Search Results (624)

Sarcomyxa edulis is a characteristic edible and medicinal mushroom found in Northeast China that is highly valued by consumers for its tender texture, pleasant flavor, and high nutritional value. To gain a deeper understanding of the molecular mechanisms underlying the development of S. edulis fruiting bodies, this study utilized the Illumina NovaSeq platform to perform transcriptome sequencing at three growth and development stages of S. edulis strain SE8, namely primordia (SE8–P), fruiting body differentiation (SE8–F), and mature fruiting body (SE8–M). A total of 54.67 Gb of clean data was obtained, with a GC content of around 51%. After assembly, 36,423 Unigenes were obtained. Functional annotation was performed on the Unigenes, resulting in 21,206 Unigene annotation results. Differential expression gene analysis showed that 79,606 and 523 DEGs were annotated in at least one database during the SE8–P vs. SE8–F, SE8–F vs. SE8–M, and SE8–P vs. SE8–M processes, respectively. Among these, the genes encoding aldehyde dehydrogenase and fungal hydrophobins were consistently downregulated, playing a negative regulatory role in the growth and development of S. edulis. The genes encoding glycoside hydrolase and AB hydrolase superfamily proteins were consistently upregulated, playing a positive regulatory role in growth and development. Among these, the genes encoding aldehyde dehydrogenase were annotated to the Tryptophan metabolism (ko00380) pathway through KEGG, suggesting that aldehyde dehydrogenase regulates indoacetate formation in the fruiting body of S. edulis. The accuracy of RNA–Seq and DEG analysis was validated using quantitative PCR. This study enriches our knowledge of the genetic information and provides a theoretical basis for the molecular mechanisms of fruiting body development of S. edulis. Full article

In this study, the differences in gene expression of Stropharia rugosoannulata at different treatment times under high temperature and drought stress were analyzed by transcriptomics. Here, a total of 74,571 transcripts and 16,233 unigenes were identified, with an average assembly length of 3002 bp. A total of 10,248 differentially expressed genes (DEGs) were identified. DEG analysis indicated that the numbers of DEGs under high-temperature stress for 1 d, 2 d, and 3 d were 798, 851, and 1484, respectively. These DEGs were involved in 96 GO functional categories and 69 KEGG metabolic pathways. Meanwhile, the numbers of DEGs under drought stress for 3 d, 6 d, and 9 d were 421, 1072, and 2880, respectively. These DEGs were involved in 108 GO functional categories and 78 KEGG metabolic pathways. Further analysis of the metabolic pathway (ko04011) commonly enriched by DEGs identified 15 candidate genes responding to high-temperature or drought stress. Eight candidate genes were randomly selected for qRT-PCR verification, and the qRT-PCR results were basically consistent with the transcriptome datasets. These findings provide critical candidate genes for understanding the molecular regulation mechanism of S. rugosoannulata in response to high temperature and drought stress and have important reference value for its stress resistance breeding. Full article

Coptis trifolia (threeleaf goldthread) offers a valuable comparative system for investigating the evolution and regulation of benzylisoquinoline alkaloid (BIA) synthesis. In this study, we analyzed the leaf and root transcriptomes of C. trifolia using both long-read and short-read RNA-Sequencing. We assembled 41,926 unigenes (≥500 bp) and identified 37 genes related to BIA biosynthesis, including two transcription factors, bHLH1 and WRKY1. The number of BIA genes identified in C. trifolia was comparable to that in other Coptis species. Transcriptome analysis revealed that most of these genes were more highly expressed in roots than leaves. Consistent with previous studies, C. trifolia contained a single (S)-stylopine synthase (SPS) gene homolog, potentially multifunctional for (S)-canadine synthase (CAS), (S)-cheilanthifoline synthase (CFS), and SPS. Transcriptome and untargeted metabolomic data indicated greater variation in root samples than leaf samples, although slightly more differentially expressed transcripts and metabolites were observed in leaves. Targeted metabolite profiling showed higher BIA accumulation in roots, with epiberberine being the most abundant, followed by coptisine, berberine, and columbamine. These results provide essential genomic resources for comparative analysis of the BIA pathway across Ranunculaceae, targeted gene function studies for metabolic bioengineering, and conservation strategies for C. trifolia, a member of an early-diverging clade within the genus with limited genetic resources. Full article

