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Mycologia, 96(5), 2004, pp. 981-989.
© 2004 by The Mycological Society of America

The mitochondrial genome of Saprolegnia ferax: organization, gene content and nucleotide sequence


W. Scott Grayburn
Deborah S. S. Hudspeth
Melody K. Gane
Michael E. S. Hudspeth 1

     Department of Biological Sciences, Northern Illinois University, DeKalb, Illinois 60115

    ABSTRACT
 TOP
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
 RESULTS
 DISCUSSION
 LITERATURE CITED
 

The mitochondrial genome of the peronosporomycete water mold Saprolegnia ferax has been characterized as a 46 930 bp circle containing an 8618 bp large inverted repeat (LIR). Eighteen reading frames encode identified subunits of respiratory complexes I, III, IV and V; 16 encode polypeptides of small and large mitoribosome subunits; and one encodes a subunit of the sec-independent protein translocation pathway. Of four additional putative reading frames three are homologues of those found in the related Phytophthora infestans genome. Protein encoding loci in the tightly compacted genome typically are arranged in operon-like clusters including three abutting and two overlapping pairs of reading frames. Translational RNAs include the mitochondrial small and large subunit rRNAs and 25 tRNA species. No tRNAs are encoded to enable translation of any threonine or the arginine CGR codons. The LIR separates the molecule into 19 274 bp large and 10 420 bp small single copy regions, and it encodes intact duplicate copies of four reading frames encoding known proteins, both rRNAs, and five tRNAs. Partial 3' sequences of three additional reading frames are duplicated at single copy sequence junctions. Active recombination between LIR elements generates two distinctive gene orders and uses the duplicated 3' sequences to maintain intact copies of the partially duplicated loci.

Key words: mitochondrial genes, mtDNA, Oomycetes, Peronosporomycetes, stramenopiles


    INTRODUCTION
 TOP
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
 RESULTS
 DISCUSSION
 LITERATURE CITED
 
Ascertaining the genetic content and mitochondrial organization of lower eukaryotes has been invaluable in providing insight into mitochondrial origins and in demonstrating the diversity of mitochondrial genomes (reviewed in Gray et al 1998Go, Lang et al 1999Go). Genetically, variation in the number of identified protein-encoding loci ranges from 3 to 67, tRNAs from 0 to 27 and rRNAs from 0 to 3. The assembled sequence data physically describe the 6–77 kb range of genomes as compact gene-rich circular or linear molecules of high AT content. Despite these variations mtDNAs of recognized eukaryotic lineages are consistent in their overall genetic and physical organization. Thus, mitochondrial genomes of protists are potentially useful tools for resolving evolutionary relationships between organisms whose morphological and biochemical characters often are limited and/or difficult to obtain.

The Peronosporomycetes (Oomycetes) are a class of fungal-like protists included in an assemblage of lower eukaryotes often referred to as stramenopiles (Patterson 1989Go, Dick 2001Go). Members of this lineage are unified taxonomically by the presence of tripartite tubular hairs (stramenopiles) at some stage of their life cycle. The diverse collection of organisms also includes autotrophic chromophytes (chlorophyll a + c containing algae such as chrysophytes, fucophytes, xanthophytes and diatoms), additional fungal-like heterotrophs (thraustochytrids, labyrinthulids and hyphochytriomycetes) and the heterotrophic bicosoecids. Complete mitochondrial DNA sequences have been determined for six of these organisms—the chromophytes Chrysodidymus synuroideus (Chesnick et al 2000Go), Laminaria digitata (Oudot-LeSeq et al 2002Go), Ochromonas danica (Burger et al 2002) and Pylaiella littoralis (Oudot-LeSeq et al 2001Go); the heterotrophic bicosecid Cafeteria roenbergensis (Burger 1999Go); and the peronosporomycete Phytophthora infestans (Paquin et al 1997Go). Like most protists, mitochondrial genomes of peronosporomycetes typically are compact mtDNAs and encode at least 30 polypeptides of known function.

