Visual Omics: a web-based platform for omics data analysis and visualization with rich graph-tuning capabilities.

SUMMARY: With the continuous development of high-throughput sequencing technology, bioinformatic analysis of omics data plays an increasingly important role in life science research. Many R packages are widely used for omics analysis, such as DESeq2, clusterProfiler and STRINGdb. And some online tools based on them have been developed to free bench scientists from programming with these R packages. However, the charts generated by these tools are usually in a fixed, non-editable format and often fail to clearly demonstrate the details the researchers intend to express. To address these issues, we have created Visual Omics, an online tool for omics data analysis and scientific chart editing. Visual Omics integrates multiple omics analyses which include differential expression analysis, enrichment analysis, protein domain prediction and protein-protein interaction analysis with extensive graph presentations. It can also independently plot and customize basic charts that are involved in omics analysis, such as various PCA/PCoA plots, bar plots, box plots, heat maps, set intersection diagrams, bubble charts and volcano plots. A distinguishing feature of Visual Omics is that it allows users to perform one-stop omics data analyses without programming, iteratively explore the form and layout of graphs online and fine-tune parameters to generate charts that meet publication requirements. AVAILABILITY AND IMPLEMENTATION: Visual Omics can be used at http://bioinfo.ihb.ac.cn/visomics. Source code can be downloaded at http://bioinfo.ihb.ac.cn/software/visomics/visomics-1.1.tar.gz. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Transcriptome analysis revealed the existence of family-specific regulation of growth traits in grass carp.

The grass carp (Ctenopharyngodon idella) is the world's most prolific freshwater fish. Little is known, however, about the functional genes and genetic regulatory networks that govern its growth traits. We created three grass carp families in this study by using two grass carp parents with fast-growing offspring and two grass carp parents with slow-growing offspring, namely the fast-growing × fast-growing family (FF), the slow-growing × slow-growing family (SS), and the fast-growing × slow-growing family (FS). Under the satiation and starvation feeding modes, the average body weight of these families' offspring exhibited a consistent ordering (FF > FS > SS). The transcriptomes of grass carp whole brain and hepatopancreas were then acquired for each family, and it was discovered that the number of differentially expressed genes (DEGs) in the different organs demonstrated family specificity. DEGs were mostly identified in the hepatopancreas of FF and the whole brain of SS, but they were more evenly distributed in FS. There were 14 DEGs that were found in all three families, including three that were negatively correlated in hepatopancreas (ahsg2, lect2) or in brain (drd5), and 11 that were positively connected in hepatopancreas (sycn, pabpc4, zgc:112294, cel, endou, ela2, prss3, zbtb41, ela3) or in brain (fabp7, endod1). The deletion of ahsg2 boosted the growth rate only in certain zebrafish, suggesting that the growth-promoting effects of ahsg2 varies among individuals. Furthermore, we examined the SNP in each family and conducted preliminary research on the probable genetic pathways of family-specific control of growth traits. The family specificity of the growth regulation mechanism of grass carp at the transcriptional level was revealed for the first time in this study, and it was discovered that growth differences among individuals in the FF family were primarily due to differences in nutrient metabolism, whereas growth differences among individuals in the SS family may be primarily due to differences in foraging ability caused by differences in brain development. This research adds to our understanding of the genetic regulatory mechanism of grass carp growth.

A systematic evaluation of bioinformatics tools for identification of long noncoding RNAs.

High-throughput RNA sequencing unveiled the complexity of transcriptome and significantly increased the records of long noncoding RNAs (lncRNAs), which were reported to participate in a variety of biological processes. Identification of lncRNAs is a key step in lncRNA analysis, and a bunch of bioinformatics tools have been developed for this purpose in recent years. While these tools allow us to identify lncRNA more efficiently and accurately, they may produce inconsistent results, making selection a confusing issue. We compared the performance of 41 analysis models based on 14 software packages and different data sets, including high-quality data and low-quality data from 33 species. In addition, computational efficiency, robustness, and joint prediction of the models were explored. As a practical guidance, key points for lncRNA identification under different situations were summarized. In this investigation, no one of these models could be superior to others under all test conditions. The performance of a model relied to a great extent on the source of transcripts and the quality of assemblies. As general references, FEELnc_all_cl, CPC, and CPAT_mouse work well in most species while COME, CNCI, and lncScore are good choices for model organisms. Since these tools are sensitive to different factors such as the species involved and the quality of assembly, researchers must carefully select the appropriate tool based on the actual data. Alternatively, our test suggests that joint prediction could behave better than any single model if proper models were chosen. All scripts/data used in this research can be accessed at http://bioinfo.ihb.ac.cn/elit.

