Perhaps the most dramatic example of sequence loss is the complete lack of TIR NBS-LRR sequences in the Poaceae, despite abundant sequence for both the grasses and the NBS-LRR gene family [ 32, 58].
Gram-negative Bacteriodetes were the second most abundant sequences identified for both fresh and dry manure samples.
In other cases of highly abundant sequences, e.g. for a plant defensin, an elongation factor 1-alpha (EF-1α), a strictosidine synthase, or a vesicle-associated membrane family protein (VAMP), B. divaricarpa clones displayed no or very few differences, while the A. thaliana genome harbored several related genes.
To address this issue, we devised a novel methodology that would allow us to reconstruct a "consensus sequence" consisting of the most abundant sequence present for each region of the HIV genome for this specific patient.
After the OTU picking step, the representative sequence for each OTU, namely, the most abundant sequences in that OTU, is chosen for subsequent analyses in order to reduce the computational power and the analysis time, without losing the frequency information.
However, this is probably the case because of the abundant sequence resources for this species.
In addition, this physical normalization procedure can be complemented – or to some degree substituted for – with bioinformatic methods for reducing highly abundant sequences (see below).
The latter suggested that the pieces derived from a global event that affected the entire genome, but was only detectable for highly abundant sequences.
The highly abundant sequences with the highest uncertainties for correct annotation (highest E-values), apolipophorin and the CUB and zona pellucida-like domain-containing protein 1, were further scrutinized by similarity searches in additional databases.
