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The eastern oyster (Crassostrea virginica) is a protandrous hermaphrodite of commercial importance. As with many marine invertebrates, little is known about sex determination and differentiation systems in this species. Such knowledge has important implications not only for understanding the evolution of sex but also for applied questions in aquaculture. In order to examine mechanistic differences in reproductive development between the sexes, we compared the transcriptomes of gonad and mantle tissues from six male and six female oysters. A total of 7675 transcripts were differentially expressed between male and female gonads (3936 and 3739 were upregulated in males and females, respectively). Transcripts identified include those associated with sex in other invertebrate and vertebrate species such asDmrt1,Sox‐30,Bindin,Dpy‐30, andHistone H4in males andFoxl2,Vitellogenin, andBystinin females. GO terms associated with transcripts upregulated in male gonads include protein modification, reproductive process, and cell projection organization, whereas RNA metabolic process and amino acid metabolic process were associated with transcripts upregulated in females. Far fewer transcripts were differentially expressed between male and female mantle tissues, with 87 transcripts upregulated in females and 16 upregulated in males. However, 41% of transcripts identified as differentially expressed between mantle tissues were also differentially expressed between male and female gonads includingHistone H4andBystin. This study represents the first characterization of eastern oyster male and female gonad transcriptomes. We further identify differing expression profiles between male and female mantle tissues, which provides evidence for sex‐specific functions of the mantle and suggests that this tissue could harbor biomarkers for identifying oyster sex non‐destructively.

 

Genome assembly can be challenging for species that are characterized by high amounts of polymorphism, heterozygosity, and large effective population sizes. High levels of heterozygosity can result in genome mis-assemblies and a larger than expected genome size due to the haplotig versions of a single locus being assembled as separate loci. Here, we describe the first chromosome-level genome for the eastern oyster, Crassostrea virginica. Publicly released and annotated in 2017, the assembly has a scaffold N50 of 54 mb and is over 97.3% complete based on BUSCO analysis. The genome assembly for the eastern oyster is a critical resource for foundational research into molluscan adaptation to a changing environment and for selective breeding for the aquaculture industry. Subsequent resequencing data suggested the presence of haplotigs in the original assembly, and we developed a post hoc method to break up chimeric contigs and mask haplotigs in published heterozygous genomes and evaluated improvements to the accuracy of downstream analysis. Masking haplotigs had a large impact on SNP discovery and estimates of nucleotide diversity and had more subtle and nuanced effects on estimates of heterozygosity, population structure analysis, and outlier detection. We show that haplotig masking can be a powerful tool for improving genomic inference, and we present an open, reproducible resource for the masking of haplotigs in any published genome. 

Atlantic killifish (Fundulus heteroclitus) residing in some urban and industrialized estuaries of theUSeastern seaboard demonstrate recently evolved and extreme tolerance to toxic aryl hydrocarbon pollutants, characterized as dioxin‐like compounds (DLCs). Here, we provide an unusually comprehensive accounting (69%) through quantitative trait locus (QTL) analysis of the genetic basis forDLCtolerance in killifish inhabiting an urban estuary contaminated withPCBcongeners, the most toxic of which areDLCs. Consistent with mechanistic knowledge ofDLCtoxicity in fish and other vertebrates, the aryl hydrocarbon receptor (ahr2) region accounts for 17% of trait variation; however,QTLon independent linkage groups and their interactions have even greater explanatory power (44%).QTLinterpreted within the context of recently availableFundulusgenomic resources and shared synteny among fish species suggest adaptation via interacting components of a complex stress response network. SomeQTLwere also enriched in other killifish populations characterized asDLC‐tolerant and residing in distant urban estuaries contaminated with unique mixtures of pollutants. Together, our results suggest thatDLCtolerance in killifish represents an emerging example of parallel contemporary evolution that has been driven by intense human‐mediated selection on natural populations.