The expanded inhibitor of apoptosis gene family in oysters possesses novel domain architectures and may play diverse roles in apoptosis following immune challenge

Background: Apoptosis plays important roles in a variety of functions, including immunity and response to environmental stress. The Inhibitor of Apoptosis (IAP) gene family of apoptosis regulators is expanded in molluscs, including eastern, Crassostrea virginica, and Pacific, Crassostrea gigas, oysters. The functional importance of IAP expansion in apoptosis and immunity in oysters remains unknown. Results: Phylogenetic analysis of IAP genes in 10 molluscs identified lineage specific gene expansion in bivalve species. Greater IAP gene family expansion was observed in C. virginica than C. gigas (69 vs. 40), resulting mainly from tandem duplications. Functional domain analysis of oyster IAP proteins revealed 3 novel Baculoviral IAP Repeat (BIR) domain types and 14 domain architecture types across gene clusters, 4 of which are not present in model organisms. Phylogenetic analysis of bivalve IAPs suggests a complex history of domain loss and gain. Most IAP genes in oysters (76% of C. virginica and 82% of C. gigas), representing all domain architecture types, were expressed in response to immune challenge (Ostreid Herpesvirus OsHV-1, bacterial probionts Phaeobacter inhibens and Bacillus pumilus, several Vibrio spp., pathogenic Aliiroseovarius crassostreae, and protozoan parasite Perkinsus marinus). Patterns of IAP and apoptosis-related differential gene expression differed between the two oyster species, where C. virginica, in general, differentially expressed a unique set of IAP genes in each challenge, while C. gigas differentially expressed an overlapping set of IAP genes across challenges. Apoptosis gene expression patterns clustered mainly by resistance/susceptibility of the oyster host to immune challenge. Weighted Gene Correlation Network Analysis (WGCNA) revealed unique combinations of transcripts for 1 to 12 IAP domain architecture types, including novel types, were significantly co-expressed in response to immune challenge with transcripts in apoptosis-related pathways. Conclusions: Unprecedented diversity characterized by novel BIR domains and protein domain architectures was observed in oyster IAPs. Complex patterns of gene expression of novel and conserved IAPs in response to a variety of ecologically-relevant immune challenges, combined with evidence of direct co-expression of IAP genes with apoptosis-related transcripts, suggests IAP expansion facilitates complex and nuanced regulation of apoptosis and other immune responses in oysters

Intensive oyster aquaculture can reduce disease impacts on sympatric wild oysters

Risks associated with disease spread from fish and shellfish farming have plagued the growth and public perception of aquaculture worldwide. However, by processing nutrients and organic material from the water column, the culture of many suspension-feeding bivalves has been proposed as a novel solution toward mitigating problems facing coastal water quality, including the removal of disease-causing parasites. Here we developed and simulated an epidemiological model describing sympatric oyster Crassostrea virginica populations in aquaculture and the wild impacted by the protozoan parasite Perkinsus marinus. Our model captured the indirect interaction between wild and cultured populations that occurs through sharing water-borne P. marinus transmission stages, and we hypothesized that oyster aquaculture can enhance wild oyster populations through reduced parasitism as long as cultured oysters are harvested prior to spreading disease. We found that the density of oysters in aquaculture, which is commonly thought to lead to the spread of disease through farms and out to nearby populations in the wild, has only indirect effects on P. marinus transmission through its interaction with the rate of aquaculture harvests. Sufficient aquaculture harvest, which varies with the susceptibility of farmed oysters to P. marinus infection and their lifespan once infected, reduces disease by diluting parasites in the environment. Our modeling results offer new insights toward the broader epidemiological implications of oyster aquaculture and effective disease management

Construction and sequence sampling of deep-coverage, large-insert BAC libraries for three model lepidopteran species

