Puregene tissue core kit a

A purebred DZ donkey was used for genome sequencing (Supplementary Note 1). Genomic DNA was extracted from blood by using the Puregene Tissue Core Kit A (Qiagen, Beijing, China).

Blood and tissue samples were obtained from eight wild guanacos, vicuñas, and domestic llamas and from seven alpacas. Sampling of guanacos and vicuñas represents the entire range of geographic distribution of each species (Additional file 1: Table S8). One adult male guanaco from Putre (Chile) and adult female vicuña from Lauca National Park (Chile) were selected for de novo assembly, representing the northern subspecies of wild South American camelids, Lama guanicoe cacsilensis and Vicugna vicugna mensalis, respectively. Llama tissues were obtained from Putre and alpaca from Temuco (Chile; Additional file 1: Table S8). Genomic DNA was extracted using the Puregene Tissue Core Kit A (Qiagen). See Additional Material S3 for further information and permit details.

Genomic DNA were extracted from fin samples for all 24 specimens using Puregene Tissue Core Kit A (Qiagen, MD, USA). Then, genomic libraries of insert size of 350 base pairs were constructed and genome resequencing with average of 24.2 X for each individual were performed using the Illumina X Ten sequencing platforms (Supplementary Table S1). To detect SNPs at the population level, the Illumina sequencing reads were mapped to the Brachymystax lenok genome with Burrows-Wheeler Alignment (BWA) tool (Li and Durbin, 2009 (link)), and polymerase chain reaction (PCR) duplicates were filtered using SAMtools (Li et al., 2009 (link)). SNP calling was performed using GATK v.4.1.2.0 (McKenna et al., 2010 (link)) with default parameters across the 24 individuals. To obtain reliable SNP, we performed a filtering step with the following set of parameters: depth ≥4, MQ ≥ 40, FS ≤ 60, QD ≥ 4, maf ≥0.05, and miss ≤0.2, according to previous study (De Mita et al., 2013 (link)).