Two distinct mtDNA organizational patterns have emerged from restriction endonuclease analyses of a variety of peronosporomycete taxa. The more prevalent LIR pattern initially was described for Achlya ambisexualis (Hudspeth et al 1983Go) and subsequently was found in at least some representatives from all other examined orders, with the exception of the Leptomitales. This pattern features a large inverted repeat, ranging from about 8.5 to 28.9 kb (Hudspeth and Hudspeth 1996Go), which separates the molecule into small and large single copy regions. Intramolecular recombination events between the repeat elements in Achlya (Hudspeth et al 1983Go, Boyd et al 1984Go) were shown to generate two equimolar orientational genome isomers, each with its own gene order.

In the less prevalent non-LIR pattern, initially described for Phytophthora infestans (Klimczak and Prell 1984Go) of the order Pythiales, the LIR is conspicuously absent. Non-LIR genomes subsequently have been described only for additional Phytophthora species (Forster et al 1987Go, Shumard-Hudspeth and Hudspeth 1990Go) and Apodachlya and Leptomitus of the Leptomitales (McNabb and Klassen 1988Go, Hudspeth 1992Go).

In this work we report the complete mtDNA sequence for the peronosporomycete Saprolegnia ferax, compare it with the non-LIR pattern P. infestans, and examine the consequences of active intramolecular recombination events between LIR elements.


    MATERIALS AND METHODS
 TOP
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
 RESULTS
 DISCUSSION
 LITERATURE CITED
 
Culturing of Saprolegnia ferax and DNA isolation. – Stock cultures of Saprolegnia ferax (ATCC 36051) were obtained from I.B. Heath (York University, Toronto, Canada), maintained on potato-dextrose or cornmeal agar (Difco Laboratories, Troy, Michigan) and stored at 4 C. Mycelia for DNA preparations were propagated as 16 L peptone yeast glucose (PYG; Griffin et al 1974Go) aerated carboys at ambient temperatures.

Total DNA was prepared from late log-phase mycelia with purified mtDNA obtained as the upper band in bis-benzimide (Hoechst 33258; Calbiochem, La Jolla, California) CsCl gradients (Hudspeth et al 1980Go, Shumard et al 1986Go). Plasmid DNAs were isolated by the alkaline lysis method (Birnboim and Doly 1979Go).

Cloning and DNA sequencing. – Before sequencing of the genome, a preliminary seven-enzyme restriction map was constructed to approximate the limits of the LIR. Initial DNAs for sequencing then were prepared from clones generated from a combination of mapped EcoRI or unmapped HindIII restriction fragments ligated into pUC19 and transformed into E. coli JM83 following established procedures (Maniatis et al 1982Go). Clones were sequenced using sequence-generated primers prepared using either a 392 or PCRmate 391 DNA synthesizer (Applied Biosystems, Foster City, California) or were obtained commercially (MWG Biotech, High Point, North Carolina). Positions of abutting EcoRI or HindIII clones were confirmed by sequencing of mtDNA PCR products generated by crossing of presumptive adjacent restriction sites. Regions of sequence not included in the initial clones were generated by direct sequencing of purified mtDNA using primers derived from sequenced noncontiguous clones. Subsequent PCR products were generated and sequenced to include these regions. DNA sequence data were obtained using a 373 DNA Sequencer (Applied Biosystems, Foster City, California) or a Beckman Coulter CEQ 2000XL automated DNA sequencer (Beckman Coulter, Fullerton, California).

Sequence data were assembled using Sequencher (Gene Codes Corp., Ann Arbor, Michigan). Protein-encoding and rRNA loci were identified using the NCBI BLASTP and BLASTN similarity searches (Altschul et al 1990Go). tRNAs were identified using tRNAscan-SE (Lowe and Eddy 1997Go). Protein alignments were performed using the Clustal X program (Thompson et al 1997Go).

The complete mtDNA sequence has been deposited in GenBank as accession number AY534144.


    RESULTS
 TOP
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
 RESULTS
 DISCUSSION
 LITERATURE CITED
 
Physical organization of S. ferax mtDNA. – The nucleotide sequence of the S. ferax mitochondrial genome assembles and restriction maps as a 46 930 bp circle (FIG. 1Go) in good agreement with the 14 µm (44.5 kb) circular molecule detected by electron microscopy for a Saprolegnia sp. (Clark-Walker and Gleason 1973Go). Located within the circle is an 8618 bp large inverted repeat (LIR) separating the genome into large (19 274 bp) and small (10 420 bp) single-copy regions. The repeat is similar in size and location to that initially described for the Achlya genome (Hudspeth et al 1983Go) and is a characteristic of the vast majority of peronosporomycete mtDNAs examined to date (Hudspeth and Hudspeth 1996Go, McNabb and Klassen 1988Go).



