Schoenle, A. | bioRxiv Science

bioRxiv2024

De Novo Genome assembly of the Caucasian dwarf goby Knipowitschia cf. caucasica, a new alien Gobiidae invadingthe River Rhine

The Caucasian dwarf goby Knipowitschia cf. caucasica is a new invasive alien Gobiidae spreading in the Lower Rhine since 2019. Little is known about the invasion biology of the species and further investigations to reconstruct the invasion history are lacking genomic resources. We assembled a high-quality chromosome-scale reference genome of Knipowitschia cf. caucasica by combining PacBio, Omni-C and Illumina technologies. The size of the assembled genome is 956.58 Mb with a N50 scaffold length of 43 Mb, which includes 92.3 % complete Actinopterygii Benchmarking Universal Single-Copy Orthologs. 98.96 % of the assembly sequence was assigned to 23 chromosome-level scaffolds, with a GC-content of 42.83 %. Repetitive elements account for 53.08 % of the genome. The chromosome-level genome contained 26,404 transcripts with 23,210 multi-exons, of which 26,260 genes were functionally annotated. In summary, the high-quality genome assembly provides a fundamental basis to understand the adaptive advantage of the species.

genomics↗

bioRxiv2024

The dilemma of underestimating freshwater biodiversity: morphological and molecular approaches

BackgroundThe Lower Rhine ecosystem has been extensively shaped by human activities, destroying, modifying, and even creating novel water bodies as habitats. Freshwater systems are hotspots of biodiversity and highly complex ecosystems. However, knowledge and description of its biodiversity across all trophic levels is still incomplete and the complexity of interactions remains unresolved, especially below the micro scale. This is even true for important international inland waterways such as the River Rhine. We here document the biodiversity of the Lower Rhine and associated water bodies, spanning from the level of protists up to the level of larger invertebrate predators and herbivores organized in faunal size classes (nano-, micro, meio- and macrofauna). This study is part of a long-term ecological research project (LTER-D REES). Our study includes two riprap sections of the rivers main channel, two oxbows and two gravel-pit lakes in the rivers flood plain. Diversity was assessed through morphotype richness and metabarcoding, as well as accounting for sediment composition. ResultsWe found high discrepancies between amplicon sequencing variants (ASVs) and morphotype richness in all size classes, as well as a problematic limitation of reference sequences from freshwater organisms in public databases. Irrespective of the size class, we observed habitat specific zoobenthos communities in each of the three investigated habitat types, with few taxa or taxonomic groups overlapping. ConclusionsOur results demonstrate the importance to integrate different methodologies and extend freshwater sequencing efforts for the assessment of biodiversity across all trophic levels, as particularly relevant for long term projects.

ecology↗