<p>Abstract</p> <p>Background</p> <p><it>Manduca sexta, Heliothis virescens</it>, and <it>Heliconius erato </it>represent three widely-used insect model species for genomic and fundamental studies in Lepidoptera. Large-insert BAC libraries of these insects are critical resources for many molecular studies, including physical mapping and genome sequencing, but not available to date.</p> <p>Results</p> <p>We report the construction and characterization of six large-insert BAC libraries for the three species and sampling sequence analysis of the genomes. The six BAC libraries were constructed with two restriction enzymes, two libraries for each species, and each has an average clone insert size ranging from 152–175 kb. We estimated that the genome coverage of each library ranged from 6–9 ×, with the two combined libraries of each species being equivalent to 13.0–16.3 × haploid genomes. The genome coverage, quality and utility of the libraries were further confirmed by library screening using 6~8 putative single-copy probes. To provide a first glimpse into these genomes, we sequenced and analyzed the BAC ends of ~200 clones randomly selected from the libraries of each species. The data revealed that the genomes are AT-rich, contain relatively small fractions of repeat elements with a majority belonging to the category of low complexity repeats, and are more abundant in retro-elements than DNA transposons. Among the species, the <it>H. erato </it>genome is somewhat more abundant in repeat elements and simple repeats than those of <it>M. sexta </it>and <it>H. virescens</it>. The BLAST analysis of the BAC end sequences suggested that the evolution of the three genomes is widely varied, with the genome of <it>H. virescens </it>being the most conserved as a typical lepidopteran, whereas both genomes of <it>H. erato </it>and <it>M. sexta </it>appear to have evolved significantly, resulting in a higher level of species- or evolutionary lineage-specific sequences.</p> <p>Conclusion</p> <p>The high-quality and large-insert BAC libraries of the insects, together with the identified BACs containing genes of interest, provide valuable information, resources and tools for comprehensive understanding and studies of the insect genomes and for addressing many fundamental questions in Lepidoptera. The sample of the genomic sequences provides the first insight into the constitution and evolution of the insect genomes.</p

The genomic landscape of rapid repeated evolutionary adaptation to toxic pollution in wild fish

Author Posting. © The Author(s), 2016. This is the author's version of the work. It is posted here under a nonexclusive, irrevocable, paid-up, worldwide license granted to WHOI. It is made available for personal use, not for redistribution. The definitive version was published in Science 354 (2016): 1305-1308, doi:10.1126/science.aah4993.Atlantic killifish populations have rapidly adapted to normally lethal levels of pollution in four urban estuaries. Through analysis of 384 whole killifish genome sequences and comparative transcriptomics in four pairs of sensitive and tolerant populations, we identify the aryl hydrocarbon receptor-based signaling pathway as a shared target of selection. This suggests evolutionary constraint on adaptive solutions to complex toxicant mixtures at each site. However, distinct molecular variants apparently contribute to adaptive pathway modification among tolerant populations. Selection also targets other toxicity-mediating genes, and genes of connected signaling pathways, indicating complex tolerance phenotypes and potentially compensatory adaptations. Molecular changes are consistent with selection on standing genetic variation. In killifish high nucleotide diversity has likely been a crucial substrate for selective sweeps to propel rapid adaptation.Primary support was from the United States National Science Foundation (collaborative research grants DEB-1265282, DEB-1120512, DEB- 1120013, DEB-1120263, DEB-1120333, DEB-1120398 to JKC, DLC, MEH, SIK, MFO, JRS, WW, and AW). Further support was provided by the National Institutes of Environmental Health Sciences (1R01ES021934-01 to AW; P42ES007381 to MEH; R01ES019324 to JRS), and the National Science Foundation (OCE-1314567 to AW). BC was supported by the Postdoctoral Research Program at the US EPA administered by the Oak Ridge Institute for Science and Education (Agreement DW92429801)

The effects of nectar volume and amino acid concentration on bee foraging preferences.

We attempted to quantify the relationship between nectar volume and pollinator visitation duration, as well as amino acid concentration and bee foraging preference. We bagged lilacs in order to let nectar accumulate. Inclement weather prevented data collection. To test preference for amino acids, we placed arrays containing five sugar/amino acid solutions (35% sucrose with 0, 0.624, 2.0, 5.5, or 15.25 umol/ml amino acids) directly in honeybee hives and measured consumption of each solution. We found no preference for any particular amino acid concentration.http://deepblue.lib.umich.edu/bitstream/2027.42/54623/1/3063.pdfDescription of 3063.pdf : Access restricted to on-site users at the U-M Biological Station

Patterns of male reproductive success in Crepidula fornicata provide new insight for sex allocation and optimal sex change