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FIG. 1. Gene map of Saprolegnia ferax mtDNA. Genes in the outermost circle are transcribed clockwise, whereas those in the adjacent circle are transcribed anticlockwise; the two innermost circles identify locations of EcoRI and PstI restriction sites. Intergenic spaces are not to scale.

 
Given the potential for intramolecular recombination events in circular molecules containing inverted repeat sequences, a restriction endonuclease analysis was used to assay for the presence of isomeric forms of the genome. In this assay PstI restriction sites, present within each single-copy region (FIG. 1Go), but absent within the LIR, were used to detect pairs of fragments resulting from the reorientation of single-copy regions as a consequence of recombination between the LIR elements (Hudspeth et al 1983Go). The results (not shown) identified two sets of such PstI fragments in apparent equimolar concentration. One pair of 26.7 kb and 14.3 kb fragments, when combined with a 5.9 kb fragment located wholly within the large single-copy region, was consistent with one orientation of the genome. A second pair of 23.7 kb and 17.3 kb fragments, when likewise combined with the 5.9 kb fragment, was consistent with the alternate genome orientation. The presence of equimolar concentrations of both sets of the larger fragment pairs in the mtDNA population was interpreted as evidence for a dual population of orientational isomers, and as support for an active intramolecular recombination mechanism.

Genetic organization and gene content. – The 66 intron-less genetic loci (77 including LIR duplicated sequences) encoded in the genome are shown in FIG. 1Go and listed in TABLE IGo. These loci, representing 92.1% of the genomic sequence, often are arranged in operon-like clusters and are densely packed in the genome. Two pairs of genes overlap (rps12-rps7, rpl2-rps19) and three pairs abut each other (rps2-rps4, rps13-rps11, rps19-rps3). Intergenic regions average only 47 bp with a range of –23 (overlapping loci) to 341 bp. The overall A+T content of 76.9% is significantly higher in intergenic regions (94.1%) than in protein-encoding (79.2%) sequences. Thirty-nine loci encode polypeptides of which 35 are readily assigned by similarity searches of the GenBank protein database. Eighteen of these are components of the mitochondrial respiratory chain, 16 are subunits of the mitoribosome, and one, secY, is a homolog of E. coli tatC—a component of the sec-independent protein translocation pathway (Bogsch et al 1998Go, Weiner et al 1998Go). Three of four unassigned reading frames (orf64, orf143 and orf273) share regions of homology (FIG. 2Go) with "unique" P. infestans ORFs (Paquin et al 1997Go, below) of approximately equivalent sizes and the carboxyl region of rps4 shares homology with orf100 of P. infestans. The remaining 27 loci (exclusive of LIR duplicated sequences) encode RNA components of the mitochondrial translational apparatus. Twenty-five are tRNAs, and the remaining two encode the small (rns) and large (rnl) subunit rRNAs. The tRNAs include both initiator and elongator trnM plus cognate species for trnG, trnI, trnL, trnR, and trnS. No trnT was detected.


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TABLE I. Genetic content of Saprolegnia ferax mtDNA
 


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FIG. 2. Comparisons of deduced amino acid sequences of S. ferax ORFs with their P. infestans counterparts. A. S. ferax ORF64 and P. infestans ORF68. B. S. ferax ORF143 and P. infestans ORF142. C. S. ferax ORF273 and P. infestans ORF217. Red identifies identical residues. Sfe, S. ferax; Pin, P. infestans; dashes indicate spaces introduced to facilitate alignments.

 
Codon-usage frequencies are shown in TABLE 2Go. Notably absent are uses of the leucine codon CUC, the arginine codons AGG and CGG and the termination codon UGA. A single use of the ACG threonine codon occurs in orf312. GUG serves as the initiator codon for atp1 and atp6, with the standard AUG employed for all other polypeptides. Similarly, the termination codon UAG is used only for rpl2 with UAA used for all other reading frames.


