The liver transcriptome of suckermouth armoured catfish (Pterygoplichthys anisitsi, Loricariidae): Identification of expansions in defensome gene families

A prototype of the mammalian sulfotransferase 1 (SULT1) family in Xenopus laevis: Characterization of a biased usage of SULT1 genes located in the S-subgenome

BLAST searches previously carried out against Xenopus genome databases, using the cloned X. laevis cytosolic sulfotransferase 1 (SULT1) cDNA sequence, revealed the presence of more than a dozen members of this gene family. Among them, 11 genes composed of five sets, four pairs and a triplet, were homeologous genes in the X. laevis allotetraploid genome consisting of S- and L-subgenomes (≥83% identity within a set). Phylogenetic and synteny analyses of tetrapod SULT1 genes demonstrated that X. laevis possessed six subfamilies, four of which were related to mammalian SULT1 gene subfamilies, while two were ectothermic vertebrate-specific and amphibian-specific SULT1 gene subfamilies. Five sets of homeologous SULT1 genes were located as a gene cluster, and showed S-subgenome-biased gene expression patterns. Acetylation levels of histone H3 at lysine 9 and H4 were also higher in the homeologous SULT1 genes on the S-subgenome than those on the L-subgenome, however, methylation levels of histone H3 at lysine 9 and DNA methylation levels showed no correlation with their transcript levels. In conclusion, histone modifications such as acetylation may be a key factor that controls the S-subgenome-biased expression of the homeologous SULT1 genes.

Comparative analysis of the mitogenomes of two Corydoras (Siluriformes, Loricarioidei) with nine known Corydoras, and a phylogenetic analysis of Loricarioidei

Corydoras is a speciose catfish genus from South America with widely investigated phylogenetic and evolutionary relationships. The complete mitogenomes of C. aeneus and C. paleatus were sequenced, assembled, and annotated using next-generation sequencing. The genome arrangements, gene contents, genome structures, base compositions, evolutionary features, codon usage, and tRNA structures of the two mitogenomes were compared and analyzed with nine published mitogenomes of Corydoras. Phylogenetic analysis was performed using concatenated nucleotide sequences with 13 protein-coding genes and two rRNAs with 44 mitogenomes of Siluriformes. These results provide information on the mitogenomes of eleven Corydoras species and evolutionary relationships within the suborder Loricarioidei, which may be applicable for further phylogenetic and taxonomic studies on Siluriformes and Loricarioidei.

On the reproductive biology of the invasive Armoured Sailfin Catfish Pterygoplicthys pardalis (Castelnau, 1855) (Siluriformes: Loricariidae) from the natural drainages in Thiruvananthapuram, India

The present paper deals with the breeding biology of the invasive fish Pterygoplicthys pardalis from the natural drainages of Thiruvananthapuram, Kerala. The specimens were collected from Amayizhanchan Thodu, a natural drainage running through the heart of the city. A total of 145 males and 142 females were collected from January to December 2018. The sex ratio was determined monthly as the percentage of males to females (M: F). Monthly mean gonadosomatic index (GSI) values were compared using R stat, and GSI was plotted monthly to identify the spawning seasons. The gonads were examined and different stages of maturity were noted using standard methods. The length at first maturity was also found out. The fish exhibit courtship behaviour and the eggs are deposited in burrows and also along the crevices in the granite walls; the burrows are guarded by the male fish till the young ones are hatched out. The sex ratio showed an average mean value of 1.04: 1 and showed no significant departure. The size at first maturity was 23.9 cm standard length. The ova diameter studies show the presence of ripe ovaries throughout the year, with peaks during March and April and between August and September and in December, indicating the fish is a batch spawner. The absolute fecundity ranges from 923 to 14,777 eggs, and the relative fecundity ranges 0.0142–0.0015. Regression analysis showed a significant relationship (P <0.001) between absolute fecundity and the total length, the total body weight, and ovary weight. The strong breeding behaviour, the presence of accessory respiratory organs, the absence of natural enemies and parental care makes Pterygoplichthys pardalis a successful invader in the natural drainage. More biological studies are needed for the successful eradication of the species from the invaded ecosystem. 

