Search Results (301)

Disparities in the functional classification of secretory genes among aphid taxa may be attributed to variations in coding sequences and gene expression profiles. However, the driving factors that regulate sequence evolution remain unclear. This study aimed to investigate the differences in coding sequences and expression patterns of secretory genes between the rose grain aphid (Metopolophium dirhodum) and the pea aphid (Acrythosiphon pisum), with a particular focus on their roles in evolutionary adaptations and functional diversity. The study involved the rearing of aphids, RNA extraction, de novo transcriptome assembly, functional annotation, secretory protein prediction, and comparative analysis of coding sequences and expression patterns across various functional categories using bioinformatics tools. The results revealed that metabolic genes exhibited greater coding sequence divergence, indicating the influence of positive selection. Moreover, significant expression divergence was noted among functional categories, particularly in metabolic and genetic information processing genes, which exhibited higher variability. This study enhances our understanding of the molecular mechanisms that contribute to phenotypic and genetic diversity among aphid species. This study elucidates the relationship between variations in coding sequences and differences in gene expression among functional categories, thereby establishing a foundation for future studies on gene evolution in response to environmental pressures. 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

Background: Gloriosa superba L., commonly known as Glory Lily, is a medicinally valuable perennial climber native to tropical and subtropical regions of India. It is known for its rich alkaloid content, including colchicine and colchicoside, which contribute to its therapeutic potential in treating various ailments. Despite its pharmacological significance, genomic research on G. superba remains limited due to the lack of genetic markers, hindering molecular studies and breeding advancements. Methods: This study utilized a previously reported de novo transcriptome assembly of G. superba, identifying 14,672 EST-SSRs as genomic markers to assess genetic variations across different accessions. Genetic diversity was examined using SSR markers, while 20 morphological traits were systematically evaluated across 19 G. superba accessions from diverse geographic regions to provide insights into trait variability. Results: The most highly variable traits included plant height, number of leaves per plant, number of branches per plant, fresh pod yield, fresh seed yield, dry seed yield, number of pods per plant, leaf width, and internodal length, with coefficients of variation (CV) ranging from 63.53% to 22.45%. Intermediate CV values (10.05% to 18.75%) were observed in eight traits, while three traits (days to flowering, days to 50% flowering, and colchicine content) had low variation (<5%). Principal component analysis (PCA) accounted for 51.3% of phenotypic variation, with PC1 and PC2 contributing 29.4% and 21.9%, respectively. Clustering analysis grouped the 19 G. superba accessions into two main clusters and four sub-clusters, highlighting significant genetic divergence, with the highest dissimilarity (81.45%) observed between accessions from Arrupukottai and Pachmarhi. SSR analysis using 112 markers revealed high polymorphism but a relatively low heterozygosity index (H = 0.277) and PIC values of individual SSRs ranged from 0.26069 in RGM-51635 to 0.4534 in RGM-24219. Conclusions: The genetic divergence observed among the collected G. superba ecotypes provides valuable insights for future breeding programs aimed at enhancing cultivation efficiency and developing superior varieties with improved yield and colchicine content. Full article

Spinach (Spinacia oleracea L.) is an important leafy vegetable but is vulnerable to viral infections that significantly affect its quality and yield. In this study, we identified virus-infected spinach exhibiting typical symptoms with yellowing, wrinkling, and mottling in Beijing. But conventional RT-PCR screening for twelve common plant viruses yielded negative results. Then, using transcriptome sequencing along with a de novo assembly approach, we obtained the complete viral genome, which consists of RNA1 (5916 nucleotides) and RNA2 (3576 nucleotides). BLASTN analysis against the NCBI viral genome database revealed high homology with broad bean wilt virus 2 (BBWV2), leading us to designate this isolate as BBWV2-SP (GenBank accession numbers PV102464 and PV102465). Phylogenetic analysis indicated that BBWV2-SP shares 96.69% nucleotide sequence identity with a Liaoning isolate from Chenopodium album MN786955 and clusters within the Chinese evolutionary lineage. We developed primers targeting the conserved region of the RNA2 coat protein, amplifying a 478-base-pair product. All symptomatic spinach samples tested positive, while asymptomatic controls remained negative, confirming the causal relationship between BBWV2-SP and the observed disease symptoms. This study provides the complete genome assembly of the spinach isolate BBWV2-SP and establishes a molecular detection protocol for BBWV2 in spinach. These findings offer essential technical support for field monitoring, epidemiological surveillance, and disease control strategies, while also enhancing our understanding of BBWV2′s genetic diversity and mechanisms of pathogenicity. Full article