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TABLE II. Codon Usage
 
The LIR extends for 8618 bp and encodes 11 intact and three partial loci. Eleven genes thus are duplicated fully in the genome and include the two rRNAs, five tRNAs, three small subunit mitoribosome polypeptides, and nad2 of respiratory complex I. It was a surprise to discover, however, that each end of the LIR terminates with the partial 3' sequence of a protein encoding gene. At the small single copy junctions, 319 nucleotides of nad5 (encoding 106 full codons) are duplicated and both a lysine and a termination codon, completing both the atp1 and cox1 reading frames, are duplicated at the large single copy junctions.


    DISCUSSION
 TOP
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
 RESULTS
 DISCUSSION
 LITERATURE CITED
 
The impetus for this study was the opportunity to compare the organizational and genetic features of two phylogenetically distant representative peronosporomycete mtDNAs. By selecting S. ferax for comparison with the available P. infestans genome (Paquin et al 1997Go) we were able to include well-studied representatives from the two major peronosporomycete subclasses (the Saprolegniomycetidae and the Peronosporomycetidae) as well as to contrast LIR and non-LIR genomes.

The overall genetic content and organization of the two genomes is similar. All 35 assignable reading frames, both rRNAs, and the 25 species of tRNAs are common to both genomes with differences reflected only in the numbers and types of ORFs.

Genome organization, with the exception of the LIR, also is strikingly similar, with the genes organized as compact blocks of loci. In S. ferax these blocks are suggestive of three major polycistronic transcripts. A 20-loci clockwise transcript (FIG. 1Go) originates at nad6 in the small single copy region and terminates with rnl in the LIR, while a 22-loci anticlockwise transcript originates at rps13 in the large single copy region and terminates following rps7 in the LIR. Finally, a 33-loci clockwise transcript extends from secY in the large single copy region to rps7 in the other LIR. This latter transcript would overlap the anticlockwise transcript at its origin and duplicates transcription for nine of the LIR encoded loci.

Gene-order conservation. – Comparison of gene order and potential transcriptional units in the S. ferax and P. infestans genomes revealed two major blocks of colinear loci. With the inclusion of a newly identified orf68 in the P. infestans genome (see below) a colinear set of 26 loci extending from trnLUAG through rps4 (FIG. 1Go) is apparent. Retained within this block are the remnants of the conserved prokaryotic ribosomal protein linkages including rps13-rps11, rpl2-rps19-rps3-rpl16 and rps14-rps8-rpl6, all previously noted for P. infestans (Lang et al 1999Go). The presumptive stramenopile linkage of rps8-rpl6-rps2-rps4 (Chesnick et al 2000Go) is similarly present. A second major block includes the eight LIR genes from nad2 through rps7.

The retention of large colinear blocks of loci in the Peronosporomycetes, even in distantly related taxa, is expected. This is based on the necessity of either retaining or acquiring promoter sites for the translocated loci. Due to the paucity of intergenic target sequences for translocation events that avoid disruption of other loci, the rate of viable translocations is expected to be low and the retention of genetic linkages to be high.

Unassigned reading frames. – Deduced amino acid sequences of the four unassigned Saprolegnia ORFs were compared with the five free-standing ORFs reported for P. infestans (Paquin et al 1997Go). Two of the ORFs lie in the largest positionally conserved gene block with orf143 located between nad7 and trnHGUG, and orf273 between trnICAU and atp8. Each ORF shares obvious regions of amino acid similarity with its P. infestans equivalent. The orf143/orf142 pair (FIG. 2bGo) encodes the more highly conserved deduced polypeptide with an amino acid identity of about 45%. The orf273/orf217 pair (FIG. 2cGo) is significantly less conserved but still clearly retains three regions of conservation—one centrally located and the others near the termini.

No homologue to Saprolegnia orf64 was identified previously in the P. infestans genome. However, because this ORF is included in a conserved 26 loci gene block (see above), and, because the corresponding block in the P. infestans genome contains an intergenic region of sufficient length to encode a comparable reading frame, we re-evaluated this region of the P. infestans genome. A short open reading frame, designated orf68, subsequently was located between secY and trnCGCA on the complementary strand as in S. ferax, but in P. infestans this ORF shares a 12-codon overlap with the carboxyl region of secY. The alignment of deduced amino acid sequences from this ORF pair revealed the conserved P. infestans polypeptide (48% identity) shown in FIG. 2aGo.

