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.