequences of fungi and algae ( Johansen et al 1996
). It also was demonstrated that a common characteristic of group I introns was their insertion in the same position of the SSU independent of the phylogeny of the host organism (Bhattacharya et al 1996
, Gargas et al 1995
, Hibbett 1996
). The group I intron present in the SSU rDNA of M. fructicola, which is located at position 943 relative to Escherichia coli ribosomal SSU (GenBank accession: ECORRD) or position 1165 relative to Saccharomyces cerevisiae ribosomal SSU (GenBank accession: YSCRGEA) is not found in M. fructigena or M. laxa. However, several more-distant fungi, green algae and amoebae have a group I intron in the same position of the SSU rDNA (Gargas et al 1995
).
PCR primers for the M. fructicola SSU rDNA intron and some of the SSU sequence were developed for species identification (Fulton and Brown 1997
). Recently there have been reports that the intron-containing PCR product does not always occur in isolates thought to be M. fructicola, suggesting that some isolates lack the intron (Förster and Adaskaveg 2000
, Hughes et al 2000
). The objective of this study was to look for the SSU rDNA intron in 13 isolates of M. fructicola by using PCR with different primer pairs and, when the intron was present, to analyze the sequence. Four M. fructicola isolates did not have the intron. By analyzing the intron sequence in the remaining isolates, we could distinguish five polymorphic groups, one of them corresponding to the sequence published by Fulton and Brown (1997)
. The intron sequence published by Snyder and Jones (1999)
and not found in this study was classified into a sixth polymorphic group.
| MATERIALS AND METHODS |
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PCR amplification (RAPD and sequence-specific).
All PCR reactions were performed with Invitrogen Canada reagents (Burlington, Ontario). All sequence-specific primers were synthesized by Invitrogen Canada (Burlington, Ontario). The random primer 353 (5'-TGG GCT CGC T-3') used for RAPD analysis was synthesized by the University of British Columbia, Canada (Dr. John Hobbs Nucleic Acid-Protein Service [NAPS] Unit Biotechnology Laboratory). PCR amplifications using specific primers were performed with 1 µL of a 1/10 or 1/100 dilution of mycelial DNA (120
g/ µL) in a solution of 20 mM Tris-HCl pH 8.4, 50 mM KCl, 200 µM of each dNTP, 2.0 mM MgCl2 and 0.025 units/µL Taq polymerase. One type of reaction included primers NS3 (5'-GCA AGT CTG GTG CCA GCA GCC-3'; White et al 1990
) and NS6 (5'-GCA TCA CAG ACC TGT TAT TGC CTC-3'; White et al 1990
) at 0.2 µM each. Another set of reactions employed primer: NS5 (5'-AAC TTA AAG GAA TTG ACG GAA G-3'; White et al 1990
) paired with mfs-3 (5'-CAC TCG AAA GCA TTG AGT TG-3'; Fulton and Brown 1997
), nu-SSI(943)-251-3'-Mf (Nomenclature: Gargas and DePriest 1996
) (5'-CCA TTC CCA TTT AGT CTC TG-3') or NS6 at 0.4 µM each. Amplification reactions were carried out in a GeneAmp 9600 PCR System thermocycler (Applied Biosystems, Foster City, California) for primer pair NS3NS6, with an initial denaturation of 94 C for 2 min, followed by 35 cycles of 94 C for 15 s, annealing at 58 C for 30 s, extension at 72 C for 1 min and, after the last cycle, a final extension at 72 C for 3 min; or in a PTC-200 DNA engine thermocycler (MJ Research, Watertown, Massachusetts) for primer pairs NS5-mfs-3 and NS5-nu-SSI(943)-251-3'-Mf using essentially the same program with a modified annealing step of 60 C for 15 s. Reactions using the primer pair NS5-NS6 differed by using 30 cycles of 95 C for 15 s, annealing at 35 C for 15 s and extension at 72 C for 1 min. The relative positions for primers are shown in FIG. 1, except for primer NS3, which is 575 bp upstream of NS5, and primer NS6, which is 270 bp downstream the intron sequence. For RAPD amplifications approximately 1 µL of a 1/20 dilution of DNA (120
g/µL) was amplified in 10 mM Tris-HCl pH 8.3, 50 mM KCl, 200 µM of each dNTP, 2.5 mM MgCl2, 0.95 µM 10-mer random primer and 0.5 unit of Taq polymerase (Invitrogen Canada, Burlington, Ontario, Canada) for a total volume of 20 µL. The reactions were carried out in a Perkin-Elmer 9600 thermocycler (Applied Biosystems, Foster City, California) with an initial denaturation at 94 C for 3 min, followed by 35 cycles of 94 C for 5 s, 35 C for 30 s, a 2 min ramping to 72 C (0.3 C/sec) and an extension at 72 C for 2.5 min and a final extension at 72 C for 3 min. Amplified products were visualized under ultraviolet light after electrophoresis in 1.5% agarose gels and staining with ethidium bromide.
