4.3. Conclusion
This study presents the potential advantages of using capture-based
target gene enrichment for biodiversity assessment of prokaryotic and
eukaryotic communities, with a specific application in poorly known
deep-sea benthic ecosystems. The results showed that capture-based
target gene enrichment has the potential for considerable added value
compared to metabarcoding in performing referenced biodiversity
inventories and phylogenetic reconstruction, improving knowledge for
both biomonitoring and management purposes. CBH showed the ability to
reach the two main goals initially established in this study: (i)
revealing a broader spectrum of metazoan diversity and (ii)
reconstructing full-length barcode regions (up to 1900 bp) allowing
better phylogenetic reconstruction, thus improving taxonomic
assignments. Consequently, provided sequencing depth is sufficient to
allow de novo reconstruction, CBH can be applied at slightly
higher costs than MTB for i) identifying taxa that are not well
represented (nor any close relatives) in databases and ii) performing
phylogenetic and phylogeographic studies.