Searches of the protein databases, using short regions of identity/similarity derived from each of the three ORF pairs noted above, failed to identify likely mitochondrial homologues. However, their positional and relative amino acid conservation in two distinct subclass peronosporomycete lineages strongly argues for their validity as functional, albeit highly derived, mitochondrial proteins.

Of the three P. infestans ORFs without obvious S. ferax homologues, orf100 is a candidate for a carboxyl extension of rps4. Similar to other protists and prokaryotes, this locus in S. ferax encodes a polypeptide with a carboxyl terminus about 75 amino acids longer than that reported for P. infestans. The proximity of orf100 five nucleotides downstream of rps4 in P. infestans prompted the inclusion of a concatenated rps4/orf100 sequence in an alignment with deduced rps4 polypeptides from the "jakobid" protist Reclinomonas americana (Lang et al 1997Go), the brown alga Pylaiella littoralis (Oudot-LeSeq et al 2001Go) and the peronosporomycete Saprolegnia (FIG. 3Go). While it is apparent that the carboxyl region of rps4 is far less conserved than the remainder of the polypeptide among these representative taxa, orf100 and the rps4 carboxyl region of S. ferax clearly are homologous. It remains to be determined if the rps4/orf100 combination of P. infestans encodes a true frame shift, represents a genomically fragmented rps4 or is a sequencing artifact.



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FIG. 3. Comparisons of deduced rps4 amino acid sequences identifying P. infestans orf100 as the carboxyl terminus of rps4. P. infestans orf100 is underlined as an extension of rps4; red identifies identical residues; Sfe is S. ferax; Pin, P. infestans; Pli, Pylaiella littoralis (brown alga); Ram, Reclinomonas Americana (protest); dashes indicate spaces introduced to facilitate alignments.

 
Assuming orf100 encodes the carboxyl region of rps4, the only unassigned ORFs not shared between the mtDNAs are orf312 of S. ferax and orf32 and orf79 of P. infestans. Of these the presence of orf32 has been reported in P. megasperma (Lang and Forget 1993Go) and has been identified subsequently in several additional nonsaprolegnealean lineages of the Peronosporomycetes (unpublished results). We similarly have identified an orf82 as an orf79 equivalent in a different P. megasperma isolate (unpublished results). Thus, only orf312 currently remains without precedent in other peronosporomycete mtDNAs.

Codon usage and tRNAs. – Twenty-five species of tRNAs with appropriate clover-leaf structures and unambiguous anticodons are encoded in S. ferax mtDNA, with five of these duplicated in the LIR. This set of tRNAs is identical to that encoded in the P. infestans genome (Paquin et al 1997Go) and is insufficient to support mitochondrial protein synthesis. Notably absent are the tRNAs required for translation of arginine CGR and all threonine codons. The two-codon arginine AGR family is accounted for by trnRUCU (only AGA codons are used in S. ferax), but the use of trnRGCG in the four-codon arginine family in lieu of the more typical trnRACG with its wobble "A" deaminated to "I" (Pfitzinger et al 1990Go) limits translation to CGY codons. Thus, as in P. infestans, it is necessary to postulate the import of cytosolic tRNAs enabling translation of arginine CGR and all threonine codons. Similarly, as originally observed in E. coli (Muramatsu et al 1988Go) and inferred for P. infestans and other protists and plants (Gray et al 1998Go), it is assumed that the wobble "C" of trnICAU is post-transcriptionally modified to lysidine to enable translation of the isoleucine AUA codon.

LIR recombination retains intact loci. – The primary architectural difference between S. ferax and P. infestans mtDNAs is the presence of the LIR. Size variation in LIR genomes has been well documented among peronosporomycete taxa and has been shown to be the major contributor to genome size variation (Hudspeth and Hudspeth 1996Go, McNabb and Klassen 1988Go). S. ferax contains the shortest described LIR, and the 8618 bp are shown here to encode intact copies of four polypeptides, five tRNAs and both rRNAs. It was a surprise to find partial protein-encoding sequences, rather than intergenic sequences, at the repeat termini. We had anticipated that, because an active recombination mechanism between repeat elements has been inferred for S. ferax and other members of the Saprolegniales (Hudspeth et al 1983Go, Boyd et al 1984Go), the LIR would terminate with intergenic sequences and thereby ensure intact encoded loci for both mtDNA orientational isomers.

