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, 10 (2), 61-74
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A Preliminary DNA Barcode Selection for the Genus Russula (Russulales, Basidiomycota)

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A Preliminary DNA Barcode Selection for the Genus Russula (Russulales, Basidiomycota)

Guo-Jie Li et al. Mycology.

Abstract

Russula is a worldwid genus which has a high species diversity . Aiming accurate and rapid species identification, candidate genes nLSU (28S), ITS, tef-1α, mtSSU, rpb1, and rpb2, were analysed as potential DNA barcodes. This analysis included 433 sequences from 38 well-circumscribed Russula species of eight subgenera. Two vital standards were analysed for success species identification using DNA barcodes, specifically inter- and intra-specific variations together with the success rates of PCR amplification and sequencing. Although the gap between inter- and intra-specific variations was narrow, ITS met the qualification standards for a target DNA barcode. Overlapping inter- and intra-specific pairwise distances were observed in nLSU, tef-1α, mtSSU, and rpb2. The success rates of PCR amplification and sequencing in mtSSU and rpb1 were lower than those of others. Gene combinations were also investigated for resolution of species recognition. ITS-rpb2 was suggested as the likely target DNA barcode for Russula, owing to the two viatal standards above. Since nLSU has the lowest minimum of inter-specific variation, and tef-1α has the highest overlap between intra- and inter-species variations among the candidate genes, they are disqualified from the selection for DNA barcode of Russula.

Keywords: Barcode gap; Russulaceae; fungal identification; intra-and inter-specific variation; species recognition.

Figures

Figure 1.
Figure 1.
Comparisons of intra- and inter-specific variations among nLSU, ITS, tef-1α, mtSSU, rpb1 and rpb2 genes of Russula generated by TaxonGap. The inter- and intra-specific variations were presented as the black and grey bars respectively. The minimums of inter-specific variations for each gene were shown as the vertical lines. Taxon names followed the black bars represented the closest species of this analysis.
Figure 2.
Figure 2.
Comparisons of frequency distribution of intra- and inter-specific variation pairwise distances among nLSU, ITS, tef-1α, mtSSU, rpb1 and rpb2 genes of Russula generated by MEGA and Excel. The interand intra-specific distances are presented as yellow and blue bars respectively.
Figure 2.
Figure 2.
Comparisons of frequency distribution of intra- and inter-specific variation pairwise distances among nLSU, ITS, tef-1α, mtSSU, rpb1 and rpb2 genes of Russula generated by MEGA and Excel. The interand intra-specific distances are presented as yellow and blue bars respectively.
Figure 3.
Figure 3.
Comparisons of intra- and inter-specific variations among ITS-mtSSU, ITS-rpb1, ITS-rpb2, mtSSUrpb1, mtSSU-rpb2 and rpb1-rpb2 gene combinations of Russula generated by TaxonGap. The inter- and intra-specific variations were presented as the black and grey bars respectively. The minimums of interspecific variations for each gene were shown as the vertical lines. Taxon names followed the black bars represented the closest species of this analysis.
Figure 4.
Figure 4.
Comparisons of frequency distribution ofintra- and inter-specific variation pairwise distances among ITS-mtSSU, ITS-rpb1, ITS-rpb2, mtSSU-rpb1, mtSSU-rpb2 and rpb1-rpb2 gene combinations of Russula generated by MEGA and Excel. The inter- and intra-specific distances are presented as yellow and blue bars respectively.
Figure 4.
Figure 4.
Comparisons of frequency distribution ofintra- and inter-specific variation pairwise distances among ITS-mtSSU, ITS-rpb1, ITS-rpb2, mtSSU-rpb1, mtSSU-rpb2 and rpb1-rpb2 gene combinations of Russula generated by MEGA and Excel. The inter- and intra-specific distances are presented as yellow and blue bars respectively.

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Grant support

This work was supported by the National Natural Science Foundation of China [grant number 31500013] to GJL, [grant number 31000013, 31360014, 31470152] to RLZ, and Beijing Innovative Consortium of Agriculture Research System [Project ID: BAIC05-2018].
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