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KMID : 0365220140510020081
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Korean Journal of Public Health
2014 Volume.51 No. 2 p.81 ~ p.89
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FGMD : Database of Fungal Genetic Markers and Multigene Analysis in Fungal Classification
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Jang Jin-Hwa
Bae Se-Eun
Jung Sung-Hoon
Kim Ha-Yeon
Ahn In-Sung
Son Hyeon-Seok
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Abstract
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FGMD (fungal genetic marker database, http://lcbb.snu.ac.kr/fgmd), which contains genetic markers for publicly reported fungal species. The 17 genetic markers used in this study can be used either singly or in combination for the phylogenetic classification of fungi. This database can provide diverse combinations of genetic markers and differs from other databases because it allows for broad systematic analyses based on all species for which sequences are publicly available. We also compared classifications made using single genetic markers to those made using a multigene approach to identify the best combination of markers based on the FGMD for the phylogenetic classification of fungal species. A phylogenetic analysis was performed using 71 species representing four fungal phyla using combinations of three marker genes. Multigene analysis was used for the classification of each species from the species to phylum levels, and error rates for each combination of markers were calculated. Multigene analyses had lower error rates than single-gene analyses. Group prediction by discriminant analysis using multigene markers, which used combinations of Rpb2, Atpase6, and β-Tubulin genes as variables, displayed high accuracy (92%). A multigene approach, such as the one described here, may be applicable as a unified genetic marker for the phylogenetic classification of diverse fungal species.
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KEYWORD
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Genetic marker, Multigene, Phylogenetic analysis, Error rate
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