Chromosome-level genome assembly and annotation of two lineages of the ant Cataglyphis hispanica: stepping stones towards genomic studies of hybridogenesis and thermal adaptation in desert ants

Abstract

Cataglyphis are thermophilic ants that forage during the day when temperatures are highest and sometimes close to their critical thermal limit. Several Cataglyphis species have evolved unusual reproductive systems such as facultative queen parthenogenesis or social hybridogenesis, which have not yet been investigated in detail at the molecular level. We generated high-quality genome assemblies for two hybridogenetic lineages of the Iberian ant Cataglyphis hispanica using long-read Nanopore sequencing and exploited chromosome conformation capture (3C) sequencing to assemble contigs into 26 and 27 chromosomes, respectively. Males of one lineage were karyotyped to confirm the number of chromosomes inferred from 3C data. We obtained transcriptomic data to assist gene annotation and built custom repeat libraries for each of the two assemblies. Comparative analyses with 19 other published ant genomes were also conducted. These new genomic resources pave the way for exploring the genetic mechanisms underlying the remarkable thermal adaptation and the molecular mechanisms associated with transitions between different genetic systems characteristics of the ant genus Cataglyphis.

A deep dive into genome assemblies of non-vertebrate animals

“…Arima Hi-C, Phase Genomics, or Dovetails Genomics), yet they still require a minimum input of about 0.5-1 million cells. Hi-C scaffolding proved efficient at bringing highly fragmented draft assemblies to chromosome-level scaffolds (Figure 6), and is now included in many genome projects for all sorts of non-vertebrate animals: the arthropods Varroa destructor [254], Carcinoscorpius rotundicauda [255], and Cataglyphis hispanica [256], the cnidarians Xenia sp. [257] and Rhopilema esculentum [258], the echinoderms Lytechinus variegatus [259] and Pisaster ochraceus [260], the molluscs Scapharca broughtonii [261], Chrysomallon squamiferum [262], and Mercenaria mercenaria [263], the nematods Caenorhabditis remanei [264] and Heterodera glycines [265], the platyhelminthe Schistosoma haemotabium [266], the poriferan Ephydatia muelleri [267], the rotifer Adineta vaga [36], the xenacoelomorph Hofstenia miamia [268], and more.…”