High-throughput SNP discovery in the rabbit (Oryctolagus cuniculus) genome by next-generation semiconductor-based sequencing

Animal Genetics

Volumn 45, Issue 2, 2014, Pages 304-307

  Bertolini, F ^a   Schiavo, G ^a   Scotti, E ^a   Ribani, A ^a   Martelli, P L ^a   Casadio, R ^a   Fontanesi, L ^a  

^a UNIVERSITY OF BOLOGNA   (Italy)

Author keywords

next generation sequencing; polymorphisms; reduced representation library; resequencing

Indexed keywords

ORYCTOLAGUS CUNICULUS;

ANIMAL; ANIMAL DISEASE; ARTICLE; GENETICS; GENOTYPING TECHNIQUE; HIGH THROUGHPUT SEQUENCING; METHODOLOGY; NEXT-GENERATION SEQUENCING; POLYMORPHISMS; RABBIT; REDUCED REPRESENTATION LIBRARY; RESEQUENCING; SINGLE NUCLEOTIDE POLYMORPHISM;

NEXT-GENERATION SEQUENCING; POLYMORPHISMS; REDUCED REPRESENTATION LIBRARY; RESEQUENCING;

ANIMALS; GENOTYPING TECHNIQUES; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; POLYMORPHISM, SINGLE NUCLEOTIDE; RABBITS;

EID: 84897654788     PISSN: 02689146     EISSN: 13652052     Source Type: Journal    
DOI: 10.1111/age.12121     Document Type: Article

References (22)

1. Altshuler D., Pollara V.J., Cowles C.R., van Etten W.J., Baldwin J., Linton L., &, Lander E.S., (2000) An SNP map of the human genome generated by reduced representation shotgun sequencing. Nature 407, 513-6.
2. Aslam M.L., Bastiaansen J.W.M., Elferink M.G., et al,. (2012) Whole genome SNP discovery and analysis of genetic diversity in Turkey (Meleagris gallopavo). BMC Genomics 13, 391.
3. Bragg L.M., Stone G., Butler M.K., Hugenholtz P., &, Tyson G.W., (2013) Shining a light on dark sequencing: characterizing errors in Ion Torrent PGM data. PLoS Computational Biology 9, e1003031.
4. Carneiro M., Blanco-Aguiar J.A., Villafuerte R., Ferrand N., &, Nachman M.W., (2010) Speciation in the European rabbit (Oryctolagus cuniculus): islands of differentiation on the X chromosome and autosomes. Evolution 64, 3443-60.
5. Carneiro M., Afonso S., Geraldes A., et al,. (2011) The genetic structure of domestic rabbits. Molecular Biology and Evolution 28, 1801-16.
6. Carneiro M., Albert F.W., Melo-Ferreira J., et al,. (2012) Evidence for widespread positive and purifying selection across the European rabbit (Oryctolagus cuniculus) genome. Molecular Biology and Evolution 29, 1837-49.
7. Fontanesi L., Forestier L., Allain D., et al,. (2010) Characterization of the rabbit agouti signaling protein (ASIP) gene: transcripts and phylogenetic analyses and identification of the causative mutation of the nonagouti black coat colour. Genomics 95, 166-75.
8. Fontanesi L., Martelli P.L., Scotti E., Russo V., Rogel-Gaillard C., Casadio R., &, Vernesi C., (2012) Exploring copy number variation in the rabbit (Oryctolagus cuniculus) genome by array comparative genome hybridization. Genomics 100, 245-51.
9. Fontanesi L., Scotti E., Cisarova K., Di Battista P., Dall'Olio S., Fornasini D., &, Frabetti A., (2013) A missense mutation in the rabbit melanocortin 4 receptor (MC4R) gene is associated with finishing weight in a meat rabbit line. Animal Biotechnology 24, 268-77.
10. Fontanesi L., Scotti E., Allain D., &, Dall'Olio S., (2014) A frameshift mutation in the melanophilin (MLPH) gene causes the dilute coat colour in rabbit (Oryctolagus cuniculus) breeds. Animal Genetics, doi: 10.1111/age.12104.
11. Li H., &, Durbin R., (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754-60.
12. Li H., &, Durbin R., (2010) Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 26, 589-95.
13. Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., &, Durbin R.,; 1000.Genome.Project.Data.Processing.Subgroup. (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25, 2078-9.
14. Lindblad-Toh K., Garber M., Zuk O., et al,. (2011) A high-resolution map of human evolutionary constraint using 29 mammals. Nature, 478, 476-82.
15. McLaren W., Pritchard B., Rios D., Chen Y., Flicek P., &, Cunningham F., (2010) Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor. Bioinformatics 26, 2069-70.
16. Ning Z., Cox A.J., &, Mullikin J.C., (2001) SSAHA: a fast search method for large DNA databases. Genome Research 11, 1725-9.
17. Rogel-Gaillard C., Ferrand N., &, Hayes H., (2009) Rabbit. In: Genome Mapping and Genomics in Animals, Volume 3; Genome Mapping and Genomics in Domestic Animals (Ed., N.E. Cockett, &, C. Kole,), pp. 165-230. Springer-Verlag Berlin Heidelberg, Germany.
18. Rothberg J.M., Hinz W., Rearick T.M., et al,. (2011) An integrated semiconductor device enabling non-optical genome sequencing. Nature 475, 348-52.
19. Smith T.F., &, Waterman M.S., (1981) Identification of common molecular subsequences. Journal of Molecular Biology 147, 195-7.
20. Thorvaldsdõttir H., Robinson J.T., &, Mesirov J.P., (2013) Integrative genomics viewer (IGV): high-performance genomics data visualization and exploration. Briefings in Bioinformatics 14, 178-92.
21. Van Tassell C.P., Smith T.P., Matukumalli L.K., et al,. (2008) SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries. Nature Methods 5, 247-52.
22. Wiedmann R.T., Smith T.P., &, Nonneman D.J., (2008) SNP discovery in swine by reduced representation and high throughput pyrosequencing. BMC Genetics 9, 81.