Differentially Expressed Unigenes Research Articles

Energy deprivation affects nitrogen assimilation and fatty acid biosynthesis leading to leaf chlorosis under waterlogging stress in the endangered Abies koreana.

Energy deprivation triggers various physiological, biochemical and molecular changes in plants under abiotic stress. We investigated the oxidative damages in the high altitude grown conifer Korean fir (Abies koreana) exposed to waterlogging stress. Our experimental results showed that waterlogging stress led to leaf chlorosis, 35days after treatment. A significant decrease in leaf fresh weight, chlorophyll and sugar content supported this phenotypic change. Biochemical analysis showed a significant increase in leaf proline, lipid peroxidase and 1,1-diphenyl-2-picrylhydrazyl (DPPH) free radical content of waterlogged plants. To elucidate the molecular mechanisms, we conducted RNA-sequencing (RNA-seq) and de novo assembly. Using RNA-seq analysis approach and filtering (P<0.05 and false discovery rate<0.001), we obtained 134 unigenes upregulated and 574 unigenes downregulated. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis placed the obtained differentially expressed unigenes in α-linoleic pathway, fatty acid degradation, glycosis, glycolipid metabolism and oligosaccharide biosynthesis process. Mapping of unigenes with Arabidopsis using basic local alignment search tool for nucleotides showed several critical genes in photosynthesis and carbon metabolism downregulated. Following this, we found the repression of multiple nitrogen (N) assimilation and nucleotide biosynthesis genes including purine metabolism. In addition, waterlogging stress reduced the levels of polyunsaturated fatty acids with a concomitant increase only in myristic acid. Together, our results indicate that the prolonged snowmelt may cause inability of A. koreana seedlings to lead the photosynthesis normally due to the lack of root intercellular oxygen and emphasizes a detrimental effect on the N metabolic pathway, compromising this endangered tree's ability to be fully functional under waterlogging stress.

Transcriptome Analysis Provides Insights into Korean Pine Tree Aging and Response to Shading

Age controls a tree’s responses to environmental cues and shading influences tree growth and physiology. These are basic principles of “Afforestation under canopy”, an approach that is widely used in the regeneration of Korean pine forests. Studying the underlying mechanism helps us to understand tree adaptation and utilize it in forest management. In this study, we investigated the transcriptomic changes in the uppermost main stems of the Korean pine tree (Pinus koraiensis, Sieb. et Zucc.) at different ages (5, 7, 10, 14, and 17 years) and in different growth conditions (open-grown and shade-grown trees) using RNA-Seq. In total, 434,005,837 reads were produced and assembled into 111,786 unigenes. After pairwise comparisons, 568 differentially expressed unigenes (DEUs) were identified. The greatest number of DEUs was identified in the comparison between 5-year-old open-grown trees and 17-year-old shade-grown trees, while no DEUs were identified in 15 pairwise comparisons. Among these 568 DEUs, 45 were assigned to gene ontology (GO) terms associated with response to environmental changes, including “response to stress” (26) and “response to light and temperature” (19); 12 were assigned to GO terms associated with sexual reproduction, such as “sexual reproduction”, “specification of floral organ identity”, “pollen tube guidance”, and “fruit ripening”; 15 were heat shock protein genes and showed decreased expression patterns with age; and one, annotated as Pinus tabuliformis DEFICIENS-AGAMOUS-LIKE 1, showed an increased expression pattern with age, independent of the reproductive state or growth conditions of Korean pine trees. Altogether, these findings not only demonstrate the molecular aspects of the developmental and physiological effects of age and shading on Korean pine trees, but also improve our understanding of the basic principles of “Afforestation under canopy”.

Integrated Transcriptomics and Metabolomics Analysis Reveals the Effects of Cutting on the Synthesis of Flavonoids and Saponins in Chinese Herbal Medicine Astragalus mongholious.

