Hydrothermal vents and methane seeps are extreme deep-sea ecosystems that support dense populations of specialized macro benthos such as mussels. But the lack of genome information hinders the understanding of the adaptation of these animals to such inhospitable environments. Here we report the genomes of a deep-sea vent/seep mussel (Bathymodiolus platifrons) and a shallow-water mussel (Modiolus philippinarum). Phylogenetic analysis shows that these mussel species diverged approximately 110.4 million years ago. Many gene families, especially those for stabilizing protein structures and removing toxic substances from cells, are highly expanded in B. platifrons, indicating adaptation to extreme environmental conditions. The innate immune system of B. platifrons is considerably more complex than that of other lophotrochozoan species, including M. philippinarum, with substantial expansion and high expression levels of gene families that are related to immune recognition, endocytosis and caspase-mediated apoptosis in the gill, revealing presumed genetic adaptation of the deep-sea mussel to the presence of its chemoautotrophic endosymbionts. A follow-up metaproteomic analysis of the gill of B. platifrons shows methanotrophy, assimilatory sulfate reduction and ammonia metabolic pathways in the symbionts, providing energy and nutrients, which allow the host to thrive. Our study of the genomic composition allowing symbiosis in extremophile molluscs gives wider insights into the mechanisms of symbiosis in other organisms such as deep-sea tubeworms and giant clams.

The family Ampullariidae includes both aquatic and amphibious apple snails. They are an emerging model for evolutionary studies due to the high diversity, ancient history, and wide geographical distribution. Insight into drivers of ampullariid evolution is hampered, however, by the lack of genomic resources. Here, we report the genomes of four ampullariids spanning the Old World ( Lanistes nyassanus ) and New World ( Pomacea canaliculata , P. maculata , and Marisa cornuarietis ) clades. The ampullariid genomes have conserved ancient bilaterial karyotype features and a novel Hox gene cluster rearrangement, making them valuable in comparative genomic studies. They have expanded gene families related to environmental sensing and cellulose digestion, which may have facilitated some ampullarids to become notorious invasive pests. In the amphibious Pomacea , novel acquisition of an egg neurotoxin and a protein for making the calcareous eggshell may have been key adaptations enabling their transition from underwater to terrestrial egg deposition.

The Pacific oyster Crassostrea gigas is one of the dominant sessile inhabitants of the estuarine intertidal zone, which is a physically harsh environment due to the presence of a number of stressors. Oysters have adapted to highly dynamic and stressful environments, but the molecular mechanisms underlying such stress adaptation are largely unknown. In the present study, we examined the proteomic responses in the gills of C. gigas exposed to three stressors (high temperature, low salinity, and aerial exposure) they often encounter in the field. We quantitatively compared the gill proteome profiles using iTRAQ-coupled 2-D LC-MS/MS. There were 3165 identified proteins among which 2379 proteins could be quantified. Heat shock, hyposalinity, and aerial exposure resulted in 50, 15, and 33 differentially expressed gill proteins, respectively. Venn diagram analysis revealed substantial different responses to the three stressors. Only xanthine dehydrogenase/oxidase showed a similar expression pattern across the three stress treatments, suggesting that reduction of ROS accumulation may be a conserved response to these stressors. Heat shock caused significant overexpression of molecular chaperones and production of S-adenosyl-l-methionine, indicating their crucial protective roles against protein denature. In addition, heat shock also activated immune responses, Ca(2+) binding protein expression. By contrast, hyposalinity and aerial exposure resulted in the up-regulation of 3-demethylubiquinone-9 3-methyltransferase, indicating that increase in ubiquinone synthesis may contribute to withstanding both the osmotic and desiccation stress. Strikingly, the majority of desiccation-responsive proteins, including those involved in metabolism, ion transportation, immune responses, DNA duplication, and protein synthesis, were down-regulated, indicating conservation of energy as an important strategy to cope with desiccation stress. There was a high consistency between the expression levels determined by iTRAQ and Western blotting, highlighting the high reproducibility of our proteomic approach and its great value in revealing molecular mechanisms of stress responses.

Nautilus is the sole surviving externally shelled cephalopod from the Palaeozoic. It is unique within cephalopod genealogy and critical to understanding the evolutionary novelties of cephalopods. Here, we present a complete Nautilus pompilius genome as a fundamental genomic reference on cephalopod innovations, such as the pinhole eye and biomineralization. Nautilus shows a compact, minimalist genome with few encoding genes and slow evolutionary rates in both non-coding and coding regions among known cephalopods. Importantly, multiple genomic innovations including gene losses, independent contraction and expansion of specific gene families and their associated regulatory networks likely moulded the evolution of the nautilus pinhole eye. The conserved molluscan biomineralization toolkit and lineage-specific repetitive low-complexity domains are essential to the construction of the nautilus shell. The nautilus genome constitutes a valuable resource for reconstructing the evolutionary scenarios and genomic innovations that shape the extant cephalopods.

