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Genomic Characteriz...
Genomic Characterization of the Barnacle Balanus improvisus Reveals Extreme Nucleotide Diversity in Coding Regions
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- Alm Rosenblad, Magnus, 1957 (författare)
- Gothenburg University,Göteborgs universitet,Institutionen för kemi och molekylärbiologi,Department of Chemistry and Molecular Biology,Univ Gothenburg, Dept Chem & Mol Biol, Gothenburg, Sweden.
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- Abramova, Anna, 1990 (författare)
- Gothenburg University,Göteborgs universitet,Institutionen för kemi och molekylärbiologi,Department of Chemistry and Molecular Biology,Univ Gothenburg, Dept Chem & Mol Biol, Gothenburg, Sweden.
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- Lind, Ulrika (författare)
- Gothenburg University,Göteborgs universitet,Institutionen för kemi och molekylärbiologi,Department of Chemistry and Molecular Biology,Univ Gothenburg, Dept Chem & Mol Biol, Gothenburg, Sweden.
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- Ólason, Páll I. (författare)
- Uppsala universitet,Science for Life Laboratory, SciLifeLab,Institutionen för cell- och molekylärbiologi
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- Giacomello, S. (författare)
- Stockholm Univ, Dept Biochem & Biophys, Natl Bioinformat Infrastruct Sweden, Sci Life Lab, Box 1031, S-17121 Solna, Sweden.
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- Nystedt, Björn, 1978- (författare)
- Uppsala universitet,Science for Life Laboratory, SciLifeLab,Institutionen för cell- och molekylärbiologi
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- Blomberg, Anders, 1956 (författare)
- Gothenburg University,Göteborgs universitet,Institutionen för kemi och molekylärbiologi,Department of Chemistry and Molecular Biology,Univ Gothenburg, Dept Chem & Mol Biol, Gothenburg, Sweden.
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(creator_code:org_t)
- 2021-05-01
- 2021
- Engelska.
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Ingår i: Marine Biotechnology. - : Springer Science and Business Media LLC. - 1436-2228 .- 1436-2236. ; 23, s. 402-416
- Relaterad länk:
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https://doi.org/10.1...
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https://gup.ub.gu.se...
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https://doi.org/10.1...
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https://urn.kb.se/re...
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Abstract
Ämnesord
Stäng
- 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 baybarnacle 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. © 2021, The Author(s).
Ämnesord
- NATURVETENSKAP -- Biologi -- Ekologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Ecology (hsv//eng)
- NATURVETENSKAP -- Biologi -- Genetik (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Genetics (hsv//eng)
- TEKNIK OCH TEKNOLOGIER -- Naturresursteknik -- Marin teknik (hsv//swe)
- ENGINEERING AND TECHNOLOGY -- Environmental Engineering -- Marine Engineering (hsv//eng)
- NATURVETENSKAP -- Biologi -- Biokemi och molekylärbiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Biochemistry and Molecular Biology (hsv//eng)
Nyckelord
- Balanus improvisus
- Barnacle
- Genome
- Nucleotide diversity
- Octopamine receptor
- Genes
- Marine biology
- Antifouling strategies
- Ecological and economic
- Genomic characterization
- Marine biotechnology
- Practical problems
- Whole genome sequencing
- Nucleotides
- Genome
Publikations- och innehållstyp
- ref (ämneskategori)
- art (ämneskategori)
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