Astragali Radix, derived from the roots of Astragalus mongholicus, is a traditional Chinese medicine containing flavonoids and saponins as its key ingredients. With a shortage in the wild sources of the herbal plant, it is especially important to explore a cultivation mode for A. mongholicus for medicinal purposes. Cutting, a physical environmental stress method, was used in this study with the objective of improving the quality of this herbal legume. We found that cutting of the top 1/3 of the aboveground part of A. mongholicus during the fruiting period resulted in a significant increase in the content of flavonoids and saponins, as well as in root growth, including length, diameter, and dry weight. Furthermore, the leaves were sampled and analyzed using a combined transcriptome and metabolome analysis approach at five different time points after the treatment. Sixteen differentially expressed unigenes (DEGs) involved in the biosynthesis of flavonoids were identified; these were found to stimulate the synthesis of flavonoids such as formononetin and calycosin-7-O-β-D-glucoside. Moreover, we identified 10 DEGs that were associated with the biosynthesis of saponins, including astragaloside IV and soyasaponin I, and found that they only regulated the mevalonic acid (MVA) pathway. These findings provide new insights into cultivating high-quality A. mongholicus, which could potentially alleviate the scarcity of this valuable medicinal plant.

Identification of Potential miRNA-mRNA Regulatory Network Associated with Growth and Development of Hair Follicles in Forest Musk Deer.

In this study, sRNA libraries and mRNA libraries of HFs of FMD were constructed and sequenced using an Illumina HiSeq 2500, and the expression profiles of miRNAs and genes in the HFs of FMD were obtained at the anagen and catagen stages. In total, 565 differentially expressed unigenes (DEGs) were identified, 90 of which were upregulated and 475 of which were downregulated. In the BP category of GO enrichment, the DEGs were enriched in the processes related to HF development and differentiation, including the hair cycle regulation and processes, HF development, skin epidermis development, regulation of HF development, skin development, the Wnt signaling pathway, and the BMP signaling pathway. Through KEGG analysis it was found that DEGs were significantly enriched in pathways associated with HF development and growth. A total of 186 differentially expressed miRNAs (DEmiRNAs) were screened (p < 0.05) in the HFs of FMD at the anagen stage vs. the catagen stage, 33 of which were upregulated and 153 of which were downregulated. Through DEmiRNA-mRNA association analysis, we found DEmiRNAs and target genes that mainly play regulatory roles in HF development and growth. The enrichment analysis of DEmiRNA target genes revealed similarities with the enrichment results of DEGs associated with HF development. Notably, both sets of genes were enriched in key pathways such as the Notch signaling pathway, melanogenesis, the cAMP signaling pathway, and cGMP-PKG. To validate our findings, we selected 11 DEGs and 11 DEmiRNAs for experimental verification using RT-qPCR. The results of the experimental validation were consistent with the RNA-Seq results.

Change in energy-consuming strategy, nucleolar metabolism and physical defense in Macrobrachium rosenbergii after acute and chronic polystyrene nanoparticles exposure

The COVID-19 pandemic has further intensified plastic pollution due to the escalated use of single-use gloves and masks, consequently leading to the widespread presence of microplastics (MPs) and nanoplastics (NPs) in major rivers and lakes worldwide. Macrobrachium rosenbergii has become an important experimental subject due to its ecological role and environmental sensitivity. In this study, we sought to comprehend the ramifications of NPs on the widely-distributed freshwater prawn, M rosenbergii, by conducting a detailed analysis of its responses to NPs after both 96 h and 30 days of exposure. The transcriptome analysis revealed 918 differentially expressed unigenes (DEGs) after 30 days of NPs exposure (356 upregulated, 562 downregulated) and 2376 DEGs after 96 h of NPs exposure (1541 upregulated, 835 downregulated). The results of DEGs expression indicated that acute NPs exposure enhanced carbohydrate transport and metabolism, fostering chitin and extracellular matrix processes. In contrast, chronic NPs exposure induced nucleolar stress in M. rosenbergii, impeding ribosome development and mRNA maturation while showing no significant changes in glucose metabolism. Our findings underscore the M. rosenbergii distinct coping mechanisms during acute and chronic NPs exposure, elucidating its vital adaptive strategies. These results contribute to our understanding of the ecological implications of NPs pollution and its impact on aquatic animals.

