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).