The black tiger shrimp (Penaeus monodon) remains the second most widely cultured shrimp species globally; however, issues with disease and domestication have seen production levels stagnate over the past two decades. To help identify innovative solutions needed to resolve bottlenecks hampering the culture of this species, it is important to generate genetic and genomic resources. Towards this aim, we have produced the most complete publicly available P. monodon transcriptome database to date based on nine adult tissues and eight early life-history stages (BUSCO - Complete: 98.2% [Duplicated: 51.3%], Fragmented: 0.8%, Missing: 1.0%). The assembly resulted in 236,388 contigs, which were then further segregated into 99,203 adult tissue specific and 58,678 early life-history stage specific clusters. While annotation rates were low (approximately 30%), as is typical for a non-model organisms, annotated transcript clusters were successfully mapped to several hundred functional KEGG pathways. Transcripts were clustered into groups within tissues and early life-history stages, providing initial evidence for their roles in specific tissue functions, or developmental transitions. We expect the transcriptome to provide an essential resource to investigate the molecular basis of commercially relevant-significant traits in P. monodon and other shrimp species.

Cooked prawn colour is known to be a driver of market price and a visual indicator of product quality for the consumer. Although there is a general understanding that colour variation exists in farmed prawns, there has been no attempt to quantify this variation or identify where this variation is most prevalent. The objectives of this study were threefold: firstly to compare three different quantitative methods to measure prawn colour or pigmentation, two different colorimeters and colour quantification from digital images. Secondly, to quantify the amount of pigmentation variation that exists in farmed prawns within ponds, across ponds and across farms. Lastly, to assess the effects of ice storage or freeze-thawing of raw product prior to cooking. Each method was able to detect quantitative differences in prawn colour, although conversion of image based quantification of prawn colour from RGB to Lab was unreliable. Considerable colour variation was observed between prawns from different ponds and different farms, and this variation potentially affects product value. Different post-harvest methods prior to cooking were also shown to have a profound detrimental effect on prawn colour. Both long periods of ice storage and freeze thawing of raw product was detrimental to prawn colour. However, ice storage immediately after cooking was shown to be beneficial to prawn colour. Results demonstrated that darker prawn colour was preserved by holding harvested prawns live in chilled seawater, limiting the time between harvesting and cooking, and avoiding long periods of ice storage or freeze thawing of uncooked product.

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These two authors contributed equally to the writing of this publication Affiliations: (which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint . http://dx.doi.org/10.1101/280420 doi: bioRxiv preprint first posted online Mar. 14, 2018; 2 DeclarationsAvailability of data and material Raw data, assembly and bioinformatics scripts will be made freely available online upon publication. . CC-BY-NC-ND 4.0 International license It is made available under a (which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint . http://dx.doi.org/10.1101/280420 doi: bioRxiv preprint first posted online Mar. 14, 2018;

The purpose of this study was to revisit the mitochondrial genetic divergence of North Atlantic populations of the subtidal gastropod Buccinum undatum, because previous mitochondrial DNA (mtDNA) analysis by Pálsson et al. (2014) included 16S ribosomal RNA sequences that were incorrectly assigned to the species. In the present study, population mtDNA variation is now assessed using COI sequences obtained from previous research (Pálsson et al., 2014) and, to increase the geographical cover of the study, data from recently assembled transcriptomes of 96 Icelandic whelks (Jónsson et al., 2019) and GenBank are also used. To estimate the mtDNA divergence in B. undatum across the North Atlantic, two species screening indices were used: automatic barcode gap discovey (ABGD; Puillandre et al., 2012a) and species screening threshold index (SSTI; Witt et al., 2006). Phylogenetic reconstruction revealed monophyletic Eastern and Western North Atlantic whelk lineages, which diverged early in the Pleistocene glaciation (2.1 Mya), followed by a subsequent divergence event between Greenlandic and Canadian populations at 1.3 Mya. Species screening indices, ABGD and SSTI, indicated cryptic speciation or allopatric divergence. Genetic distances between populations from the two continents were similar to or greater than interspecific genetic distances across several North Pacific and North Atlantic Buccinum species.

The Giant or Black Tiger Shrimp, Penaeus monodon, is an economically significant aquaculture species globally, producing 4.5 million tonnes of product annually at a value of US$ 23.5 billion (FAO, 2016a). Recent innovations in the domestication and selective breeding of P. monodon have resulted in significant improvements in growth rate, survival and pathogen tolerance. However, the reproductive performance of domesticated stocks is inferior compared to that of wild-caught broodstock. Significant reductions in the number of females maturing, egg and nauplii production and hatch rates are commonly reported for domesticated stocks relative to their wild-caught counterparts.The complexities surrounding reduced reproductive performance in domesticated P. monodon are underpinned by two critical issues: 1) a poor understanding of the specific nutritional requirements for reproduction in the species and; 2) a lack of clarity as to the characteristics that define a 'good spawner' -particularly on a biochemical and molecular level. The studies that make up this thesis employed a multidisciplinary approach to assess nutritional, biochemical, and molecular factors that relate to broodstock reproductive performance. Primarily this thesis sought to: (1) investigate whether the current constraints to reproductive performance in domesticated stocks could be overcome by including the microbial biomass derived bioactive Novacq™ (Patent #2008201886) within pelleted diets; (2) evaluate whether current broodstock maturation diets are limiting in relation to repeated spawning and; (3) characterise key interactions between micronutrients and regulatory gene(s) and/or pathways linked to reproduction.A series of reproductive performance trials were undertake to assess the effect of incorporating microbial biomass (Novacq™) within pelleted maturation diets. Preliminary farm-based trials observed significant increases to maturation rate, egg production and nauplii production when domesticated broodstock were fed an experimental pelleted diet containing the Novacq™ ingredient (20% Novacq™ inclusion rate, 2.4% of total diet fed). However, in a subsequent trial conducted under controlled experimental conditions, broodstock fed commercial-grade pelleted diets (30% Novacq™, 5.5% of total diet fed) exhibited a significant decrease in egg hatch rate. Reductions in reproductive performance under controlled experimental conditions were attributed to a decrease in the quality of basal pellet diets, both as a function of increased Novacq™ inclusion and their commercial-based formulation. The above studies suggest the capacity to improve reproductive performance in domesticated P. monodon, using biofloc and its substituents, is highly dependent on the quality of the basal maturation diet fed.ii In response to the aforementioned studies, a trial was undertaken to identify potential factors limiting reproductive performance within current broodstock maturation diets. The effect of repeated spawning on reproductive performance and tissue bioche...

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The reconstruction of spatial genetic structure can provide valuable insights into the evolutionary processes affecting speciessuch as genetic drift, adaptive selection, and gene flow between populations (Crawford & Oleksiak, 2016; Funk et al., 2012; Kohn et al., 2006)-while facilitating the characterization of historical demographic events and ongoing evolutionary trajectories (Emerson et al., 2010). Marine invertebrate phylogeography in the north Atlantic Ocean has been shaped by climate variation during the Pleistocene Epoch; glacial cycles have repeatedly altered species' distributions over the last two million years. Several marine invertebrate species have gone extinct in North America and have subsequently been recolonized from Europe (Ingolfsson, 1992;