Hybrid Genome Assembly of a Neotropical Mutualistic Ant.

Juliane Hartke,Tilman Schell,Juraj Paule,Erich Bornberg-Bauer,Evelien Jongepier,Barbara Feldmeyer,Philipp P Sprenger,Markus Pfenninger,Hanno Schmidt,Thomas Schmitt,Florian Menzel

doi:10.1093/gbe/evz159

Abstract

The success of social insects is largely intertwined with their highly advanced chemical communication system that facilitates recognition and discrimination of species and nest-mates, recruitment, and division of labor. Hydrocarbons, which cover the cuticle of insects, not only serve as waterproofing agents but also constitute a major component of this communication system. Two cryptic Crematogaster species, which share their nest with Camponotus ants, show striking diversity in their cuticular hydrocarbon (CHC) profile. This mutualistic system therefore offers a great opportunity to study the genetic basis of CHC divergence between sister species. As a basis for further genome-wide studies high-quality genomes are needed. Here, we present the annotated draft genome for Crematogaster levior A. By combining the three most commonly used sequencing techniques—Illumina, PacBio, and Oxford Nanopore—we constructed a high-quality de novo ant genome. We show that even low coverage of long reads can add significantly to overall genome contiguity. Annotation of desaturase and elongase genes, which play a role in CHC biosynthesis revealed one of the largest repertoires in ants and a higher number of desaturases in general than in other Hymenoptera. This may provide a mechanistic explanation for the high diversity observed in C. levior CHC profiles.

Highlights

The genomic basis of chemical communication is still mostly unknown, despite its importance in animal behaviour
Genome size, assessed by the peak coverage approach (Schell et al 2017), was estimated to be 355.52 Mbp. This estimate is at the higher end but still within range compared with other ant genomes
When correcting the original G. max calibration (Dolezel et al 1994) for the newest human reference genome assembly (GRCh38.p13), the 2C value corresponds to 409.96 Mbp (1 pg 1⁄4 978 Mbp, Dolezel et al 2003), which is within range of previously reported estimates, significantly larger than estimates for the same genus (Crematogaster hespera: 275.9 Mbp; Tsutsui et al 2008)

Summary

Introduction

The genomic basis of chemical communication is still mostly unknown, despite its importance in animal behaviour. A prime example are social insects, in which cuticular hydrocarbons (CHCs) represent the most important means of communication and facilitate the functioning of complex social organization. They enable the expression and recognition of various attributes, such as species and nest-mate status, caste, sex, and fertility (Lahav et al 1999; Dietemann et al 2003; Leonhardt et al 2016). One of the most successful families of social insects is ants with $13,000 recognized species (Chomicki and Renner 2017) They occur in virtually all terrestrial habitats, barring the polar regions, and evolved a striking diversity in life-history traits, morphology and behavior.

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