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Identifying the causes and consequences of assembly gaps using a multiplatform genome assembly of a bird‐of‐paradise

Peona, Valentina (författare)
Uppsala universitet,Evolutionsbiologi,Systematisk biologi,Science for Life Laboratory, SciLifeLab
Blom, Mozes P. K. (författare)
Department of Bioinformatics and Genetics Swedish Museum of Natural History Stockholm Sweden;Museum für Naturkunde Leibniz Institut für Evolutions‐ und Biodiversitätsforschung Berlin Germany,Swedish Museum Nat Hist, Dept Bioinformat & Genet, Stockholm, Sweden.;Leibniz Inst Evolut & Biodiversitatsforsch Berlin, Museum Nat Kunde, Berlin, Germany.
Xu, Luohao (författare)
Department of Neurosciences and Developmental Biology University of Vienna Vienna Austria,Univ Vienna, Dept Neurosci & Dev Biol, Vienna, Austria.
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Burri, Reto (författare)
Department of Population Ecology Institute of Ecology and Evolution Friedrich‐Schiller‐University Jena Jena Germany,Friedrich Schiller Univ Jena, Inst Ecol & Evolut, Dept Populat Ecol, Jena, Germany.
Sullivan, Shawn (författare)
Phase Genomics Seattle WA USA,Phase Genom, Seattle, WA USA.
Bunikis, Ignas (författare)
Uppsala universitet,Institutionen för immunologi, genetik och patologi,uppsala genomcenter
Liachko, Ivan (författare)
Phase Genomics Seattle WA USA,Phase Genom, Seattle, WA USA.
Haryoko, Tri (författare)
Research Centre for Biology Museum Zoologicum BogorienseIndonesian Institute of Sciences (LIPI) Cibinong Indonesia,Indonesian Inst Sci UPI, Res Ctr Biol, Museum Zool Bogoriense, Cibinong, Indonesia.
Jønsson, Knud A. (författare)
Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark,Univ Copenhagen, Nat Hist Museum Denmark, Copenhagen, Denmark.
Zhou, Qi (författare)
Department of Neurosciences and Developmental Biology University of Vienna Vienna Austria;MOE Laboratory of Biosystems Homeostasis & Protection Life Sciences Institute Zhejiang University Hangzhou China;Center for Reproductive Medicine The 2nd Affiliated Hospital School of Medicine Zhejiang University Hangzhou China,Univ Vienna, Dept Neurosci & Dev Biol, Vienna, Austria.;Zhejiang Univ, Life Sci Inst, MOE Lab Biosyst Homeostasis & Protect, Hangzhou, Peoples R China.;Zhejiang Univ, Affiliated Hosp 2, Ctr Reprod Med, Sch Med, Hangzhou, Peoples R China.
Irestedt, Martin (författare)
Naturhistoriska riksmuseet,Enheten för bioinformatik och genetik,Department of Bioinformatics and Genetics Swedish Museum of Natural History Stockholm Sweden,Swedish Museum Nat Hist, Dept Bioinformat & Genet, Stockholm, Sweden.
Suh, Alexander (författare)
Uppsala universitet,Evolutionsbiologi,Science for Life Laboratory, SciLifeLab,Systematisk biologi,Univ East Anglia, Sch Biol Sci Organisms & Environm, Norwich, Norfolk, England.
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 (creator_code:org_t)
2020-10-10
2020
Engelska.
Ingår i: Molecular Ecology Resources. - : Wiley. - 1755-098X .- 1755-0998. ; 21:1, s. 263-286
Relaterad länk:
https://onlinelibrar...
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https://doi.org/10.1...
https://uu.diva-port... (primary) (Raw object)
https://urn.kb.se/re...
https://doi.org/10.1...
https://urn.kb.se/re...
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  • Tidskriftsartikel (refereegranskat)
Abstract Ämnesord
Stäng  
  • Genome assemblies are currently being produced at an impressive rate by consortia and individual laboratories. The low costs and increasing efficiency of sequencing technologies now enable assembling genomes at unprecedented quality and contiguity. However, the difficulty in assembling repeat-rich and GC-rich regions (genomic “dark matter”) limits insights into the evolution of genome structure and regulatory networks. Here, we compare the efficiency of currently available sequencing technologies (short/linked/long reads and proximity ligation maps) and combinations thereof in assembling genomic dark matter. By adopting different de novo assembly strategies, we compare individual draft assemblies to a curated multiplatform reference assembly and identify the genomic features that cause gaps within each assembly. We show that a multiplatform assembly implementing long-read, linked-read and proximity sequencing technologies performs best at recovering transposable elements, multicopy MHC genes, GC-rich microchromosomes and the repeat-rich W chromosome. Telomere-to-telomere assemblies are not a reality yet for most organisms, but by leveraging technology choice it is now possible to minimize genome assembly gaps for downstream analysis. We provide a roadmap to tailor sequencing projects for optimized completeness of both the coding and noncoding parts of nonmodel genomes.

Ämnesord

NATURVETENSKAP  -- Biologi -- Genetik (hsv//swe)
NATURAL SCIENCES  -- Biological Sciences -- Genetics (hsv//eng)

Nyckelord

Genetics
Ecology
Evolution
Behavior and Systematics
Biotechnology
Ecosystems and species history
Ekosystem och arthistoria

Publikations- och innehållstyp

ref (ämneskategori)
art (ämneskategori)

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