Transcriptomes of Zebrafish in Early Stages of Multiple Viral Invasions Reveal the Role of Sterols in Innate Immune Switch-On.

Although it is widely accepted that in the early stages of virus infection, fish pattern recognition receptors are the first to identify viruses and initiate innate immune responses, this process has never been thoroughly investigated. In this study, we infected larval zebrafish with four different viruses and analyzed whole-fish expression profiles from five groups of fish, including controls, at 10 h after infection. At this early stage of virus infection, 60.28% of the differentially expressed genes displayed the same expression pattern across all viruses, with the majority of immune-related genes downregulated and genes associated with protein synthesis and sterol synthesis upregulated. Furthermore, these protein synthesis- and sterol synthesis-related genes were strongly positively correlated in the expression pattern of the rare key upregulated immune genes, IRF3 and IRF7, which were not positively correlated with any known pattern recognition receptor gene. We hypothesize that viral infection triggered a large amount of protein synthesis that stressed the endoplasmic reticulum and the organism responded to this stress by suppressing the body's immune system while also mediating an increase in steroids. The increase in sterols then participates the activation of IRF3 and IRF7 and triggers the fish's innate immunological response to the virus infection.

Comprehensive analysis of hub mRNA, lncRNA and miRNA, and associated ceRNA networks implicated in grass carp (Ctenopharyngodon idella) growth traits.

Grass carp (Ctenopharyngodon idella) is the most productive freshwater aquaculture fish in worldwide. However, the molecular mechanism of its growth traits has not been fully elucidated. Whole transcriptome analysis of the brain and hepatopancreas of 29 six-month-old grass carp with different growth rates was performed. Weighted gene co-expression network analysis (WGCNA) was used to construct a weighted gene co-expression network of mRNA, miRNA and lncRNA separately. A total of 35 hub mRNAs, 47 hub lncRNAs and 33 hub miRNAs were identified from the brain, 37 hub mRNAs, 110 hub lncRNAs and 36 hub miRNAs were identified from the hepatopancreas. The ceRNA networks in the brain and hepatopancreas were involved in brain development and nutrient metabolism, respectively. Overall, this is the first investigation of the growth-related transcriptomic characteristics in the brain and hepatopancreas of grass carp, thus will help us to further explore the molecular mechanism of grass carp growth rate.

Dynamic Transcriptional Landscape of Grass Carp (Ctenopharyngodon idella) Reveals Key Transcriptional Features Involved in Fish Development.

A high-quality baseline transcriptome is a valuable resource for developmental research as well as a useful reference for other studies. We gathered 41 samples representing 11 tissues/organs from 22 important developmental time points within 197 days of fertilization of grass carp eggs in order to systematically examine the role of lncRNAs and alternative splicing in fish development. We created a high-quality grass carp baseline transcriptome with a completeness of up to 93.98 percent by combining strand-specific RNA sequencing and single-molecule real-time RNA sequencing technologies, and we obtained temporal expression profiles of 33,055 genes and 77,582 transcripts during development and tissue differentiation. A family of short interspersed elements was preferentially expressed at the early stage of zygotic activation in grass carp, and its possible regulatory components were discovered through analysis. Additionally, after thoroughly analyzing alternative splicing events, we discovered that retained intron (RI) alternative splicing events change significantly in both zygotic activation and tissue differentiation. During zygotic activation, we also revealed the precise regulatory characteristics of the underlying functional RI events.

