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The 140 000 or so fungal species reported so far are heterogeneously defined based on varying criteria such as morphological, physiological, mating, and (or) molecular features. Incongruences are common among traits used to separating closely related species and it is often difficult to compare fungal taxonomic groups defined based on different species recognition criteria. Though DNA sequence-based classification and identification have been made, a consensus has not been reached, primarily due to intrinsic limitations in the proposed one or a few genes. Here, I argue that the fundamental reason for the observed inconsistencies is that speciation is a stochastic process with the emergence and fixation of different traits influenced differently by many nondeterministic factors such as population size, random mutation, mode(s) of reproduction, selection imposed by interacting biotic and abiotic factors, and chance events. Each species concept attempts to capture one or a few traits emerged in the continuous process of speciation. I propose that a genome sequence-based classification and identification system could unify and stabilize fungal taxonomy and help integrate taxonomy with other fields of fungal biology. The genomic species concept could be similarly argued for other groups of eukaryotic microbes as well as for plants and animals. Key words: species concepts, yeasts, molds, mushrooms, trait evolution, genome sequence, genome species concept. Il existe environ 140 000 espèces fongiques rapportées à ce jour, mais elles ont été définies sur des bases hétérogènes selon divers critères, que ce soit morphologiques, physiologiques, de reproduction ou de propriétés moléculaires. Les incohérences sont nombreuses parmi les caractères employés pour séparer des espèces proches et il est souvent difficile de comparer les groupes taxonomiques de champignons définis sur des bases différentes en matière de reconnaissance des espèces. Bien que la classification et l'identification fondées sur des séquences d'ADN ait été faite, aucun consensus n'a encore été trouvé principalement en raison des limitations intrinsèques liées au(x) gène(s) proposé(s). Dans cet article, l'auteur avance que la raison principale pour les incohérences observées est que la spéciation est un processus stochastique où l'émergence et la fixation de différents caractères est influencée par plusieurs facteurs non-déterministes distincts tels que la taille de la population, une mutation aléatoire, le mode de reproduction, la sélection imposée par des facteurs biotiques et abiotiques, ainsi que le hasard. Chaque concept de l'espèce tente de capturer un ou plusieurs caractères apparus au cours du processus continu de spéciation. L'auteur propose qu'un système d'identification et de classification fondé sur la séquence du génome pourrait unifier et stabiliser la taxonomie des champignons et aider à intégrer la taxonomie avec d'autres champs d'étude en biologie des champignons. Le concept d'espèce fondée sur le génome pourrait également s'appliquer à d'autres groupes de microorganismes eucaryotes, de même qu'aux plantes et aux animaux. [Traduit par la Rédaction] Mots-clés: concepts d'espèce, levures, moisissures, champignons, évolution des caractères, séquence du génome, concept d'espèce fondée sur le génome., Introduction Species is a fundamental term in biology. However, species can mean different things for scientists in different fields and (or) working on different groups of organisms. While most biologists [...]

This open-access special issue features 12 full articles representing emerging trends from the international DNA barcoding community. Several articles highlight how DNA-based techniques are elucidating the species diversity, biogeography, and [...]

The two special issues--Barcodes to Biomes--mark the one-year anniversary of the 6th International Barcode of Life Conference held in Guelph, Canada. The 6th Conference brought together 601 delegates from 51 [...]

