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Published June 14, 2013 | Version v1
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Data from: Mass production of SNP markers in a nonmodel passerine bird through RAD sequencing and contig mapping to the zebra finch genome

Authors/Creators

  • 1. French National Centre for Scientific Research
  • 2. Département de Génétique Animale
  • 3. University of Edinburgh
  • 4. Société Calédonienne d'Ornithologie Nord; BP 236; F-98822; Poindimié; Nouvelle Calédonie; France*
  • 5. Laboratory Evolution and Biological Diversity
  • 6. Museo Nacional de Ciencias Naturales

Description

Here, we present an adaptation of restriction-site-associated DNA sequencing (RAD-seq) to the Illumina HiSeq2000 technology that we used to produce SNP markers in very large quantities at low cost per unit in the Réunion grey white-eye (Zosterops borbonicus), a nonmodel passerine bird species with no reference genome. We sequenced a set of six pools of 18–25 individuals using a single sequencing lane. This allowed us to build around 600 000 contigs, among which at least 386 000 could be mapped to the zebra finch (Taeniopygia guttata) genome. This yielded more than 80 000 SNPs that could be mapped unambiguously and are evenly distributed across the genome. Thus, our approach provides a good illustration of the high potential of paired-end RAD sequencing of pooled DNA samples combined with comparative assembly to the zebra finch genome to build large contigs and characterize vast numbers of informative SNPs in nonmodel passerine bird species in a very efficient and cost-effective way.

Notes

SNPs validated with different MAC (2 or 3) and a sequencing depth of 10 or 20X
This archive contains three types of files with extensions '.n', '.y' and '.alleles'. '.n' files list for each library the number of reads associated at each SNP position. '.y' files list the number of times a SNP is detected. '.alleles' files give the name of the contig displaying a given SNP, then the position of the SNP from the restriction site, the total number of reads for the whole dataset, the count of the minor allele, the count of the major allele, and the two possible nucleotides encountered at this position
Files_with_contigs_names_and_allele_counts_for_several_stringency_criteria.zip
Fasta file listing contigs
consensus_reads_1_2_UDBA.zip

Files

consensus_reads_1_2_UDBA.zip

Files (100.4 MB)

Additional details

Related works

Is cited by
10.1111/1755-0998.12137 (DOI)