CrusTome: a transcriptome database resource for large-scale analyses across Crustacea.

Transcriptomes from nontraditional model organisms often harbor a wealth of unexplored data. Examining these data sets can lead to clarity and novel insights in traditional systems, as well as to discoveries across a multitude of fields. Despite significant advances in DNA sequencing technologies and in their adoption, access to genomic and transcriptomic resources for nontraditional model organisms remains limited. Crustaceans, for example, being among the most numerous, diverse, and widely distributed taxa on the planet, often serve as excellent systems to address ecological, evolutionary, and organismal questions. While they are ubiquitously present across environments, and of economic and food security importance, they remain severely underrepresented in publicly available sequence databases. Here, we present CrusTome, a multispecies, multitissue, transcriptome database of 201 assembled mRNA transcriptomes (189 crustaceans, 30 of which were previously unpublished, and 12 ecdysozoans for phylogenetic context) as an evolving and publicly available resource. This database is suitable for evolutionary, ecological, and functional studies that employ genomic/transcriptomic techniques and data sets. CrusTome is presented in BLAST and DIAMOND formats, providing robust data sets for sequence similarity searches, orthology assignments, phylogenetic inference, etc. and thus allowing for straightforward incorporation into existing custom pipelines for high-throughput analyses. In addition, to illustrate the use and potential of CrusTome, we conducted phylogenetic analyses elucidating the identity and evolution of the cryptochrome/photolyase family of proteins across crustaceans.

Application of commercial kits using DNA-based and immunochemical methods for determination of shrimp allergens in kimchi and its ingredients.

Shrimps cause a significant part of crustacea-related allergies. It is used in processed foods, including fermented Korean foods, such as kimchi. Even low amounts of shrimp allergens can provoke reactions in consumers allergic to shrimp. Accurate food labeling is the most effective means of preventing the consumption of allergenic ingredients. To validate labeling compliance and minimize the risk of cross-contaminations, the effectiveness of methodologies used for the detection of allergens in foods should be compared. Here, seven commercial kits, based on quantitative real-time polymerase chain reaction (PCR) or enzyme-linked immunosorbent assay (ELISA), were assessed for their ability to detect the presence of shrimp allergens in food. Our results showed that SureFood real-time PCR kit and Ridascreen ELISA kit had the highest recovery, whereas five other kits underperformed in the determination of allergen content of kimchi and its ingredients. The variation in recovery among the kits depended on the limit of detection and reactivity to the shrimp allergens, tropomyosin, and sarcoplasmic calcium-binding protein. PRACTICAL APPLICATION: This research confirms the performance of commercial kits to detect the presence of shrimp allergens in kimchi, and demonstrates that the sensitivity of these kits depends on reactivity to the specific shrimp allergenic proteins. These results can be used to food allergy labeling and can be applied by the food industry to develop allergen test kits for fermented foods with improved performance.

CrusTF: a comprehensive resource of transcriptomes for evolutionary and functional studies of crustacean transcription factors.

BACKGROUND: Crustacea, the second largest subphylum of Arthropoda, includes species of major ecological and economic importance, such as crabs, lobsters, crayfishes, shrimps, and barnacles. With the rapid development of crustacean aquaculture and biodiversity loss, understanding the gene regulatory mechanisms of growth, reproduction, and development of crustaceans is crucial to both aquaculture development and biodiversity conservation of this group of organisms. In these biological processes, transcription factors (TFs) play a vital role in regulating gene expression. However, crustacean transcription factors are still largely unknown, because the lack of complete genome sequences of most crustacean species hampers the studies on their transcriptional regulation on a system-wide scale. Thus, the current TF databases derived from genome sequences contain TF information for only a few crustacean species and are insufficient to elucidate the transcriptional diversity of such a large animal group. RESULTS: Our database CrusTF ( http://qinlab.sls.cuhk.edu.hk/CrusTF ) provides comprehensive information for evolutionary and functional studies on the crustacean transcriptional regulatory system. CrusTF fills the knowledge gap of transcriptional regulation in crustaceans by exploring publicly available and newly sequenced transcriptomes of 170 crustacean species and identifying 131,941 TFs within 63 TF families. CrusTF features three categories of information: sequence, function, and evolution of crustacean TFs. The database enables searching, browsing and downloading of crustacean TF sequences. CrusTF infers DNA binding motifs of crustacean TFs, thus facilitating the users to predict potential downstream TF targets. The database also presents evolutionary analyses of crustacean TFs, which improve our understanding of the evolution of transcriptional regulatory systems in crustaceans. CONCLUSIONS: Given the importance of TF information in evolutionary and functional studies on transcriptional regulatory systems of crustaceans, this database will constitute a key resource for the research community of crustacean biology and evolutionary biology. Moreover, CrusTF serves as a model for the construction of TF database derived from transcriptome data. A similar approach could be applied to other groups of organisms, for which transcriptomes are more readily available than genomes.

