2.4 Locating the sex chromosomes and autosomes with short reads
Male and female DNA reads were mapped separately to the genomic scaffolds using Bowtie2 with default parameters (Langmead & Salzberg, 2012). The resulting alignments were filtered to remove the low-quality mapped reads by SAMtools (view -b -q 30). The read counts of each chromosome were calculated by using SAMtools idxstats (Li et al., 2009). The mapped reads per million (MRPM) of each chromosome was calculated for both female reads and male reads. Syntenic blocks of genes were identified between the chromosome-level genome assemblies of S. chinensis , Acyrthosiphon pisum , Rhopalosiphum maidis ,E. lanigerum use TBtools (version 1.09, Chen et al., 2020).