The size-advantage model and sex-allocation theory are frequently invoked to explain the evolution and maintenance of sequential hermaphroditism in many taxa. A test of current theory requires quantitative estimates of reproductive success and knowledge of the relationship between reproduction and size for each gender. Reproductive success can be difficult to measure. In species where polyandry occurs, it can be quantified only by determining paternity of offspring. We employed microsatellite loci to establish paternity for 12 families of Crepidula fornicata, where a family is defined as a single female, her brood, and the males stacked on top of her. Genetic data were analyzed and paternity was assigned to a single potential father for more than 83% of the offspring tested. Estimates of reproductive success revealed that one male within the family fathered the majority of offspring and that he was usually the largest male and the one closest to the brooding female. The dominant male\u27s success also tended to decrease as the number of mature males within the family increased. Our results suggest that sperm competition could be a driving force in determining male reproductive success and the timing of sex change in C. fornicata. © 2008 Marine Biological Laboratory

Data from: Targeted approach to identify genetic loci associated with evolved dioxin tolerance in Atlantic Killifish (Fundulus heteroclitus)

Background: The most toxic aromatic hydrocarbon pollutants are categorized as dioxin-like compounds (DLCs) to which extreme tolerance has evolved independently and contemporaneously in (at least) four populations of Atlantic killifish (Fundulus heteroclitus). Surprisingly, the magnitude and phenotype of DLC tolerance is similar among these killifish populations that have adapted to varied, but highly aromatic hydrocarbon-contaminated urban/industrialized estuaries of the US Atlantic coast. Multiple tolerant and neighboring sensitive killifish populations were compared with the expectation that genetic loci associated with DLC tolerance would be revealed. Results: Since the aryl hydrocarbon receptor (AHR) pathway partly or fully mediates DLC toxicity in vertebrates, single nucleotide polymorphisms (SNPs) from 42 genes associated with the AHR pathway were identified to serve as targeted markers. Wild fish (N = 36/37) from four highly tolerant killifish populations and four nearby sensitive populations were genotyped using 59 SNP markers. Similar to other killifish population genetic analyses, strong genetic differentiation among populations was detected, consistent with isolation by distance models. When DLC-sensitive populations were pooled and compared to pooled DLC-tolerant populations, multi-locus analyses did not distinguish the two groups. However, pairwise comparisons of nearby tolerant and sensitive populations revealed high differentiation among sensitive and tolerant populations at these specific loci: AHR 1 and 2, cathepsin Z, the cytochrome P450s (CYP1A and 3A30), and the NADH dehydrogenase subunits. In addition, significant shifts in minor allele frequency were observed at AHR2 and CYP1A loci across most sensitive/tolerant pairs, but only AHR2 exhibited shifts in the same direction across all pairs. Conclusions: The observed differences in allelic composition at the AHR2 and CYP1A SNP loci were identified as significant among paired sensitive/tolerant populations of Atlantic killifish with multiple statistical tests. The genetic patterns reported here lend support to the argument that AHR2 and CYP1A play a role in the adaptive response to extreme DLC contamination. Additional functional assays are required to isolate the exact mechanism of DLC tolerance

Developing tools for the study of molluscan immunity: Thesequencing of the genome of the eastern oyster, Crassostrea virginica

The eastern oyster, Crassostrea virginica, provides important ecological and economical services, making it the target of restoration projects and supporting a significant fishery/aquaculture industry with landings valued at more than $100 million in 2012 in the United States of America. Due to the impact of infectious diseases on wild, restored, and cultured populations, the eastern oyster has been the focus of studies on host-pathogen interactions and immunity, as well as the target of selective breeding efforts for disease resistant oyster lines. Despite these efforts, relatively little is known about the genetic basis ofresistance to diseases or environmental stress, not only in eastern oyster, but also in other molluscan species of commercial interest worldwide. In order to develop tools and resources to assist in the elucidation of the genomic basis of traits of commercial, biological, and ecological interest in oysters, ateam of genome and bioinformatics experts, in collaboration with the oyster research community, is sequencing, assembling, and annotating the first reference genome for the eastern oyster and producing an exhaustive transcriptome from a variety of oyster developmental stages and tissues in response to adiverse set of environmentally-relevant stimuli. These transcriptomes and reference genome for theeastern oyster, added to the already available genome and transcriptomes for the Pacific oyster (Crassostrea gigas) and other bivalve species, will be an essential resource for the discovery of candidate genes and markers associated with traits of commercial, biological, and ecologic importance in bivalve molluscs, including those related to host-pathogen interactions and immunity