A caste differentiation mutant elucidates the evolution of socially parasitic ants

Most ant species have two distinct female castes – queens and workers – yet the developmental and genetic mechanisms that produce these alternative phenotypes remain poorly understood. Working with the clonal raider ant, Ooceraea biroi, we discovered a variant strain that expresses queen-like traits in individuals that would normally become workers. The variants show changes in morphology, behavior, and fitness that cause them to rely on workers in wild-type (WT) colonies for survival. Overall, they resemble the queens of many obligately parasitic ants that have evolutionarily lost the worker caste and live inside colonies of closely related hosts. To understand the genetic basis of this variant strain, which we term the queen-like mutants (QLM), we re-analyzed published PacBio and Hi-C data (McKenzie and Kronauer 2018) using the Falcon pipeline. 

,
To improve the assembly of Chromosome 13, we re-analyzed published data using the Falcon pipeline. First, we ran Falcon-unzip using published PacBio data (McKenzie & Kronauer 2018, Genome Biology). This yielded primary (212Mbp, 322 contigs with N50 of 2.2Mbp) and alternate (67.8Mbp, 2685 contigs with N50 of 27.37kbp) assemblies. These assemblies were phased with published Hi-C data (McKenzie & Kronauer 2018, Genome Biology) using Falcon-phase, and then scaffolded using the NCBI Obir v5.4 genome assembly using RaGOO. Finally, this primary assembly, which we refer to as the Obir v5.6 assembly, was polished and masked as described previously. These assemblies were uploaded as primary_chroms_ragoo.fasta and secondary_chroms_ragoo.fasta, respectively.Next, we performed high molecular weight extractions of O. biroi following a published protocol and sequenced two barcoded libraries using the Oxford Nanopore PromethION platform. Raw reads were assembled de novo using Flye (version 2.8..., The falcon pipeline (falcon-unzip and falcon-phase) and RaGOO were used to generate the primary and secondary 5.6 assemblies. RaGOO also generated structural variant statistics. Contigs from the de-novo Flye assemblies were aligned to the primary RaGOO assembly using Mauve.Â