Understanding the Early Evolutionary Stages of a Tandem Drosophilamelanogaster-Specific Gene Family: A Structural and Functional Population Study.

Gene families underlie genetic innovation and phenotypic diversification. However, our understanding of the early genomic and functional evolution of tandemly arranged gene families remains incomplete as paralog sequence similarity hinders their accurate characterization. The Drosophila melanogaster-specific gene family Sdic is tandemly repeated and impacts sperm competition. We scrutinized Sdic in 20 geographically diverse populations using reference-quality genome assemblies, read-depth methodologies, and qPCR, finding that ∼90% of the individuals harbor 3-7 copies as well as evidence of population differentiation. In strains with reliable gene annotations, copy number variation (CNV) and differential transposable element insertions distinguish one structurally distinct version of the Sdic region per strain. All 31 annotated copies featured protein-coding potential and, based on the protein variant encoded, were categorized into 13 paratypes differing in their 3' ends, with 3-5 paratypes coexisting in any strain examined. Despite widespread gene conversion, the only copy present in all strains has functionally diverged at both coding and regulatory levels under positive selection. Contrary to artificial tandem duplications of the Sdic region that resulted in increased male expression, CNV in cosmopolitan strains did not correlate with expression levels, likely as a result of differential genome modifier composition. Duplicating the region did not enhance sperm competitiveness, suggesting a fitness cost at high expression levels or a plateau effect. Beyond facilitating a minimally optimal expression level, Sdic CNV acts as a catalyst of protein and regulatory diversity, showcasing a possible evolutionary path recently formed tandem multigene families can follow toward long-term consolidation in eukaryotic genomes.

Construction of a high-density genetic map and mapping of growth related QTLs in the grass carp (Ctenopharyngodon idellus).

BACKGROUND: Grass carp (Ctenopharyngodon idellus) are important species in Asian aquaculture. A draft genome for grass carp has already been published in 2015. However, there is still a requirement for a suitable genetic linkage map to arrange scaffolds on chromosomal frameworks. QTL analysis is a powerful tool to detect key locations for quantitative traits, especially in aquaculture. There no growth related QTLs of grass carp have been published yet. Even the growth trait is one of the focuses in grass carp culture. RESULTS: In this study, a pair of distantly related parent grass carps and their 100 six-month-old full-sib offspring were used to construct a high-density genetic map with 6429 single nucleotide polymorphisms (SNPs) by 2b-RAD technology. The total length of the consensus map is 5553.43 cM with the average marker interval of 1.92 cM. The map has a good collinearity with both the grass carp draft genome and the zebrafish genome, and it assembled 89.91% of the draft genome to a chromosomal level. Additionally, according to the growth-related traits of progenies, 30 quantitative trait loci (QTLs), including 7 for body weight, 9 for body length, 5 for body height and 9 for total length, were identified in 16 locations on 5 linkage groups. The phenotypic variance explained for these QTLs varies from 13.4 to 21.6%. Finally, 17 genes located in these regions were considered to be growth-related because they either had functional mutations predicted from the resequencing data of the parents. CONCLUSION: A high density genetic linkage map of grass carp was built and it assembled the draft genome to a chromosomal level. Thirty growth related QTLs were detected. After the cross analysis of Parents resequencing data, 17 candidate genes were obtained for further researches.

Glutathione peroxidase 5 deficiency induces lipid metabolism regulated by reactive oxygen species in Chlamydomonas reinhardtii.

