ena-STUDY-ESTACION BIOLOGICA DONANA-02-11-2015-12:13:50:181-25
Genome-wide surveys of nucleotide variation using single-digest RAD-Seq Illumina libraries in sixty specimens of yellow-billed pintail, cinnamon teal, and speckled teal specimens collected from high- and low-altitude localities in the Andes
Sixty duck specimens representing three species of Andean ducks, cinnamon teal (Anas cyanoptera), speckled teal (Anas georgica) and yellow-billed pintails (Anas flavirostris) from high- and low-altitude localities in the Andes were selected for genome-wide surveys of nucleotide variation using single-digest RAD-Seq and single-end Illumina sequencing. Total genomic DNA was extracted using a DNeasy Tissue Kit (Qiagen, Valencia, California, USA) and normalized using a Qubit Fluorometer (Invitrogen, Grand Island, New York, USA). DNA samples were submitted to Floragenex (Eugene, Oregon, USA) for single-digest RAD-Seq using SbfI, which recognizes an 8-nucleotide (CCTGCAGG) restriction site. Digested DNAs were ligated to barcodes and sequencing adaptors and then sequenced on the Illumina HiSeq 2000 with single-end 100 bp chemistry. Following Illumina sequencing, sequences were demultiplexed and trimmed to yield RAD sequences of 90 bp. Data analysis and bioinformatics pipelines were provided by Floragenex. A total of 372 million sequence reads were obtained with an average depth of 7.6 (±2.4 SD) million reads per sample for yellow-billed pintail and speckled teal and 3.3 (±1.4 SD) million reads per sample for cinnamon teal, corresponding to an average of 140,671 (±27,856) RAD loci representing ~1% of a typical 1.1 gigabase avian genome.
Sixty duck specimens representing three species of Andean ducks, cinnamon teal (Anas cyanoptera), speckled teal (Anas georgica) and yellow-billed pintails (Anas flavirostris) from high- and low-altitude localities in the Andes were selected for genome-wide surveys of nucleotide variation using single-digest RAD-Seq and single-end Illumina sequencing. Total genomic DNA was extracted using a DNeasy Tissue Kit (Qiagen, Valencia, California, USA) and normalized using a Qubit Fluorometer (Invitrogen, Grand Island, New York, USA). DNA samples were submitted to Floragenex (Eugene, Oregon, USA) for single-digest RAD-Seq using SbfI, which recognizes an 8-nucleotide (CCTGCAGG) restriction site. Digested DNAs were ligated to barcodes and sequencing adaptors and then sequenced on the Illumina HiSeq 2000 with single-end 100 bp chemistry. Following Illumina sequencing, sequences were demultiplexed and trimmed to yield RAD sequences of 90 bp. Data analysis and bioinformatics pipelines were provided by Floragenex. A total of 372 million sequence reads were obtained with an average depth of 7.6 (±2.4 SD) million reads per sample for yellow-billed pintail and speckled teal and 3.3 (±1.4 SD) million reads per sample for cinnamon teal, corresponding to an average of 140,671 (±27,856) RAD loci representing ~1% of a typical 1.1 gigabase avian genome.