Ancient expansion of the hox cluster in lepidoptera generated four homeobox genes implicated in extra-embryonic tissue formation

Abstract

Gene duplications within the conserved Hox cluster are rare in animal evolution, but in Lepidoptera an array of divergent Hox-related genes (Shx genes) has been reported between pb and zen. Here, we use genome sequencing of five lepidopteran species (Polygonia c-album, Pararge aegeria, Callimorpha dominula, Cameraria ohridella, Hepialus sylvina) plus a caddisfly outgroup (Glyphotaelius pellucidus) to trace the evolution of the lepidopteran Shx genes. We demonstrate that Shx genes originated by tandem duplication of zen early in the evolution of large clade Ditrysia; Shx are not found in a caddisfly and a member of the basally diverging Hepialidae (swift moths). Four distinct Shx genes were generated early in ditrysian evolution, and were stably retained in all descendent Lepidoptera except the silkmoth which has additional duplications. Despite extensive sequence divergence, molecular modelling indicates that all four Shx genes have the potential to encode stable homeodomains. The four Shx genes have distinct spatiotemporal expression patterns in early development of the Speckled Wood butterfly (Pararge aegeria), with ShxC demarcating the future sites of extraembryonic tissue formation via strikingly localised maternal RNA in the oocyte. All four genes are also expressed in presumptive serosal cells, prior to the onset of zen expression. Lepidopteran Shx genes represent an unusual example of Hox cluster expansion and integration of novel genes into ancient developmental regulatory networks.

Figure 1. Shx genes originated as tandem duplications of zen within the Hox gene cluster.

(A) Phylogenetic tree of Shx among lepidopteran Hox genes reconstructed using Phylobayes (C20), support values are posterior probabilies. (B) Shx complement of 8 lepidopteran species and the Trichoptera outgroup with available linkage information. Presence of multiple genes on the same genomic scaffolding is indicated by a plain line and gene duplication within a paralogy group as stacked boxes.

Figure 2. Lowest energy structural models of deduced (A) ShxA, (B) ShxB, (C) ShxC, (D) ShxD and (E) zen homeodomains from Speckled Wood Pararge aegeria bound to DNA sequences predicted through in silico evolution.

Sequence logos generated from DNA sequences of 50 lowest energy predicted protein-DNA complexes for each protein.

Figure 3. (A) Expression of Shx genes throughout embryonic stages of P. aegeria.

Agarose gel electrophoresis of RT-PCR products obtained using intron-crossing primers (Figure S10). (B) Schematic overview of serosa formation in P. aegeria. Diagrammatic cross section through a developing embryo and associated extra-embryonic cell layers inside a 10–12 h AEL egg. Chorion (brown), vitelline membrane (violet), extraembryonic region/serosa (red), germ anlage (green) and presumptive amniotic cells (blue) are illustrated during serosal specification, maturation and closure. Top row shows ventral half while bottom row shows dorsal half, anterior is top in both. Embryo-vitelline cavity following germ anlage sinking is shown in the middle panel. Orientation 3D axis indicates anterior (A), left (L) and ventral (V) or dorsal (D). AEL, after egg-laying (hours).

Figure 4. Spatiotemporal expression of Shx genes.

Localisation of ShxA, ShxB, ShxC, ShxD, and Pa-zen transcripts in P. aegeria ovarioles (A–E), 10 h embryos (F–J) and 12 h embryos (K–O). Embryos and oocytes are orientated with the anterior to the top. Embryos dorsal side facing while lower and upper oocytes in C show dorsal and ventral faces respectively. Note that in 12 h embryos the serosal cells have migrated over the germ anlage forming an enveloping layer. Some follicle cells in E are removed to show absence of staining in the oocyte. Labels indicate nurse cells (nc), follicle cells (fc), oocyte (oc), germ anlage (g), and extra embryonic anlage (ee) which differentiates into the serosa (s). Orientation for each panel is indicated in bottom right 3D axis indicating anterior (A), left (L) and ventral (V) when known. AEL, after egg-laying (hours). Scale bars 200 µm.