Prospects for fungus identification using CO1 DNA barcodes, with Penicillium as a test case - PubMed (original) (raw)
Prospects for fungus identification using CO1 DNA barcodes, with Penicillium as a test case
Keith A Seifert et al. Proc Natl Acad Sci U S A. 2007.
Abstract
DNA barcoding systems employ a short, standardized gene region to identify species. A 648-bp segment of mitochondrial cytochrome c oxidase 1 (CO1) is the core barcode region for animals, but its utility has not been tested in fungi. This study began with an examination of patterns of sequence divergences in this gene region for 38 fungal taxa with full CO1 sequences. Because these results suggested that CO1 could be effective in species recognition, we designed primers for a 545-bp fragment of CO1 and generated sequences for multiple strains from 58 species of Penicillium subgenus Penicillium and 12 allied species. Despite the frequent literature reports of introns in fungal mitochondrial genomes, we detected introns in only 2 of 370 Penicillium strains. Representatives from 38 of 58 species formed cohesive assemblages with distinct CO1 sequences, and all cases of sequence sharing involved known species complexes. CO1 sequence divergences averaged 0.06% within species, less than for internal transcribed spacer nrDNA or beta-tubulin sequences (BenA). CO1 divergences between species averaged 5.6%, comparable to internal transcribed spacer, but less than values for BenA (14.4%). Although the latter gene delivered higher taxonomic resolution, the amplification and alignment of CO1 was simpler. The development of a barcoding system for fungi that shares a common gene target with other kingdoms would be a significant advance.
Conflict of interest statement
The authors declare no conflict of interest.
Figures
Fig. 1.
Number, size, and position of introns in CO1 of fungi and fungus-like Oomycota. (a) Neighbor-joining tree of 56 fungal species for which complete mitochondrial genomes and/or complete CO1 genes are available in GenBank. The tree is constructed with the 648-bp CO1 barcode region. The circled numbers indicate the number of introns in the barcode region for all taxa to the right of the symbol, and the arrow indicates the approximate taxonomic location of the fine-scale analysis. (b) Exon and intron lengths in the 648-bp CO1 barcode region for the 56 fungal species. Exons are shaded dark gray, and introns are shaded white. Exon–intron boundaries are based on annotations provided by the GenBank records.
Fig. 2.
Neighbor-joining tree of 70 species and 354 isolates from the subgenus Penicillium and related species. The tree is constructed with 545 bp of CO1. Bracketed numbers represent the number of strains sequenced for each species.
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