The LIR ends encode 3' termini for three polypeptides but still maintain available intact copies for the three loci. At the small single copy junctions, the LIR terminates with 106 codons of nad5. When the genome assumes the orientational isomer presented in FIG. 1Go, the right-handed repeat element generates an intact nad5 locus while the left-handed element retains only the carboxyl-encoding fragment. In the alternate configuration it is the left-handed repeat that forms the intact locus. A different approach to retaining intact loci is used for the large single copy junctions. Here the LIR termini encode two in-frame codons—lysine and termination—that are common to the flanking loci. These codons provide translational termination for both atp1 and cox1 in both mtDNA orientations. Thus, the extension of coding sequences into the LIR still provides intact nad5, atp1 and cox1 loci for either mtDNA isomer.


    ACKNOWLEDGMENTS
 
We thank Barbara Ball for assistance with the figures. This study was supported by the Northern Illinois University Plant Molecular Biology Center and NSF grants DEB-9806785 and DEB-0213076.


    FOOTNOTES
 
Accepted for publication February 21, 2004.

1 Corresponding author. E-mail: mykes{at}niu.edu


    LITERATURE CITED
 TOP
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
 RESULTS
 DISCUSSION
 LITERATURE CITED
 
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J Mol Biol 215:403–410.[Medline]

Bogsch EG, Sargent F, Stanley NR, Berks BC, Robinson C, Palmer T. 1998. An essential component of a novel bacterial protein export system with homologues in plastids and mitochondria. J Biol Chem 273:18003–18006.[Abstract/Free Full Text]

Birnboim HC, Doly J. 1979. A rapid alkaline extraction procedure for screening recombinant plasmid DNA. Nucleic Acids Res 7:1513–1523.[Abstract/Free Full Text]

Boyd DA, Hobman TC, Gruenke SA, Klassen GR. 1984. Evolutionary stability of mitochondrial DNA organization in Achlya. Can J Biochem Cell Biol 62:571–576.

Burger G. 1999. GenBank accession No. AF193903.

———, Lang BF, Gray MW. 2000. GenBank accession No. AF287134.

Chesnick JM, Goff M, Graham J, Ocampo C, Lang BF, Seif E, Burger G. 2000. The mitochondrial genome of the stramenopile alga Chrysodidymus synuroideus. Complete sequence, gene content and genome organization. Nucleic Acids Res 28:2512–2518.[Abstract/Free Full Text]

Clark-Walker GD, Gleason FH. 1973: Circular DNA from the water mold Saprolegnia. Arch. Mikrobiol 92:209–216.

Dick MW. 2001. Straminipilous Fungi. Dordrecht, The Netherlands: Kluwer Academic Publishers.

Forster H, Kinscherf TG, Leong SA, Maxwell DP. 1987. Molecular analysis of the mitochondrial genome of Phytophthora. Curr Genet 12:215–218.

Gray MW, Lang BF, Cedergren R, Golding G, Lemieux C, Sankoff D, Turmel M, Brossard N, Delage E, Littlejohn TG, Plante I, Rioux P, Saint-Louis D, Zhu Y, Burger G. 1998. Genome structure and gene content in protist mitochondrial DNAs. Nucleic Acids Res 26: 865–878.[Abstract/Free Full Text]

Griffin DH, Timberlake WE, Cheney JC. 1974. Regulation of macromolecular synthesis, colony development, and specific growth rate of Achlya bisexualis during balanced growth. J Gen Microbiol 80:381–388.

Hudspeth MES. 1992. The fungal mitochondrial genome—a broader perspective. In Arora DK, Elander RP, Mukerji KG, eds. Handbook of applied mycology. Fungal biotechnology. Vol. 4. New York: Marcel Dekker Inc. p 213–241.

