Comparative analysis and synteny detection

Protein sequences of the annotated genes in Brazil A4 were used for BLASTP search against all genes in Y C6, and only the top two hits with an e-value < 10⁻⁵ were kept as homologous pairs. These homologous pairs were used for syntenic block detection through MCscanX [93] with a match score of 50, match size of 5, gap penalty of -1, overlap window of 5, e-value of 1e-5, and max gaps of 25. The output of MCScanX was further parsed using in-house script, and was submitted to Circa (OMGenomics, http://omgenomics.com/circa/) to draw comparative plot. The same workflow was applied to detect synteny blocks between smaller scaffolds and chromosomes for identifying allelic variations.