Hybridization is a potent mechanism for generating unique strains with broad host ranges and increased virulence in fungal pathogens. In the opportunistic basidiomycete pathogen Cryptococcus neoformans, intervarietal hybrids are commonly found infecting patients. The two parental varieties C. neoformans var. grubii and C. neoformans var. neoformans mate readily under laboratory conditions, but the hybrid basidiospores have germination rates about four times lower than those from intravarietal crosses. Here, we used microdissection to collect basidiospores from a hybrid cross and analysed the genotypes of germinated basidiospores to identify potentially antagonistic allelic combinations between loci that impact basidiospore germination. Our analyses showed clear evidence for Bateson-Dobzhansky-Muller (BDM) incompatibility affecting basidiospore viability. Antagonistic combinations of alleles from both two loci and three loci were found. Interestingly, most of the hybrid progeny showed segregation distortion in favour of the alleles from var. neoformans, consistent with large-scale epistatic interactions among loci affecting basidiospore viability. Our study presents the first evidence of BDM incompatibility between nuclear genes affecting post-zygotic reproductive isolation in this model basidiomycete yeast. Key words: hybridization, heterozygosity, homozygosity, basidiospore viability, genetic incompatibility, Cryptococcus neoformans. Chez les champignons pathogenes, l'hybridation est un puissant mecanisme pour generer des souches uniques ayant une large gamme d'hotes et une virulence accrue. Chez le basidiomycete pathogene opportuniste Cryptococcus neoformans, les hybrides inter-varietaux sont frequemment retrouves chez des patients infectes. Les deux varietes parentales C. neoformans var. grubii et C. neoformans var. neoformans forment aisement des hybrides en laboratoire, mais les basidiospores hybrides presentent des taux de germination environ quatre fois plus faibles que ceux issus de croisements intra-varietaux. Dans ce travail, les auteurs ont employe la micro-dissection pour obtenir des basidiospores issues d'un hybride et ils ont analyse les genotypes des basidiospores germees pour identifier de possibles combinaisons alleliques antagonistes entre des locus qui affectent la germination des basidiospores. Ces analyses ont montre des evidences claires d'incompatibilite Bateson-Dobzhansky-Muller (BDM) affectant la viabilite des basidiospores. Des combinaisons alleliques antagonistes impliquant soit deux locus ou trois locus ont ete observees. Fait interessant, la plupart des descendants hybrides affichaient une distorsion de segregation en faveur des alleles de la var. neoformans, une observation concordant avec des interactions epistatiques de grande ampleur parmi les locus affectant la viabilite des basidiospores. Cette etude presente les premieres evidences d'incompatibilite BDM entre des genes nucleaires affectant l'isolement reproductif post-zygotique chez cette levure basidiomycete modele. [Traduit par la Redaction] Mots-cles: hybridation, heterozygotie, homozygotie, viabilite des basidiospores, incompatibilite genetique, Cryptococcus neoformans., Introduction Cryptococcus neoformans is an encapsulated, basidiomycetous yeast that can cause meningoencephalitis in individuals with compromised immunity (Mitchell and Perfect 1995). Besides its unicellular growth, the fungus also has a [...]

The 53rd annual conference of the Genetics Society of Canada was held at McMaster University in Hamilton, Ontario, from 17 to 20 June 2010. About 100 geneticists from across Canada and the US attended the meeting, with a total of 27 posters and 55 oral presentations. The presentations highlighted the power of genetics for understanding a variety of biological issues from sex and recombination to alcoholism and cancer, from DNA replication to antimicrobial resistance, horizontal gene transfer, foraging, and courtship. Large-scale genomic and trans criptomic comparisons were included in many presentations to demonstrate the impact of genomics in biomedical research. The combined molecular, developmental, and evolutionary genetic investigations presented at the meeting, especially those on model organisms, highlighted that genes and genetic systems can evolve very rapidly. Key words: model organisms, rapid evolution, molecular genetics, developmental genetics, evolutionary genetics, genomics, bio informatics. La 53ieme conference annuelle de la Societe de genetique du Canada a eu lieu a l'Universite McMaster a Hamilton en Ontario du 17 au 20 juin 2010. Environ 100 geneticiens de partout au Canada et des Etats-Unis ont participe a cette conference ou ont ete presentees 27 affiches et 55 communications. Les presentations ont mis en lumiere la puissance de la genetique pour contribuer a la comprehension d'une gamine de processus biologiques allant du sexe et de la recombinaison a l'alcoolisme et au cancer, de la replication de l'ADN a la resistance antimicrobienne, au transfert horizontal de genes, aux comportements alimentaires et sexuels. Des comparaisons genomiques et transcriptomiques a grande echelle faisaient partie de nombreuses presentations et demontrent l'impact de la genomique en recherche biomedicale. Les investigations combinant la genetique moleculaire, du developpement el de l'evolution presentees lors de cette conference, parliculierement chez les especes modeles, ont fait ressortir que les genes et les systemes genetiques peuvent evoluer tres rapidement. Mots-cles : organismes modeles, evolution rapide, genetique moleculaire, genetique du developpement, genetique de l'evolution, genomique, bioinformatique. [Traduit par la Redaction], Introduction Genetics investigates the variation and inheritance of traits in living organisms. The inheritance of traits from parents to offspring has been noted and used since prehistoric times to improve [...]

