Detecting selection in the blue crab, Callinectes sapidus, using DNA sequence data from multiple nuclear protein-coding genes

Nematode gene annotation by machine-learning-assisted proteotranscriptomics enables proteome-wide evolutionary analysis

Nematodes encompass more than 24,000 described species, which were discovered in almost every ecological habitat, and make up >80% of metazoan taxonomic diversity in soils. The last common ancestor of nematodes is believed to date back to ∼650-750 million years, generating a large and phylogenetically diverse group to be explored. However, for most species high-quality gene annotations are incomprehensive or missing. Combining short-read RNA sequencing with mass spectrometry-based proteomics and machine-learning quality control in an approach called proteotranscriptomics, we improve gene annotations for nine genome-sequenced nematode species and provide new gene annotations for three additional species without genome assemblies. Emphasizing the sensitivity of our methodology, we provide evidence for two hitherto undescribed genes in the model organism Caenorhabditis elegans Extensive phylogenetic systems analysis using this comprehensive proteome annotation provides new insights into evolutionary processes of this metazoan group.

Regulatory function of the trehalose-6-phosphate synthase gene TPS3 on chitin metabolism in brown planthopper, Nilaparvata lugens

Brown planthopper (Nilaparvata lugens) is one of the important pests that damage rice. Trehalose-6-phosphate synthase (TPS) is a key enzyme responsible for catalysing the biosynthesis of trehalose, which is the energy substance of insects. In this study, combined with the reported N. lugens TPS1, TPS2 and newly discovered TPS3, we studied the regulation of TPS in chitin metabolism by RNA interference. Firstly, we found that the relative expression levels of TRE1-1, TRE1-2 and TRE2 increased significantly after 48 h of dsTPS3 injection, and the activity of TRE1 enhanced significantly. Secondly, abnormal and lethal phenotypes were observed after dsTPS3 and dsTPSs injection. The relative expression levels of PGM2, G6PI2, Cht1-4, Cht6-10 and IDGF decreased significantly after 48 h of dsTPS3 injection. At 72 h after injection of dsTPS3, the relative expression levels of CHS1, Cht2, Cht4, Cht7 and Cht8 reduced significantly, but the expression levels of G6PI1, Cht5 and ENGase increased significantly. The relative expression levels of GFAT, UAP, PGM2, G6PI2, CHS1, CHS1a, CHS1b, Cht2, Cht4, Cht8, Cht9 and Cht10 decreased significantly after 48 h of dsTPSs injection. However, at 72 h after the injection of dsTPSs, the expression levels of GNPNA, UAP, PGM1, G6PI1, HK, CHS1, CHS1a, CHS1b, Cht3, Cht5, Cht7 and ENGase increased significantly. Finally, the chitin content decreased in dsTPS1, dsTPS2 and dsTPSs treatments. In conclusion, the inhibition of TPS expression affected the metabolism of trehalose and chitin in N. lugens. The related research results provide a theoretical basis for pest control.

Population genetics and historical demographic inferences of the blue crab Callinectes sapidus in the US based on microsatellites

The native range of the blue crab Callinectes sapidus spans Nova Scotia to northern Argentina. In the US, it constitutes a keystone species in estuarine habitats of the Atlantic coast and Gulf of Mexico (GOM), serving as both predator and prey to other species, and also has historically represented a multi-billion dollar fishery. Knowledge relevant to effective management and monitoring of this ecologically and economically important species, such as levels of population genetic differentiation and genetic diversity, is necessary. Although several population genetics studies have attempted to address these questions in one or more parts of its distribution, conflicting results and potential problems with the markers used, as well as other issues, have obscured our understanding on them. In this study, we examined large-scale genetic connectivity of the blue crab in the US, using 16 microsatellites, and genotyped individuals from Chesapeake Bay, in the US Atlantic, and from nine localities along the US GOM coast. Consistent with the high long-distance dispersal potential of this species, very low levels of genetic differentiation were detected for the blue crab among the ten US localities examined, suggesting it constitutes a large panmictic population within this region. Estimations of genetic diversity for the blue crab appear to be high in the US, and provide a baseline for monitoring temporal changes in this species. Demographic analyses indicate a recent range expansion of the US population, probably during the Holocene. In addition, capitalizing on published microsatellite data from southern Brazil, our analyses detected high genetic differentiation between localities in the US and Brazil. These results point to the need for examination of genetic diversity and differentiation along the area spanning the US to southern Brazil.