The phenotypic variation mechanisms of Atractylodes lancea post-cultivation revealed by conjoint analysis of rhizomic transcriptome and metabolome

The wild Atractylodes lancea rhizomes have been traditionally used as herbal medicine. As the increasingly exhaustion of wild A. lancea, the artificial cultivation mainly contributed to the medicinal material production. However, besides the phenotypic variation of rhizome phenotypic trait alteration, the qualities of cultivated A. lancea decrease compared with the wild counterpart. To unveil the physiological and molecular mechanism beneath the phenotypic variation, GC-MS-based volatile organic compounds (VOCs) profiling and RNAseq-based transcriptome analysis were conducted.The volatile metabolomics profiling revealed 65 differentially accumulated metabolites (DAMs) while the transcriptomic profiling identified 12 009 differentially expressed unigenes (DEGs) post-cultivation. The volatile active compounds including atractylone, and eudesmol accumulated more in wild rhizome than in the cultivated counterpart, and several unigenes in terpene synthesis were downregulated under cultivated condition. Compared with the wild A. lancea rhizome, the contents of bioactive Jasmonic Acid (JAs) in cultivated A. lancea rhizome were higher, and evidences that JAs negatively regulate the terpenes biosynthesis in the cultivated A. lancea rhizome were also provided. The combinational omics analysis further indicated the high correlation between the ten cultivation-suppressed VOCs and the cultivation-altered genes for sesquiterpenoids biosynthesis in A. lancea.The network of the cultivation-altered transcription factors (TFs) and the ten VOCs suggested TFs (e.g. Arabidopsis ERF13 homologs and WRKY50) are involved in the regulation of terpenes biosynthesis. These results laid a theoretical basis for developing geo-herbalism medicinal plants with “high quality and optimal shape".

Changes in the gut bacterial community affect miRNA profiles in Riptortus pedestris under different rearing conditions

Insects possess complex and dynamic gut microbial system, which contributes to host nutrient absorption, reproduction, energy metabolism, and protection against stress. However, there are limited data on interactions of host-gut bacterial microbiota through miRNA (microRNA) regulation in a significant pest, Riptortus pedestris. Here, we performed the 16S rRNA amplicon sequencing and small RNA sequencing from the R. pedestris gut under three environmental conditions and antibiotic treatment, suggesting that we obtained a large amount of reads by assembly, filtration and quality control. The 16S rRNA amplicon sequencing results showed that the abundance and diversity of gut bacterial microbiota were significantly changed between antibiotic treatment and other groups, and they are involved in metabolism and biosynthesis-related function based on functional prediction. Furthermore, we identified different numbers of differentially expressed unigenes (DEGs) and differentially expressed miRNAs (DEMs) based on high-quality mappable reads, which were enriched in various immune-related pathways, including Toll-like receptor, RIG-I-like receptor, NOD-like receptor, JAK/STAT, PI3K/Akt, NF-κB, MAPK signaling pathways, and so forth, using GO and KEGG enrichment analysis. Later on, the identified miRNAs and their target genes in the R. pedestris gut were predicted and randomly selected to construct an interaction network. Finally, our study indicated that alterations in the gut bacterial microbiota are significantly positively or negatively associated with DEMs of the Toll/Imd signaling pathway with Pearson correlation analysis. Taken together, the results of our study lay the foundation for further deeply understanding the interactions between the gut microbiota and immune responses in R. pedestris through miRNA regulation, and provide the new basis for pest management in hemipteran pests.

Integrated transcriptomic and metabolomic analysis reveals the molecular basis of tissue-specific accumulation of bioactive steroidal alkaloids in Fritillaria unibracteata

