Abstract
Barnacles are key marine crustaceans in several habitats, and they constitute a common practical problem by causing biofouling on man-made marine constructions and ships. Despite causing considerable ecological and economic impacts, there is a surprising void of basic genomic knowledge, and a barnacle reference genome is lacking. We here set out to characterize the genome of the bay barnacle Balanus improvisus (= Amphibalanus improvisus) based on short-read whole-genome sequencing and experimental genome size estimation. We show both experimentally (DNA staining and flow cytometry) and computationally (k-mer analysis) that B. improvisus has a haploid genome size of ~ 740 Mbp. A pilot genome assembly rendered a total assembly size of ~ 600 Mbp and was highly fragmented with an N50 of only 2.2 kbp. Further assembly-based and assembly-free analyses revealed that the very limited assembly contiguity is due to the B. improvisus genome having an extremely high nucleotide diversity (π) in coding regions (average π ≈ 5% and average π in fourfold degenerate sites ≈ 20%), and an overall high repeat content (at least 40%). We also report on high variation in the α-octopamine receptor OctA (average π = 3.6%), which might increase the risk that barnacle populations evolve resistance toward antifouling agents. The genomic features described here can help in planning for a future high-quality reference genome, which is urgently needed to properly explore and understand proteins of interest in barnacle biology and marine biotechnology and for developing better antifouling strategies.
Highlights
Barnacles are sessile marine crustaceans encompassing around 1200 species that are usually gregarious and can be found at high densities in shallow and tidal waters around the globe (Newman and Abbott 1980)
De novo genome assembly based on 157 Gbp shortread Illumina sequences from one adult individual of B. improvisus, which corresponds to > 200 × coverage, resulted in 587,357 contigs > 200 bp in size (Table 1)
The poor contiguity in the pilot assembly suggested that a future reference genome assembly effort will pose a considerable challenge
Summary
Barnacles are sessile marine crustaceans encompassing around 1200 species that are usually gregarious and can be found at high densities in shallow and tidal waters around the globe (Newman and Abbott 1980). Marine Biotechnology (2021) 23:402–416 as an easy and less energetically demanding food (Dernbach and Freeman 2015). Barnacles are of importance for diverse aspects of marine biotechnology. They are one of the main biofouling organisms on man-made underwater constructions, such as the piping of cooling units and ship hulls, causing considerable ecological and economic impacts. Barnacles produce one of the strongest underwater adhesives (Kamino 2006; Berglin et al 2001) and are of great interest in many applications
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