1 INTRODUCTION
Collembolans have a long evolutionary history (~410 Mya) and are among the most abundant arthropods on Earth (more than 9,000 known species) (Bellinger et al., 1996‒2021). Most species in this group consume fungi in soil and leaf litter; they have radiated from the littoral zone to mountaintops and are particularly abundant in epiphytes of tropical rainforests. Collembolans are an integral component of soil ecosystems and are vulnerable to the effects of soil contamination. The abundance, diversity and molecular data of collembolans have been widely used to assess the environmental impacts of a range of pollutants on soils (Hopkin, 1997; Gunstone et al., 2021). Collembola represents a monophyletic lineage forming an early branch off the line leading to insects. Understanding the evolution of collembolans is pivotal to clarifying the origin of insects and the early diversification of Hexapoda (Nardi et al., 2003; Misof et al., 2014).
The collembolan Folsomia candida Willem, 1902, is widely distributed in soils throughout the world and plays an important role in soil ecosystems (Fountain & Hopkin, 2005). The species is easy to maintain in the laboratory and has been used as a “standard” test organism for more than 50 years in the fields of population biology, evolutionary ecology, soil biology and ecotoxicology (ISO 11267:2014). In addition, F. candida is increasingly being used in bioassays of soil remediation methods (Lock & Janssen, 2003) and risk assessments of industrial chemicals and genetically modified crops (Huang et al., 2019).
As a cosmopolitan species, several strains of F. candida from different geographical origins have been collected and used by many laboratories (Tully et al., 2006; Tully & Potapov, 2015). Most strains of F. candida show parthenogenesis, which is probably induced by the endosymbiont Wolbachia (Ma et al., 2016). F. candidais questioned as an ideal “standard” because of the cryptic genetic diversity revealed in different strains based on COI and COII gene (Frati et al., 2004), RAPD-PCR and 18S/28S rDNA marker analyses (Tully et al., 2006). Tully and Potapov (2015) comprehensively compared the morphological characteristics of eleven clonal strains from Europe and America and one sexual lineage from our lab in Shanghai (FCSH). They identified all 66 individuals (8 to 12 individuals per strain) as the previously recognized F. candida morphospecies sensu stricto , with characteristic long furca, the same sensillar chaetotaxy and ventral setae on the third thoracic segment (Potapov & Yan, 2012). However, most studied characters vary among individuals and show overlap between strains. FCSH showed the greatest morphological peculiarity, and differed from all parthenogenetic strains by number of setae on thorax, dens and manubrium (Tully & Potapov, 2015). These previous studies indicate the possibility of an interesting evolutionary scenario in the cryptic speciation of F. candida .
Despite the importance of F. candida in evolution and ecotoxicology studies, the genomic resources of F. candida are limited. Faddeeva-Vakhrusheva et al. (2017) reported a reference genome for F. candida (FCBL, Berlin strain) of 221.7 Mbp, comprising 162 scaffolds. They found that substantial gene family expansions were linked to the stress response and that over 800 genes related to lignocellulose degradation had been acquired by horizontal gene transfer (HGT). It will be very useful to further obtain and compare high-quality genome information from different strains of F. candida to understand its speciation pattern and evolutionary history and to reveal the molecular mechanisms of its response to environmental stressors and reproductive regulation. In this study, by incorporating chromatin conformation (Hi-C) data and sequences obtained from the PacBio and Illumina platforms, we present chromosome-level genome assemblies of the parthenogenetic Danish strain (FCDK) and the sexual Shanghai strain ofF. candida (FCSH). Interestingly, our comparative genome analyses revealed that FCDK and FCSH separated as early as 10 million years ago (Mya). Despite minor morphological divergences, FCDK and FCSH have accumulated striking genetic differences, including different genome sizes, chromosome structures, gene numbers, mitogenome sequences, and microRNA (miRNA) distributions, suggesting they have evolved into two separate species.