Repeated inversions within a pannier intron drive diversification of intraspecific colour patterns of ladybird beetles

Abstract

How genetic information is modified to generate phenotypic variation within a species is one of the central questions in evolutionary biology. Here we focus on the striking intraspecific diversity of >200 aposematic elytral (forewing) colour patterns of the multicoloured Asian ladybird beetle, Harmonia axyridis, which is regulated by a tightly linked genetic locus h. Our loss-of-function analyses, genetic association studies, de novo genome assemblies, and gene expression data reveal that the GATA transcription factor gene pannier is the major regulatory gene located at the h locus, and suggest that repeated inversions and cis-regulatory modifications at pannier led to the expansion of colour pattern variation in H. axyridis. Moreover, we show that the colour-patterning function of pannier is conserved in the seven-spotted ladybird beetle, Coccinella septempunctata, suggesting that H. axyridis’ extraordinary intraspecific variation may have arisen from ancient modifications in conserved elytral colour-patterning mechanisms in ladybird beetles.

Development and evolution of color patterns in ladybird beetles: A case study in Harmonia axyridis

“…Interestingly, the genome of H. axyridis has been sequenced again by researchers experienced in Drosophila genetics, as in the classical genetic studies. Two groups, one led by Benjamin Prud'homme and Arnaud Estoup and the other by Teruyuki Niimi, have sequenced the H. axyridis genome (Gautier et al., and Ando et al., , respectively). Prud'homme had previously revealed the importance of modifications in cis‐regulatory elements (CREs) in organismal evolution using different Drosophila species at the laboratory of Sean Carroll (Gompel, Prud'homme, Wittkopp, Kassner, & Carroll, ; Prud'homme et al., ).…”

“…Niimi learned Drosophila genetics at Walter Gehring's laboratory and have compiled the tools necessary for molecular genetic studies on H. axyridis (Hatakeyama et al., ; Kawaguchi & Niimi, ; Kuwayama, Yaginuma, Yamashita, & Niimi, ; Kuwayama et al., ; Niimi, Kuwayama, & Yaginuma, ). Niimi's group delimited the relevant genomic region of the four major h alleles to an approximately 660‐kb region using GWAS based on classical genetic crossing and the 10× linked‐read sequencing platform (Ando et al., ). Through functional analyses using larval RNA interference (RNAi), both groups discovered a transcription factor gene, pannier , is responsible for the four major color pattern alleles found in >95% of the population.…”

“…Ando et al. () reported on the elytral pigmentation process during pupal development. Ladybird beetles are holometabolous insects, having both larval and pupal developmental stages before emerging as adults.…”

“…Gene regulatory network (GRN) for red and black pigmentation of adult elytra begins at approximately 80 hr AP. During this stage, red pigments (carotenoids; Bezzerides, McGraw, Parker, & Husseini, ) begin to accumulate within the thickened ventral epidermis of the developing elytra in only the forthcoming red‐pigmented regions (Figure , “Carotenoids”) (Ando et al., ). Black pigmentation (melanin; Bezzerides et al., ) begins immediately after eclosion (~108 hr AP) in the regions complementary to the red‐pigmented regions; however, the enzymatic activity for synthesis of melanin can be observed as early as 80 hr AP (Ando et al., ).…”

“…During this stage, red pigments (carotenoids; Bezzerides, McGraw, Parker, & Husseini, ) begin to accumulate within the thickened ventral epidermis of the developing elytra in only the forthcoming red‐pigmented regions (Figure , “Carotenoids”) (Ando et al., ). Black pigmentation (melanin; Bezzerides et al., ) begins immediately after eclosion (~108 hr AP) in the regions complementary to the red‐pigmented regions; however, the enzymatic activity for synthesis of melanin can be observed as early as 80 hr AP (Ando et al., ). The black‐pigmented layer within an elytron is located in the dorsal cuticle (Figure , “Melanin”), and different from the red‐pigmented layer (the ventral epidermal cells; Figure , “Carotenoids”) (Ando et al., ).…”