A prototype of the mammalian sulfotransferase 1 (SULT1) family in Xenopus laevis: molecular and enzymatic properties of XlSULT1B.S

The cytosolic sulfotransferase 1 (SULT1) proteins are a family of highly divergent proteins that show variable expansion in different species during vertebrate evolution. To clarify the evolutionary origin of the mammalian lineage of the SULT1 family, we compiled Xenopus laevis and X. tropicalis SULT1 (XSULT1) sequences from public databases. The XSULT1 family was found to comprise at least six subfamilies, which corresponded in part to five mammalian SULT1 subfamilies but only poorly to zebrafish SULT1 subfamilies. SULT1C was most highly expanded, and could be divided into at least five subfamilies. A cDNA for X. laevis SULT1B (XlSULT1B.S), a homolog of mammalian SULT1B1, was cloned and its recombinant protein was expressed in a bacterial system. XlSULT1B.S, unlike mammalian SULT1B1, was found to be a monomeric protein of ~34 kDa, and displayed sulfonating activity toward 2-naphthol and p-nitrophenol (pNP). However, we could not detect such sulfonating activity toward any endogenous compounds including thyroid hormones, steroid hormones and dopamine, despite the fact that X. laevis and Rana catesbeiana liver cytosols contained sulfonating activity toward most of these endogenous compounds. At optimum pH (6.4), the Michaelis-Menten constant (K_m) for pNP was two orders of magnitude greater in XlSULT1B.S (1.04 mM) than in the cytosol preparations (8-15 μM). Our results indicate that Xenopus possesses a prototype of the mammalian SULT1 family, and that XlSULT1B.S showed overall similarities in primary sequence to, and significant differences in molecular and enzymatic properties from, mammalian SULT1B1.

Characterization of the Aryl Hydrocarbon Receptor (AhR) Pathway in Anabas testudineus and Mechanistic Exploration of the Reduced Sensitivity of AhR2a

Field investigations have revealed the ability of the climbing perch Anabas testudineus to survive in highly contaminated water bodies. The aryl hydrocarbon receptor (AhR) pathway is vital in mediating the toxicity of aromatic hydrocarbon contaminants, and genotypic variation in the AhR can confer resistance to these contaminants. Thus, we characterized the AhR pathway in A. testudineus in order to understand the mechanism(s) underlying the resistance of this species to contaminants and to broaden current knowledge on teleost AhR. In A. testudineus, four AhRs, two AhR nuclear translocators (ARNTs), and one AhR repressor (AhRR) were found. Transient transfection assays revealed that AhR1a, AhR1b, and AhR2b were functional, whereas AhR2a was poorly activated by the potent agonist 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). Two ARNTs (partner of AhR) and one AhRR (repressor of AhR) all were functional with each of the active AhR. As a major form, the insensitivity of AhR2a might serve as a potential mechanism for A. testudineus' reduced sensitivity to severe contamination. We explored the key residues that may account for AhR2a's insensitivity in silico and then functionally validated them in vitro. Two sites (VCS_322-324, M₃₇₀) in its ligand-binding domain (LBD) were proved critical for its sensitivity to TCDD. This systematic exploration of the AhR pathway showed that most members have maintained their traditional functions as expected, whereas a nonfunctionalization event has occurred for AhR2a.

Development of SNVs and indels markers mined out of the first multi-organ transcriptomes from Hypancistrus zebra (Loricariidae), an endangered Amazonian catfish

Hypancistrus zebra is a catfish, endemic from the Xingu River, threatened with extinction due to the impacts of Belo Monte dam, of its illegal capture, of gold mining activities and of climate change. Currently, there are three nucleotide sequences from this species in GenBank, what impedes the development of genetic markers to assist on its conservation. A total of 217 million RNA-Seq reads from seven organs were sequenced and used to assemble 566,607 transcripts, including 98% of BUSCO vertebrates orthologs, 11,321 transcripts with SNVs and 1,724 transcripts with indels. Three transcripts with SNVs and five transcripts with indels were validated as the best candidate markers to conservation practices. This work illustrates the use of transcriptomics in conservation, by the development of a bigger toolbox for an endangered fish, and shall further contribute to studies on this and others related species reproduction, physiology, and adaptability to environmental changes.

