Anonymous nuclear loci in non-model organisms: Making the most of high-throughput genome surveys

Bioinformatics

Volumn 28, Issue 14, 2012, Pages 1807-1810

  Bertozzi, Terry ^a,b   Sanders, Kate L ^b   Sistrom, Mark J ^c   Gardner, Michael G ^b,d  

^a SOUTH AUSTRALIAN MUSEUM   (Australia)

^b UNIVERSITY OF ADELAIDE   (Australia)

^c YALE UNIVERSITY   (United States)

^d FLINDERS UNIVERSITY   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

REPTILIA;

ANIMAL; ARTICLE; BIOLOGY; CELL NUCLEUS; DNA SEQUENCE; GENE LIBRARY; GENE LOCUS; GENETICS; GENOMICS; METHODOLOGY; REPTILE;

ANIMALS; CELL NUCLEUS; COMPUTATIONAL BIOLOGY; GENE LIBRARY; GENETIC LOCI; GENOMICS; REPTILES; SEQUENCE ANALYSIS, DNA;

EID: 84864145464     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/bts284     Document Type: Article

References (18)

1. Abdelkrim, J. et al. (2009) Fast, cost-effective development of species-specific microsatellite markers by genomic sequencing. Biotechniques, 46, 185-192.
2. Allentoft, M. E. et al. (2009) Identification of microsatellites from an extinct moa species using high-throughput (454) sequence data. Biotechniques, 46, 195-200.
3. Brugmans, B. et al. (2003) A new and versatile method for the successful conversion of AFLP markers into simple single locus markers. Nucleic Acids Res., 31, e55-e55.
4. Gardner, M. G. et al. (2011) Rise of the machines, recommendations for ecologists using next generation sequencing for microsatellite development. Mol. Ecol. Resour., 11, 1093-1101.
5. Jennings, W. B. and Edwards, S. V. (2005) Speciational history of Australian grass finches (Poephila) inferred from thirty gene trees. Evolution, 59, 2033-2047.
6. Jurka, J. et al. (2005) Repbase Update, a database of eukaryotic repetitive elements. Cytogent. Genome Res., 110, 462-467.
7. Karl, S. A. and Avise, J. C. (1993) PCR-based assays of Mendelian polymorphisms from anonymous single-copy nuclear DNA: techniques and applications for population genetics. Mol. Biol. Evol., 10, 342-361.
8. Lee, J. Y. and Edwards, S. V. (2008) Divergence across Australia's carpentarian barrier: statistical phylogeography of the red-backed fairy wren (Malurus melanocephalus). Evolution, 62, 3117-3134.
9. Librado, P. and Rozas, J. (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics, 25, 1451-1452.
10. Lowe, A. J. et al. (1998) Identification and characterization of nuclear, cleaved amplified polymorphic sequence (CAPS) loci in Irvingia gabonensis and I. wombolu, indigenous fruit trees of west and central Africa. Mol. Ecol., 7, 1771-1788.
11. Price, A. L. et al. (2005) De novo identification of repeat families in large genomes. Bioinformatics, 21, i351-i358.
12. Rasmussen, D. A. and Noor, M. A. F. (2009) What can you do with 0. 1x genome coverage? A case study based on a genome survey of the scuttle fly Megaselia scalaris (Phoridae). BMC Genomics, 10, 382.
13. Rosenblum, E. B. et al. (2007) Anonymous nuclear markers for the eastern fence lizard, Sceloporus undulatus. Mol. Ecol. Notes, 7, 113-116.
14. Rozen, S. and Skaletsky, H. (2000) Primer3 on the WWW for general users and for biologist programmers. Methods Mol. Biol., 132, 365-386.
15. Smit, A. F. A. et al. (1996-2010) RepeatMasker Open-3. 0. Available at http://www.repeatmasker.org (last accessed date November 11, 2011).
16. Thomson, R. C. et al. (2008) Developing markers for multilocus phylogenetics in nonmodel organisms: a test case with turtles. Mol. Phylogen. Evol., 49, 514-525.
17. Thomson, R. C. et al. (2010) Genome-enabled development ofDNAmarkers for ecology, evolution and conservation. Mol. Ecol., 19, 2184-2195.
18. Townsend, T. M. et al. (2008) Rapid development of multiple nuclear loci for phylogenetic analysis using genomic resources: an example from squamate reptiles. Mol. Phylogenet. Evol., 47, 129-142.