Fritillaria unibracteata is an endangered medicinal plant whose bulb has been used as a Chinese herb to suppress cough, asthma and excessive phlegm for centuries. Steroidal alkaloids, which are synthesized via the steroid synthesis pathways, are their significant bioactive constituents. However, few studies on genes involved in steroidal alkaloid biosynthesis in F. unibracteata have been reported, mainly due to the lack of the F. unibracteata genome. In this paper, comparative transcriptomic and metabolomic analyses of four different tissues of F. unibracteata (leaves, flowers, stems, and bulbs) were performed. Imperialine, peiminine, and peimisine were among the significant bioactive compounds that were considerably abundant in bulb tissue, according to the metabolomic findings. Then, 83.60 Gb transcriptome sequencing of four different tissues was performed, of which one gene encoding phosphomevalonate kinase was directly functionally characterized to verify the accuracy of sequences obtained from the transcriptome. A total of 9217 differentially expressed unigenes (DEGs) were identified in four different tissues of F. unibracteata. GO and KEGG enrichments revealed that phenylpropanoid biosynthesis, MVA-mediated terpenoid backbone biosynthesis, and steroid biosynthesis were enriched in bulb tissue, whereas enrichment of MEP-mediated terpenoid backbone biosynthesis, photosynthesis, photosynthesis-antenna protein and carotenoid biosynthesis was observed in aerial tissues. Moreover, clustering analysis indicated that the downstream steroid biosynthesis pathway was more important in steroidal alkaloid biosynthesis compared to the upstream terpenoid backbone biosynthesis pathway. Hence, MVA-mediated biosynthesis of steroidal alkaloids was proposed, in which 15 bulb-clustered DEGs were positively correlated with a high accumulation of bioactive steroid alkaloids, further validating our proposal. In addition, 36 CYP450s showing a positive correlation with bioactive steroidal alkaloids provided candidate enzymes to catalyze the subsequent steps of steroidal alkaloid biosynthesis. In addition, the transcription factors and ABC transporters clustered in bulb tissue might be responsible for the regulation and transportation of steroidal alkaloid biosynthesis. Protein-protein interaction analysis implied a highly complex steroid alkaloid biosynthesis network in which delta (24)-sterol reductase might be one of the central catalysts. Based on the integrated transcriptome and metabolome, this current study is a first step in understanding the tissue-specific biosynthesis of steroidal alkaloids in F. unibracteata. Furthermore, key genes and regulators identified herein could facilitate metabolic engineering to improve steroidal alkaloids in F. unibracteata.

An integrated transcriptome and metabolome analysis reveals the gene network regulating flower development in Pogostemon cablin.

Pogostemon cablin is a well-known protected species widely used in medicine and spices, however the underlying molecular mechanisms and metabolite dynamics of P. cablin flower development remain unclear due to the difficulty in achieving flowering in this species. A comparison of the transcriptome and widely targeted metabolome during P. cablin flower development was first performed in this study. Results showed that a total of 13,469 differentially expressed unigenes (DEGs) and 371 differentially accumulated metabolites (DAMs) were identified. Transcriptomic analysis revealed that the DEGs were associated with starch and sucrose metabolism, terpenoid biosynthesis and phenylpropanoid biosynthesis. Among these DEGs, 75 MIKC-MADS unigenes were associated with the development of floral organs. Gibberellins (GAs), auxin, and aging signaling might form a cross-regulatory network to regulate flower development in P. cablin. According to the metabolic profile, the predominant DAMs were amino acids, flavonoids, terpenes, phenols, and their derivatives. The accumulation patterns of these predominant DAMs were closely associated with the flower developmental stage. The integration analysis of DEGs and DAMs indicated that phenylpropanoids, flavonoids, and amino acids might be accumulated due to the activation of starch and sucrose metabolism. Our results provide some important insights for elucidating the reproductive process, floral organ, and color formation of P. cablin flowers at the molecular level. These results will improve our understanding of the molecular and genetic mechanisms involved in the floral development of P. cablin.

Transcriptome analysis of Euwallacea interjectus reveals differentially expressed unigenes related to developmental stages and egg laying

Euwallacea interjectus (Curculionidae: Scolytinae) is an ambrosia beetle species in its early stages of research. Therefore, studying the related molecular mechanism associated with the development and egg laid is essential. Transcriptome sequencing was used in this study to compare the gene expression of the beetles at different developmental stages and female adults before and after oviposition. A total of 40,047 annotated unigenes were obtained. There were 4225 differentially expressed unigenes (DEUs) from larva to prepupa stage, 3651 DEUs between prepupa and pupa, 1675 DEUs generated from pupa to adult, and 4762 DEUs between females before and after oviposition. The most significant pathway differences between different development stages and before and after oviposition were selected through functional annotation of DEUs between different stages. Among them, there were many pathways related to protein metabolism including: neuroactive ligand-receptor interaction, endoplasmic reticulum and RNA transport. This study provides valuable information on the molecular regulation mechanism of development and the egg laid of E. interjectus.

