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.
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RBINS Staff Publications 2024
Marine populations are genetically structured through historical processes, environmental or physical barriers and life history characteristics. Divergent patterns of demographic history, even among closely-related species sharing climatic changes, raise questions about the influence of species-specific traits on population structure. The Southern Ocean features comparatively high biodiversity, which has been attributed to frequent local extinction-recolonization cycles that have driven benthic, Antarctic organisms into temporary refugia. In contrast, organisms in the Arctic were able to shift latitude in response to changing Pleistocene climate. We therefore hypothesize that Arctic populations were historically less constrained in their distribution than Antarctic fish populations and hence show lower levels of genetic structure. For assessing the role of lifestyle in influencing demographic history in the Southern Ocean closely related notothenioid fish with benthic (Trematomus bernacchii, T. hansoni) and semi-pelagic or even cryopelagic (T. newnesi) lifestyles were genetically analysed. In the Arctic, polar cod (Boreogadus saida), which is often found in association with sea ice, but also throughout the water column to the bottom, can be regarded as semi- or cryopelagic too. The Antarctic species were analysed by six microsatellite and one mitochondrial marker before (Van de Putte et al., 2012) and we extend these analyses with data from nine microsatellite markers in polar cod. Antarctic species showed significant genetic population structure between High-Antarctic and Peninsular regions and much lower differentiation in pelagic than benthic species. It suggests that the observed patterns are indeed related to ecological traits of Antarctic fish. In the Arctic, we hypothesize genetic structuring inside fjords in Svalbard relative to shelf specimens, which we expect to show low or absent structure as in Antarctic species with a similar lifestyle. Identifying common driving factors for population structure is important in order to enable forecasting, particularly in light of dramatically increasing rates of environmental change. Comparing population genetic patterns and exploring underlying causes from both poles may thus help to shed light on how fish populations survived in the past and may persist in the future. Reference - Van de Putte A., Janko K., Kasparova E., Maes G.E., Rock, J., Koubbi P., Volckaert F.A.M., Choleva L., Fraser K.P.P., Smykla J., Van Houdt J.K.J., Marshall C. 2012 Comparative phylogegraphy of three trematomid fishes reveals contrasting genetic structure patterns in benthic and pelagic species. Marine Genomics 8:23-34.
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RBINS Staff Publications 2018
