Genomic characterization of the barnacle Balanus improvisus reveals extreme nucleotide diversity in coding regions

Pilot short-read genome assembly of one single adult barnacle, Balanus improvisus (=Amphibalanus imrpovisus), used to estimate genome size and heterocygosity. Bi01.clean.fa.gz is the final assembly with contaminations etc removed.<br> Alm Rosenblad et al., Marine Biotechnology 2021<br><b><br></b><b>Abstract </b>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 <i>Balanus improvisus</i> (= <i>Amphibalanus improvisus</i>) based on short-read whole genome sequencing and experimental genome size estimation.<br>We show both experimentally (DNA staining and flow cytometry) and computationally (<i>k</i>-mer analysis) that <i>B. improvisus</i> 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 <i>B. improvisus</i> genome having an extremely high nucleotide diversity (π) in coding regions (average π ≈ 5% and average π in 4-fold 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 towards 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.