Giants among Cnidaria: Large Nuclear Genomes and Rearranged Mitochondrial Genomes in Siphonophores.

Siphonophores (Cnidaria: Hydrozoa) are abundant predators found throughout the ocean and are important constituents of the global zooplankton community. They range in length from a few centimeters to tens of meters. They are gelatinous, fragile, and difficult to collect, so many aspects of the biology of these roughly 200 species remain poorly understood. To survey siphonophore genome diversity, we performed Illumina sequencing of 32 species sampled broadly across the phylogeny. Sequencing depth was sufficient to estimate nuclear genome size from k-mer spectra in six specimens, ranging from 0.7 to 2.3 Gb, with heterozygosity estimates between 0.69% and 2.32%. Incremental k-mer counting indicates k-mer peaks can be absent with nearly 20× read coverage, suggesting minimum genome sizes range from 1.4 to 5.6 Gb in the 25 samples without peaks in the k-mer spectra. This work confirms most siphonophore nuclear genomes are large relative to the genomes of other cnidarians, but also identifies several with reduced size that are tractable targets for future siphonophore nuclear genome assembly projects. We also assembled complete mitochondrial genomes for 33 specimens from these new data, indicating a conserved gene order shared among nonsiphonophore hydrozoans, Cystonectae, and some Physonectae, revealing the ancestral mitochondrial gene order of siphonophores. Our results also suggest extensive rearrangement of mitochondrial genomes within other Physonectae and in Calycophorae. Though siphonophores comprise a small fraction of cnidarian species, this survey greatly expands our understanding of cnidarian genome diversity. This study further illustrates both the importance of deep phylogenetic sampling and the utility of k-mer-based genome skimming in understanding the genomic diversity of a clade.

Unique trajectory of gene family evolution from genomic analysis of nearly all known species in an ancient yeast lineage.

Gene gains and losses are a major driver of genome evolution; their precise characterization can provide insights into the origin and diversification of major lineages. Here, we examined gene family evolution of 1,154 genomes from nearly all known species in the medically and technologically important yeast subphylum Saccharomycotina. We found that yeast gene family and genome evolution are distinct from plants, animals, and filamentous ascomycetes and are characterized by small genome sizes and smaller gene numbers but larger gene family sizes. Faster-evolving lineages (FELs) in yeasts experienced significantly higher rates of gene losses-commensurate with a narrowing of metabolic niche breadth-but higher speciation rates than their slower-evolving sister lineages (SELs). Gene families most often lost are those involved in mRNA splicing, carbohydrate metabolism, and cell division and are likely associated with intron loss, metabolic breadth, and non-canonical cell cycle processes. Our results highlight the significant role of gene family contractions in the evolution of yeast metabolism, genome function, and speciation, and suggest that gene family evolutionary trajectories have differed markedly across major eukaryotic lineages.

Effects of exposure to nanoplastics on the gill of mussels Mytilus galloprovincialis: An integrated perspective from multiple biomarkers.

The pervasive presence of nanoplastics (NPs) in marine environments poses a threat to marine organisms. Gills, as the organ in direct contact with the environment in marine invertebrates, maybe the first to accumulate NPs. To date, the toxic effects of NPs on the gills of marine invertebrates are still largely unknown. In this study, the response of multiple biomarkers (i.e., total antioxidant capacity, the activity of acetylcholine, ion content and transport enzyme, metabolic enzymes, and lipids content) in mussels Mytilus galloprovincialis exposed to polystyrene nanoplastics (PS-NPs) for 7 days were evaluated. Significant inductions of total antioxidant capacity (T-AOC) and inhibition of acetylcholine (AChE) activity were detected after 7 days of PS-NPs exposure. PS-NPs also triggered significant alteration in ion content (Na+ and K+) and suppressed the activities of the ion transport enzyme (Na+/K+-ATPase). Moreover, we found the activity of metabolic enzymes (succinate dehydrogenase and pyruvate kinase) and lipids content (triacylglycerol and cholesterol) were significantly altered, suggesting the interference of PS-NPs on energy metabolism and lipid metabolism. This investigation provides substantial information to understand the physical responses of invertebrate gills to PS-NPs exposure. Given the crucial ecological roles of invertebrates, the presence of PS-NPs in the marine environment may have far-reaching impacts on population abundance, biodiversity, and stability of the marine ecosystem.

Evaluation of antioxidant capacity and digestive enzyme activities in Mytilus galloprovincialis exposed to nanoplastics under different patterns of hypoxia.

In the marine environment, plastic pollution may occur simultaneously with hypoxia. However, current ecological risk assessments of nanoplastics have rarely considered the impact of additional environmental factors, such as hypoxia. In this study, we investigated the effect of polystyrene nanospheres (PS-NPs) on the digestive performance (antioxidant system and digestive enzymes) of mussels Mytilus galloprovincialis under different patterns of hypoxia (normoxia, constant hypoxia, and fluctuating hypoxia). The result showed that PS-NPs caused oxidative damage in the digestive glands of mussels, while all patterns of hypoxia exacerbated this oxidative damage. Activities of four digestive enzymes (α-amylase, cellulase, trypsin, and lipase) were examined. Among these, the activity of the α-amylase was inhibited by PS-NPs, and the inhibition was aggravated by all the hypoxia patterns. The cellulase activity and trypsin activity was enhanced by PS-NPs, and the increase was further stimulated by hypoxia. Lipase activity was not affected by PS-NPs alone, but significant inhibition was detected after the coexposure to PS-NPs and hypoxia. Conclusively, the combined stress of hypoxia and nanoplastics can significantly affect the digestive performance of mussels and may alter the mussel nutrient uptake strategy. Our work has provided new insight into the ecological risk assessment of plastics under global climate change.