The Origin of Large-Bodied Shrimp that Dominate Modern Global Aquaculture

Integrase-associated niche differentiation of endogenous large DNA viruses in crustaceans

IMPORTANCE

Crustacean genomes harbor sequences originating from a family of large DNA viruses called nimaviruses, but it is unclear why they are present. We show that endogenous nimaviruses selectively insert into repetitive sequences within the host genome, and this insertion specificity was correlated with different types of integrases, which are DNA recombination enzymes encoded by the nimaviruses themselves. This suggests that endogenous nimaviruses have colonized various genomic niches through the acquisition of integrases with different insertion specificities. Our results point to a novel survival strategy of endogenous large DNA viruses colonizing the host genomes. These findings may clarify the evolution and spread of nimaviruses in crustaceans and lead to measures to control and prevent the spread of pathogenic nimaviruses in aquaculture settings.

ACD-containing chaperones reveal the divergent thermo-tolerance in penaeid shrimp

The α-crystallin domain-containing (ACD-containing) gene family, which includes typical small heat shock proteins (sHSPs), is the most ubiquitous and diverse family of putative chaperones in all organisms, including eukaryotes and prokaryotes. In the present study, approximately 54-117 ACD-containing genes were identified in five penaeid shrimp species, yielding a significant expansion in comparison with other crustaceans (generally 6-20 ACD-containing genes). Unlike typical sHSPs, which contain a single ACD domain, the ACD-containing genes of penaeid shrimp contain additional ACD domains (3-7 domains, in general), thus having a larger molecular weight and a more complex 3D structure. As indicated by the RNA-seq and qRT-PCR results, the ACD-containing genes of penaeid shrimp showed a strong response to high temperatures. Furthermore, heterologous expression and citrate synthase assays of three representative ACD-containing genes confirmed that their chaperone activity could enhance the thermo-tolerance of E. coli and prevent the aggregation of substrate proteins at high temperatures. Compared with penaeid shrimp species with a relatively low thermo-tolerance (Fenneropenaeus chinensis and Marsupenaeus japonicus), the species with high thermo-tolerance (Litopenaeus vannamei and Fenneropenaeus indicus) contained more ACD-containing genes due to tandem duplication and exhibited biased expression levels under high temperatures. This can explain the divergent thermo-tolerance of different penaeid shrimp species. In conclusion, the ACD-containing genes in penaeid shrimp could be assigned as new chaperones and contribute to their divergent thermo-tolerance phenotypes and adaptations to the ecological environment.

Phylogenetic relations and mitogenome-wide similarity metrics reveal monophyly of Penaeus sensu lato

Splitting of the genus Penaeus sensu lato into six new genera based on morphological features alone has been controversial in penaeid shrimp taxonomy. Several studies focused on building phylogenetic relations among the genera of Penaeus sensu lato. However, they lack in utilizing full mitochondrial DNA genome of shrimp representing all the six controversial genera. For the first time, the present study targeted the testing of all the six genera of Penaeus sensu lato for phylogenetic relations utilizing complete mitochondrial genome sequence. In addition, the study reports for the first time about the complete mitochondrial DNA genome sequence of Fenneropenaeus indicus, an important candidate species in aquaculture and fisheries, and utilized it for phylogenomics. The maximum likelihood and Bayesian approaches were deployed to generate and comprehend the phylogenetic relationship among the shrimp in the suborder, Dendrobranchiata. The phylogenetic relations established with limited taxon sampling considered in the study pointed to the monophyly of Penaeus sensu lato and suggested collapsing of the new genera to a single genus. Further, trends in mitogenome-wide estimates of average amino acid identity in the order Decapoda and the genus Penaeus sensu lato supported restoration of the old genus, Penaeus, rather promoting the creation of new genera.

