Suitable DNA barcode for DNA metabarcoding
Whether a soil sample could be traced back to its original source
localities depends on the suitable DNA barcode to be used. Although
there is incompatibility between the universality of primers and the
resolution of barcodes for higher plants, the universality of primers is
more important for DNA metabarcoding of lower plants in soil samples
because almost all DNA barcodes are variable enough to resolve most
known taxonomic units (Liu et al., 2020b). Lower plants have shorter
lifetime, evolve much more quickly and accumulate more genetic
variations in their genomes than higher plants. However, lower plants
are the least known creatures to taxonomists and quite large of them can
only be identified to genus or even family levels. For example,rbcL is one of the least variable gene of seed plants, but its
variability in lower plants is much higher (Dong et al., 2014) and can
serve as a DNA barcode for lower plants such as diatoms (Liu et al.,
2020a).
Another advantage of using rbcL as a DNA barcode for lower plants
is that this gene locates in plastid genome, implying that
contaminations of plastid genome free organisms bring no trouble to the
data analyses. There is usually a vast range of microorganisms in soil
samples, for example, insects, fungi, bacteria, etc.. When using DNA
barcodes from nuclear genome such as 18S, amplification of these
organisms is usually inevitable, which needs quite large experimental
and analysis resources.