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多数蚂蚁物种拥有两类截然不同的雌性品级（caste）——蚁后与工蚁，但调控这两种差异化表型的发育与遗传机制仍未得到充分阐明。本研究以克隆掠蚁（clonal raider ant）双刺猛蚁（*Ooceraea biroi*）为研究对象，发现了一种变异品系，该品系在本应发育为工蚁的个体中表达类蚁后性状。该变异个体在形态、行为与适合度上均发生改变，使其依赖野生型（wild-type, WT）蚁群中的工蚁才能存活。总体而言，这类变异个体与许多专性寄生蚁的蚁后相似——这类寄生蚁在演化过程中丢失了工蚁品级，寄生于近缘宿主蚁群中。为解析该变异品系的遗传基础，我们将其命名为类蚁后突变体（queen-like mutants, QLM），并使用Falcon流程重新分析了已发表的PacBio与Hi-C测序数据（McKenzie与Kronauer，2018）。 为优化13号染色体的基因组组装，我们再次使用Falcon流程对已发表数据进行重分析。首先，我们基于已发表的PacBio测序数据（McKenzie & Kronauer，2018，*Genome Biology*）运行Falcon-unzip工具，得到初级组装序列（212Mbp，322个重叠群（contig），N50值为2.2Mbp）与次级组装序列（67.8Mbp，2685个重叠群，N50值为27.37kbp）。随后，我们利用Falcon-phase工具结合已发表的Hi-C测序数据（McKenzie & Kronauer，2018，*Genome Biology*）对上述组装结果进行分型，并通过RaGOO工具以NCBI Obir v5.4基因组作为参考进行支架挂载。最终，我们将该初级组装版本命名为Obir v5.6组装，并按照此前的方法对其进行序列抛光与重复序列屏蔽。上述组装结果分别以primary_chroms_ragoo.fasta与secondary_chroms_ragoo.fasta的形式上传。 随后，我们按照已发表的实验流程对双刺猛蚁进行高分子量基因组DNA提取，并使用Oxford Nanopore PromethION平台对两个带条码的文库进行测序。原始reads通过Flye软件（版本2.8…）进行从头组装。本研究使用Falcon流程（包含falcon-unzip与falcon-phase模块）与RaGOO工具生成了初级与次级5.6版组装序列，RaGOO同时还生成了结构变异统计数据。我们使用Mauve工具将Flye从头组装得到的重叠群比对至RaGOO初级组装序列上。