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Alm Rosenblad M, Abramova A, Lind U, Ólason P, Giacomello S, Nystedt B, Blomberg A. Genomic Characterization of the Barnacle Balanus improvisus Reveals Extreme Nucleotide Diversity in Coding Regions. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2021; 23:402-416. [PMID: 33931810 PMCID: PMC8270832 DOI: 10.1007/s10126-021-10033-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 04/05/2021] [Indexed: 05/11/2023]
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.
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Affiliation(s)
- Magnus Alm Rosenblad
- Deparment of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg , Sweden
| | - Anna Abramova
- Deparment of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg , Sweden
| | - Ulrika Lind
- Deparment of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg , Sweden
| | - Páll Ólason
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Husargatan 3, 752 37, Uppsala, Sweden
| | - Stefania Giacomello
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Box 1031, 17121, Solna, Sweden
| | - Björn Nystedt
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Husargatan 3, 752 37, Uppsala, Sweden
| | - Anders Blomberg
- Deparment of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg , Sweden.
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Nunez JCB, Rong S, Ferranti DA, Damian-Serrano A, Neil KB, Glenner H, Elyanow RG, Brown BRP, Alm Rosenblad M, Blomberg A, Johannesson K, Rand DM. From tides to nucleotides: Genomic signatures of adaptation to environmental heterogeneity in barnacles. Mol Ecol 2021; 30:6417-6433. [PMID: 33960035 PMCID: PMC9292448 DOI: 10.1111/mec.15949] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 04/28/2021] [Accepted: 04/30/2021] [Indexed: 12/25/2022]
Abstract
The northern acorn barnacle (Semibalanus balanoides) is a robust system to study the genetic basis of adaptations to highly heterogeneous environments. Adult barnacles may be exposed to highly dissimilar levels of thermal stress depending on where they settle in the intertidal (i.e., closer to the upper or lower tidal boundary). For instance, barnacles near the upper tidal limit experience episodic summer temperatures above recorded heat coma levels. This differential stress at the microhabitat level is also dependent on the aspect of sun exposure. In the present study, we used pool‐seq approaches to conduct a genome wide screen for loci responding to intertidal zonation across the North Atlantic basin (Maine, Rhode Island, and Norway). Our analysis discovered 382 genomic regions containing SNPs which are consistently zonated (i.e., SNPs whose frequencies vary depending on their position in the rocky intertidal) across all surveyed habitats. Notably, most zonated SNPs are young and private to the North Atlantic. These regions show high levels of genetic differentiation across ecologically extreme microhabitats concomitant with elevated levels of genetic variation and Tajima's D, suggesting the action of non‐neutral processes. Overall, these findings support the hypothesis that spatially heterogeneous selection is a general and repeatable feature for this species, and that natural selection can maintain functional genetic variation in heterogeneous environments.
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Affiliation(s)
- Joaquin C B Nunez
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI, USA
| | - Stephen Rong
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI, USA.,Center for Computational Molecular Biology, Brown University, Providence, RI, USA
| | - David A Ferranti
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI, USA
| | | | - Kimberly B Neil
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI, USA
| | - Henrik Glenner
- Department of Biological Sciences, University of Bergen, Bergen, Norway.,Center of Macroecology and Climate, GLOBE, University of Copenhagen, Copenhagen, Denmark
| | - Rebecca G Elyanow
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI, USA.,Center for Computational Molecular Biology, Brown University, Providence, RI, USA
| | - Bianca R P Brown
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI, USA
| | - Magnus Alm Rosenblad
- Department of Chemistry and Molecular Biology, University of Gothenburg, Lundberg Laboratory, Göteborg, Sweden
| | - Anders Blomberg
- Department of Chemistry and Molecular Biology, University of Gothenburg, Lundberg Laboratory, Göteborg, Sweden
| | - Kerstin Johannesson
- Department of Marine Sciences, University of Gothenburg, Tjärnö Marine Laboratory, Strömstad, Sweden
| | - David M Rand
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI, USA.,Center for Computational Molecular Biology, Brown University, Providence, RI, USA
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Labriere C, Elumalai V, Staffansson J, Cervin G, Le Norcy T, Denardou H, Réhel K, Moodie LWK, Hellio C, Pavia H, Hansen JH, Svenson J. Phidianidine A and Synthetic Analogues as Naturally Inspired Marine Antifoulants. JOURNAL OF NATURAL PRODUCTS 2020; 83:3413-3423. [PMID: 33054188 DOI: 10.1021/acs.jnatprod.0c00881] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Stationary and slow-moving marine organisms regularly employ a natural product chemical defense to prevent being colonized by marine micro- and macroorganisms. While these natural antifoulants can be structurally diverse, they often display highly conserved chemistries and physicochemical properties, suggesting a natural marine antifouling pharmacophore. In our current report, we investigate the marine natural product phidianidine A, which displays several chemical properties found in highly potent marine antifoulants. Phidianidine A and synthetic analogues were screened against the settlement and metamorphosis of Amphibalanus improvisus cyprids, and several of the compounds displayed inhibitory activities at low micromolar concentrations with IC50 values down to 0.7 μg/mL observed. The settlement study highlights that phidianidine A is a potent natural antifoulant and that the scaffold can be tuned to generate simpler and improved synthetic analogues. The bioactivity is closely linked to the size of the compound and to its basicity. The study also illustrates that active analogues can be prepared in the absence of the natural constrained 1,2,4-oxadiazole ring. A synthetic lead analogue of phidianidine A was incorporated in a coating and included in antifouling field trials, where it was shown that the coating induced potent inhibition of marine bacteria and microalgae settlement.
