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A broad range of fungi were isolated from different geographic regions and substrates and identified according to traditional and modern methods. A total of 120 different isolates were assigned to the phyla, Basidiomycota with 8 isolates, Ascomycota with 75 isolates, and ˵Zygomycota″ with 37 isolates. Although morphological characters were able to differentiate the isolates to their phyla and in most cases to the correct genera, a combination of several methods is always recommended because characterization and identification of unknown fungal isolates is highly error-prone if relying on single methods. Sequence-based identification turned out to be reliable for most Ascomycetes and Zygomycetes. But with the ongoing questionable trend to rely on sequences as first source information for species separation, the most serious problems are the annotation problems in public reference databases, the inconsistency of described taxa, and the available reference data. [ABSTRACT FROM AUTHOR]

Fusarium oxysporum is a ubiquitous inhabitant of soils worldwide and causes diseases such as wilt, yellows, and damping-off in different plant species. Rapid and reliable detection of the pathogen is essential for undertaking appropriate and timely disease management measures. The time-consuming and laborious classical detection methods are now being increasingly replaced by culture-independent molecular detection techniques, which are much faster, more specific, and sensitive. Molecular techniques like microarrays, whole genome sequencing, DNA barcoding, metagenomics etc. can identify a large number of isolates in a single assay. Some of the emerging tools will also allow complete analysis of developmental processes that are characteristics of the fungus, including the molecular nature of pathogenicity. [ABSTRACT FROM AUTHOR]

The DNA barcoding is a promising technique for identifications of biological species based on a relatively short sequence of COI gene. A research area to improve the DNA barcoding is to study the classification techniques that utilize common properties of DNA and amino acid sequences such as variable lengths of gene sequences, and the comparison of different reference genes. In this study, we evaluate a classification model for DNA barcoding induced by genetic programming. The proposed method can be adapted for both DNA and amino acid sequences. The performance is evaluated by representing the two types of sequences and one based on their properties. The proposed method evaluates common significant sites on the reference genes which are useful to differentiate between species. [ABSTRACT FROM AUTHOR]

DNA-based species assignment and delimitation are two important problems in systematic biology. In a recent work of O΄Meara, species delimitation is investigated through coupling it with species tree inference in the framework of gene tree and species tree reconciliation. We present a polynomial time algorithm for splitting individuals into species to minimize the deep coalescence cost of the gene tree and species tree reconciliation, a species assignment problem arises from species delimitation via gene tree and species tree reconciliation. How to incorporate this proposed algorithm into the heuristic search strategy of O΄Meara for species delimitation is also discussed. The proposed algorithm is implemented in C++. [ABSTRACT FROM AUTHOR]

The detection and identification of plant pathogens currently relies upon a very diverse range of techniques and skills, from traditional culturing and taxonomic skills to modern molecular-based methods. The wide range of methods employed reflects the great diversity of plant pathogens and the hosts they infect. The well-documented decline in taxonomic expertise, along with the need to develop ever more rapid and sensitive diagnostic methods has provided an impetus to develop technologies that are both generic and able to complement traditional skills and techniques. Real-time polymerase chain reaction (PCR) is emerging as one such generic platform technology and one that is well suited to high-throughput detection of a limited number of known target pathogens. Real-time PCR is now exploited as a front line diagnostic screening tool in human health, animal health, homeland security, biosecurity as well as plant health. Progress with developing generic techniques for plant pathogen identification, particularly of unknown samples, has been less rapid. Diagnostic microarrays and direct nucleic acid sequencing (de novo sequencing) both have potential as generic methods for the identification of unknown plant pathogens but are unlikely to be suitable as high-throughput detection techniques. This paper will review the application of generic technologies in the routine laboratory as well as highlighting some new techniques and the trend towards multi-disciplinary studies. [ABSTRACT FROM AUTHOR]