Invertebrate Trehalose-6-Phosphate Synthase Gene: Genetic Architecture, Biochemistry, Physiological Function, and Potential Applications

The non-reducing disaccharide trehalose is widely distributed among various organisms. It plays a crucial role as an instant source of energy, being the major blood sugar in insects. In addition, it helps countering abiotic stresses. Trehalose synthesis in insects and other invertebrates is thought to occur via the trehalose-6-phosphate synthase (TPS) and trehalose-6-phosphate phosphatase (TPP) pathways. In many insects, the TPP gene has not been identified, whereas multiple TPS genes that encode proteins harboring TPS/OtsA and TPP/OtsB conserved domains have been found and cloned in the same species. The function of the TPS gene in insects and other invertebrates has not been reviewed in depth, and the available information is quite fragmented. The present review discusses the current understanding of the trehalose synthesis pathway, TPS genetic architecture, biochemistry, physiological function, and potential sensitivity to insecticides. We note the variability in the number of TPS genes in different invertebrate species, consider whether trehalose synthesis may rely only on the TPS gene, and discuss the results of in vitro TPS overexpression experiment. Tissue expression profile and developmental characteristics of the TPS gene indicate that it is important in energy production, growth and development, metamorphosis, stress recovery, chitin synthesis, insect flight, and other biological processes. We highlight the molecular and biochemical properties of insect TPS that make it a suitable target of potential pest control inhibitors. The application of trehalose synthesis inhibitors is a promising direction in insect pest control because vertebrates do not synthesize trehalose; therefore, TPS inhibitors would be relatively safe for humans and higher animals, making them ideal insecticidal agents without off-target effects.

The Atlantic blue crab Callinectes sapidus in southern European coastal waters: Distribution, impact and prospective invasion management strategies

The native distribution of the blue crab Callinectes sapidus in the western Atlantic extends from Nova Scotia to Argentina. Introduced to Europe at the beginning of the 20th century, it is currently recorded almost ubiquitously in the Mediterranean and in the Black Sea. An overview of the occurrence, abundance, and ecological impact of the species in southern European waters is provided; additionally, we present a pragmatic assessment of its management scenarios, explicitly considering the dual nature of C. sapidus as both an invasive species and a fishery resource. We emphasise that the ongoing expansion of C. sapidus in the region may represent a stimulating challenge for the identification and implementation of future strategies in the management of invasive crustaceans. The impact of the invader could be converted into an enhancement of the services delivered by southern European coastal ecosystems, while mitigation costs could be transformed into profits for local populations.

The Atlantic blue crab Callinectes sapidus in southern European coastal waters: Distribution, impact and prospective invasion management strategies

The native distribution of the blue crab Callinectes sapidus in the western Atlantic extends from Nova Scotia to Argentina. Introduced to Europe at the beginning of the 20th century, it is currently recorded almost ubiquitously in the Mediterranean and in the Black Sea. An overview of the occurrence, abundance, and ecological impact of the species in southern European waters is provided; additionally, we present a pragmatic assessment of its management scenarios, explicitly considering the dual nature of C. sapidus as both an invasive species and a fishery resource. We emphasise that the ongoing expansion of C. sapidus in the region may represent a stimulating challenge for the identification and implementation of future strategies in the management of invasive crustaceans. The impact of the invader could be converted into an enhancement of the services delivered by southern European coastal ecosystems, while mitigation costs could be transformed into profits for local populations.

Genetic load in marine animals: a review

Marine invertebrates and fish are well known for their remarkable genetic diversity, which is commonly explained by large population size and the characteristic dispersive nature of their early, planktonic life history. Other potential sources of diversity in marine animals, such as a higher mutation rate, have been much less considered, though evidence for a high genetic load in marine bivalves has been accumulating for nearly half a century. In this review, I examine evidence for a higher genetic load in marine animals from studies of molecular marker segregation and linkage over the last 40 years, and survey recent work examining mutational load with molecular evolution approaches. Overall, marine animals appear to have higher genetic load than terrestrial animals (higher dn/ds ratios, inbreeding load, and segregation dis`tortion), though results are mixed for marine fish and data are lacking for many marine animal groups. Bivalves (oysters) have the highest loads observed among marine animals, comparable only to long-lived plants; however, more data is needed from other bivalves and more marine invertebrate taxa generally. For oysters, a higher load may be related to a chronically lower effective population size that, in concert with a higher mutational rate, elevate the number of deleterious mutations observed. I suggest that future studies use high-throughput sequencing approaches to examine (1) polymorphism in genome-scale datasets across a wider range of marine animals at the population level and (2) intergenerational mutational changes between parents and offspring in crosses of aquaculture species to quantify mutation rates.

