A chromosome-level genome assembly of “a living fossil”, the tadpole shrimp Lepidurus arcticus (Pallas, 1793)

Abstract

We present the first chromosome-level reference genome for Lepidurus arcticus (Pallas, 1793), a freshwater crustacean with circumpolar distribution. L. arcticus belongs to the small order of freshwater Notostracan crustaceans that are representatives of the ancient group Branchiopoda. This group has a remarkable morphological stability and is frequently labelled “living fossils”. Its ancient origin, streamlined genome and reproductive flexibility makes this a very interesting candidate for genomic studies.

The pseudo-haplotype-resolved assemblies, hap1 and hap2, span 81.2 megabases (Mb) and 81.8 Mb, respectively, and were each scaffolded into six chromosomes. Both hap1 and hap2 showed high completeness, with identical BUSCO completeness scores of 98.3%. Scaffold N50 lengths were 13.4 Mb for hap1 and 13.9 Mb for hap2, and k-mer completeness estimated from PacBio HiFi reads was 95.79% and 96.18%, respectively. The pseudo-haplotypes showed very low estimated genome-wide heterozygosity of 0.133%. Gene annotation identified 10,901 protein-coding genes in hap1 and 10,910 in hap2. Repetitive elements comprised approximately 24–25% of each assembly, with long terminal repeat retrotransposons representing the most abundant transposable element class at approximately 8–9%.

Comparison with the near chromosome-level genome of Lepidurus packardi revealed substantial intrachromosomal rearrangements, despite similar chromosome numbers and chromosome sizes. Differences in transposable element content between L. arcticus and L. packardi were primarily driven by retrotransposons, particularly LTR and LINE elements. This reference genome provides a valuable resource for future population genomic studies and for investigating evolutionary stasis at the genome level.