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First de novo whole genome sequencing and assembly of the pink-footed goose.
Pujolar, J M; Dalén, L; Olsen, R A; Hansen, M M; Madsen, J.
Afiliação
  • Pujolar JM; Department of Bioscience, Aarhus University, Ny Munkegade 114, Bldg. 1540, DK-8000 Aarhus C, Denmark. Electronic address: martipujolar@gmail.com.
  • Dalén L; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, SE-104 05 Stockholm, Sweden.
  • Olsen RA; Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Box 1031, SE-17121 Solna, Sweden.
  • Hansen MM; Department of Bioscience, Aarhus University, Ny Munkegade 114, Bldg. 1540, DK-8000 Aarhus C, Denmark.
  • Madsen J; Department of Bioscience-Kalø, Aarhus University, Grenåvej 14, DK-8410 Rønde, Denmark.
Genomics ; 110(2): 75-79, 2018 03.
Article em En | MEDLINE | ID: mdl-28860085
ABSTRACT
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 1.38×10-7 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.
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Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Genoma / Gansos Limite: Animals Idioma: En Revista: Genomics Assunto da revista: GENETICA Ano de publicação: 2018 Tipo de documento: Article

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Genoma / Gansos Limite: Animals Idioma: En Revista: Genomics Assunto da revista: GENETICA Ano de publicação: 2018 Tipo de documento: Article