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Simple Summary: Kanglang white minnow (KWM, Anabarilius grahami), is a typical "3E" (Endangered, Endemic and Economic) fish species in Yunnan-Guizhou Plateau. As one of the traditional "Four Famous Fishes" in Yunnan province, it has become the major local aquaculture species with increasing demand after the success of artificial breeding. However, this economically important fish is highly susceptible to the infection of a parasite ciliate, Ichthyophthirius multifiliis (Ich), during the practical procedure of artificial breeding. To examine the host immune responses to Ich, we divided the experimental fishes into three groups (including control, early-infected stage, and late-infected stage) for transcriptome sequencing to analyze the differentially expressed genes (DEGs) and immune response mechanisms. The notorious parasite Ichthyophthirius multifiliis (Ich) has been recorded worldwide in fish species and causes white spot disease, posing major threats and resulting in severe losses to international fish production. Extensively effective strategies for treating Ich are not available yet, and genetic mechanisms of hosts in response to the parasite are still largely unknown. In this study, we selected Kanglang white minnow (KWM, Anabarilius grahami) to examine its liver transcriptional changes after Ich infection, as white spot disease is one bottleneck problem in exploring this economically important species. We divided the experimental fishes into three groups (control, early-infected, and late-infected) to examine differentially expressed genes (DEGs). A total of 831 DEGs were identified and classified into 128 significantly enriched GO (Gene Ontology) terms and 71 significantly enriched KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways. Most of these terms or pathways were functionally enriched in immunity, inflammatory response, and apoptosis, such as nucleotide-binding oligomerization domain-like (NOD-like) receptor signaling, tumor necrosis factor (TNF) signaling, interleukin-17 (IL-17) signaling, and apoptosis pathways. We also identified 178 putative antimicrobial peptides (AMPs) and AMP precursors based on our previously reported genome assembly of KWM, and revealed that the expressional patterns varied according to different types. In summary, our work reported the first comprehensive transcriptional changes in KWM in response to the exogenous infection of Ich, which would lay a solid foundation for in-depth studies on disease defense or resistant strains selection in this valuable fish. [ABSTRACT FROM AUTHOR]

• rGO network in polymer matrix was easily tuned by the loading of rGO. • Formed rGO network was determined by a facile method. • The anticorrosion mechanism as function of rGO network was investigated. A facile method of measuring electrical conductivity was developed to characterize the formation of rGO network in polymer matrix. The electrical conductivity, barrier and anticorrosion of PVP@rGO/epoxy nanocomposite coating were investigated as function of rGO' loading. When the electrical conductivity sharply increased to be seven orders, it indicated the formation of rGO network in polymer matrix in the loading of 0.75wt%. Furthermore, it also confirmed that although a conducting rGO network could effectively hinder the diffusion of electrolytes, yet it also accelerated corrosion at the interface. This strategy dose not only provide a facile method to determine the formation of rGO network in polymer matrix, but also proposes a new insight about effect of rGO' loading on anticorrosion of polymer coating. [ABSTRACT FROM AUTHOR]

Widely distributing in aquaculture waters, ammonia threatens the survival of orange-spotted grouper (Epinephelus coioides) when its concentration become very high. However, the molecular mechanisms underlying ammonia tolerance in this economically important fish have not been well uncovered. In this work, based on genome resequencing of a natural population of 300 individuals, we performed a genome-wide association study (GWAS) to identify those loci that are associated with the ammonia resistance. Multiple association analysis methods were employed to verify the accuracy and reliability of our GWAS results. A total of 2,783,352 single nucleotide polymorphisms (SNPs) were identified, in which 25 SNPs were determined to be correlated with the ammonia tolerance. Interestingly, more than half of these notable SNPs were clustered on the chromosomes 9 and 16. According to their localization in our genome assembly, we founda total of 7 candidate genes, including complement component 3 (c3), clusterin (clu), SCO-spondin (sspo), carboxypeptidase A6 (cpa6), ephrin type-B receptor 3 (ephb3), plexin A2 (plxna2), and serum/glucocorticoid regulated kinase family member 3 (sgk3). Among them, the sgk3 gene may be critical since it has been reported to activate many ion channels and transporters, suggesting its potential to transport ammonium (NH 4 +) ex vivo for decreasing ammonia toxicity. The SNPs in this study therefore provide valuable foundation for future marker-assisted selection, which may improve ammonia tolerance to breed high-quality orange-spotted grouper and other fish species. • GWAS with both MLM and FarmCPU was used to identify SNPs associated with ammonia tolerance in orange-spotted grouper. • We identified 25 ammonia-resistant SNPs and 7 candidate genes, and sgk3 gene may be involved in ammonia excretion. • This study will provide valuable genomic resources for future marker-assisted selection. [ABSTRACT FROM AUTHOR]

