Although barcodes are appealing as a powerful tool to identify already described species, the cautious among us argue that the use of a single locus for identification may produce misleading results especially considering the different evolutionary histories of organellar and nuclear genomes within a single species [11].
Under some situations, this characteristic makes them useful loci for strain identification [ 28, 29].
The use of multiple loci for strain identification is preferred [ 23, 25] as a single locus cannot differentiate all the strains.
The system also helps to design primer sequences for flanking regions of repeat loci for PCR identification of polymorphism within populations.
We reanalyzed the macaroni penguin isolates with multilocus sequence typing (MLST), a method that uses sequence data from 7 unlinked loci for genetic identification (8 ), complemented with flaA gene sequencing.
As a multi-copy and easily amplified region, the nrDNA internal transcribed spacer (ITS) region has become the standard locus for fungal identification, often even species demarcation, because of its high interspecific variability [7], [8].
We used the Powerplex16 System amplification kit (Promega, Fitchburg, WI, USA) for 15 autosomal STR loci and the Amelogenin locus for gender identification.
The Agrobacterium genome encompasses more than a hundred of PBPs, of which some of them were already described as key-loci for species identification.
ITS2 sequences have a relatively high divergence rate; thus, it can be used as a complementary locus to CO1 for identification of animal species.
Our results suggest a high potential of the combined use of rbcL and trnL-F as a two-locus cpDNA barcode for identification of fern species.
However, dependence on only two sequence loci for accurate species identification lacks discrimination, especially for fine-scale ecological and evolutionary interaction studies between orchids and their mycorrhizal symbionts.