Isolation, Characterization, and Transcriptome Analysis of an ISKNV-Like Virus from Largemouth Bass.

Largemouth bass (Micropterus salmoides) is an important commercial fish farmed in China. Challenges related to diseases caused by pathogens, such as iridovirus, have become increasingly serious. In 2017, we detected iridovirus-infected diseased largemouth bass in Zunyi, Guizhou Province. The isolated virus was identified as an infectious spleen and kidney necrosis virus (ISKNV)-like virus (ISKNV-ZY). ISKNV-ZY induces a cytopathic effect after infecting mandarin fish brain (MFB) cells. Abundant hexagonal virus particles were observed in the cytoplasm of ISKNV-ZY-infected MFB cells, using electron microscopy. The whole genome of ISKNV-ZY contained 112,248 bp and 122 open reading frames. Phylogenetic tree analysis showed that ISKNV-ZY was most closely related to BCIV, indicating that it is an ISKNV-like megalocytivirus. ISKNV-ZY-infected largemouth bass started to die on day six and reached a death peak on days 7-8. Cumulative mortality reached 100% on day 10. Using RNA sequencing-based transcriptome analysis after ISKNV-ZY infection, 6254 differentially expressed unigenes (DEGs) were identified, of which 3518 were upregulated and 2673 downregulated. The DEGs were associated with endocytosis, thermogenesis, oxidative phosphorylation, the JAK-STAT signaling pathway, the MAPK signaling pathway, etc. These results contribute to understanding the molecular regulation mechanism of ISKNV infection and provide a basis for ISKNV prevention.

Transcriptome profiling of lung immune responses potentially related to acute respiratory distress syndrome in forest musk deer

BackgroundForest musk deer is an endangered species globally. The death of captive forest musk deer can be caused by certain respiratory system diseases. Acute respiratory distress syndrome (ARDS) is a huge threat to the life of forest muck deer that breed in our department.MethodsLung histopathologic analysis was conducted by hematoxylin and eosin (HE) staining. The lung gene changes triggered by ARDS were examined by RNA sequencing and related bioinformatics analysis in forest musk deer. The potential functions of unigenes were investigated by NR, SwissProt KOG, GO, and KEGG annotation analyses. Vital biological processes or pathways in ARDS were examined by GO and KEGG enrichment analyses.ResultsA total of 3265 unigenes were differentially expressed (|log2fold-change|> 2 and adjusted P value < 0.01) in lung tissues of 3 forest musk deer with ARDS compared with normal lung tissues of the non-ARDS group. These differentially expressed unigenes (DEGs) played crucial roles in immunity and defense responses to pathogens. Moreover, we identified the DEGs related to one or more of the following biological processes: lung development, immunity, and bacterial/viral/fungal infection. And six DEGs that might be involved in lung injury caused by immune dysregulation or viral/fungal infection were identified.ConclusionARDS-mediated lung gene alterations were identified in forest musk deer. Moreover, multiple genes involved in lung development and lung defense responses to bacteria/viruses/fungi in ARDS were filtered out in forest musk deer.

Comparative transcriptomics analyses of chemosensory genes of antenna in male red swamp crayfish Procambarus clarkii