Development of genome- and transcriptome-derived microsatellites in related species of snapping shrimps with highly duplicated genomes.

Molecular markers are powerful tools for studying patterns of relatedness and parentage within populations and for making inferences about social evolution. However, the development of molecular markers for simultaneous study of multiple species presents challenges, particularly when species exhibit genome duplication or polyploidy. We developed microsatellite markers for Synalpheus shrimp, a genus in which species exhibit not only great variation in social organization, but also interspecific variation in genome size and partial genome duplication. From the four primary clades within Synalpheus, we identified microsatellites in the genomes of four species and in the consensus transcriptome of two species. Ultimately, we designed and tested primers for 143 microsatellite markers across 25 species. Although the majority of markers were disomic, many markers were polysomic for certain species. Surprisingly, we found no relationship between genome size and the number of polysomic markers. As expected, markers developed for a given species amplified better for closely related species than for more distant relatives. Finally, the markers developed from the transcriptome were more likely to work successfully and to be disomic than those developed from the genome, suggesting that consensus transcriptomes are likely to be conserved across species. Our findings suggest that the transcriptome, particularly consensus sequences from multiple species, can be a valuable source of molecular markers for taxa with complex, duplicated genomes.

A re-assessment of Konarus Bamber, 2006 and sympatric leptocheliids from Australasia, and of Pseudoleptochelia Lang, 1973 (Crustacea: Peracarida: Tanaidacea).

Following recent revelations regarding males with subchelate chelipeds in the tanaidacean genus Parakonarus, a number of Australian leptocheliid taxa are re-assessed, and their males and females variously re-allocated. To assist the interpretation of taxa with subchelate males, Heterotanais anomalus Sars is redescribed based on material from the Balearic Islands. The males of Konarus are now known to have a subchelate cheliped. The male (only) of Pseudoleptochelia bulbus from Melanesia is reassigned to Konarus cheiris, while Pseudoleptochelia bulbus sensu stricto is reassigned to Leptochelia together with its "minuta"-type male, as Leptochelia bulbus. Pseudoleptochelia straddi is rassigned to Konarus, together with its females from Queensland, Australia, which were previously assigned to Konarus cheiris. Pseudoleptocheliafairgo is confirmed as a member of Parakonarus, but material from Queensland is re-described as a new species. Other species previously assigned to Pseudoleptochelia are re-assessed: P. inermis, P. mercantilis and P. mortenseni sensu stricto are transferred to Leptochelia. The "small females" and males of P. mortenseni are transferred to Parakonarus as a new species. P. antarctica is provisionally reverted to Heterotanais, P. mergellinae to Leptochelia, and P. filum is tentatively transferred to Pseudonototanais. Pseudoleptochelia magna is synonymized with P. anomala. Pseudoleptochelia provincialis is tentatively transferred to Parakonarus. Pseudoleptochelia occiporta (females only) is reassigned to Leptochelia; the male of P. occiporta is considered to represent a species of Parakonarus. Pseudoleptocheliajuliae is reassigned to Parakonarus. Konarus, Makraleptochelia, Bassoleptochelia, Parakonarus and Pseudoleptochelia are placed in the new subfamily Konariinae. Generic relationships in this subfamily were confirmed by Principle Components Analysis. Catenarius is placed in the new subfamily Catenariinae.

