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A chromosome-level ...
A chromosome-level assembly of the seed beetle Callosobruchus maculatus genome with annotation of its repetitive elements
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- Arnqvist, Göran, Professor, 1961- (author)
- Uppsala universitet,Zooekologi
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- Westerberg, Ivar, 1996- (author)
- Stockholms universitet,Uppsala universitet,Systematisk biologi,Stockholm Univ, Dept Ecol Environm & Plant Sci, SE-10691 Stockholm, Sweden,Institutionen för ekologi, miljö och botanik,Uppsala University, Sweden
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- Galbraith, James (author)
- Univ Adelaide, Sch Biol Sci, Adelaide 5005, Australia.;Univ Exeter, Fac Environm Sci & Econ, Cornwall TR10 9FE, England.
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- Sayadi, Ahmed (author)
- Uppsala universitet,Reumatologi
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- Scofield, Douglas G., 1966- (author)
- Uppsala universitet,Evolutionsbiologi,UPPMAX
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- Olsen, Remi-André, 1985- (author)
- Stockholms universitet,Institutionen för biokemi och biofysik,Science for Life Laboratory (SciLifeLab),Stockholm Univ, Dept Biochem & Biophys, Sci Life Lab, SE-10691 Stockholm, Sweden.
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- Immonen, Elina (author)
- Uppsala universitet,Evolutionsbiologi
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- Bonath, Franziska, 1985- (author)
- Stockholms universitet,Science for Life Laboratory (SciLifeLab),Institutionen för molekylär biovetenskap, Wenner-Grens institut,Stockholm Univ, Wenner Gren Inst, Dept Mol Biosci, Sci Life Lab, SE-10691 Stockholm, Sweden.
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- Ewels, Philip (author)
- Seqera Labs, Barcelona 08005, Spain.
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- Suh, Alexander (author)
- Uppsala universitet,Systematisk biologi
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(creator_code:org_t)
- Oxford University Press, 2024
- 2024
- English.
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In: G3. - : Oxford University Press. - 2160-1836. ; 14:2
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https://uu.diva-port... (primary) (Raw object)
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Abstract
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- Callosobruchus maculatus is a major agricultural pest of legume crops worldwide and an established model system in ecology and evolution. Yet, current molecular biological resources for this species are limited. Here, we employ Hi-C sequencing to generate a greatly improved genome assembly and we annotate its repetitive elements in a dedicated in-depth effort where we manually curate and classify the most abundant unclassified repeat subfamilies. We present a scaffolded chromosome-level assembly, which is 1.01 Gb in total length with 86% being contained within the 9 autosomes and the X chromosome. Repetitive sequences accounted for 70% of the total assembly. DNA transposons covered 18% of the genome, with the most abundant superfamily being Tc1-Mariner (9.75% of the genome). This new chromosome-level genome assembly of C. maculatus will enable future genetic and evolutionary studies not only of this important species but of beetles more generally.
Subject headings
- NATURVETENSKAP -- Biologi -- Genetik (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Genetics (hsv//eng)
- NATURVETENSKAP -- Biologi -- Evolutionsbiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Evolutionary Biology (hsv//eng)
Keyword
- Chrysomelidae
- chromosome conformation capture
- X chromosome assembly
- transposable elements
- Tc1-Mariner
Publication and Content Type
- ref (subject category)
- art (subject category)
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- By the author/editor
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Arnqvist, Göran, ...
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Westerberg, Ivar ...
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Galbraith, James
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Sayadi, Ahmed
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Scofield, Dougla ...
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Olsen, Remi-Andr ...
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show more...
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Immonen, Elina
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Bonath, Franzisk ...
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Ewels, Philip
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Suh, Alexander
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- About the subject
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- NATURAL SCIENCES
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NATURAL SCIENCES
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and Biological Scien ...
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and Genetics
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- NATURAL SCIENCES
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NATURAL SCIENCES
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and Biological Scien ...
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and Evolutionary Bio ...
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G3
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Uppsala University
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Stockholm University