Simple Summary: Mudskippers are important ecological components of intertidal ecosystems. It was proposed that their guts may play significant roles for terrestrial adaptations of these amphibious fishes. However, their gastrointestinal components and differences in microbiota with other vertebrates were never reported. Here, we performed a comparative metagenome analysis among various vertebrate groups, classified by living habitats and feeding habits, and also acquired microbial gene catalogs of five common fish species. Our findings confirmed the dominant microbial genera in each vertebrate group, as well as bacteriocin-related genes in the five common fish species, for discussion of their relationships with fish pathogenic diseases. Our big data will support in-depth investigations into potential roles of gastrointestinal microbiota to hosts and related applications in aquaculture practices. Gut microbiomes in various fish species were widely investigated with the rapid development of next-generation sequencing technologies. However, little is known about gastrointestinal (GI) microbial communities in mudskippers, a representative group of marine amphibious fishes, and their comparisons with other vertebrate animals from different habitats. Here, we performed a comprehensive analysis on microbial composition in five representative vertebrate groups (including amphibious mudskippers, marine and freshwater aquatic fishes, amphibians, and terrestrial animals) via operational taxonomic unit (OTU) survey and obtained a microbial gene catalog of five common fish species by metagenome sequencing. We observed that Cyanobacteria, Proteobacteria, Firmicutes, Bacteroidetes, and Fusobacteria were the most substantial bacteria in mudskippers. Differential variances in composition patterns of GI microbiota among the vertebrate groups were determined, although Proteobacteria and Firmicutes were the shared phyla with high abundance. In addition, Cetobacterium and Photobacterium were the most abundant genera in core OTUs of these examined omnivores, carnivores, and herbivores. Our metagenomic analysis also showed significant differences between the representative blue-spotted mudskipper and grass carp (both are herbivorous fishes) in microbes at the phylum and class levels and functional gene terms. Moreover, several bacteriocin-related genes were identified in the five common fishes, suggesting their potential contributions to pathogen resistance. In summary, our present work not only sheds new light on the correlation of GI microbiota composition with living habitats and feeding habits of the hosts, but also provides valuable bacterial genetic resources for healthy growth of aquaculture fishes. [ABSTRACT FROM AUTHOR]

Many Viola plants growing in mining areas exhibit high levels of cadmium (Cd) tolerance and accumulation, and thus are ideal organisms for comparative studies on molecular mechanisms of Cd hyperaccumulation. However, transcriptomic studies of hyperaccumulative plants in Violaceae are rare. Viola baoshanensis is an amazing Cd hyperaccumulator in metalliferous areas of China, whereas its relative V. inconspicua is a non-tolerant accumulator that resides at non-metalliferous sites. Here, comparative studies by transcriptome sequencing were performed to investigate the key pathways that are potentially responsible for the differential levels of Cd tolerance between these two Viola species. A cascade of genes involved in the ubiquitin proteosome system (UPS) pathway were observed to have constitutively higher transcription levels and more activation in response to Cd exposure in V. baoshanensis, implying that the enhanced degradation of misfolded proteins may lead to high resistance against Cd in this hyperaccumulator. Many genes related to sucrose metabolism, especially those involved in callose and trehalose biosynthesis, are among the most differentially expressed genes between the two Viola species, suggesting a crucial role of sucrose metabolism not only in cell wall modification through carbon supply but also in the antioxidant system as signaling molecules or antioxidants. A comparison among transcriptional patterns of some known transporters revealed that several tonoplast transporters are up-regulated in V. baoshanensis under Cd stress, suggesting more efficient compartmentalization of Cd in the vacuoles. Taken together, our findings provide valuable insight into Cd hypertolerance in V. baoshanensis, and the corresponding molecular mechanisms will be useful for future genetic engineering in phytoremediation. [ABSTRACT FROM AUTHOR]

Serotonin is a neurotransmitter involved in various physiological processes in the central and peripheral nervous systems. Serotonin is also a precursor for melatonin biosynthesis, which mainly occurs in the pineal gland of vertebrates. Tryptophan hydroxylase (TPH) acts as the rate-limiting enzyme in serotonin biosynthesis and is the initial enzyme involved in the synthesis of melatonin. Recently, two enzymes—TPH1 and TPH2—were reported to form the TPH family in vertebrates and to play divergent roles in serotonergic systems. Here, we examined the evolution of the TPH family from 70 vertebrate genomes. Based on the sequence similarity, we extracted 184 predicted tph homologs in the examined vertebrates. A phylogenetic tree, constructed on the basis of these protein sequences, indicated that tph genes could be divided into two main clades (tph1 and tph2), and that the two clades were further split into two subgroups of tetrapods and Actinopterygii. In tetrapods, and some basal non-teleost ray-finned fishes, only two tph isotypes exist. Notably, tph1 in most teleosts that had undergone the teleost-specific genome duplication could be further divided into tph1a and tph1b. Moreover, protein sequence comparisons indicated that TPH protein changes among vertebrates were concentrated at the NH2-terminal. The tertiary structures of TPH1 and TPH2 revealed obvious differences in the structural elements. Five positively selected sites were characterized in TPH2 compared with TPH1; these sites may reflect the functional divergence in enzyme activity and substrate specificity. In summary, our current work provides novel insights into the evolution of tph genes in vertebrates from a comprehensive genomic perspective. [ABSTRACT FROM AUTHOR]

