Fig. 5
Methodology for the development of sex-specific Z and W inferred probes. Step 1. Generate single-tube long fragment reads and Illumina paired-end reads for female and male individuals, assemble and map reads. Step 2. Identify sex-linked reads from read depth coverage. Step 3. BLAST search sex-linked reads against high quality reference genome (V. komodoensis). Step 4. Generate hybrid assembly to identify genomewide repeats and mask repeats regions along sex-linked scaffolds. Step 5. Identify single copy sequences and design myTags® libraries. In step 2, the male to female (M/F) ratio of the Z-specific scaffolds in males is close to 2 whereas the W-specific scaffolds is close to 0. In females, the Z-specific and W-specific scaffolds are close to 1. Steps 4 and 5 were provided by Arbor Biosciences using proprietary methods (Ann Arbor, MI, United States). These probes targeted the single copy regions and functional genes and avoided repetitive elements and were used for FISH (Fluorescence in situ Hybridisation) (Fig modified after).