Plants have evolved sophisticated embryo defences by kinetically-stable non-digestible storage proteins that lower the nutritional value of seeds, a strategy that have not been reported in animals. To further understand antinutritive defences in animals, we analysed PmPV1, massively accumulated in the eggs of the gastropod Pomacea maculata, focusing on how its structure and structural stability features affected its capacity to withstand passage through predator guts. The native protein withstands >50 min boiling and resists the denaturing detergent sodium dodecyl sulphate (SDS), indicating an unusually high structural stability (i.e., kinetic stability). PmPV1 is highly resistant to in vitro proteinase digestion and displays structural stability between pH 2.0–12.0 and 25–85 °C. Furthermore, PmPV1 withstands in vitro and mice digestion and is recovered unchanged in faeces, supporting an antinutritive defensive function. Subunit sequence similarities suggest a common origin and tolerance to mutations. This is the first known animal genus that, like plant seeds, lowers the nutritional value of eggs by kinetically-stable non-digestible storage proteins that survive the gut of predators unaffected. The selective pressure of the harsh gastrointestinal environment would have favoured their appearance, extending by convergent evolution the presence of plant-like hyperstable antinutritive proteins to unattended reproductive stages in animals.

The apple snail Pomacea canaliculata is a freshwater gastropod with a remarkable ability to withstand seasonal or unpredictable dry conditions by entering estivation. Studies of P. canaliculata using conventional biochemical and the individual gene approaches have revealed the expressional changes of several enzymes and antioxidative genes in response to estivation and arousal. In this study, we applied iTRAQ-coupled two-dimensional LC-MS/MS to identify and quantify the global protein expression during the estivation and arousal of P. canaliculata. A total of 1040 proteins were identified, among which 701 proteins were quantified and compared across four treatments (i.e., control, active snails; short-term estivation, 3 days of exposure to air; prolonged estivation, 30 days of exposure to air; and arousal, 6 h after resubmergence in water) revealing 53 differentially expressed proteins. A comparison of protein expression profiles across treatments indicated that the proteome of this species was very insensitive to initial estivation, with only 9 proteins differentially expressed as compared with the control. Among the 9 proteins, the up-regulations of two immune related proteins indicated the initial immune response to the detection of stress cues. Prolonged estivation resulted in many more differentially expressed proteins (47 compared with short-term estivation treatment), among which 16 were down-regulated and 31 were up-regulated. These differentially expressed proteins have provided the first global picture of a shift in energy usage from glucose to lipid, prevention of protein degradation and elevation of oxidative defense, and production of purine for uric acid production to remove toxic ammonia during prolonged estivation in a freshwater snail. From prolonged estivation to arousal, only 6 proteins changed their expression level, indicating that access to water and food alone is not a necessary condition to reactivate whole-sale protein expression. A comparison with hibernation and diapause revealed many similar molecular mechanisms of hypometabolic regulation across the animal kingdom.

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The eggs of the freshwater Pomacea apple snails develop above the water level, exposed to varied physical and biological stressors. Their high hatching success seems to be linked to their proteins or perivitellins, which surround the developing embryo providing nutrients, sunscreens and varied defenses. The defensive mechanism has been unveiled in P. canaliculata and P. maculata eggs, where their major perivitellins are pigmented, non-digestible and provide a warning coloration while another perivitellin acts as a toxin. In P. scalaris, a species sympatric to the former, the defense strategy seems different, since no toxin was found and the major perivitellin, PsSC, while also colored and non-digestible, is a carbohydrate-binding protein. In this study we examine the structure and function of PsSC by sequencing its subunits, characterizing its carbohydrate binding profile and evaluating its effect on gut cells. Whereas cDNA sequencing and database search showed no lectin domain, glycan array carbohydrate binding profile revealed a strong specificity for glycosphingolipids and ABO group antigens. Moreover, PsSC agglutinated bacteria in a dose-dependent manner. Inspired on the defensive properties of seed lectins we evaluated the effects of PsSC on intestinal cells both in vitro (Caco-2 and IEC-6 cells) and in the gastrointestinal tract of rats. PsSC binds to Caco-2 cell membranes without reducing its viability, while a PsSC-containing diet temporarily induces large epithelium alterations and an increased absorptive surface. Based on these results, we propose that PsSC is involved in embryo defenses by altering the gut morphophysiology of potential predators, a convergent role to plant defensive lectins.