High‐quality genomes reveal significant genetic divergence and cryptic speciation in the model organism Folsomia candida (collembola)

The collembolan Folsomia candida Willem, 1902, is widely distributed throughout the world and has been frequently used as a test organism in soil ecology and ecotoxicology studies. However, it is questioned as an ideal “standard” because of differences in reproductive modes and cryptic genetic diversity between strains from various geographical origins. In this study, we obtained two high‐quality chromosome‐level genomes of F. candida, for a parthenogenetic strain (named FCDK, 219.08 Mb, 25,139 protein‐coding genes) and a sexual strain (named FCSH, 153.09 Mb, 21,609 protein‐coding genes), reannotated the genome of the parthenogenetic strain reported by Faddeeva‐Vakhrusheva et al. in 2017 (named FCBL, 221.7 Mb, 25,980 protein‐coding genes) and conducted comparative genomic analyses of the three strains. High genome similarities between FCDK and FCBL based on synteny, genome architecture, mitochondrial and nuclear gene sequences suggest that they are conspecific. The seven chromosomes of FCDK are each 25%–54% larger than the corresponding chromosomes of FCSH, showing obvious repetitive element expansions and large‐scale inversions and translocations but no whole‐genome duplication. The strain‐specific genes, expanded gene families and genes in nonsyntenic chromosomal regions identified in FCDK are highly related to the broader environmental adaptation of parthenogenetic strains. In addition, FCDK has fewer strain‐specific microRNAs than FCSH, and their mitochondrial and nuclear genes have diverged greatly. In conclusion, FCDK/FCBL and FCSH have accumulated independent genetic changes and evolved into distinct species after 10 million years ago. Our work provides important genomic resources for studying the mechanisms of rapidly cryptic speciation and soil arthropod adaptation to soil ecosystems.