Unraveling the genetic secrets of ancient Baikal amphipods

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

Stochastic particle packing with specified granulometry and porosity

This work presents a technique for particle size generation and placement in arbitrary closed domains. Its main application is the simulation of granular media described by disks. Particle size generation is based on the statistical analysis of granulometric curves which are used as empirical cumulative distribution functions to sample from mixtures of uniform distributions. The desired porosity is attained by selecting a certain number of particles, and their placement is performed by a stochastic point process. We present an application analyzing different types of sand and clay, where we model the grain size with the gamma, lognormal, Weibull and hyperbolic distributions. The parameters from the resulting best fit are used to generate samples from the theoretical distribution, which are used for filling a finite-size area with non-overlapping disks deployed by a Simple Sequential Inhibition stochastic point process. Such filled areas are relevant as plausible inputs for assessing Discrete Element Method and similar techniques

Unraveling the genetic secrets of ancient Baikal amphipods

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

Indication of ongoing amphipod speciation in Lake Baikal by genetic structures within endemic species

Abstract Background The ancient Lake Baikal is characterized by an outstanding diversity of endemic faunas with more than 350 amphipod species and subspecies. We determined the genetic diversity within the endemic littoral amphipod species Eulimnogammarus verrucosus, E. cyaneus and E. vittatus and investigated whether within those species genetically separate populations occur across Lake Baikal. Gammarus lacustris from water bodies in the Baikal area was examined for comparison. Results Genetic diversities within a species were determined based on fragments of cytochrome c oxidase I (COI) and for E. verrucosus additionally of 18S rDNA. Highly location-specific haplogroups of E. verrucosus and E. vittatus were found at the southern and western shores of Baikal that are separated by the Angara River outflow; E. verrucosus from the eastern shore formed a further, clearly distinct haplotype cluster possibly confined by the Selenga River and Angarskiy Sor deltas. The genetic diversities within these haplogroups were lower than between the different haplogroups. Intraspecific genetic diversities within E. verrucosus and E. vittatus with 13 and 10%, respectively, were similar to interspecies differences indicating the occurrence of cryptic, morphologically highly similar species; for E. verrucosus this was confirmed with 18S rDNA. The haplotypes of E. cyaneus and G. lacustris specimens were with intraspecific 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. Conclusions Our finding of separation of subgroups of Baikal endemic amphipods to different degrees points to a species-specific ability of dispersal across areas with adverse conditions and to potential geographical dispersal barriers in Lake Baikal

Thermal reaction norms of key metabolic enzymes reflect divergent physiological and behavioral adaptations of closely related amphipod species

Lake Baikal is inhabited by more than 300 endemic amphipod species, which are narrowly adapted to certain thermal niches due to the high interspecific competition. In contrast, the surrounding freshwater fauna is commonly represented by species with large‐scale distribution and high phenotypic thermal plasticity. Here, we investigated the thermal plasticity of the energy metabolism in two closely‐related endemic amphipod species from Lake Baikal (Eulimnogammarus verrucosus; stenothermal and Eulimnogammarus cyaneus; eurythermal) and the ubiquitous Holarctic amphipod Gammarus lacustris (eurythermal) by exposure to a summer warming scenario (6–23.6 °C; 0.8 °C d−1). In concert with routine metabolic rates, activities of key metabolic enzymes increased strongly with temperature up to 15 °C in E. verrucosus, whereupon they leveled off (except for lactate dehydrogenase). In contrast, exponential increases were seen in E. cyaneus and G. lacustris throughout the thermal trial (Q10‐values: 1.6–3.7). Cytochrome‐c‐oxidase, lactate dehydrogenase, and 3‐hydroxyacyl‐CoA dehydrogenase activities were found to be higher in G. lacustris than in E. cyaneus, especially at the highest experimental temperature (23.6 °C). Decreasing gene expression levels revealed some thermal compensation in E. cyaneus but not in G. lacustris. In all species, shifts in enzyme activities favored glycolytic energy generation in the warmth. The congruent temperature‐ dependencies of enzyme activities and routine metabolism in E. verrucosus indicate a strong feedback‐ regulation of enzymatic activities by whole organism responses. The species‐specific thermal reaction norms reflect the different ecological niches, including the spatial distribution, distinct thermal behavior such as temperature‐dependent migration, movement activity, and mating season

Activities of key metabolic enzymes and their respective mRNA transcript levels in amphipods exposed to an experimental warming scenario

