3.2 Sex chromosomes and autosomes
Male and female Illumina paired-end reads were mapped separately to
genomic scaffolds to estimate MRPM. The MRPM value of female reads for
chrX1, chrX2 and chrX3 were 1,439,092, 1,333,387 and 1,051,602, whereas
those for the corresponding male reads were 781,901, 726,210 and 576,946
respectively. As expected, MRPM values of female reads were roughly
twice as high as those of male reads in chrX1, chrX2 and chrX3. For the
other 10 chromosomes, no significant difference in total reads was
observed between females and males, with the female-to-male ratio
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 for autosomes (Li et al. 2021,
Mathers et al. 2021). The syntenic blocks were compared between theS. chinensis assembly and that of Ac. pisum from
Macrosiphini (Li, et al., 2020), R. maidis from Aphidini (Chen et
al. 2019), and E. lanigerum from Eriosomatinae (Figure 3B). The
comparisons revealed high levels of genome rearrangements between
autosomes. The three S. chinensis chromosomes were mapped to the
conserved X chromosome of Macrosiphini and Aphidini, and two X
chromosomes of E. lanigerum . The observed multiple X chromosomes
were consistent with previous reports (Biello et al., 2020), which were
speculated to result from the fragmentation of the X chromosome inS. chinensis and E. lanigerum or from the ancient fusion
event of the large X chromosome in Aphidinae (Macrosiphini + Aphidini).
This observation strongly supports that chrX1, chrX2 and chrX3 are the
sex chromosomes and the karyotype
of S. chinensis is XX+X (Yuan et al., 2021).