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First de novo whole...
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Pujolar, J. M.
(författare)
First de novo whole genome sequencing and assembly of the pink-footed goose
- Artikel/kapitelEngelska2018
Förlag, utgivningsår, omfång ...
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Elsevier BV,2018
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printrdacarrier
Nummerbeteckningar
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LIBRIS-ID:oai:DiVA.org:su-154827
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https://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-154827URI
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https://doi.org/10.1016/j.ygeno.2017.08.008DOI
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https://urn.kb.se/resolve?urn=urn:nbn:se:nrm:diva-3135URI
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Språk:engelska
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Sammanfattning på:engelska
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Ämneskategori:ref swepub-contenttype
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Ämneskategori:art swepub-publicationtype
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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 och genrebeteckningar
Biuppslag (personer, institutioner, konferenser, titlar ...)
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Dalén, L.Naturhistoriska riksmuseet,Enheten för bioinformatik och genetik(Swepub:nrm)lovedale
(författare)
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Olsen, Remi-AndréStockholms universitet,Institutionen för biokemi och biofysik,Science for Life Laboratory (SciLifeLab)(Swepub:su)rolse
(författare)
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Hansen, M. M.
(författare)
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Madsen, J.
(författare)
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Naturhistoriska riksmuseetEnheten för bioinformatik och genetik
(creator_code:org_t)
Sammanhörande titlar
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Ingår i:Genomics: Elsevier BV110:2, s. 75-790888-75431089-8646
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Genomics
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