Differences in genome size and gene content are among the most important signatures of microbial adaptation and genome evolution. Here, we investigated the patterns of genome variation among 10 natural strains of the symbiotic nitrogen-fixing bacterium Sinorhizobium meliloti, using pulse field gel electrophoresis (PFGE) and whole-genome microarray hybridizations. Our PFGE analysis showed a genome size range of 6.45-7.01 Mbp, with the greatest variation arising from the pSymA replicon, followed by pSymB; no size difference was evident among the chromosomes. Consistent with this pattern of size differences, 41.2% of open reading frames (ORFs) on pSymA were variably absent/present, followed by 12.7% on pSymB and 3.7% on the chromosome. However, the ORFs that were variably duplicated were more evenly distributed among the three replicons: 11.0%, 16.5%, and 15.3% of ORFs on pSymA, pSymB, and the chromosome, respectively. Among the 10 strains, the percentage of ORFs that were absent ranged from 1.51% to 6.35%, and the percentage of ORFs that were duplicated ranged from 0.27% to 8.56%. Our analyses showed that host plants, geographic origins, multilocus enzyme electrophoretic types, and replicon sizes had little influence on the distribution patterns of absent or duplicated ORFs. The proportions of ORFs that were either variably absent/present or variably duplicated differed greatly among the functional categories, for each of the three replicons as well as for the whole genome. Interestingly, we observed positive correlations among the three replicons in the number of absent ORFs as well as the number of duplicated ORFs, consistent with coordinated gene gains and losses in this important bacterium in nature. Key words: pulse field gel electrophoresis, comparative microarray hybridization, genome variation, [N.sub.2]-fixing bacteria. Les differences en ce qui a trait a la taille du genome ou au contenu genique comptent parmi les evidences les plus claires de l'adaptation et de l'evolution du genome chez les microbes. Dans ce travail, les auteurs ont examine la variation du genome chez 10 souches naturelles de la bacterie fixatrice d'azote Sinorhizobium meliloti par electrophorese en champs pulses (PFGE) et par hybridation genomique sur puces a ADN. L'analyse en PFGE a revele que la taille du genome variait entre 6,45 et 7,01 Mb, la plus grande variation etant observee au sein de replicon pSymA, suivi du replicon pSymB. Aucune difference detectable n'a ete notee chez les chromosomes. Conformement aux differences de taille observe es, 41,2% des ORF sur pSymA etaient variables quant a leur presence/absence, de meme que 12,7% des ORF sur pSymB et 3,7% des ORF sur le chromosome. Cependant, la proportion d'ORF qui etaient dupliques de maniere variable etait plus egalement repartie: respectivement 11,0, 16,5 et 15,3% des ORF sur pSymA, pSymB et le chromosome. Parmi les 10 souches, la proportion des ORF absents variait entre 1,51 et 6,35%, tandis que les ORF dupliques variaient entre 0,27 et 8,56%. Des analyses montrent que les plantes hotes, l'origine geographique, les types isoenzymatiques a plusieurs locus et la taille des replicons avaient peu d'influence sur la distribution des ORF absents ou dupliques. La proportion des ORF qui etaient variables quant a leur presence/absence ou leur duplication differait grandement parmi les categories fonctionnelles pour chacun des trois replicons de meme que pour le genome entier. De plus, les auteurs ont observe des correlations positives entre les trois replicons pour ce qui est du nombre d'ORF absents ou dupliques, une observation qui est conforme a l'hypothese de gains/pertes geniques coordonnes chez cette importante espece bacterienne en nature. Mots-cles: electrophorese en champs pulses, hybridation comparee sur puces a ADN, variation genomique, bacteries fixatrices d'azote. [Traduit par la Redaction], Introduction Differences in genome size and gene content are among the most prominent features in comparative studies of bacterial genomes. Among the currently sequenced bacterial genomes, the genome sizes vary [...]