FLOCK provides reliable solutions to the "number of populations" problem.

Identifying groups of individuals forming coherent genetic clusters is relevant to many fields of biology. This paper addresses the K-partition problem: given a collection of genotypes, partition those genotypes into K groups, each group being a sample of the K source populations that are represented in the collection of genotypes. This problem involves allocating genotypes to genetic groups while building those groups at the same time without the use of any other a priori information. FLOCK is a non-Markov chain Monte Carlo (MCMC) algorithm that uses an iterative method to partition a collection of genotypes into k groups. Rules to estimate K are formulated and their validity firmly established by running simulations under several migration rates, migration regimes, number of loci, and values of K. FLOCK tended to build clusters largely consistent with the source samples. The performance of FLOCK was also compared with that of STRUCTURE and BAPS. FLOCK provided more accurate allocations to clusters and more reliable estimates of K; it also ran much faster than STRUCTURE. FLOCK is based on an entirely novel approach and provides a true alternative to the existing, MCMC based, algorithms. FLOCK v.2.0 for microsatellites or for AFLP markers can be downloaded from http://www.bio.ulaval.ca/no_cache/departement/professeurs/fiche_des_professeurs/professeur/11/13/.

Assessment of hypoxia-inducible factor-1α mRNA expression in mantis shrimp as a biomarker of environmental hypoxia exposure.

Efforts to assess the ecological impacts of the marked increase in coastal hypoxia worldwide have been hampered by a lack of biomarkers of hypoxia exposure in marine benthic organisms. Here, we show that hypoxia-inducible factor-1α (HIF-1α) transcript levels in the heart and cerebral ganglion of mantis shrimp (Oratosquilla oratoria) collected from hypoxic sites in Tokyo Bay are elevated several-fold over those in shrimp collected from normoxic sites. Upregulation of HIF-1α mRNA levels in the heart after exposure to sub-lethal hypoxia was confirmed in controlled laboratory experiments. HIF-1α transcript levels were increased at approximately threefold after 7 and 14 days of hypoxia exposure and declined to control levels within 24 h of restoration to normoxic conditions. The results provide the first evidence for upregulation of HIF-1α transcript levels in two hypoxia-sensitive organs, heart and cerebral ganglion, in a marine invertebrate exposed to environmental hypoxia. These results suggest that upregulation of HIF-1α transcript levels is an important component in adaptation of mantis shrimp to chronic hypoxia and is a potentially useful biomarker of environmental hypoxia exposure.

Additive vs non-additive genetic components in lethal cadmium tolerance of Gammarus (Crustacea): novel light on the assessment of the potential for adaptation to contamination.

Questioning the likelihood that populations adapt to contamination is critical for ecotoxicological risk assessment. The appraisal of genetic variance in chemical sensitivities within populations is currently used to evaluate a priori this evolutionary potential. Nevertheless, conclusions from this approach are questionable since non-additive genetic components in chemical tolerance could limit the response of such complex phenotypic traits to selection. Coupling quantitative genetics with ecotoxicology, this study illustrates how the comparison between cadmium sensitivities among Gammarus siblings enabled discrimination between genetic variance components in chemical tolerance. The results revealed that, whereas genetically determined differences in lethal tolerance exist within the studied population, such differences were not significantly heritable since genetic variance mainly relied on non-additive components. Therefore the potential for genetic adaptation to acute Cd stress appeared to be weak. These outcomes are discussed in regard to previous findings for asexual daphnids, which suggest a strong potency of genetic adaptation to environmental contamination, but which contrast with compiled field observations where adaptation is not the rule. Hereafter, we formulate the reconciling hypothesis of a widespread weakness of additive components in tolerance to contaminants, which needs to be further tested to gain insight into the question of the likelihood of adaptation to contamination.