Transcriptomic analysis of Anabas testudineus and its defensive mechanisms in response to persistent organic pollutants exposure

The freshwater climbing perch (Anabas testudineus) can tolerate water environments contaminated with persistent organic pollutants (POPs). The mechanisms underlying this tolerance are unknown. We used de novo transcriptomic analysis to investigate the defensive mechanisms of A. testudineus against POPs based on its genetic features and biological responses to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) exposure. Our results revealed a specific expansion of cytochrome P450 (CYP) 3A subfamily, which may be involved in the elimination of certain POPs. In xenobiotic responses, the aryl-hydrocarbon receptor (AhR) pathway represents a critical signaling mechanism, and we characterized four AhR and two AhR nuclear translocator homologs and one AhR repressor (AhRR) gene in A. testudineus. TCDD-induced AhRR and CYP1A mRNA upregulation suggests that negative-feedback regulation of AhR signaling through AhRR helps avoid excessive xenobiotic responses. Furthermore, liver and gill transcriptomic profiles were markedly altered after TCDD exposure, with some of the altered genes being related to common defensive responses reported in other species. Based on the newly identified TCDD-altered genes, several A. testudineus-specific responses are proposed, such as enhanced fatty acid β-oxidation. The genetic features of CYP3A subfamily and AhR pathway and the TCDD-induced defensive biological processes elucidated here enhance our understanding of A. testudineus defensive responses against POPs.

Biological Entanglement-Like Effect After Communication of Fish Prior to X-Ray Exposure

The phenomenon by which irradiated organisms including cells in vitro communicate with unirradiated neighbors is well established in biology as the radiation-induced bystander effect (RIBE). Generally, the purpose of this communication is thought to be protective and adaptive, reflecting a highly conserved evolutionary mechanism enabling rapid adjustment to stressors in the environment. Stressors known to induce the effect were recently shown to include chemicals and even pathological agents. The mechanism is unknown but our group has evidence that physical signals such as biophotons acting on cellular photoreceptors may be implicated. This raises the question of whether quantum biological processes may occur as have been demonstrated in plant photosynthesis. To test this hypothesis, we decided to see whether any form of entanglement was operational in the system. Fish from 2 completely separate locations were allowed to meet for 2 hours either before or after which fish from 1 location only (group A fish) were irradiated. The results confirm RIBE signal production in both skin and gill of fish, meeting both before and after irradiation of group A fish. The proteomic analysis revealed that direct irradiation resulted in pro-tumorigenic proteomic responses in rainbow trout. However, communication from these irradiated fish, both before and after they had been exposed to a 0.5 Gy X-ray dose, resulted in largely beneficial proteomic responses in completely nonirradiated trout. The results suggest that some form of anticipation of a stressor may occur leading to a preconditioning effect or temporally displaced awareness after the fish become entangled.

Reducing the information gap on Loricarioidei (Siluriformes) mitochondrial genomics

Background

The genetic diversity of Neotropical fish fauna is underrepresented in public databases. This distortion is evident for the order Siluriformes, in which the suborders Siluroidei and Loricarioidei share equivalent proportion of species, although far less is known about the genetics of the latter clade, endemic to the Neotropical Region. Recently, this information gap was evident in a study about the structural diversity of fish mitochondrial genomes, and hampered a precise chronological resolution of Siluriformes. It has also prevented molecular ecology investigations about these catfishes, their interactions with the environment, responses to anthropogenic changes and potential uses.

Results

Using high-throughput sequencing, we provide the nearly complete mitochondrial genomes for 26 Loricariidae and one Callichthyidae species. Structural features were highly conserved. A notable exception was identified in the monophyletic clade comprising species of the Hemiancistrus, Hypostomini and Peckoltia-clades, a ~60 nucleotide-long deletion encompassing the seven nucleotides at the 3′ end of the Conserved Sequence Block (CSB) D of the control region. The expression of mitochondrial genes followed the usual punctuation pattern. Heteroplasmic sites were identified in most species. The retrieved phylogeny strongly corroborates the currently accepted tree, although bringing to debate the relationship between Schizolecis guntheri and Pareiorhaphis garbei, and highlighting the low genetic variability within the Peckoltia-clade, an eco-morphologically diverse and taxonomically problematic group.

Conclusions

Herein we have launched the use of high-throughput mitochondrial genomics in the studies of the Loricarioidei species. The new genomic resources reduce the information gap on the molecular diversity of Neotropical fish fauna, impacting the capacity to investigate a variety of aspects of the molecular ecology and evolution of these fishes. Additionally, the species showing the partial CSB-D are candidate models to study the replication and transcription of vertebrate mitochondrial genome.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-3709-3) contains supplementary material, which is available to authorized users.