The water ﬂea Daphnia carinata is emerging as a new model for biological
studies due to its natural cyclical parthenogenesis and small genome.
However, no genomic information for the D. carinata is currently
available. Here, we reported a chromosome-scale genome assembly of D.
carinata. The assembled D. carinata (WSL) genome was consisted of 131.58
Mb, and 92.23% (121.36 Mb) of the assembly was anchored onto 10
chromosomes. Basing on the whole genome information, we further compared
the transcriptomic and epigenomic characterization among parthenogenetic
females (PF), sexual females (SF) and males (M) in D. carinata.
Transcriptomic analysis showed that the highly expressed genes in M were
mainly grouped into the cuticle, phototransduction, hypoxia-response,
sex differentiation, and methyl farnesoate synthesis. Besides, compared
to M and SF, the highly expressed genes in PF were mainly grouped into
energy metabolism, mitosis, DNA replication, and RNA splicing. miRNAomic
analysis showed that several miRNA-mRNA pairs may be the functional
modules in the reproductive regulation of D. carinata, such as
novel-miR-4—brat, novel-miR-21—lin-9 pairs, novel-miR-110—gl,
novel-miR-4—eIF3-S9. The whole-genome DNA methylation analysis showed
that genome-wide methylation rate was very low in D. carinata, and DNA
methylation sites were mainly enriched in the gene body region.
Comparative analysis showed that the genome-wide methylation rate in PF
was higher than that in SF and M. Differentially methylation
region-related genes were all mainly grouped in metabolic process,
catalytic activity, binding/ion binding, and cellular process.