———, Hudspeth DSS. 1996. Mitochondrial genomes of the zoosporic fungi. In Dayal R, ed. Advances in zoosporic fungi. New Delhi: MD Publications Pvt Ltd. p 173–199.

———, Shumard DS, Bradford CJR, Grossman LI. 1983. Organization of Achlya mtDNA: a population with two orientations and a large inverted repeat containing the rRNA genes. Proc Natl Acad Sci USA 80:142–146.[Abstract/Free Full Text]

———, ———, Tatti KM, Grossman LI. 1980. Rapid purification of yeast mitochondrial DNA in high yield. Biochim Biophys Acta 61:221–228.

Klimczak J, Prell HH. 1984. Isolation and characterization of mitochondrial DNA of the oomycetous fungus Phytophthora infestans. Curr Genet 8:323–326.

Lang BF, Burger G, O’Kelly CJ, Cedergren R, Golding GB, Lemieux C, Sankoff D, Turmel M, Gray MW. 1997. An ancestral mitochondrial DNA resembling a eubacterial genome in miniature. Nature 387:493–497.[Medline]

———, Forget L. 1993. The mitochondrial genome of Phytophthora infestans. In O’Brien SJ, ed. Genetic Maps. Locus maps of complex genomes. Book 3 Lower Eukaryotes. 6th ed. Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press. p 3.133.

———, Gray MW, Burger G. 1999. Mitochondrial genome evolution and the origin of eukaryotes. Ann Rev Genet 33:351–397.[Medline]

Lowe TM, Eddy SR. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25:955–964.[Abstract/Free Full Text]

Maniatis T, Fritsch EF, Sambrook J. 1982. Molecular cloning: a laboratory manual. Cold Spring Harbor, New York: Cold Spring Harbor Laboratory.

McNabb SA, Klassen GR. 1988. Uniformity of mitochondrial complexity in oomycetes and the evolution of the inverted repeat. Expt Mycol 12:233–242.

Muramatsu T, Nishikawa K, Nemoto F, Kuchino Y, Nishimura S, Miyazawa T, Yokoyama S. 1988. Codon and amino-acid specificities of a transfer RNA are both converted by a single post-transcriptional modification. Nature 336:179–181.[Medline]

Patterson DJ. 1989. Stramenopiles: chromophytes from a protistan perspective. In Green JP, Leadbeater BSC, Diver WC, eds. The chromophyte algae: problems and perspectives. Oxford, UK: Clarendon Press. p 357–379.

Oudot-LeSecq M-P, Fontaine JM, Rousvoal S, Kloareg B, Loiseaux-DeGoer S. 2001. The complete sequence of a brown algal mitochondrial genome, the ectocarpale Pylaiella littoralis (L.) Kjellm. J Mol Evol 53:80–88.[Medline]

———, Kloareg B, Loiseaux-DeGoer S. 2002. The mitochondrial genome of the brown alga Laminaria digitata: a comparative analysis. Eur J Phycol 37:163–172.

Paquin B, LaForest M-J, Forget L, Roewer I, Wang Z, Long-core J, Lang BF. 1997. The fungal mitochondrial genome project: evolution of fungal mitochondrial genomes and their gene expression. Curr Genet 31:380–395.[Medline]

Pfitzinger H, Weil JH, Pillay DTN, Guillemaut P. 1990. Codon recognition in plant chloroplasts. Plant Mol Biol 14:805–814.[Medline]

Shumard-Hudspeth DS, Hudspeth MES. 1990. Genic rearrangements in Phytophthora mitochondrial DNA. Curr Genet 17:413–417.[Medline]

Shumard DS, Grossman LI, Hudspeth MES. 1986. Achlya mitochondrial DNA: gene localization and analysis of inverted repeats. Mol Gen Genet 202:16–23.[Medline]

Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. 1997. The Clustal X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 24:4876–4882.

Weiner JH, Bilous PT, Shaw GM, Lubitz SP, Frost L, Thomas GH, Cole JA, Turner RJ. 1998. A novel and ubiquitous system for membrane targeting and secretion of cofactor-containing proteins. Cell 93:93–101.[Medline]




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Agricola
Right arrow Articles by Grayburn, W. S.
Right arrow Articles by Hudspeth, M. E. S.


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