BACKGROUND: Reactive oxygen species (ROS) are generated incidentally during natural metabolism process of aerobic photosynthetic organisms which could be either harmful for cellular components. How ROS regulated lipid metabolism and the transcriptomes of stressed cells respond to ROS in aerobic photosynthetic organisms are unclear. Glutathione peroxidases (GPXs) detoxify hydrogen peroxide or organic hydroperoxides, which are important enzymes of the antioxidant system. So the function of GPXs matters the cellular redox state. How the lipid metabolism respond to the GPXs deficiency remains to be explored. METHODS: In this study, we employed a Chlamydomonas reinhardtii gpx5 knockout mutant to examine the effects of ROS on lipid metabolism. The redox state and lipid content of the parental strain CC4348 and the gpx5 mutant were detected. Besides, the transcriptomes of CC4348 and the gpx5 mutant were sequenced before and after treatment with nitrogen-free medium to obtain genome wide respond. Then we performed the functional annotation, classification and enrichment analysis based on KEGG database for the differentially expressed genes (DEGs) before and after nitrogen deprivation of CC4348 and the gpx5 mutant. RESULTS: In the CC4348 cells, the lipid accumulated accompanying with increasing ROS level after treatment with nitrogen-free media. However, in the gpx5 mutant, the ROS level is much higher than that in the parental strain CC4348, unexpectedly with reduced lipid accumulation. By comparing the transcriptomes of CC4348 and gpx5 mutant, we found that both CC4348 and gpx5 mutant cells displayed upregulation of transcripts related to protein, nucleic acid, carbon metabolism and chlorophyll biosynthesis, but more proportion of genes related to lipid metabolism were up-regulated in CC4348 than that in the gpx5 mutant. CONCLUSION: In CC4348, lipid metabolism was up-regulated with increasing ROS level. But in the gpx5 mutant, Lipid accumulation was less with higher ROS level, which was due to the inhibited lipid biosynthesis. Therefore, ROS provides dual-directional regulation of lipid metabolism induced by GPX5 in Chlamydomonas.

Rapid Functional and Sequence Differentiation of a Tandemly Repeated Species-Specific Multigene Family in Drosophila.

Gene clusters of recently duplicated genes are hotbeds for evolutionary change. However, our understanding of how mutational mechanisms and evolutionary forces shape the structural and functional evolution of these clusters is hindered by the high sequence identity among the copies, which typically results in their inaccurate representation in genome assemblies. The presumed testis-specific, chimeric gene Sdic originated, and tandemly expanded in Drosophila melanogaster, contributing to increased male-male competition. Using various types of massively parallel sequencing data, we studied the organization, sequence evolution, and functional attributes of the different Sdic copies. By leveraging long-read sequencing data, we uncovered both copy number and order differences from the currently accepted annotation for the Sdic region. Despite evidence for pervasive gene conversion affecting the Sdic copies, we also detected signatures of two episodes of diversifying selection, which have contributed to the evolution of a variety of C-termini and miRNA binding site compositions. Expression analyses involving RNA-seq datasets from 59 different biological conditions revealed distinctive expression breadths among the copies, with three copies being transcribed in females, opening the possibility to a sexually antagonistic effect. Phenotypic assays using Sdic knock-out strains indicated that should this antagonistic effect exist, it does not compromise female fertility. Our results strongly suggest that the genome consolidation of the Sdic gene cluster is more the result of a quick exploration of different paths of molecular tinkering by different copies than a mere dosage increase, which could be a recurrent evolutionary outcome in the presence of persistent sexual selection.

PMSeeker: A Scheme Based on the Greedy Algorithm and the Exhaustive Algorithm to Screen Low-Redundancy Marker Sets for Large-Scale Parentage Assignment with Full Parental Genotyping.

Parentage assignment is a genetic test that utilizes genetic characteristics, such as molecular markers, to identify the parental relationships within populations, which, in commercial fish farming, are almost always large and where full information on potential parents is known. To accurately find the true parents, the genotypes of all loci in the parentage marker set (PMS) are required for each individual being tested. With the same accuracy, a PMS containing a smaller number of markers will undoubtedly save experimental costs. Thus, this study established a scheme to screen low-redundancy PMSs using the exhaustive algorithm and greedy algorithm. When screening PMSs, the greedy algorithm selects markers based on the parental dispersity index (PDI), a uniquely defined metric that outperforms the probability of exclusion (PE). With the conjunctive use of the two algorithms, non-redundant PMSs were found for more than 99.7% of solvable cases in three groups of random sample experiments in this study. Then, a low-redundancy PMS can be composed using two or more of these non-redundant PMSs. This scheme effectively reduces the number of markers in PMSs, thus conserving human and experimental resources and laying the groundwork for the widespread implementation of parentage assignment technology in economic species breeding.