Protein hydrolysates have potential as sustainable functional feed ingredients or additives for the aquaculture industry. This study examined the growth-promoting effects of duck-blood protein hydrolysate (DBPH, <10 kDa) on the flowerhorn cichlid (Amphilophus citrinellus × Cichlasoma trimaculatum). Fish with an average weight of 3.24 ± 0.22 g were randomly assigned to four dietary treatments: a negative control (basal diet) and basal diets supplemented with 0.5%, 1%, and 2% DBPH. After 90 days of the feeding trial, growth parameters indicated that supplementation with 1% and 2% DBPH enhanced growth. However, the muscle composition and skin coloration did not differ significantly. Transcriptome sequencing of the liver tissue yielded 39.83 GB of high-quality clean data. De novo transcriptome assembly identified 32,824 unigenes, of which 21,385 were successfully annotated based on public databases. Differential expression analysis identified 269 upregulated and 232 downregulated genes. To clarify the growth-promoting effects of DBPH, five glycolysis/gluconeogenesis-related genes (tpi, gapdh, pck1, ldh, and adh) were validated by liver qRT-PCR, and the results were consistent with those of the transcriptomic analysis. These findings provide new insights into the mechanisms by which DBPH supplementation could enhance growth, as evidenced by alterations in glycolysis and gluconeogenesis pathways, indicating potential as a novel feed additive in aquaculture. Full article

The swimming crab is a commercially and nutritionally important marine resource with the highest catch volumes in Mexico occurring along the East Pacific coast. Among the Pacific species of the genus Callinectes, the blue crab C. arcuatus has the widest distribution and is found throughout the year. Its close resemblance to the well-studied Atlantic blue swimming crab (C. sapidus) makes it an excellent model for molecular reproductive studies in the Mexican Pacific. Using next-generation sequencing, this study aimed to characterize maturation-associated genes in an ovary–hepatopancreas transcriptome of C. arcuatus, with a particular focus on vitellogenin (Vtg) and its expression in the ovaries and hepatopancreas across different gonadal maturity stages. The transcriptome library generated from pooled samples produced 27,729 unigenes, of which, 196 (1.81%) were identified as reproduction-related genes. Notably, 33 of these genes, including the complete Vtg sequence, have not been previously reported in this species. Vtg expression was found to be tissue-specific, with levels in the hepatopancreas up to 13 orders of magnitude higher than in the ovary. In the hepatopancreas, Vtg expression increased exponentially from stage I to stage V of gonadal maturity, whereas in the ovaries, its expression showed the opposite trend. These findings highlight that the hepatopancreas, with its abundant nutrient reserves, serves as the primary site of Vtg expression and synthesis. Full article

Salinity is a pivotal environmental factor that governs crustacean survival and development through its regulatory effects on key physiological processes, including osmoregulation and metabolic homeostasis. In the mud crab Scylla paramamosain, salinity tolerance of the megalopa plays an important role in larval survival rates and aquaculture yield. Here, we employed a combined transcriptomic and proteomic strategy to comprehensively dissect the molecular adaptive mechanisms of S. paramamosain megalopa exposed to acute and prolonged low-salinity stress (8‰) compared to control condition (17‰). Illumina-based transcriptome sequencing generated 81.71 Gb of high-quality clean data, which were assembled into 42,210 unigenes. LC-MS/MS-based proteomic profiling identified 51,390 unique peptides, corresponding to 5909 confidently quantified proteins. Transcriptomic profiling identified 2627 differentially expressed genes (DEGs) under acute low-salinity stress, comprising 1332 upregulated and 1295 downregulated genes compared to the control group. In contrast, a total of 733 DEGs were identified under prolonged low-salinity exposure, including 390 upregulated and 343 downregulated genes. Parallel proteomic analysis identified 199 differentially expressed proteins (DEPs) in the acute stress group, with 105 upregulated and 94 downregulated relative to the control group. Under prolonged stress, 206 DEPs were detected, including 124 upregulated and 82 downregulated proteins compared to the control group. Significant GO term and KEGG pathway enrichments contained metal ion binding, oxidoreductase activity, nucleus, apoptotic process, innate immune response, and amino acid metabolism, suggesting that megalopa employ coordinated regulatory mechanisms involving metabolic reprogramming, immunity system modulation, ion homeostasis maintenance and cell cycle regulation to adapt to hypoosmotic stress. Integrated multi-omics analysis identified 17 genes displaying significant concordant differential expression at both mRNA and protein levels during acute hypoosmotic stress, versus only 5 gene-protein pairs during prolonged stress exposure, indicating extensive post-transcriptional regulation and protein turnover mechanisms in sustained hypoosmotic condition. To the best of our knowledge, this study established the first integrative transcriptome-proteome framework elucidating hypoosmotic adaptation (8‰) mechanisms in S. paramamosain megalopa. The identified molecular signatures offer actionable targets for selective breeding of salinity-tolerant strains and precision management of megalopa culture under suboptimal salinity condition, while fundamentally advancing our mechanistic understanding of osmoregulatory plasticity across decapod crustaceans. Full article

