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.