Lake Baikal is the oldest, by volume, the largest, and the deepest freshwater lake on Earth. It is characterized by an outstanding diversity of endemic faunas with more than 350 amphipod species and subspecies (Amphipoda, Crustacea, Arthropoda). They are the dominant benthic organisms in the lake, contributing substantially to the overall biomass. Eulimnogammarus verrucosus, E. cyaneus, and E. vittatus, in particular, serve as emerging models in ecotoxicological studies.
It was, then, necessary to investigate whether these endemic littoral amphipods species form genetically separate populations across Baikal, to scrutinize if the results obtained --~for example, about stress responses~-- with samples from one single location (Bolshie Koty, where the biological station is located), could be extrapolated to the complete lake or not. The genetic diversity within those three endemic littoral amphipod species was determined based on fragments of Cytochrome C Oxidase I (COI) and 18S rDNA (only for E. verrucosus). Gammarus lacustris, a Holarctic species living in water bodies near Baikal, was examined for comparison. The intra-specific genetic diversities within E. verrucosus and E. vittatus (13% and 10%, respectively) were similar to the inter-species differences, indicating the occurrence of cryptic, morphologically highly similar species. This was confirmed with 18S rDNA for E. verrucosus. The haplotypes of E. cyaneus and G. lacustris specimens were, with intra-specific genetic distances of 3% and 2%, respectively, more homogeneous, indicating no --or only recent disruption of-- gene flow of E. cyaneus across Baikal, and recent colonization of water bodies around Baikal by G. lacustris. The data provide the first clear evidence for the formation of cryptic (sub)species within endemic littoral amphipod species of Lake Baikal and mark the inflows/outflow of large rivers as dispersal barriers.
Lake Baikal has provided a stable environment for millions of years, in stark contrast to small, transient water bodies in its immediate vicinity. A highly diverse endemic amphipod fauna is found in one but not the other habitat. To gain more insights and explain the immiscibility barrier between Lake Baikal and non-Baikal environments faunas, the differences in the stress response pathways were studied. To this end, exposure experiments to increasing temperature and a heavy metal (cadmium) as proteotoxic stressors were conducted in Russia. High-quality de novo transcriptome assemblies were obtained, covering multiple conditions, for three amphipod species: E. verrucosus and E. cyaneus -Baikal endemics-, and G. lacustris -Holarctic- as a potential invader. After comparing the transcriptomic stress responses, it was found that both Baikal species possess intact stress response systems and respond to elevated temperature with relatively similar changes in their expression profiles. G. lacustris reacts less strongly to the same stressors, possibly because its transcriptome is already perturbed by acclimation conditions (matching the Lake Baikal littoral).
Comprehensive genomic resources are of utmost importance for ecotoxicological and ecophysiological studies in an evolutionary context, especially considering the exceptional value of Baikal as a UNESCO World Heritage Site. In that context, the results presented here, on the genome of Eulimnogammarus verrucosus, have been the first massive step to establish genomic sequence resources for a Baikalian amphipod (other than mitochondrial genomes and gene expression data in the form of de novo transcriptomes assemblies). Based on the data from a survey of its genome (a single lane of paired-end Illumina HiSeq 2000 reads, 3X) as well as a full dataset (two complete flow cells, 46X) the genome size was estimated as nearly 10 Gb based on the k-mer spectra and the coverage of highly conserved miRNA, hox genes, and other Sanger-sequenced genes. At least two-thirds of the genome are non-unique DNA, and no less than half of the genomic DNA is composed of just five families of repetitive elements, including low complexity sequences. Some of the repeats families found in high abundance in E. verrucosus seem to be species-specific, or Baikalian-specific.
Attempts to use off-the-shelf assembly tools on the available low coverage data, both before and after the removal of highly repetitive components, as well as on the full dataset, resulted in extremely fragmented assemblies. Nevertheless, the analysis of coverage in Hox genes and their homeobox showed no clear evidence for paralogs, indicating that a genome duplication did not contribute to the large genome size. Several mate-pair libraries with bigger insert sizes than the 2kb used here and long reads sequencing technology combined with semi-automated methods for genome assembly seem to be necessary to obtain a reliable assembly for this species.
| Identifer | oai:union.ndltd.org:DRESDEN/oai:qucosa:de:qucosa:75770 |
| Date | 24 August 2021 |
| Creators | Rivarola-Duarte, Lorena |
| Contributors | Universität Leipzig |
| Source Sets | Hochschulschriftenserver (HSSS) der SLUB Dresden |
| Language | English |
| Detected Language | English |
| Type | info:eu-repo/semantics/publishedVersion, doc-type:doctoralThesis, info:eu-repo/semantics/doctoralThesis, doc-type:Text |
| Rights | info:eu-repo/semantics/openAccess |
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