Characterization of the complete mitochondrial genomes of two species of Penaeidae (Decapoda: Dendrobranchiata) and the phylogenetic implications for Penaeoidea

In the present study, mitogenomes of the species Trachypenaeus curvirostris and Parapenaeus fissuroides (Decapoda: Dendrobranchiata: Penaeidae) were sequenced. The total lengths of the two species were 15,956 bp and 15,937 bp in length with A + T biases of 67.08% and 67.69%, respectively. Both two species showed positive AT skews (0.016, 0.058) and negative GC skews (-0.254, -0.310). Both mitogenomes contained 13 protein-coding genes, 22 transfer RNA genes, and 2 ribosomal RNA genes. Results of phylogenetic analyses support close relationships among Aristeidae, Benthesicymidae and Solenoceridae. The family Sicyoniidae was observed to be deeply nested within Penaeidae. Within Penaeidae, T. curvirostris and P. fissuroides were most closely related to the genus Parapenaeopsis and Metapenaeopsis, respectively, indicated that these two species belong to Penaeidae. These results will help to better understand the evolutionary position of Penaeidae and provide reference for further phylogenetic research on Penaeoidea species.

Effects of chlorpyrifos on the crustacean Litopenaeus vannamei

Shrimps can be used as indicators of the quality of aquatic systems exposed to a variety of pollutants. Chlorpyrifos is one of the most common pesticides found in environmental samples. In order to evaluate the effects of chlorpyrifos, adult organisms of Litopenaeus vannamei were exposed to two sublethal concentrations of the pesticide (0.7 and 1.3 μg/L) for four days. The LC₅₀ (96-hours) value was determined and Lipid oxidation levels (LPO) and the activities of catalase (CAT), glutathion peroxidase (GPx), glutathion-S-transferase (GST) were assessed on the muscle, hepatopancreas and gills from the exposed organisms. In addition, inhibition of acetylcholinesterase (AChE) was determined in the brain. LC₅₀ (96-hours) was 2.10 μg/L of chlorpyrifos. Catalase activity and LPO were elevated in the three tissues, whereas a decrease of AChE activities in the brain and an increase of GST activity in the hepatopancreas were observed.

A phylogenomic framework, evolutionary timeline and genomic resources for comparative studies of decapod crustaceans

Comprising over 15 000 living species, decapods (crabs, shrimp and lobsters) are the most instantly recognizable crustaceans, representing a considerable global food source. Although decapod systematics have received much study, limitations of morphological and Sanger sequence data have yet to produce a consensus for higher-level relationships. Here, we introduce a new anchored hybrid enrichment kit for decapod phylogenetics designed from genomic and transcriptomic sequences that we used to capture new high-throughput sequence data from 94 species, including 58 of 179 extant decapod families, and 11 of 12 major lineages. The enrichment kit yields 410 loci (greater than 86 000 bp) conserved across all lineages of Decapoda, more clade-specific molecular data than any prior study. Phylogenomic analyses recover a robust decapod tree of life strongly supporting the monophyly of all infraorders, and monophyly of each of the reptant, 'lobster' and 'crab' groups, with some results supporting pleocyemate monophyly. We show that crown decapods diverged in the Late Ordovician and most crown lineages diverged in the Triassic-Jurassic, highlighting a cryptic Palaeozoic history, and post-extinction diversification. New insights into decapod relationships provide a phylogenomic window into morphology and behaviour, and a basis to rapidly and cheaply expand sampling in this economically and ecologically significant invertebrate clade.

Phylogenetic incongruence and homoplasy in the appendages and bodies of arthropods: why broad character sampling is best

Notwithstanding the rapidly increasing sampling density of molecular sequence data, morphological characters still make an important contribution to our understanding of the evolutionary relationships of arthropod groups. In many clades, characters relating to the number and morphological specialization of appendages are ascribed particular phylogenetic significance and may be preferentially sampled. However, previous studies have shown that partitions of morphological character matrices often imply significantly different phylogenies. Here, we ask whether a similar incongruence is observed in the appendage and non-appendage characters of arthropods. We apply tree length (incongruence length difference, ILD) and tree distance (incongruence relationship difference, IRD) tests to these partitions in an empirical sample of 53 published neontological datasets for arthropods. We find significant incongruence about one time in five: more often than expected, but markedly less often than in previous partition studies. We also find similar levels of homoplasy in limb and non-limb characters, both in terms of internal consistency and consistency relative to molecular trees. Taken together, these findings imply that sampled limb and non-limb characters are of similar phylogenetic utility and quality, and that a total evidence approach to their analysis is preferable.