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First de novo whole...
First de novo whole genome sequencing and assembly of the pink-footed goose
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Pujolar, J. M. (författare)
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- Dalén, L. (författare)
- Naturhistoriska riksmuseet,Enheten för bioinformatik och genetik
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- Olsen, Remi-André (författare)
- Stockholms universitet,Institutionen för biokemi och biofysik,Science for Life Laboratory (SciLifeLab)
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Hansen, M. M. (författare)
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Madsen, J. (författare)
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(creator_code:org_t)
- Elsevier BV, 2018
- 2018
- Engelska.
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Ingår i: Genomics. - : Elsevier BV. - 0888-7543 .- 1089-8646. ; 110:2, s. 75-79
- Relaterad länk:
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https://doi.org/10.1...
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https://urn.kb.se/re...
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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
- Annotated genomes can provide new perspectives on the biology of species. We present the first de novo whole genome sequencing for the pink-footed goose. In order to obtain a high-quality de novo assembly the strategy used was to combine one short insert paired-end library with two mate-pair libraries. The pink-footed goose genome was assembled de novo using three different assemblers and an assembly evaluation was subsequently performed in order to choose the best assembler. For our data, ALLPATHS-LG performed the best, since the assembly produced covers most of the genome, while introducing the fewest errors. A total of 26,134 genes were annotated, with bird species accounting for virtually all BLAST hits. We also estimated the substitution rate in the pink-footed goose, which can be of use in future demographic studies, by using a comparative approach with the genome of the chicken, the mallard and the swan goose. A substitution rate of 1.38 x 10(-7) per nucleotide per generation was obtained when comparing the genomes of the two closely-related goose species (the pink-footed and the swan goose). Altogether, we provide a valuable tool for future genomic studies aiming at particular genes and regions of the pink-footed goose genome as well as other bird species.
Ämnesord
- TEKNIK OCH TEKNOLOGIER -- Miljöbioteknik (hsv//swe)
- ENGINEERING AND TECHNOLOGY -- Environmental Biotechnology (hsv//eng)
- NATURVETENSKAP -- Biologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences (hsv//eng)
- NATURVETENSKAP -- Biologi -- Genetik (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Genetics (hsv//eng)
Nyckelord
- Avian genome
- Birds
- Geese
- Substitution rate
- Whole genome sequences
- Diversity of life
Publikations- och innehållstyp
- ref (ämneskategori)
- art (ämneskategori)
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