Olfaction plays a crucial role in fish feeding behaviors and ecological adaptation. However, systematic studies on its transcriptional regulation and molecular evolutionary mechanisms in herbivorous and carnivorous fishes remain scarce. In this study, we analyzed four Xenocyprididae species: two herbivorous (Ctenopharyngodon idella and Megalobrama amblycephala) and two carnivorous (Elopichthys bambusa and Culter alburnus), using olfactory rosette transcriptome sequencing and cross-species comparisons. The number of unigenes per species ranged from 40,229 to 42,405, with BUSCO completeness exceeding 89.2%. Functional annotation was performed using six major databases. Olfactory-related candidate genes were identified based on Pfam domains (7tm_4) and KEGG pathways (ko04740), revealing 8–19 olfactory receptor genes per species. These candidate genes were predominantly enriched in the olfactory transduction and neuroactive ligand–receptor interaction pathways. A total of 3681 single-copy orthologous genes were identified, and their expression profiles exhibited clear interspecific divergence without forming strict clustering by dietary type. High-threshold differentially expressed trend genes (|log₂FC| ≥ 4) were enriched in pathways related to RNA processing, metabolite transport, and xenobiotic metabolism, suggesting that the olfactory system may participate in diverse adaptive responses. Ka/Ks analysis indicated that most homologous genes were under purifying selection, with only 0.87–2.07% showing positive selection. These positively selected genes were enriched in pathways related to immune response and neural regulation, implying potential roles in adaptive evolution associated with ecological behavior. Furthermore, the olfactory-related gene oard1 exhibited Ka/Ks > 1 in the E. bambusa vs. C. idella comparison. qRT-PCR validation confirmed the reliability of the RNA-Seq data. This work is the first to integrate two complementary indicators—expression trends and evolutionary rates—to systematically investigate the transcriptional regulation and molecular evolution of the olfactory system in Xenocyprididae species under the context of dietary differentiation, providing valuable reference data for understanding the perceptual basis of dietary adaptation in freshwater fish. Full article

Background: Grassland desertification has garnered significant attention as a pressing issue. Among the key pests affecting plateau meadows, the Gynaephora qinghaiensis (Lepidoptera: Lymantriidae) poses a substantial threat in the Qinghai-Tibet Plateau region, highlighting the urgent need for effective, environmentally friendly control strategies. Insect sex pheromones are increasingly employed in pest monitoring and management. Methods: This study aims to identify and analyze genes associated with sex pheromone synthesis in grassland caterpillars through transcriptome sequencing and tissue-specific expression analysis. Results: A total of 139,599 transcripts and 56,403 Unigenes were obtained from the sex pheromone glands transcriptome database. A total of 31 genes related to sex pheromone synthesis were identified, including 1 ACC, 8 DES, 6 AR, 7 FAR, 5 FAS, and 4 ACT genes. The expression levels of these genes varied significantly across different tissues in both male and female caterpillars (p < 0.05). GqinACC1, GqinDES1, GqinDES4, GqinDES8, GqinAR3, GqinFAR6, GqinACT2, and GqinACT3 exhibited significantly higher expression levels in the female gonads compared to other tissues (p < 0.01). Conclusions: We hypothesize that specific genes play specific roles in the pheromone synthesis pathways of pests, Key genes were identified based on expression patterns for subsequent functional studies. The results of this study offer valuable data support for subsequent investigations into the mechanisms underlying sex pheromone synthesis in G. qinghaiensis. Additionally, these findings may identify potential targets for future research on genes associated with pheromone biosynthesis, which could disrupt their chemical communication and contribute to grassland conservation efforts. Full article

Background: Indigofera pseudotinctoria, a traditional Chinese forage and medicine widely used in East Asia, holds significant economic and agricultural value. Despite this, genomic information regarding I. pseudotinctoria remains conspicuously lacking. Methods: In this study, we utilized genome survey sequencing to elucidate the complete genome sequence of this species. Results: The genome size of I. pseudotinctoria to be around 637–920 Mb with a heterozygosity rate of 0.98% and a repeat rate of 66.3%. A total of 240,659 simple sequence repeat (SSR) markers were predicted in the genome of I. pseudotinctoria. Substantial differences were observed among nucleotide repeat types, for instance, mononucleotide repeats were found to be predominant (62.47%), whereas pentanucleotide repeats were notably scarce (0.24%). Furthermore, among dinucleotide and trinucleotide repeats, sequence motifs AT/AT (66.57%) and AAT/ATT (54.15%) were found to be particularly abundant. Among the identified unigenes, 58,790 exhibited alignment with known genes in established databases, including 33,218 genes within the Gene Ontology (GO) database and 10,893 genes in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Conclusions: This study marks the first attempt to both sequence and delineate the genomic landscape of I. pseudotinctoria. Importantly, it will serve as a foundational reference for subsequent comprehensive genome-wide deep sequencing and the development of SSR molecular markers within the scope of I. pseudotinctoria research. Full article

