Genomic Characterization of the Barnacle Balanus improvisus Reveals Extreme Nucleotide Diversity in Coding Regions

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.

Comparative genomics reveals the dynamic evolutionary history of cement protein genes of barnacles from intertidal to deep‐sea hydrothermal vents

“…In addition, the heterozygosity of barnacle genomes is supported by the range of concordance rates of orthologues (Table 1). Consistent with previous studies, these findings suggest that barnacles possess heterozygous genomes with high genetic diversity (Alm Rosenblad et al., 2021; Ip et al., 2021; Kim et al., 2019). The establishment of high‐quality and complete reference genome assemblies for thoracican barnacles presents formidable challenges due to the elevated levels of heterozygosity and the abundance of repetitive sequences within their genomes.…”

Draft Genome of Tanacetum Coccineum: Genomic Comparison of Closely Related Tanacetum-Family Plants

“…Since the distribution with the maximum coverage = 1 was considered to be caused by sequencing errors, we treated the data after coverage = 11, which is the minimum value between the two distributions, as the k-mer derived from the correct genome. In accordance with previous studies [8], the genome size estimated from the k-mer distribution with a maximum of 44 for coverage = 11 and above was 9.8 Gb. These analyses led to the conclusion that the T. coccineum used in the present study has a genome size of approximately 9 Gb.…”

“…Separately, the genome size was estimated using k-mer depth analysis, as described previously [8]. Briefly, the occurrence of each k-mer was counted using the Jellyfish software [7], and the homozygous k-mer depth peak (C) was determined from a histogram of the k-mer depths.…”

Ten years of marine evolutionary biology—Challenges and achievements of a multidisciplinary research initiative

“…By developing reference genomes for our target species, we aimed to make progress beyond earlier achievements that had used standard molecular tools for that time, such as mtDNA and microsatellite markers. However, the large size and high variability of the genomes (such as a high content [>40%] of genomic repeats, and extremely high genetic diversity with ~5% nucleotide diversity in coding regions of the barnacle Balanus ( Amphibalanus ) improvisus ; Alm Rosenblad et al, 2021 ), meant that our ambitious aim to establish seven new genomes from different major groups of organisms (Figure 2 ) became a substantial challenge. Following the first Illumina‐based reference genomes, we have continued to improve several of the reference genomes by long read (PacBio) sequencing with the invaluable help of many collaborators.…”