FishSNP: a high quality cross-species SNP database of fishes.

The progress of aquaculture heavily depends on the efficient utilization of diverse genetic resources to enhance production efficiency and maximize profitability. Single nucleotide polymorphisms (SNPs) have been widely used in the study of aquaculture genomics, genetics, and breeding research since they are the most prevalent molecular markers on the genome. Currently, a large number of SNP markers from cultured fish species are scattered in individual studies, making querying complicated and data reuse problematic. We compiled relevant SNP data from literature and public databases to create a fish SNP database, FishSNP ( http://bioinfo.ihb.ac.cn/fishsnp ), and also used a unified analysis pipeline to process raw data that the author of the literature did not perform SNP calling on to obtain SNPs with high reliability. This database presently contains 45,690,243 (45 million) nonredundant SNP data for 13 fish species, with 30,288,958 (30 million) of those being high-quality SNPs. The main function of FishSNP is to search, browse, annotate and download SNPs, which provide researchers various and comprehensive associated information.

FishGET: A fish gene expression and transcriptome database with improved accuracy and visualization.

With the rapid expansion of transcriptome studies in many fishes, a great number of RNA-seq data have been published, allowing for a more systematic understanding of the general profiles and details of gene expression in fish. FishGET is dedicated to gathering and curating fish RNA-seq data to discover more new RNAs, including mRNA and lncRNA, thereby getting a more complete reference transcriptome and providing more comprehensive and accurate transcriptome annotations. We obtained a total of 1362 RNA-seq paired-end data of 8 fishes from 97 different studies, and then we performed transcript assembly, meta-assembly, weighted gene co-expression network analysis (WGCNA), functional annotations, neighbor location annotation, lncRNA type annotation, homology annotation. To promote research into fish genes at the transcriptional level, we developed a user-friendly web interface that allows users to view all information and makes use of multiple types of dynamic interactive visualization services.

Profiling the Spatial Expression Pattern and ceRNA Network of lncRNA, miRNA, and mRNA Associated with the Development of Intermuscular Bones in Zebrafish.

Intermuscular bones (IBs) are small spicule-like bones in the muscular septum of fish, which affect their edible and economic value. The molecular mechanism of IB development is still uncertain. Numerous studies have shown that the ceRNA network, which is composed of mRNA, lncRNA, and miRNA, plays an important regulatory role in bone development. In this study, we compared the mRNA, lncRNA, and miRNA expression profiles in different IB development segments of zebrafish. The development of IBs includes two main processes, which are formation and growth. A series of genes implicated in the formation and growth of IBs were identified through gene differential expression analysis and expression pattern analysis. Functional enrichment analysis showed that the functions of genes implicated in the regulation of the formation and growth of IBs were quite different. Ribosome and oxidative phosphorylation signaling pathways were significantly enriched during the formation of IBs, suggesting that many proteins are required to form IBs. Several pathways known to be associated with bone development have been shown to play an important role in the growth of IBs, including calcium, ECM-receptor interaction, Wnt, TGF-ß, and hedgehog signaling pathways. According to the targeting relationship and expression correlation of mRNA, lncRNA, and miRNA, the ceRNA networks associated with the growth of IBs were constructed, which comprised 33 mRNAs, 9 lncRNAs, and 7 miRNAs. This study provides new insight into the molecular mechanism of the development of IBs.

Dietary Inclusion of Seabuckthorn (Hippophae rhamnoides) Mitigates Foodborne Enteritis in Zebrafish Through the Gut-Liver Immune Axis.

