4 DISCUSSION
Based on the comparative genomic analyses of the two strains of F.
candida , we found significant differences between them in terms of both
genome structure and gene distributions. The genome of FCDK (219.08 M)
was 65.18 M (42.4%) larger than that of FCSH (153.90 M); half of this
difference consisted of repetitive elements (34.1 M); and each
chromosome of FCDK was 25‒54% longer than the corresponding chromosome
of FCSH (Figure 1). The seven pairs of chromosomes showed obvious
large-scale chromosomal inversions and translocations, and several large
distal regions of FCDK chromosomes 1, 3, 4 and 7 did not share any
syntenic blocks with FCSH (Figure 2). There were 3,530 more PCGs
annotated in FCDK than in FCSH (Table 1). The numbers of FCDK-specific
gene families and genes (572/2285) were far greater than the numbers of
FCSH-specific sequences (204/820) (Table S7). In addition, FCDK and FCSH
showed obvious divergence between their mitochondrial genomes and miRNA
distributions. The overall sequence identity of the two mitogenomes was
only 78.2%, and the pairwise identity of their standard DNA barcodes
(658 bp of COI) was 80.9%, which is much lower than the similarity
observed in individuals from the same insect species (Hebert et al.,
203). Although 91 common miRNAs of FCDK and FCSH showed conserved
synteny on their homologous chromosomes, there were many more
strain-specific miRNAs in FCSH (39 miRNAs from 15 predicted families)
than in FCDK (9 miRNAs from 6 predicted families). Moreover, most
FCDK-specific miRNA families had only one copy, but many FCSH-specific
miRNA families showed multiple duplications, which tended to form
clusters on chromosome 7 (Figure 6). All of these genetic differences
demonstrated that after 10 million years of divergence (Figure 3), FCDK
and FCSH have evolved into distinct species.
In F. candida , parthenogenetic strains usually show a wider
distribution and stronger environmental adaptability than bisexual
strains (Tully & Potapov, 2015). The genomic differences revealed in
this study demonstrated obvious evolutionary advantages of the
parthenogenetic FCDK genome. Relative to bisexual FCSH, FCDK showed more
strain-specific and expanded gene families, many of which were involved
in resistance to environmental xenobiotics, such as the ABC, CYP and GST
families (Table 2). Interestingly, histone H2A, one of the core
histones, showed obvious expansion in FCDK (Figure 3b).
The sequences and expression
patterns of core histones can profoundly alter chromatin properties, and
their posttranslational modifications, such as acetylation, methylation,
and ubiquitination, are involved in the regulation of nucleosome
dynamics (Lawrence et al., 2016). In particular, variants of histone H2A
are associated with DNA repair and gametogenesis (Hanson et al., 2013)
as well as environmental responses (Talbert & Henikoff, 2014). The
potential roles of expanded H2A genes in FCDK deserve further study. In
addition, FCDK genes exhibited longer introns than FCSH genes (Table 1).
Introns can provide selective advantages to cells by regulating
alternative splicing, gene expression, chromatin assembly, etc. (Jo &
Choi, 2015), and they might play roles in determining species-specific
characteristics and complexities (Carvunis et al., 2012).
The genetic drivers of species differentiation have always been a hot
research topic. Our study reveals several possible factors contributing
to the genetic divergence between FCDK and FCSH. First, the increase in
transposon copies is a very important driving force leading to the
enlargement of the genome (Chalopin et al., 2015; Talla et al., 2017),
and transposable elements may contribute significantly to divergent
chromatin structures (Diehl et al., 2020). In this study, we found that
transposons were significantly enriched in the FCDK-specific regions of
Chr1, Chr3, Chr4, and Chr7 (Figure 2), and many repeat families were
obviously expanded in FCDK (Figure 3b). Most chromosomal regions with a
high transposon density showed a low gene density and high recombination
(Figure 1). Second, a large number of genes acquired through HGT located
in FCDK-specific chromosome regions probably play important roles in the
spread of antibiotic resistance and genome evolution
(Faddeeva-Vakhrusheva et al., 2017). Significantly, Wolbachiainfection may induce or accelerate speciation and contribute to
reproductive isolation (Werren, 1998), which is probably associated with
increased recombination (Singh, 2019). Although we did not find any
obvious genomic characteristics related to the differences in
reproductive mechanisms between FCDK and FCSH based on comparative
genomic analyses, our high-quality genome data provide a basis for
further mechanistic studies. In addition, strain-specific miRNAs could
drive the adaptive diversification of the genomic regulatory mechanisms
of FCDK and FCSH. Novel miRNAs could be gained and lost relatively
rapidly across closely related groups, especially when these groups
undergo extensive adaptive diversification (Xiong et al., 2019). It
would be interesting to further study how miRNA genes evolve and
contribute to speciation.
In conclusion, we generated two high-quality chromosome-level genomes of
the Folsomia candida DK and SH strains, revealed their genomic
differences, and proposed that they have differentiated into two
separate species. Our work provides important genomic resources for
studying speciation and the effect of Wolbachia on host
reproduction and genetic differentiation, as well as the basis for
mechanistically understanding soil
arthropods in the context of soil ecology, and the evolution links
between insects and crustaceans.