Abstract
The collembolan Folsomia candida Willem, 1902, is an important
representative soil arthropod that 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 present two high-quality chromosome-level
genomes of F. candida , for the parthenogenetic Danish strain
(FCDK, 219.08 Mb, N50 of 38.47 Mb, 25,139 protein-coding genes) and the
sexual Shanghai strain (FCSH, 153.09 Mb, N50 of 25.75 Mb, 21,609
protein-coding genes). 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 its broader
environmental adaptation. In addition, the overall sequence identity of
the two mitogenomes is only 78.2%, and FCDK has fewer strain-specific
microRNAs than FCSH. In
conclusion, FCDK and FCSH have
accumulated independent genetic changes and evolved into distinct
species since diverging 10 Mya. Our work shows that F. candidarepresents a good model of rapidly
cryptic speciation. Moreover, it provides important genomic resources
for studying the mechanisms of
species differentiation, soil arthropod adaptation to soil ecosystems,
and Wolbachia -induced parthenogenesis as well as the evolution of
Collembola, a pivotal phylogenetic clade between Crustacea and Insecta.
KEY WORDS: cryptic species; chromosome-level genome; genome synteny;
repetitive element expansion; comparative mitogenomics; miRNA
distribution