Comparative genomics

Genome alignment among RYP1 and Lovell v2.0 was performed using NUCmer embedded in MUMmer with the parameters of “-mumreference -g 1000 -c 90 -l 40.” The delta-filter program was used to remove the mapping noise and determine the one-to-one alignment blocks with parameters “-r -q.” Gene duplications were analyzed with BLASTP with the parameters of “-evalue < 1e−0, -v 5, -b 5” for determination of the pairwise similarity between protein sequences of RYP1 and Lovell v2.0 genomes; the MCScanX package [94] was used for classification. OrthoFinder version 2.3.9 program [46] with the default parameters was used to create the orthogroups between proteomes of RYP1 and Lovell v2.0 genomes. To identify the presence/absence variations (PAVs) in the RYP1 genome, we divided the RYP1 genome into 500 bp overlapping windows with a step size of 100 bp. Each 500 bp window was then aligned against the Lovell v2.0 genome using BWA-MEM with the parameters of “-w 500 --M.” The sequences of the windows that failed to align with the Lovell v2.0 genome or those that aligned with less than 25% coverage were defined as RYP1-specific sequences. Overlapping windows that could not be aligned were merged. The Lovell-specific sequences were then identified following the same method.