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ATP) primers NS5, NS6, nu-SSI(943)-251-3'-Mf and nu-SSI(943)-231-5'-Mf (5'-CGC ATC CTT TCC CTT CAT ACG C-3', see FIG. 1 for relative position) using the Thermo Sequenase Cycle Sequencing Kit (USB Corp., Cleveland, Ohio), following the manufacturers instructions. Sequencing reactions were fragmented on 6% polyacrylamide-8M urea gel, and after autoradiography the sequences were read with a Hitachi Tablet Digitizer and analyzed with DNASIS® Sequencing Analysis software for Windows (Helixx Technologies Inc., Toronto, Ontario, Canada). | RESULTS |
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| DISCUSSION |
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A group I intron has been characterized in the ribosomal SSU of M. fructicola (Fulton and Brown 1997
). PCR primers designed to amplify a region containing 26 bp of the ribosomal SSU rDNA upstream region and most of the intron sequence failed to produce an amplified product from some M. fructicola isolates (this study, Förster and Adaskaveg 2000
, Hughes et al 2000
). Furthermore, some Japanese isolates of M. fructicola were shown to lack the intron (Fulton et al 1999
). The present study showed that the absence of amplification can result not only from the absence of an intron but also from nucleotide variations in the intron mfs-3 priming site (FIG. 1).
The sequence of the polymorphic type A intron (Fulton and Brown 1997
) was folded into its presumed secondary structure following the structural conventions for group I introns of Burke et al (1984) (FIG. 4). Nucleotide variations observed among the sequences of the different polymorphic types of the M. fructicola introns are indicated on the secondary structure shown in FIG. 4. It was observed that none of the nucleotide variations occur in the conserved elements P, Q, R, S, and most of the variations do not occur in the pairing (P) segments responsible for the secondary structure of the group I intron (Waring and Davies 1984
) (FIG. 4). When a nucleotide substitution occurs in a pairing segment, it is expected that there will be either a compensating change in the pairing nucleotide or the variation will have a minor effect on the integrity of the pairing segment (FIG. 4). The optional presence of group I introns in SSU rDNA within a fungal species, and also within fungal populations, has been well documented (DePriest and Been 1992
, DePriest 1993
). Optional group I introns in SSU rDNA, at position 1165 relative to Saccharomyces cerevisiae SSU rDNA, in some or most isolates of the same species of fungi have been reported for Beauveria bassiana (Coates et al 2002
), Histoplasma capsulatum (Lasker et al 1998
), Hymenoscyphus ericae (Perotto et al 2000
) and Ophiosphaerella narmari (Wetzel et al 1999
). All of the above ribosomal SSU introns are located at the same position as the M. fructicola ribosomal SSU intron and their sequences aligned properly. It was demonstrated that the presence of the Ophiosphaerella narmari intron was not evenly distributed among all ribosomal tandem repeats (Wetzel et al 1999
). Therefore, it was possible that the presence of one copy of the M. fructicola intron remained undetected in a PCR reaction using primers NS5NS6 by simply having been out-competed by the intronless PCR product that would be favored by its size and number of copies. This possibility was assessed by using a reverse primer complementary to the conserved R internal element (Waring and Davies 1984
) paired with NS5 so it would amplify any polymorphic type of intron present at low copy number. From our experiment, we conclude that the absence of the ribosomal SSU intron in the four M. fructicola isolates would be uniform throughout the ribosomal tandem repeats.
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The accumulation of nucleotide variation among introns from isolates of M. fructicola, together with the broad distribution of isolates possessing introns, would suggest a long association between the intron at position 1165 and this species. If so, the occurrence of intron-containing and intronless isolates from the same locations in Ontario and British Columbia therefore might reflect random intron deletion events. On the other hand, it is possible that the intron has an evolutionary history apart from that of M. fructicola and that the current intron distribution in M. fructicola represents multiple insertion events. To address this question fully, more isolates of M. fructicola from different locations will have to be investigated and relationships among isolates will have to be compared with relationships among introns.
In summary, PCR and sequence analysis of the ribosomal SSU of M. fructicola isolates confirmed the absence of the previously characterized group I intron in some of the isolates. Furthermore, the analysis demonstrated that across isolates the intron displays nucleotide substitutions and insertions. Comparisons among the intron sequences obtained in this study and those published previously (Fulton and Brown 1997
, Snyder and Jones 1999
) resulted in the identification of six polymorphic types (FIG. 1) that may relate in part to isolate origin.
| ACKNOWLEDGMENTS |
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| FOOTNOTES |
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1 Corresponding author. E-mail: cotemj{at}inspection.gc.ca
| LITERATURE CITED |
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