The red swamp crayfish, Procambarus clarkii, is a globally invasive species and has caused huge damage to aquaculture, biodiversity, and ecology worldwide. Antenna-expressed receptors are important for P. clarkii to detect chemosensory cues for mate attraction. In this study, we tested the behavior of male P. clarkii to the conditioned water from female P. clarkii during the mating and non-mating periods, and performed RNA sequencing to investigate the chemosensory-related genes of the antenna of male P. clarkii. The results of the behavioral assay have shown that for the female-conditioned water, male P. clarkii within the mating period can be significantly attracted, but not during the non-mating period. This suggested that the expressions of chemosensory-related genes in the antenna of male P. clarkii may change significantly with mating seasonal variation. Antenna transcriptomes found that a total of 59,218 unigenes with an average length of 1,056.41 bp, and 4,889 differentially expressed unigenes (DEGs), among which 2,128 were upregulated, while 2,761 were downregulated were obtained. A total of 12 upregulated and nine downregulated DEGs were associated with chemical reception, including four ionotropic receptors (IRs) or ionotropic glutamate receptors (iGluRs), eight G-protein-coupled receptors (GPCRs), five transient receptor potential channels (TRP channels), one sodium–calcium exchanger, one isomerase, and two uncharacterized proteins (chemosensory proteins-like, CSPs). CSPs were preliminarily classified as pheromone receptors in the antenna of male P. clarkii. Furthermore, the calcium transduction-related pathways may play an important role in the sex pheromone reception of the male P. clarkii’s antenna. The results of quantitative real-time reverse transcriptase PCR (RT-qPCR) showed that the trends of expression of eight selected unigenes were consistent with RNA-Seq results. Our results provide more comprehensive data for chemical communication mechanisms after P. clarkii enter the mating period and eventually would develop better control strategies in further.

Transcriptome profiles of yellowish-white and fuchsia colored flowers in the Rheum palmatum complex reveal genes related to color polymorphism.

Flower color variation is ubiquitous in many plant species, and several studies have been conducted to elucidate the underlying molecular mechanism. There are two flower color variants (yellowish-white and fuchsia) in the Rheum palmatum complex, however, few studies have investigated this phenomenon. Here, we used transcriptome sequencing of the two color variants to shed light on the molecular and biochemical basis for these color morphs. Comparison of the two transcriptomes identified 9641 differentially expressed unigenes (DEGs), including 6477 up-regulated and 3163 down-regulated genes. Functional analyses indicated that several DEGs were related to the anthocyanin biosynthesis pathway, and the expression profiles of these DEGs were coincident with the qRT-PCR validation results, indicating that expression levels of structural genes have a profound effect on the color variation in the R. palmatum complex. Our results suggested that the interaction of transcription factors (MYB, bHLH and WRKY) also regulated the anthocyanin biosynthesis in the R. palmatum complex. Estimation of selection pressures using the dN/dS ratio showed that 1106 pairs of orthologous genes have undergone positive selection. Of these positively selected genes, 21 were involved in the anthocyanin biosynthetic pathway, indicating that they may encode the proteins for structural alteration and affect flower color in the R. palmatum complex.

Transcriptome and Metabolome Analyses Reveal Differences in Terpenoid and Flavonoid Biosynthesis in Cryptomeria fortunei Needles Across Different Seasons.

Cryptomeria fortunei (Chinese cedar) has outstanding medicinal value due to its abundant flavonoid and terpenoid contents. The metabolite contents of C. fortunei needles differ across different seasons. However, the biosynthetic mechanism of these differentially synthesized metabolites (DSMs) is poorly understood. To improve our understanding of this process, we performed integrated non-targeted metabolomic liquid chromatography and gas chromatography mass spectrometry (LC-MS and GC-MS), and transcriptomic analyses of summer and winter needles. In winter, the C. fortunei needle ultrastructure was damaged, and the chlorophyll content and Fv/Fm were significantly (p < 0.05) reduced. Based on GC-MS and LC-MS, we obtained 106 and 413 DSMs, respectively; based on transcriptome analysis, we obtained a total of 41.17 Gb of clean data and assembled 33,063 unigenes, including 14,057 differentially expressed unigenes (DEGs). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed that these DSMs/DEGs were significantly (p < 0.05) enriched in many biosynthesis pathways, such as terpenoids, photosynthates, and flavonoids. Integrated transcriptomic and metabonomic analyses showed that seasonal changes have the greatest impact on photosynthesis pathways, followed by terpenoid and flavonoid biosynthesis pathways. In summer Chinese cedar (SCC) needles, DXS, DXR, and ispH in the 2-methyl-pentaerythritol 4-phosphate (MEP) pathway and GGPS were highly expressed and promoted the accumulation of terpenoids, especially diterpenoids. In winter Chinese cedar (WCC) needles, 9 genes (HCT, CHS, CHI, F3H, F3'H, F3'5'H, FLS, DFR, and LAR) involved in flavonoid biosynthesis were highly expressed and promoted flavonoid accumulation. This study broadens our understanding of the metabolic and transcriptomic changes in C. fortunei needles caused by seasonal changes and provides a reference regarding the adaptive mechanisms of C. fortunei and the extraction of its metabolites.

