Genomic DNA Extraction and SLAF Library Construction for Cyprinidae

Genomic DNA was extracted from muscle tissue using the standard phenol-chloroform method [23 ]. DNA quality was first assessed using 1% agarose gel and was further quantified using a NanoDrop^® ND-1000 spectrophotometer (Thermo Scientific, Waltham, MA, USA). SLAF sequence strategy with specific modifications was utilised in library construction. Briefly, the reference sequence of Cyprinus carpio (GenBank accession number: GCA_000951615.2) [24 (link)] was used to conduct the pre-experiment on silico simulation of the number of markers generated by various endonuclease combinations. The SLAF library was constructed based on the SLAF pilot experiment in accordance with the predesigned scheme, and eventually two endonuclease combinations of HaeIII and Hpy166II (New England Biolabs, Ipswich, MA, USA) were applied to genomic DNA digestion in the fish populations. Zhang et al. described the details of the SLAF sequence strategy [25 (link)]. The sequencing data were generated using Illumina HiSeq2500 platform. Raw data had been submitted to the National Center for Biotechnology Information (NCBI) Sequence Read Archive with the Bioproject number PRJNA599030.