To help prevent foodborne enteritis in aquaculture, several feed additives, such as herbal medicine, have been added to fish diets. Predictions of effective herb medicines for treating fish foodborne enteritis from key regulated DEGs (differentially expressed genes) in transcriptomic data can aid in the development of feed additives using the Traditional Chinese Medicine Integrated Database. Seabuckthorn has been assessed as a promising candidate for treating grass carp soybean-induced enteritis (SBMIE). In the present study, the SBMIE zebrafish model was used to assess seabuckthorn's therapeutic or preventative effects. The results showed that intestinal and hepatic inflammation was reduced when seabuckthorn was added, either pathologically (improved intestinal villi morphology, less oil-drops) or growth-related (body fat deposition). Moreover, seabuckthorn may block the intestinal p53 signaling pathway, while activating the PPAR signaling pathway and fatty acid metabolism in the liver. 16S rRNA gene sequencing results also indicated a significant increase in OTU numbers and skewed overlapping with the fish meal group following the addition of seabuckthorn. Additionally, there were signs of altered gut microbiota taxa composition, particularly for reduced TM7, Sphingomonas, and Shigella, following the addition of seabuckthorn. Hindgut imaging of fluorescent immune cells in SBMIE larvae revealed the immune regulatory mechanisms at the cellular level. Seabuckthorn may significantly inhibit the inflammatory gathering of neutrophils, macrophages, and mature T cells, as well as cellular protrusions' formation. On the other hand, in larvae, seabuckthorn inhibited the inflammatory aggregation of lck+ T cells but not immature lymphocytes, indicating that it affected intestinal adaptive immunity. Although seabuckthorn did not affect the distribution of intestinal CD4+ cells, the number of hepatic CD4+ cells were reduced in fish from the seabuckthorn supplementation group. Thus, the current data indicate that seabuckthorn may alleviate foodborne gut-liver symptoms by enhancing intestinal mucosal immunity and microbiota while simultaneously inhibiting hepatic adipose disposition, making it a potential additive for preventing fish foodborne gut-liver symptoms.

Integrative Transcriptomic Analysis Reveals the Immune Mechanism for a CyHV-3-Resistant Common Carp Strain.

Anti-disease breeding is becoming the most promising solution to cyprinid herpesvirus-3 (CyHV-3) infection, the major threat to common carp aquaculture. Virus challenging studies suggested that a breeding strain of common carp developed resistance to CyHV-3 infection. This study illustrates the immune mechanisms involved in both sensitivity and anti-virus ability for CyHV3 infection in fish. An integrative analysis of the protein-coding genes and long non-coding RNAs (lncRNAs) using transcriptomic data was performed. Tissues from the head kidney of common carp were extracted at days 0 (the healthy control) and 7 after CyHV-3 infection (the survivors) and used to analyze the transcriptome through both Illumina and PacBio sequencing. Following analysis of the GO terms and KEGG pathways involved, the immune-related terms and pathways were merged. To dig out details on the immune aspect, the DEGs were filtered using the current common carp immune gene library. Immune gene categories and their corresponding genes in different comparison groups were revealed. Also, the immunological Gene Ontology terms for lncRNA modulation were retained. The weighted gene co-expression network analysis was used to reveal the regulation of immune genes by lncRNA. The results demonstrated that the breeding carp strain develops a marked resistance to CyHV-3 infection through a specific innate immune mechanism. The featured biological processes were autophagy, phagocytosis, cytotoxicity, and virus blockage by lectins and MUC3. Moreover, the immune-suppressive signals, such as suppression of IL21R on STAT3, PI3K mediated inhibition of inflammation by dopamine upon infection, as well as the inhibition of NLRC3 on STING during a steady state. Possible susceptible factors for CyHV-3, such as ITGB1, TLR18, and CCL4, were also revealed from the non-breeding strain. The results of this study also suggested that Nramp and PAI regulated by LncRNA could facilitate virus infection and proliferation for infected cells respectively, while T cell leukemia homeobox 3 (TLX3), as well as galectin 3 function by lncRNA, may play a role in the resistance mechanism. Therefore, immune factors that are immunogenetically insensitive or susceptible to CyHV-3 infection have been revealed.

De novo screening of disease-resistant genes from the chromosome-level genome of rare minnow using CRISPR-cas9 random mutation.

