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Ostracods are microscopic, bi-valved crustaceans with the best fossil record of all living arthropods. Their fossil record, starting 400 million years ago, together with a high prevalence of parthenogenetic reproduction and putative ancient asexuality, make non-marine ostracods fascinating evolutionary model organisms. In the absence of high quality ostracod reference genomes, we here compare transposon landscapes between two Illumina genome assemblies from the putative ancient asexual Darwinula stevensoni and the fully sexual ostracod Notodromas monacha. Both assemblies have around 60,000 contigs, sizes of 360-380 Mb, more than 100X coverage and BUSCO scores of 93 and 94%, respectively. Because homology-based programs are not sensitive enough to detect families of transposable elements (TEs) in species missing from Repbase or Dfam, we used three different pipelines for de novo analyses: REPET, RepeatMasker2 (RM2) and EarlGrey (RM2-based, with automated curation). 

TE diversity between the two genomes differs substantially regardless which pipeline was used. The Illumina assembly of N. monacha is dominated by LTR retrotransposons (6.5%) with some DNA transposons (3.7%), whereas DNA (15.5%), LINE-like (5.9%) and rolling circle Helitron elements (1.5%) were most abundant in the assembly of D. stevensoni. Our results on the dominance of DNA (Tc/mar, hAT) and LINE-like (CR1, RTE) TEs in D. stevensoni parallel earlier findings from a partial genomic library, and differ from those of other asexuals. TE copies with a low number of nucleotide substitutions are only observed with REPET (“L” shape landscape)in both genomes.

Although the presented results may underestimate TE abundance, they indicate pronounced differences of the transposon landscapes and diversity between these two ostracod species. Analysis of related species should determine whether the differences are correlated with the reproductive mode or are lineage specific. We are currently curating TEs in an Oxford Nanopore draft assembly of D. stevensoni to further confirm our initial results.