3.4 Identification of DEGs between winged and wingless M.
dirhodum
All aphids are born through viviparous reproduction with wing primordia,
but they degenerate by the second instar in the unwinged morph (Ding et
al., 2017). In the winged individuals, the wing primordia continue to
slowly develop from first- to third-instar nymphs and then rapidly grow
in the fourth instar. In M. dirhodum , winged and wingless
individuals can be distinguished from third-instar nymphs to adults
under a microscope (Ishikawa et al., 2008, 2013). To identify potential
genes related to wing dimorphism and development, RNA-seq was performed
between populations of winged and wingless M. dirhodum in third-
and fourth-instar nymphs and adults using our assembled genome as a
reference.
As a result, 4641 DEGs were detected between the wingless (WW) and
winged (WY) third-instar nymphs (WW3/WY3), including 2114 upregulated
and 2527 downregulated genes in the wingless nymphs, compared to the
winged individuals (Fig. 4A, Table S4). A total of 4349 DEGs were
detected between the wingless and winged fourth-instar nymphs (WW4/WY4),
including 1936 upregulated and 2413 downregulated genes in the wingless
nymphs, compared to the winged individuals (Fig. 4B, Table S4). In
addition, 4375 DEGs were detected between the wingless and winged adults
(WWA/WYA), including 1877 upregulated and 2498 downregulated genes in
the wingless adults, compared to the winged individuals (Fig. 4C, Table
S4). Among them, 3638 genes were differentially expressed in both the
WW3/WY3 and WW4/WY4 groups, 3362 genes were differentially expressed in
both the WW3/WY3 and WWA/WYA groups, 3433 genes were differentially
expressed in both the WW4/WY4 and WYA/WWA groups, and 3050 genes were
differentially expressed in all three comparison groups (WW3/WY3,
WW4/WY4 and WWA/WYA) (Fig. 4D, Table S4).
Juvenile hormone or ecdysone signals, c-Jun NH2-terminal kinases (JNK),
and insulin/insulin-like growth factor signaling (IIS) pathways have
been reported to contribute to the regulation of wing dimorphism in many
insects (Xu et al., 2015, 2017; Zhang et al., 2019). Moreover, Wnt2, Fng
(fringe), Uba1 (ubiquitin-activating enzyme E1), Hh (hedgehog), Foxo,
Dpp (decapentaplegic), Brk (Brinker), Ap (alar process), Dll
(distal-less), Hth (helix-turn-helix), Tsh (thyroid-stimulating
hormone), Nub (nubbin), Scr (sex combs reduced), Antp (antennapedia),
Ubx (ultrathorax), Asc, Srf (serum response factor) and Fl (flugellos)
have been also reported to play important roles in regulating wing
polyphenism or development (Zhang et al., 2019). All the DEGs annotated
as these genes were selected and are listed in Tables 2, 3 and 4,
including insulin receptor substrate, insulin-like receptor, ecdysone
receptor, broad-complex core protein, and Foxo. In addition, many genes
related to muscle composition, energy metabolism and reproduction were
also identified between the winged and wingless aphids.