3.2 Sex chromosomes and autosomes
The male and female Illumina paired-end DNA reads were mapped separately to the genomic scaffolds to estimate the MRPM. In chrX1, chrX2, chrX3, the MRPM of female reads length is 1,439,092, 1,333,387 and 1,051,602 and the MRPM of female reads length is 781,901, 726,210 and 576,946 respectively. The MRPM of female reads was nearly twice as high as that of male reads in chrX1, chrX2 and chrX3. The other 10 chromosomes exhibited no significant differences between females and males, with female/male ratios ranging from 0.90 to 1.00 (Table S5). It has been shown that the X chromosome is conserved in aphids while chromosomal rearrangements are common on autosomes (Li et al. 2021, Mathers et al. 2021). The syntenic block between the S. chinensis assembly andAc. pisum from Macrosiphini (Li, et al., 2020), R. maidisfrom Aphidini (Chen et al. 2019), and E. lanigerum (Figure 3C) from Eriosomatinae were identified. All comparisons reveal high levels of genome rearrangements between autosomes. Interestingly, threeS. chinensis chromosomes were mapped the conserved X chromosome of Macrosiphini and Aphidini, and two X chromosomes of E. lanigerum . The observed multiple X chromosomes are consistent with previous reports (Biello et al., 2020). We speculate that it may be fragmentation of the X chromosome in S. chinensis and E. lanigerum or the result of an ancient fusion event of the large X chromosome in Aphidinae (Macrosiphini + Aphidini). The above evidence strongly suggests that chrX1, chrX2 and chrX3 is sex chromosomes and the karyotype of S. chinensis is XX+X.