Due to limited land resources and traditional farming practices, continuous cassava cropping is common in China. This practice leads to soil degradation, including reduced fertility, imbalanced microbial communities, and lower crop yields. In this study, we investigated the impacts of continuous cassava cropping (CC) and cassava–maize rotation (RC) systems on soil physicochemical properties, microbial community composition, and functional gene abundance related to carbon and nitrogen cycling. The RC system consists of a five-year rotation cycle: cassava is planted in the first year, followed by two consecutive years of maize, and then, cassava is planted again in the last two years. The soil type is classified as Haplic Acrisols with a clay loam texture in this research. Soil samples from both cropping systems were analyzed for physicochemical properties and enzyme activities, and the results showed significant decreases in soil pH, available nitrogen, available phosphorus, and available potassium in CC. Using metagenomic sequencing, 1,280,928 and 1,224,958 unigenes were identified under RC and CC, respectively, with differences in microbial taxonomic and functional profiles. Bacteria accounted for 89.257% of the soil community in RC, whereas the proportion was 88.72% in CC. The proportions of eukaryota and viruses in RC were 0.031% and 0.006%, respectively; in contrast, their proportions were 0.04% and 0.02% in CC, respectively. Cassava–maize rotation promoted the metabolic activities of soil microbes, leading to a significant enhancement in functional genes related to nitrogen and carbon cycling, such as nasA, nasD, nrtC, coxA, porA, and frdA. This shows that microbial activity and nutrient cycling improved in the crop rotation system. Thus, these findings highlight the importance of crop rotation for maintaining soil health, enhancing microbial functions, and improving sustainable cassava production. This study provides valuable insights into the management of cassava agroecosystems and the mitigation of the adverse effects of continuous cropping. Full article

The nutritional value of lipids depends not only on their fatty acid composition but also on their stereospecific positioning on the glycerol backbone. This study investigated the fatty acid composition and sn-2 positional distribution of triacylglycerols (TAG), as well as the composition of major phospholipids in golden pompano (Trachinotus ovatus) juveniles (initial weight: 10 g) fed five diets including graded levels of dietary n-3 highly unsaturated fatty acids (HUFA; 0.64–2.10%) for 56 days. With increasing dietary n-3 HUFA levels, the proportions of eicosapentaenoic acid (EPA), docosapentaenoic acid (DPA), docosahexaenoic acid (DHA), and total n-3 HUFA in muscle TAG, phosphatidylcholine (PC), and phosphatidylethanolamine (PE) significantly increased. Phospholipids, especially PC and PE, were preferentially enriched with n-3 HUFA, and the sn-2 positions of TAG showed a significantly increased deposition of DHA and reduced n-6/n-3 ratios. RNA-Seq analysis was performed on muscle tissues of T. ovatus subjected to different dietary n-3 HUFA levels to further investigate the molecular mechanisms of lipid compositional and structural changes. A total of 126,792 unigenes were obtained, of which 47.78% were successfully annotated. KEGG pathway enrichment analysis implicated the glycerophospholipid, glycerolipid, and sphingolipid metabolism pathways in lipid composition and distribution regulation, identifying gpat4, agpat3, agpat8, lpeat1, and lpgat1 as potential regulators. These findings offer insights into lipid remodeling in marine fish and support strategies to enhance aquaculture product quality. Full article

