Draft genomes and genomic divergence of two Lepidurus tadpole shrimp species (Crustacea, Branchiopoda, Notostraca)

Crustaceans of the order Notostraca (Branchiopoda) are worldwide-distributed and known for their remarkable morphological stasis between extant and Permian fossil species. Moreover, they show relevant ecological traits and a wide panel of reproductive strategies. However, genomic studies on notostracans are fairly limited. We here present the genome sequences of two notostracan taxa, Lepidurus arcticus and L. apus lubbocki. Taking advantage of the small genome size (~0.11 pg), we set the sequencing on Illumina HiSeq X platform for a single run on a single individual per species. We finally assembled 73.2 Mbp - L. arcticus - and 90.3 Mbp - L. apus lubbocki long genomes. Assembly cover up to 80% of estimated genome size, with a gene completeness >97% for both genomes. 10-15% of assembled genomes consist of repeats and, although L. apus lubbocki experienced a marked increase of LTR and DNA transposons, there is no significant difference in copy number. The analysis of 2,376 ortholog genes indicates a ~7% of divergence between the two Lepidurus species, with a nucleotide substitution rate significantly lower than the Daphnia one. Ka/Ks analyses suggests purifying selection in both branchiopod lineages, raising the question whether the lower substitution rate is correlated with the Lepidurus morphological conservation or it is attributable to specific biological traits. Our analysis demonstrates that in these organisms it is possible to obtain draft genomes with high completeness from single individuals with a relatively small sequencing effort. This makes Lepidurus, and Notostraca, an interesting model for studies in population, ecological and evolutionary genomics.