Lake Baikal is inhabited by more than 300 endemic amphipod species, which are narrowly adapted to certain thermal niches due to the high interspecific competition. In contrast, the surrounding freshwater fauna is commonly represented by species with large-scale distribution and high phenotypic thermal plasticity. Here, we investigated the thermal plasticity of the energy metabolism in two closely-related endemic amphipod species from Lake Baikal (Eulimnogammarus verrucosus; stenothermal and Eulimnogammarus cyaneus; eurythermal) and the ubiquitous Holarctic amphipod Gammarus lacustris (eurythermal) by exposure to a summer warming scenario (6-23.6 °C; 0.8 °C d-1). In concert with routine metabolic rates, activities of key metabolic enzymes increased strongly with temperature up to 15 °C in E. verrucosus, whereupon they leveled off (except for lactate dehydrogenase). In contrast, exponential increases were seen in E. cyaneus and G. lacustris throughout the thermal trial (Q10-values: 1.6-3.7). Cytochrome-c-oxidase, lactate dehydrogenase, and 3-hydroxyacyl-CoA dehydrogenase activities were found to be higher in G. lacustris than in E. cyaneus, especially at the highest experimental temperature (23.6 °C). Decreasing gene expression levels revealed some thermal compensation in E. cyaneus but not in G. lacustris. In all species, shifts in enzyme activities favored glycolytic energy generation in the warmth. The congruent temperature-dependencies of enzyme activities and routine metabolism in E. verrucosus indicate a strong feedback-regulation of enzymatic activities by whole organism responses. The species-specific thermal reaction norms reflect the different ecological niches, including the spatial distribution, distinct thermal behavior such as temperature-dependent migration, movement activity, and mating season

eulimno.dvi

Abstract Eulimnogammarus verrucosus is an amphipod endemic to the unique ecosystem of Lake Baikal and serves in particular as an emerging model in ecotoxicological studies. We report here on a survey sequencing of its genome as a first step to establish sequence resources for this species. From a single lane of paired-end sequencing data we estimated the genome size as nearly 10 Gb and we obtained an overview of the repeat content. At least two thirds of the genome are non-unique DNA, and a third of the genomic DNA is composed of just five families of repetitive elements, including low-complexity sequences. Attempts to use off-the-shelf assembly tools failed on the available low-coverage data both before and after removal of highly repetitive components. Using a seed-based approach we nevertheless assembled short contigs covering 33 pre-microRNAs and the homeodomain-containing exon of nine Hox genes. The absence of clear evidence for paralogs implies that a genome duplication did not contribute to the large genome size. We furthermore report the assembly of the mitochondrial genome using a new, guided "crystallization" procedure. The initial results presented here set the stage for a more complete sequencing and analysis of this large genome

Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells

The unprecedented outbreak of Ebola in West Africa resulted in over 28,000 cases and 11,000 deaths, underlining the need for a better understanding of the biology of this highly pathogenic virus to develop specific counter strategies. Two filoviruses, the Ebola and Marburg viruses, result in a severe and often fatal infection in humans. However, bats are natural hosts and survive filovirus infections without obvious symptoms. The molecular basis of this striking difference in the response to filovirus infections is not well understood. We report a systematic overview of differentially expressed genes, activity motifs and pathways in human and bat cells infected with the Ebola and Marburg viruses, and we demonstrate that the replication of filoviruses is more rapid in human cells than in bat cells. We also found that the most strongly regulated genes upon filovirus infection are chemokine ligands and transcription factors. We observed a strong induction of the JAK/STAT pathway, of several genes encoding inhibitors of MAP kinases (DUSP genes) and of PPP1R15A, which is involved in ER stress-induced cell death. We used comparative transcriptomics to provide a data resource that can be used to identify cellular responses that might allow bats to survive filovirus infections

Genome sequence of the progenitor of the wheat D genome Aegilops tauschii.

Aegilops tauschii is the diploid progenitor of the D genome of hexaploid wheat (Triticum aestivum, genomes AABBDD) and an important genetic resource for wheat. The large size and highly repetitive nature of the Ae. tauschii genome has until now precluded the development of a reference-quality genome sequence. Here we use an array of advanced technologies, including ordered-clone genome sequencing, whole-genome shotgun sequencing, and BioNano optical genome mapping, to generate a reference-quality genome sequence for Ae. tauschii ssp. strangulata accession AL8/78, which is closely related to the wheat D genome. We show that compared to other sequenced plant genomes, including a much larger conifer genome, the Ae. tauschii genome contains unprecedented amounts of very similar repeated sequences. Our genome comparisons reveal that the Ae. tauschii genome has a greater number of dispersed duplicated genes than other sequenced genomes and its chromosomes have been structurally evolving an order of magnitude faster than those of other grass genomes. The decay of colinearity with other grass genomes correlates with recombination rates along chromosomes. We propose that the vast amounts of very similar repeated sequences cause frequent errors in recombination and lead to gene duplications and structural chromosome changes that drive fast genome evolution