Identification

Dynodydd

Identifier

NRW_DS125331

Laith Metadata

Metadata Language

English

Lineage

This investigation used 16 buccal swab DNA extractions which had been collected previously as part of a PhD investigation in Bangor University. DNA extraction was carried out using a Qiagen DNeasy Blood and Tissue Kit. Buccal swabs were processed by cutting half of the spongy tip of the swab and treating it as ‘tissue’ when following the manufacturers protocol. DNA quantification was assessed using a Qubit 3 fluorometer with the dsDNA HS assay kit, following the manufacturer’s protocol. Library preparation, quality control and whole genome sequencing on an Illumina NovaSeq Instrument (2x 150 bp PE reads) to a target 8x coverage was carried out by Novagene Ltd. Initial data processing involved trimming adapter sequences (synthetic DNA sequences that can occur as part of the sequencing process) from PE reads, requiring a single base overlap between adapter and read (setting “-O 1”), and removing short reads < 30 bp in length (setting -m 30), using the program Cutadapt v. 1.18 (Martin 2011). Overlapping PE read pairs were then identified and merged using the program FLASH v. 1.2.11 (Magoč & Salzberg 2011) using default parameter settings. The merged and unmerged PE reads were then mapped to the reference genome assembly of the sand lizard in separate analyses using the “mem” algorithm of the program bwa v. 0.7.17, using default parameter settings. The program samtools v. 1.3.1 (Li et al. 2009) was then used to filter out unmapped reads (setting “-F 4”), secondary mapped reads (setting “-F 256”) and reads with low mapping quality (setting “-q 30”). Samtools was then used to sort reads by their 5’ mapping position (command “sort”) and remove potential PCR duplicates. Finally, samtools was used to combine the merged and unmerged PE read data into a single file in bam format. Finally, samtools was used to combine the merged and unmerged PE read data into a single file in bam format for further analysis. Further Genetic Analysis is described fully in report.

Additional Information

Owens JB, Wilkinson JW, Wüster W, Barlow A, Papadopulos A. 2022. Genetic ancestry of introduced populations of sand lizard (Lacerta agilis) in Wales. NRW Evidence Report. Report No: 596, 30pp, Natural Resources Wales, Bangor.

Dyddiad cyfeirnod y set ddata (Cyhoeddiad)

Dataset Reference Date (Publication)

2022-09-16

Extent

Extent

Hyd

Geographic Extent

Wales (WLS)

N

W

E

S

 

Distribution

Quality

Keywords

Spatial Reference System

Content

Constraints