Complete mitochondrial genome of Ovalona pulchella (Branchiopoda, Cladocera) as the first representative in the family Chydoridae: Gene rearrangements and phylogenetic analysis of Cladocera

The Complete Mitochondrial Genome of Mytilisepta virgata (Mollusca: Bivalvia), Novel Gene Rearrangements, and the Phylogenetic Relationships of Mytilidae

The circular mitochondrial genome of Mytilisepta virgata spans 14,713 bp, which contains 13 protein-coding genes (PCGs), 2 ribosomal RNA genes, and 22 transfer RNA genes. Analysis of the 13 PCGs reveals that the mitochondrial gene arrangement of Mytilisepta is relatively conserved at the genus level. The location of the atp8 gene in Mytilisepta keenae differs from that of other species. However, compared with the putative molluscan ancestral gene order, M. virgata exhibits a high level of rearrangement. We constructed phylogenetic trees based on concatenated 12 PCGs from Mytilidae. As a result, we found that M. virgata is in the same clade as other Mytilisepta spp. The result of estimated divergence times revealed that M. virgata and M. keenae diverged around the early Paleogene period, although the oldest Mytilisepta fossil was from the late or upper Eocene period. Our results provide robust statistical evidence for a sister-group relationship within Mytilida. The findings not only confirm previous results, but also provide valuable insights into the evolutionary history of Mytilidae.

Genome Assembly of a Relict Arabian Species of Daphnia O. F. Müller (Crustacea: Cladocera) Adapted to the Desert Life

The water flea Daphnia O.F. Müller 1776 (Crustacea: Cladocera) is an important model of recent evolutionary biology. Here, we report a complete genome of Daphnia (Ctenodaphnia) arabica (Crustacea: Cladocera), recently described species endemic to deserts of the United Arab Emirates. In this study, genome analysis of D. arabica was carried out to investigate its genomic differences, complexity as well as its historical origins within the subgenus Daphnia (Ctenodaphnia). Hybrid genome assembly of D. arabica resulted in ~116 Mb of the assembled genome, with an N50 of ~1.13 Mb (BUSCO score of 99.2%). From the assembled genome, in total protein coding, 5374 tRNA and 643 rRNA genes were annotated. We found that the D. arabica complete genome differed from those of other Daphnia species deposited in the NCBI database but was close to that of D. cf. similoides. However, its divergence time estimate sets D. arabica in the Mesozoic, and our demographic analysis showed a great reduction in its genetic diversity compared to other Daphnia species. Interestingly, the population expansion in its diversity occurred during the megadrought climate around 100 Ka ago, reflecting the adaptive feature of the species to arid and drought-affected environments. Moreover, the PFAM comparative analysis highlights the presence of the important domain SOSS complex subunit C in D. arabica, which is missing in all other studied species of Daphnia. This complex consists of a few subunits (A, B, C) working together to maintain the genome stability (i.e., promoting the reparation of DNA under stress). We propose that this domain could play a role in maintaining the fitness and survival of this species in the desert environment. The present study will pave the way for future research to identify the genes that were gained or lost in this species and identify which of these were key factors to its adaptation to the harsh desert environment.