Hepatic transcriptome profiles reveal the hepatoprotective effects of dietary quercetin and sodium quercetin-5′-sulfonates supplementation in hybrid grouper (Epinephelus fuscoguttatus♀ × Epinephelus polyphekadion♂)

Plant flavonoids, such as quercetin (QE), are traditionally used to treat liver injuries. Given the limited bioavailability of quercetin, sodium quercetin-5′-sulfonates (QS) were synthesised and characterised. Although beneficial effects of QE on the fatty liver are observed in vertebrates, the exact mechanism is still unclear, particularly in fish livers. As a result, RNA-sequencing was conducted on hepatic libraries from hybrid groupers (Epinephelus fuscoguttatus♀ × Epinephelus polyphekadion♂) after QE and QS exposure for 56 d. In total, 49,411 unigenes were generated with a control group (FM, 0 mmol/kg), QE (QE, 3.2 mmol/kg), and QS (QS, 3.2 mmol/kg) supplementation group. The N50 for the unigenes is 2047 bp, whereas the mean length is 1198.55 bp. Compared with FM, we identified 788 and 848 differentially expressed unigenes (DEGs) in the liver in response to QE and QS, including 423 up- and 365 down-regulated in the QE group and 402 up- and 446 down-regulated in the QS group. Furthermore, ten genes were selected for real-time quantitative PCR to verify the reliability of our transcriptome data, and the result has shown that both up-and down-regulated genes were consistent with the RNA-seq results. Results showed that QE down-regulated hepatic genes involved in the steroid biosynthesis pathway, while QS up-regulated genes related to polyamine synthesis. More importantly, glutaminase1 (GLS1) is the initial and rate-limiting enzyme responsible for glutamine catabolism, down-regulated by QE and QS exposure. Our results will provide valuable information to help understand the underlying molecular mechanism for QE and QS preventing fatty liver of grouper.

Comparing the Transcriptomes of Two Different Tissues in Helicoverpa assulta (Guenée)

Helicoverpa assulta (Guenée), a moth species belonging to the Noctuidae (Lepidoptera) family, is a destructive agricultural pest that infests multiple cash crops. To assess differences in the gene expression profiles of different tissues in H. assulta, we analyzed the transcriptomes of two tissue types (midgut and hemocytes) using the Illumina Hiseq 2000 platform, on the basis of which we obtained 52076750 and 53404200 high-quality clean reads, respectively. De novo assembly yielded 46146 and 33707 unigenes from the midgut and hemocytes, respectively. After screening, we identified 23726 unigenes differentially expressed between the midgut and hemocytes. Taking the midgut as the control, we detected 7448 and 16278 unigenes that were up- and downregulated in hemocytes, respectively. Gene Ontology functional annotation divided the differentially expressed unigenes (DEUs) into three categories (biological process, cellular component, and molecular function) and 51 branches, whereas the Kyoto Encyclopedia of Genes and Genomes metabolic pathway annotation assigned the DEUs to six categories, mapping these to 258 pathways. In addition, we detected 224918 single-nucleotide polymorphic sites. Our findings based on transcriptome sequencing, data assembly, and functional gene annotation of two different tissues in H. assulta will provide a valuable reference for further excavation and study of functional genes in H. assulta.

Gene Co-expression Network and Regression Analysis Identify the Transcriptomic, Physiological, and Biochemical Indicators of the Response of Alpine Woody Plant Rhododendron rex to Drought Stress.