Abstract: The opportunistic human fungal pathogen Cryptococcus neoformans includes two varieties, C. neoformans var. grubii and C. neoformans var. neoformans, which correspond to serotypes A and D, respectively. Recent population [...]

Copyright of Genome is the property of Canadian Science Publishing and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Fungi are ubiquitous in both natural and human-made environments. They play important roles in the health of plants, animals, and humans, and in broad ecosystem functions. Thus, having an efficient species-level identification system could significantly enhance our ability to treat fungal diseases and to monitor the spatial and temporal patterns of fungal distributions and migrations. DNA barcoding is a potent approach for rapid identification of fungal specimens, generating novel species hypothesis, and guiding biodiversity and ecological studies. In this mini-review, I briefly summarize ( i) the history of DNA sequence-based fungal identification; ( ii) the emergence of the ITS region as the consensus primary fungal barcode; ( iii) the use of the ITS barcodes to address a variety of issues on fungal diversity from local to global scales, including generating a large number of species hypothesis; and ( iv) the problems with the ITS barcode region and the approaches to overcome these problems. Similar to DNA barcoding research on plants and animals, significant progress has been achieved over the last few years in terms of both the questions being addressed and the foundations being laid for future research endeavors. However, significant challenges remain. I suggest three broad areas of research to enhance the usefulness of fungal DNA barcoding to meet the current and future challenges: ( i) develop a common set of primers and technologies that allow the amplification and sequencing of all fungi at both the primary and secondary barcode loci; ( ii) compile a centralized reference database that includes all recognized fungal species as well as species hypothesis, and allows regular updates from the research community; and ( iii) establish a consensus set of new species recognition criteria based on barcode DNA sequences that can be applied across the fungal kingdom. [ABSTRACT FROM AUTHOR]

Copyright of Genome is the property of Canadian Science Publishing and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Copyright of Genome is the property of Canadian Science Publishing and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Although lichens (lichen-forming fungi) play an important role in the ecological integrity of many vulnerable landscapes, only a minority of lichen-forming fungi have been barcoded out of the currently accepted ∼18 000 species. Regular Sanger sequencing can be problematic when analyzing lichens since saprophytic, endophytic, and parasitic fungi live intimately admixed, resulting in low-quality sequencing reads. Here, high-throughput, long-read 454 pyrosequencing in a GS FLX+ System was tested to barcode the fungal partner of 100 epiphytic lichen species from Switzerland using fungal-specific primers when amplifying the full internal transcribed spacer region (ITS). The present study shows the potential of DNA barcoding using pyrosequencing, in that the expected lichen fungus was successfully sequenced for all samples except one. Alignment solutions such as BLAST were found to be largely adequate for the generated long reads. In addition, the NCBI nucleotide database-currently the most complete database for lichen-forming fungi-can be used as a reference database when identifying common species, since the majority of analyzed lichens were identified correctly to the species or at least to the genus level. However, several issues were encountered, including a high sequencing error rate, multiple ITS versions in a genome (incomplete concerted evolution), and in some samples the presence of mixed lichen-forming fungi (possible lichen chimeras). [ABSTRACT FROM AUTHOR]