Thesium chinense Turcz. (T. chinense), a perennial herb in the Santalaceae family, exhibits potent antibacterial and anti-inflammatory properties. Transcriptome sequencing was performed on one- and two-year-old T. chinense plants across seedling, flowering, and fruiting stages (all sampled from the same location) using the illumina NovaSeq 6000 platform. A total of 58,706 unigenes were identified, including 1656 transcription factors (TFs). Further analysis classified these TFs into seven functional categories, enabling the reconstruction of a representative TF regulatory network. Differential expression analysis revealed that the number of differentially expressed genes (DEGs) ranged from 2000 to 5000 during different developmental stages in first-year plants, while varying between 1000 and 2000 in second-year plants. Comparative analysis of DEGs between one- and two-year-old plants showed that they were primarily associated with sesquiterpene, triterpene, and terpene skeleton biosynthesis, as well as other metabolic pathways. Additionally, analysis of key genes involved in flavonoid biosynthesis—the major bioactive compounds in T. chinense—revealed their predominant accumulation during the first year of growth. This study provides valuable insights into the developmental biology of T. chinense and establishes a foundation for future research on flavonoid biosynthesis pathway genes and their therapeutic applications. Full article

Flowering is a key agronomic trait that directly influences the yield of the tea-oil tree (Camellia oleifera). Floral initiation, which precedes flower bud differentiation, represents a critical developmental stage affecting the flowering outcomes. However, the molecular mechanisms underlying floral initiation in C. oleifera remain poorly understood. In this study, buds from five key developmental stages of a 12-year-old C. oleifera cultivar ‘changlin53’ were collected as experimental samples. Scanning electron microscopy was employed to identify the stage of floral initiation. UPLC-MS/MS was used to analyze endogenous gibberellin (GA) concentrations, while transcriptomic analysis was performed to reveal the underlying transcriptional regulatory network. Six GA types were detected during floral initiation and petal development. GA₄ was exclusively detected at the sprouting stage (BII), while GA₃ was present in all samples but was significantly lower in BII and the flower bud primordium formation stage (BIII) than in the other samples. A total of 64 differentially expressed genes were concurrently enriched in flower development, reproductive shoot system development, and shoot system development. Weighted gene co-expression network analysis (WGCNA) identified eight specific modules significantly associated with different developmental stages. The magenta module, containing Unigene0084708 (CoFT) and Unigene0037067 (CoLEAFY), emerged as a key regulatory module driving floral initiation. Additionally, GA20OX1 and GA2OX8 were identified as candidate genes involved in GA-mediated regulation of floral initiation. Based on morphological and transcriptomic analyses, we conclude that floral initiation of C. oleifera is a continuous regulatory process governed by multiple genes, with the FT-LFY module playing a central role in the transition from apical meristem to floral meristem. Full article

Camellia azalea is an endemic species within the genus Camellia that exhibits the trait of summer flowering, which is of significant ornamental and research value. Nevertheless, research on the regulatory mechanisms of flower formation in C. azalea is still limited, so in this study, transcriptome sequencing and analysis of endogenous hormone contents were conducted at three distinct growth stages: floral induction, floral organ maturation, and anthesis. Illumina sequencing yielded a total of 20,643 high-quality unigenes. Comparative analyses of representative samples from the three growth stages identified 6681, 1925, and 8400 differentially expressed genes (DEGs), respectively. These DEGs were further analyzed for functional enrichment using the GO and KEGG databases. Additionally, core genes from each flowering pathway underwent expression pattern analysis and network diagram construction. This revealed that the flower development process in C. azalea is linked to the specific expression of the genes involved in the photoperiod, temperature, and autonomous pathways and is subject to comprehensive regulation by multiple pathways. Further analysis of the dynamic trends of five endogenous hormone contents and plant hormone signal transduction genes revealed significant differences in the requirements of endogenous hormones, such as gibberellins and indoleacetic acid, by C. azalea at distinct growth stages. Additionally, the majority of genes on the phytohormone signal transduction pathway demonstrated a high correlation with the changes in the contents of each hormone. The present study integrates physiological and molecular approaches to identify key genes and metabolic pathways that regulate the summer flowering of C. azalea, thereby laying a theoretical foundation for further investigations into its flowering mechanism and related functional genes. Full article

Megalobrama terminalis is a significant aquatic fish in South China, renowned for its tasty meat. Nonetheless, related studies are deficient concerning the gonadal development of M. terminalis. This paper presents the first comparative transcriptome analysis of the gonads of female and male M. terminalis. A total of 84,886 unigenes were assembled, with 42,322 effectively annotated to the Nr, SwissProt, KEGG, KOG, and GO databases. Furthermore, comparative transcriptomic analysis of M. terminalis was conducted to examine its gonadal development. A total of 14,972 differentially expressed genes (DEGs) were discovered. In the testis, the expression of 11,928 unigenes was significantly upregulated, while 3044 were significantly downregulated. Numerous DEGs associated with steroidogenesis, gonadal differentiation and development, and gametogenesis in teleost fish were identified. The results provide empirical support for further study of genes and pathways associated with sex determination and gonadal differentiation in teleost fish. Full article