In Silico Evaluation of Mitochondrial Genes As DNA Barcode for Basidiomycota

In silico evaluation of mitochondrial genes as DNA barcode for Basidiomycota

A. Vialle (1), N. Feau (2), R. Hamelin (1,2)

(1) Centre d’étude de la forêt, Université Laval, Québec (QC), Canada, G1K7P4 (2) Service canadien des forêts, Ressources naturelles Canada, Centre de foresterie des Laurentides, 1055 du PEPS, P.O. Box 3800, Québec, (QC), Canada, G1V4C7

A DNA barcode is a short and standardized sequence of nucleotides providing a rapid and accurate species identification. A 648-bp region of the mitochondrial cytochrome c oxidase subunit I gene (CO1) is the core barcode region for animals and has been proposed for fungi. However, some characteristics of the fungal mitochondrial genome can compromise the utilization of this gene for the elaboration of a barcode. In particular, the presence of introns and of nuclear copies of CO1 have been cited as potential problems. The goal of our study consisted in an in silico evaluation of the potential of 14 mitochondrial genes, including CO1, commonly found in mitochondrial genomes of Basidiomycota as barcode. First, we inventoried all mitochondrial DNA data publicly available for Basidiomycota and designed mitochondrial genome recovery and assembly strategies. Thirteen complete and partial mitochondrial genomes were recovered and characterized, included the 14 genes encoding for the subunits of the respiratory chain complexes. Second, each gene retrieved was evaluated with a particular emphasis on: 1) intron position and size; 2) the occurrence of full and partial copies of the gene in both nuclear and mitochondrial genomes and; 3) the information provided in context of barcoding e.g. the compromise between the need for universal application across taxa and discrimination among taxa. The genes targeted showed high values of molecular divergence (measured by K2P distances) indicating a good potential for the resolution of lower- level relationships. However, numerous introns, potentially interfering with PCR amplification of the target barcode sequence, occurred in CO1 as well as 6 other genes. Considering these results and the optimal length of 600-bp recommended for a fungal barcode, we propose three alternative genes to CO1, coding for the ATPase subunit 6, the cytochrome oxidase subunit 3 and the NADH deshydrogenase subunit 6, to elaborate a mitochondrial DNA barcode for Basidiomycota.