Naturally derived toxins from animals are good raw materials for drug development. As a representative venomous teleost, Chinese yellow catfish (Pelteobagrus fulvidraco) can provide valuable resources for studies on toxin genes. Its venom glands are located in the pectoral and dorsal fins. Although with such interesting biologic traits and great value in economy, Chinese yellow catfish is still lacking a sequenced genome. Here, we report a high-quality genome assembly of Chinese yellow catfish using a combination of next-generation Illumina and third-generation PacBio sequencing platforms. The final assembly reached 714 Mb, with a contig N50 of 970 kb and a scaffold N50 of 3.65 Mb, respectively. We also annotated 21,562 protein-coding genes, in which 97.59% were assigned at least one functional annotation. Based on the genome sequence, we analyzed toxin genes in Chinese yellow catfish. Finally, we identified 207 toxin genes and classified them into three major groups. Interestingly, we also expanded a previously reported sex-related region (to ≈6 Mb) in the achieved genome assembly, and localized two important toxin genes within this region. In summary, we assembled a high-quality genome of Chinese yellow catfish and performed high-throughput identification of toxin genes from a genomic view. Therefore, the limited number of toxin sequences in public databases will be remarkably improved once we integrate multi-omics data from more and more sequenced species. [ABSTRACT FROM AUTHOR]

Previous phylogenetic analyses of the Chinese sisorid catfishes have either been poorly resolved or have not included all the 12 sisorid genera. Here, we successfully assembled the first complete mitochondrial genome of the sisorid fish Glyptothorax macromaculatus. Based on this novel mitochondrial genome and previously published mitochondrial genomes in the Sisoridae, we generated maximum likelihood and Bayesian phylogenies. We dated our preferred topology using fossil calibration points. We also tested the protein-coding genes in the mitochondrial genomes of the glyptosternoid fishes for signals of natural selection by comparing the nucleotide substitution rate along the branch ancestral to the glyptosternoid fishes to other branches in our topology. The mitochondrial sequence structure of G. macromaculatus was similar to those known from other vertebrates, with some slight differences. Our sisorid phylogenies were well-resolved and well-supported, with exact congruence between the different phylogenetic methods. This robust phylogeny clarified the relationships among the Chinese sisorid genera and strongly supported the division of the family into three main clades. Interestingly, the glyptosternoid divergence time predicted by our molecular dating analysis coincided with the uplift of the Tibetan Plateau, suggesting that geology may have influenced speciation in the Sisoridae. Among the mitochondrial protein-coding genes, atp8 may have most rapidly evolved, and atp6 may have been subjected to positive selection pressure to adapt to high elevations. In summary, this study provided novel insights into the phylogeny, evolution and high-altitude adaptions of the Chinese sisorid fishes. [ABSTRACT FROM AUTHOR]

In our previous work, we reported comparative genomics studies on 3Sinocyclocheilusfishes, including the surface-dwellingS. graham(Sg), the semi-cave-dewllingS. rhinocerous(Sr) and the cave-restrictedS. anshuiensis(Sa). Here, we performed a genomic survey on the immunity differences among the 3 fishes by combination of the genome and transcriptome data. Our results demonstrate that immune-related genetic pathways in Sa and Sr present more similarities than Sg. The innate immune activity in Sa seems to be higher than Sg and Sr, while Sr owns more copy numbers of MHC-related genes (related with the acquired immune system) than Sg and Sa. These differential immune activities in the 3Sinocyclocheilusspecies may be due to their differential habitats. Generally speaking, most immunity genes transcribe the lowest levels in Sa when compared with Sg and Sr, which may be associate with a less various microbial environment in the cave-restricted habitat. However, Sr has more members of MHC-related genes than those in Sg and Sa, suggesting a great contribution from the semi-cave-dwelling condition. [ABSTRACT FROM PUBLISHER]

A correction to the article “The genome sequence of the orchid Phalaenopsis equestris" that was published online on November 24, 2014 is presented.