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Affiliation(s)
- Christophe Labriere
- Department of Chemistry, Chemical Synthesis and Analysis Group, UiT The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Vijayaragavan Elumalai
- Department of Chemistry, Chemical Synthesis and Analysis Group, UiT The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Jannie Staffansson
- Department of Chemistry, Chemical Synthesis and Analysis Group, UiT The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Gunnar Cervin
- Department of Marine Sciences, Tjärnö Marine Laboratory, University of Gothenburg, SE-452 96 Strömstad, Sweden
| | - Tiffany Le Norcy
- Univ. Bretagne-Sud, EA 3884, LBCM, IUEM, F-56100 Lorient, France
| | - Hugo Denardou
- Department of Chemistry, Chemical Synthesis and Analysis Group, UiT The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Karine Réhel
- Univ. Bretagne-Sud, EA 3884, LBCM, IUEM, F-56100 Lorient, France
| | - Lindon W K Moodie
- Department of Medicinal Chemistry and Uppsala Antibiotic Centre, Biomedical Centre, Uppsala University, 75123 Uppsala, Sweden
| | - Claire Hellio
- Univ. Brest, Laboratoire des Sciences de l'Environnement MARin (LEMAR), CNRS, IRD, IFREMER, Brest 29285, France
| | - Henrik Pavia
- Department of Marine Sciences, Tjärnö Marine Laboratory, University of Gothenburg, SE-452 96 Strömstad, Sweden
| | - Jørn H Hansen
- Department of Chemistry, Chemical Synthesis and Analysis Group, UiT The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Johan Svenson
- Department of Chemistry, Chemical Synthesis and Analysis Group, UiT The Arctic University of Norway, N-9037 Tromsø, Norway
- Department of Chemistry, Biomaterial & Textile, RISE Research Institutes of Sweden, Box 857, 501 15 Borås, Sweden
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Abramova A, Alm Rosenblad M, Blomberg A, Larsson TA. Sensory receptor repertoire in cyprid antennules of the barnacle Balanus improvisus. PLoS One 2019; 14:e0216294. [PMID: 31048879 PMCID: PMC6497305 DOI: 10.1371/journal.pone.0216294] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 04/17/2019] [Indexed: 11/19/2022] Open
Abstract
Barnacle settlement involves sensing of a variety of exogenous cues. A pair of antennules is the main sensory organ that the cyprid larva uses to explore the surface. Antennules are equipped with a number of setae that have both chemo- and mechanosensing function. The current study explores the repertoire of sensory receptors in Balanus improvisus cyprid antennules with the goal to better understand sensory systems involved in the settling behavior of this species. We carried out transcriptome sequencing of dissected B. improvisus cyprid antennules. The generated transcriptome assembly was used to search for sensory receptors using HMM models. Among potential chemosensory genes, we identified the ionotropic receptors IR25a, IR8a and IR93a, and several divergent IR candidates to be expressed in the cyprid antennules. We found one gustatory-like receptor but no odorant receptors, chemosensory or odorant-binding proteins. Apart from chemosensory receptors, we also identified 13 potential mechanosensory genes represented by several transient receptor potential channels (TRP) subfamilies. Furthermore, we analyzed changes in expression profiles of IRs and TRPs during the B. improvisus settling process. Several of the sensory genes were differentially expressed during the course of larval settlement. This study gives expanded knowledge about the sensory systems present in barnacles, a taxonomic group for which only limited information about receptors is currently available. It furthermore serves as a starting point for more in depth studies of how sensory signaling affects settling behavior in barnacles with implications for preventing biofouling.
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Affiliation(s)
- Anna Abramova
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Magnus Alm Rosenblad
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Anders Blomberg
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Tomas Axel Larsson
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
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Abramova A, Lind U, Blomberg A, Rosenblad MA. The complex barnacle perfume: identification of waterborne pheromone homologues in Balanus improvisus and their differential expression during settlement. BIOFOULING 2019; 35:416-428. [PMID: 31142149 DOI: 10.1080/08927014.2019.1602123] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 03/22/2019] [Accepted: 03/24/2019] [Indexed: 06/09/2023]
Abstract
A key question in barnacle biology is the nature of cues that induce gregarious settlement. One of the characterised cues is the waterborne settlement pheromone (WSP). This study aimed to identify WSP homologues in Balanus improvisus and to investigate their expression during settlement. Six WSP homologues were identified, all containing an N-terminal signal peptide, a conserved core region, and a variable C-terminus comprising several -GR- and -HDDH- motifs. The B. improvisus WSP homologues were expressed in all settlement stages but showed different expression patterns. The homologue most similar to the B. amphitrite WSP was the most abundant and was constantly expressed during settlement. In contrast, several of the other WSP homologues showed the greatest expression in the juvenile stage. The presence of several WSP homologues suggests the existence of a pheromone mix, where con-specificity might be determined by a combination of sequence characteristics and the concentration of the individual components.
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Affiliation(s)
- Anna Abramova
- a Department of Chemistry and Molecular Biology , University of Gothenburg , Gothenburg , Sweden
| | - Ulrika Lind
- a Department of Chemistry and Molecular Biology , University of Gothenburg , Gothenburg , Sweden
| | - Anders Blomberg
- a Department of Chemistry and Molecular Biology , University of Gothenburg , Gothenburg , Sweden
| | - Magnus Alm Rosenblad
- a Department of Chemistry and Molecular Biology , University of Gothenburg , Gothenburg , Sweden
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