By contrast to the mean number of genes recovered
with high coverage (1207 genes), there was
some variation among species and individuals. As a
consequence, the number of genes recovered in all 10
species was relatively low (449 genes with ≥ 90%
sequence coverage). Apart from the factors considered
(e.g. storage media and phylogenetic distance),
there are others that may affect the capture success
inherent to the short fragment length of Illumina
sequencing. Multiple filtering stages and overly short
sequence length for contig recovery and BLAST
results can negatively affect gene sequence recovery.
Minor adjustments to blast parameters, such as
sequence length or expected value, may mean important
portions of genes are not ‘recovered’ for the final
analysis (Altschul et al., 1997; Moreno-Hagelsieb &
Latimer, 2008).