{"entity": "publication", "iuid": "ef91de67722040beadef03c2bedd39f1", "timestamp": "2026-07-11T23:29:18.419Z", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ef91de67722040beadef03c2bedd39f1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ef91de67722040beadef03c2bedd39f1"}}, "title": "Genomic Characterization of the Barnacle Balanus improvisus Reveals Extreme Nucleotide Diversity in Coding Regions.", "authors": [{"family": "Alm Rosenblad", "given": "Magnus", "initials": "M", "orcid": "0000-0002-4077-7821", "researcher": {"href": "https://publications.scilifelab.se/researcher/1db3e7106016494bb4365e099a8493ef.json"}}, {"family": "Abramova", "given": "Anna", "initials": "A"}, {"family": "Lind", "given": "Ulrika", "initials": "U"}, {"family": "\u00d3lason", "given": "P\u00e1ll", "initials": "P"}, {"family": "Giacomello", "given": "Stefania", "initials": "S"}, {"family": "Nystedt", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0001-7809-7664", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0af5a168baa4b00a6fab8d3447ebfb4.json"}}, {"family": "Blomberg", "given": "Anders", "initials": "A", "orcid": "0000-0002-1260-3920", "researcher": {"href": "https://publications.scilifelab.se/researcher/5eec83537e954ff49431042e168a5f20.json"}}], "type": "journal article", "published": "2021-06-00", "journal": {"title": "Mar Biotechnol (NY)", "issn": "1436-2236", "volume": "23", "issue": "3", "pages": "402-416", "issn-l": null}, "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 (\u03c0) in coding regions (average \u03c0 \u2248 5% and average \u03c0 in fourfold degenerate sites \u2248 20%), and an overall high repeat content (at least 40%). We also report on high variation in the \u03b1-octopamine receptor OctA (average \u03c0 = 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.", "doi": "10.1007/s10126-021-10033-8", "pmid": "33931810", "labels": {"Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Stockholm (Genomics Production)": null, "NGI Stockholm (Genomics Applications)": null, "National Genomics Infrastructure": null, "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1007/s10126-021-10033-8"}, {"db": "pmc", "key": "PMC8270832"}], "notes": [], "created": "2021-05-06T15:00:04.738Z", "modified": "2024-01-16T13:48:39.618Z"}