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.

藤壶是几个栖息地中的关键海洋甲壳类动物，它们通过对人造海洋建筑和船舶造成生物污垢构成了一个常见的实际问题。尽管造成了相当大的生态和经济影响，但基本基因组知识却令人惊讶，并且缺乏藤壶参考基因组。我们在这里着手基于短读全基因组测序和实验基因组大小估计来表征海湾藤壶Balanus improvisus (=  Amphibalanus improvisus ) 的基因组。我们通过实验（DNA 染色和流式细胞术）和计算（k聚体分析）表明B. improvisus具有约 740 Mbp 的单倍体基因组大小。试点基因组组装使总组装大小约为 600 Mbp，并且高度碎片化，N50 仅为 2.2 kbp。进一步的基于组装和无组装的分析表明，非常有限的组装连续性是由于B. improvisus基因组在编码区具有极高的核苷酸多样性 (π)（平均 π ≈ 5%，四重简并位点的平均 π ≈ 20%），以及整体高重复含量（至少 40%）。我们还报告了 α-章鱼胺受体 OctA（平均 π = 3.6%）的高度变化，这可能会增加藤壶种群对防污剂产生抗性的风险。这里描述的基因组特征可以帮助规划未来的高质量参考基因组，这是正确探索和理解藤壶生物学和海洋生物技术中感兴趣的蛋白质以及开发更好的防污策略所迫切需要的。