Increasing severity of drought stress due to global change and extreme weather has been affecting the biodiversity, function, and stability of forest ecosystems. However, despite being an important component in the alpine and subalpine vegetation in forest ecosystems, Rhododendron species have been paid rare attention in the study of molecular mechanism of tolerance or response to drought. Herein, we investigated the correlation of transcriptomic changes with the physiological and biochemical indicators of Rhododendron rex under drought stress by using the co-expression network approach and regression analysis. Compared with the control treatment, the number of significantly differentially expressed unigenes (DEGs) increased with the degree of drought stress. The DEGs were mainly enriched in the cell wall metabolic process, signaling pathways, sugar metabolism, and nitrogen metabolism. Coupled analysis of the transcriptome, physiological, and biochemical parameters indicated that the metabolic pathways were highly correlated with the physiological and biochemical indicators under drought stress, especially the chlorophyll fluorescence parameters, such as the actual photosynthetic efficiency of photosystem II, electron transport rate, photochemical quenching coefficient, and the maximum quantum efficiency of photosystem II photochemistry. The majority of the response genes related to the metabolic pathways, including photosynthesis, sugar metabolism, and phytohormone signal pathway, were highly expressed under drought stress. In addition, genes associated with cell wall, pectin, and galacturonan metabolism also played crucial roles in the response of R. rex to drought stress. The results provided novel insight into the molecular response of the alpine woody species under drought stress and may improve the understanding of the response of forest ecosystems to the global climate change.

Effect of glutamine supplementation against soybean meal-induced growth retardation, hepatic metabolomics and transcriptome alterations in hybrid sturgeon Acipenser baerii♀× A. schrenckii ♂

This study aimed to evaluate the effects of glutamine supplementation to soybean meal (SBM) diet in hybrid sturgeon (25.00 ± 1.00 g). Three diets, including fishmeal (FM) diet, SBM diet, and SBMG diet (glutamine addition to SBM diet), were formulated to feed sturgeons for 8 weeks. Growth parameters and muscular crude lipid content were reduced by SBM substitution, and were further increased in SBMG-diet group. In liver morphology detection, moderate lipid droplets accumulation in hepatocytes found in fish fed SBM diet were partially retrieved by glutamine addition. Hepatic gas chromatography–mass spectrometry analysis detected 156 up-regulated metabolites and 15 related KEGG pathways affected by SBM replacement. Glutamine addition resulted in 102 down-regulated metabolites, together with 9 KEGG pathways enriched. In liver transcriptome sequencing analysis, 1074 and 1564 differentially expressed unigenes (DEGs) were detected by SBM/FM and SBMG/SBM pairwise comparisons, respectively. The least number of DEGs (143) was present in pairwise comparison of SBMG /FM. Our results indicated that glutamine addition attenuated the SBM-based negative effect including growth retardation, and muscle proximate composition alteration. Glutamine supplementation alleviated the liver damage caused by SBM substitution possibly through down regulating the elevated levels of metabolites or gene as well as related metabolic pathways.

Comparison of miRNA and mRNA Expression in Sika Deer Testes With Age.

To elucidate the complex physiological process of testis development and spermatogenesis in Sika deer, this study evaluated the changes of miRNA and mRNA profiles in the four developmental stages of testis in the juvenile (1-year-old), adolescence (3-year-old), adult (5-year-old), and aged (10-year-old) stages. The results showed that a total of 198 mature, 66 novel miRNAs, and 23,558 differentially expressed (DE) unigenes were obtained; 14,918 (8,413 up and 6,505 down), 4,988 (2,453 up and 2,535 down), and 5,681 (2,929 up and 2,752 down) DE unigenes, as well as 88 (43 up and 45 down), 102 (44 up and 58 down), and 54 (18 up and 36 down) DE miRNAs were identified in 3- vs. 1-, 5- vs. 3-, and 10- vs. 5-year-old testes, respectively. By integrating miRNA and mRNA expression profiles, we predicted 10,790 mRNA–mRNA and 69,883 miRNA–mRNA interaction sites. The target genes were enriched by GO and KEGG pathways to obtain DE mRNA (IGF1R, ALKBH5, Piwil, HIF1A, BRDT, etc.) and DE miRNA (miR-140, miR-145, miR-7, miR-26a, etc.), which play an important role in testis development and spermatogenesis. The data show that DE miRNAs could regulate testis developmental and spermatogenesis through signaling pathways, including the MAPK signaling pathway, p53 signaling pathway, PI3K-Akt signaling pathway, Hippo signaling pathway, etc. miR-140 was confirmed to directly target mutant IGF1R-3′UTR by the Luciferase reporter assays. This study provides a useful resource for future studies on the role of miRNA regulation in testis development and spermatogenesis.