The Genomic Basis of Color Pattern Polymorphism in the Harlequin Ladybird

Abstract

SummaryMany animal species comprise discrete phenotypic forms. A common example in natural populations of insects is the occurrence of different color patterns, which has motivated a rich body of ecological and genetic research [1, 2, 3, 4, 5, 6]. The occurrence of dark, i.e., melanic, forms displaying discrete color patterns is found across multiple taxa, but the underlying genomic basis remains poorly characterized. In numerous ladybird species (Coccinellidae), the spatial arrangement of black and red patches on adult elytra varies wildly within species, forming strikingly different complex color patterns [7, 8]. In the harlequin ladybird, Harmonia axyridis, more than 200 distinct color forms have been described, which classic genetic studies suggest result from allelic variation at a single, unknown, locus [9, 10]. Here, we combined whole-genome sequencing, population-based genome-wide association studies, gene expression, and functional analyses to establish that the transcription factor Pannier controls melanic pattern polymorphism in H. axyridis. We show that pannier is necessary for the formation of melanic elements on the elytra. Allelic variation in pannier leads to protein expression in distinct domains on the elytra and thus determines the distinct color patterns in H. axyridis. Recombination between pannier alleles may be reduced by a highly divergent sequence of ∼170 kb in the cis-regulatory regions of pannier, with a 50 kb inversion between color forms. This most likely helps maintain the distinct alleles found in natural populations. Thus, we propose that highly variable discrete color forms can arise in natural populations through cis-regulatory allelic variation of a single gene.

Nanopore sequencing: Review of potential applications in functional genomics

“…Therefore, homogenization and DNA extraction methods should be optimized for each species, especially for plants or arthropods that harbor thick cell walls and cuticular exoskeletons. Likewise, in insects such as harlequin ladybird or fruit fly, a dissected tissue or a whole specimen frozen with liquid nitrogen is ground using a pestle, and HMW DNA extraction is subsequently performed with Genomic-tip 500/G kit (QIAGEN) or Blood & Cell Culture kit (QIAGEN) (Gautier et al, 2018;Miller, Staber, Zeitlinger, & Hawley, 2018). After sufficient homogenization, samples are then resuspended in detergent-based extraction buffers containing cetyltrimethylammonium bromide (CTAB).…”

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., ).…”

“…(a) Comparison of the DNA sequences between the h and h Sp alleles, adapted from Gautier et al. (), Fig. d with some modifications.…”

“…This analysis revealed that the allele with black spots within a red background (the h allele) and those with red spots within a black background ( h A , h S p , and h C alleles) diverged first in an ancestor, and the latter three alleles diverged more recently (Figure ). Furthermore, a comparison of the DNA sequence at the pannier locus among all allelic combinations (Ando et al., ; Gautier et al., ) revealed that traces of chromosomal inversion were consistently found within pannier 's first intron (Figure , the regions highlighted with yellow trapezoids), which suggests that recurrent inversion events within a pannier intron resulted in the diversification of CREs at the pannier locus by suppressing a recombination within its intron (Figure ).…”

“…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, 2005;Prud'homme et al, 2006). Prud'homme and Estoup's group delimited the relevant genomic regions of the four major h alleles to an approximately 170-kb region using population genomics-based genome-wide association studies (GWAS) and the nanopore sequencing platform (Gautier et al, 2018). 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, 2016;Kawaguchi & Niimi, 2018;Kuwayama, Yaginuma, Yamashita, & Niimi, 2006;Kuwayama et al, 2014;Niimi, Kuwayama, & Yaginuma, 2005).…”