Population dynamics of Anopheles nuneztovari in Colombia

Anopheles nuneztovari is an important Colombian malaria vector widespread on both sides of the Andean Mountains, presenting morphological, behavioral and genetic heterogeneity throughout the country. The aim of this study was to evaluate whether the population structure and distribution of An. nuneztovari in Colombia are associated with ecological and physical barriers present in a heterogeneous landscape. Further, differences in behavior were addressed. A total of 5392 specimens of An. nuneztovari were collected. Mitochondrial and nuclear marker analyses detected subdivision among the northwest-west, northeast and east populations. For both markers, isolation by distance (~53%) and isolation by resistance (>30%) were determinants of population genetic differentiation. This suggests that physical barriers, geographical distance and ecological differences on both sides of the Andean Mountains promoted the genetic differentiation and population subdivision of An. nuneztovari in Colombia. This species showed the highest biting activity after 20:00h; indoor and outdoor preferences were found in all localities. These results indicated that the most effective interventions for controlling vector populations on both sides of the Andes need to be region-specific.

Behavior and population structure of Anopheles darlingi in Colombia

Anopheles darlingi is a widely distributed and important malaria vector in Colombia. Biogeographical and ecological heterogeneity across the Colombian distribution led to the hypothesis of behavioral and genetic differentiation among A. darlingi populations. A total of 2017 A. darlingi specimens were collected during 222 h of sampling. This vector was the most abundant anopheline species in most of the localities sampled. Subdivision between samples collected west and east of the Andes was indicated by 1) mitochondrial COI and nuclear CAD sequences from NW-W and CE-S populations (COI ΦST=0.48761-0.81974, CAD FST=0.11319-0.21321), 2) a COI haplotype network, and 3) SAMOVA. Endo- and exophagy were detected in populations west of the Andes, whereas exophagy was evident in PTG, a locality east of the Andes. Isolation by resistance was significant for COI and explained 26% of the genetic differentiation. We suggest that at a macrogeographic scale, the Andes influence the differentiation of A. darlingi in Colombia and may drive divergence, and, at a microgeographic scale, ecological differences have a significant impact on structure. These data could constitute a baseline for the design of effective vector interventions, locality-specific for the east and similar for panmictic populations west of the Andes.

De novo assembly of a transcriptome from juvenile blue crabs (Callinectes sapidus) following exposure to surrogate Macondo crude oil

Background

The blue crab, Callinectes sapidus, is economically and ecologically important in western Atlantic and Gulf of Mexico coastal estuaries. In 2010 blue crabs in the northern Gulf of Mexico were exposed to crude oil and chemical dispersants from the Deepwater Horizon oil spill. To characterize the blue crab transcriptome and identify genes that could be regulated in response to oil exposure we sequenced transcriptomes from hepatopancreas and gill tissues of juvenile blue crabs after exposing them to a water-accommodated fraction of surrogate Macondo crude oil in the laboratory and compared them to transcriptomes from an unexposed control group.

Results

Illumina sequencing provided 42.5 million paired-end sequencing reads for the control group and 44.9 million paired-end reads for the treatment group. From these, 73,473 transcripts and 52,663 genes were assembled. Comparison of control and treatment transcriptomes revealed about 100 genes from each tissue type that were differentially expressed. However, a much larger number of transcripts, approximately 2000 from each tissue type, were differentially expressed. Several examples of alternatively spliced transcripts were verified by qPCR, some of which showed significantly different expression patterns. The combined transcriptome from all tissues and individuals was annotated to assign putative gene products to both major gene ontology categories as well as specific roles in responses to cold and heat, metabolism of xenobiotic compounds, defence, hypoxia, osmoregulation and ecdysis. Among the annotations for upregulated and alternatively-spliced genes were candidates for the metabolism of oil-derived compounds.

Conclusions

Previously, few genomic resources were available for blue crabs or related brachyuran crabs. The transcriptome sequences reported here represent a major new resource for research on the biology of blue crabs. These sequences can be used for studies of differential gene expression or as a source of genetic markers. Genes identified and annotated in this study include candidates for responses of the blue crab to xenobiotic compounds, which could serve as biomarkers for oil exposure. Changes in gene expression also suggest other physiological changes that may occur as the result of exposure to oil.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1739-2) contains supplementary material, which is available to authorized users.