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First de novo whole genome sequencing and assembly of the pink-footed goose
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
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Number of Authors: 52018 (English)In: Genomics, ISSN 0888-7543, E-ISSN 1089-8646, Vol. 110, no 2, p. 75-79Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
2018. Vol. 110, no 2, p. 75-79
Keywords [en]
Avian genome, Birds, Geese, Substitution rate, Whole genome sequences
National Category
Environmental Biotechnology Biological Sciences
Identifiers
URN: urn:nbn:se:su:diva-154827DOI: 10.1016/j.ygeno.2017.08.008ISI: 000425875500001PubMedID: 28860085OAI: oai:DiVA.org:su-154827DiVA, id: diva2:1196794
Available from: 2018-04-11 Created: 2018-04-11 Last updated: 2018-04-11Bibliographically approved

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Dalén, L.Olsen, Remi-André
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CiteExportLink to record
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