BACKGROUND: Mutants are important for the discovery of functional genes and creation of germplasm resources. Mutant acquisition depends on the efficiency of mutation technology and screening methods. CRISPR-Cas9 technology is an efficient gene editing technology mainly used for editing a few genes or target sites, which has not been applied for the construction of random mutant libraries and for the de novo discovery of functional genes. RESULTS: In this study, we first sequenced and assembled the chromosome-level genome of wild-type rare minnow (Gobiocypris rarus) as a susceptible model of hemorrhagic disease, obtained a 956.05 Mb genome sequence, assembled the sequence into 25 chromosomes, and annotated 26,861 protein-coding genes. Thereafter, CRISPR-Cas9 technology was applied to randomly mutate the whole genome of rare minnow with the conserved bases (TATAWAW and ATG) of the promoter and coding regions as the target sites. The survival rate of hemorrhagic disease in the rare minnow gradually increased from 0% (the entire wild-type population died after infection) to 38.24% (F3 generation). Finally, 7 susceptible genes were identified via genome comparative analysis and cell-level verification based on the rare minnow genome. CONCLUSIONS: The results provided the genomic resources for wild-type rare minnow, and confirmed that the random mutation system designed using CRISPR-Cas9 technology in this study is simple and efficient and is suitable for the de novo discovery of functional genes and creation of a germplasm resource related to qualitative traits.

Transcriptomic and Physiological Responses to Oxidative Stress in a Chlamydomonas reinhardtii Glutathione Peroxidase Mutant.

Aerobic photosynthetic organisms such as algae produce reactive oxygen species (ROS) as by-products of metabolism. ROS damage biomolecules such as proteins and lipids in cells, but also act as signaling molecules. The mechanisms that maintain the metabolic balance in aerobic photosynthetic organisms and how the cells specifically respond to different levels of ROS are unclear. Glutathione peroxidase (GPX) enzymes detoxify hydrogen peroxide or organic hydroperoxides, and thus are important components of the antioxidant system. In this study, we employed a Chlamydomonas reinhardtii glutathione peroxidase knockout (gpx5) mutant to identify the genetic response to singlet oxygen (1O2) generated by the photosensitizer rose bengal (RB). To this end, we compared the transcriptomes of the parental strain CC4348 and the gpx5 mutant sampled before, and 1 h after, the addition of RB. Functional annotation of differentially expressed genes showed that genes encoding proteins related to ROS detoxification, stress-response-related molecular chaperones, and ubiquitin-proteasome pathway genes were upregulated in CC4338. When GPX5 was mutated, higher oxidative stress specifically induced the TCA cycle and enhanced mitochondrial electron transport. Transcription of selenoproteins and flagellar-associated proteins was depressed in CC4348 and the gpx5 mutant. In addition, we found iron homeostasis played an important role in maintaining redox homeostasis, and we uncovered the relationship between 1O2 stress and iron assimilation, as well as selenoproteins. Based on the observed expression profiles in response to different levels of oxidative stress, we propose a model for dose-dependent responses to different ROS levels in Chlamydomonas.

Global gene expression profile under low-temperature conditions in the brain of the grass carp (Ctenopharyngodon idellus).

Grass carp is an important commercial fish widely cultivated in China. A wide range of temperatures, particularly extremely low temperatures, have dramatic effects on the aquaculture of this teleost. However, relatively few studies have characterized the molecular responses of grass carp exposed to acute cooling in natural environment. Here, we investigated the transcriptome profiles of the grass carp brain in response to cooling. Through regulation pattern analyses, we identified 2,513 differentially expressed genes (DEGs) that responded to moderate cold stress (12°C), while 99 DEGs were induced by severe low temperature (4°C).The pathway analyses revealed that the DEGs sensitive to moderate cold were largely enriched in steroid biosynthesis, spliceosome, translation, protein metabolism, phagosome, gap junction and estrogen signaling pathways. Additionally, we discerned genes most likely involved in low temperature tolerance, of which the MAPK signaling pathway was dominantly enriched. Further examination and characterization of the candidate genes may help to elucidate the mechanisms underpinning extreme plasticity to severe cold stress in grass carp.