Taraxacum, a genus in the Asteraceae family, is widely distributed across temperate regions and plays a vital ecological role by providing nectar and pollen to pollinators during the early flowering season. Floral nectar is a key reward that plants use to attract pollinators, and its production is tightly regulated by genes such as SWEET sugar transporters and CELL WALL INVERTASE (CWIN), which govern sugar efflux and hydrolysis. Despite their ecological importance, the molecular mechanisms underlying nectar secretion in Taraxacum remain poorly understood. In this study, we performed RNA sequencing of flower tissues from five Taraxacum species—T. coreanum, T. monogolicum, T. ohwianum, T. hallaisanense, and T. officinale—to investigate the expression of nectar-related genes. De novo transcriptome assembly revealed that T. coreanum had the highest unigene count (74,689), followed by T. monogolicum (69,234), T. ohwianum (64,296), T. hallaisanense (59,599), and T. officinale (58,924). Functional annotation and phylogenetic analyses identified 17 putative SWEET and 18 CWIN genes across the five species. Differential gene expression analysis highlighted tarSWEET9 and tarCWIN4 as consistently up-regulated during the flowering stage. Quantitative PCR in T. officinale further validated that tarSWEET9, tarCWIN4, tarCWIN6, and tarSPAS2 show significant expression during floral development but are down-regulated after pollination. These genes are likely central to the regulation of nectar secretion in response to pollination cues. Our findings suggest that T. officinale may have evolved to have an efficient, pollinator-responsive nectar secretion system, contributing to its global adaptability. This study sheds light on how pollinator interactions influence gene expression patterns and may drive evolutionary divergence among Taraxacum species. Full article

Schistosomiasis remains a major global public health challenge. Bulinus serves as an intermediate host for Schistosoma, including S. haematobium, S. intercalatum, and S. guineensis. Emerging evidence suggests that temperature fluctuations associated with global climate change are key factors influencing the survival and distribution of Bulinus. The ecological shifts in intermediate host snails may significantly influence schistosomiasis transmission dynamics, thereby exacerbating threats to human health. However, the physiological effects of temperature stress on the survival of B. globosus at the molecular level, including gene expression and underlying mechanisms, remain unclear. Our experimental study found that extreme temperature stress significantly reduced the survival rates of Bulinus globosus (B. globosus). De novo transcriptome sequencing revealed key genes associated with lipid metabolism, carbohydrate metabolism, homeostasis regulation, and the antioxidant system. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis identified significant enrichment of differentially expressed genes (DEGs) in heat shock protein pathways, propanoate metabolism, and N-acylethanolamine metabolism pathways. Overall, this work provides the first transcriptomic characterization of the thermal stress response in B. globosus, extending genomic resources for annotation and stress-related gene discovery. These findings establish a solid foundation for developing control strategies to mitigate climate-driven risks of schistosomiasis transmission. Full article

Sapindus delavayi is a drought-resistant tree species endemic to the dry–hot valleys of Southwestern China and is of great significance for soil and water conservation and ecological restoration. In this study, we sequenced the transcriptome of its leaves using the Illumina HiSeq 4000 platform and obtained 96.12 Gb of high-quality data (Q20 = 98.68%, Q30 = 95.62%), which were de novo assembled to obtain 89,228 unigenes (N50 = 1538 bp), of which 63,005 (70.61%) were successfully annotated to at least one database (NR, NT, SwissProt, KOG, KEGG, GO, Pfam). Overall, 53.96% of the unigenes in the S. delavayi leaves were annotated to Acer yangbiense, which belongs to the same family as S. delavayi. A total of 42,870 CDSs and 21,488 SSR loci were detected, with the highest mononucleotide repeat rate at 42.72% of the total number. Drought stress experiments identified 669–1203 differentially expressed genes (DEGs). Through our research, the first high-quality transcriptome database of S. delavayi has been constructed and its drought-resistance-related gene features have been analyzed, laying an important foundation for future functional gene mining, molecular marker development, molecular diversity studies, molecular breeding, and ecological adaptation research. Full article

Edwardsiella tarda is a gram-negative bacterium reported to be one of the most harmful pathogens in aquaculture. In this study, we conducted transcriptome profiling of the head kidney, liver, and spleen in spotted sea bass (Lateolabrax maculatus) infected with E. tarda. A total of 22,015 unigenes were detected by de novo assembly and annotated by comparison with the major databases (NR, GO, COG, KEGG, Swiss-Prot), with 21,065 (NR:95.68%), 11,320 (GO:51.42%), 20,464 (COG:92.95%), 21,295 (KEGG:96.73%), 18,791 (Swiss-Prot:82%). Subsequently, a substantial number of differentially expressed genes (DEGs) were identified (p-adjust < 0.05). In the head kidney, liver, and spleen, there were 1302 upregulated genes and 503 downregulated genes, 377 upregulated genes and 530 downregulated genes, and 1240 upregulated genes and 736 downregulated genes, respectively. Additionally, the expression levels of eight immune-related DEGs were validated by qRT-PCR, further verifying the reliability of the transcriptome data. To the best of our knowledge, this is the first analysis of the transcriptome profile of L. maculatus in response to E. tarda. These findings not only offer fundamental insights into the antibacterial immune mechanisms of spotted sea bass but also serve as a reference for formulating more effective fish disease management strategies. Full article

Despite its ecological and economic importance, many aspects of Varroa destructor’s biology remain poorly understood, particularly its defense mechanisms against pathogens. The limited knowledge of Varroa’s immunity has hindered the development of RNA interference (RNAi)-based strategies targeting immune-related genes. In this study, we investigated the immune gene repertoire of V. destructor by querying its NCBI nr protein database and comparing it to model species of ticks (Ixodes scapularis) and mites (Galendromus occidentalis and Tetranychus urticae). Transcription of candidate immune genes was confirmed by analyzing a de novo assembled transcriptome of V. destructor. Our findings reveal that V. destructor shares key immunological traits with ticks, including lysozymes, chitinases, and thioester-containing proteins (TEPs), but also shares the absence of transmembrane peptidoglycan recognition proteins (PGRPs), Gram-negative binding proteins, and several lectin families involved in pathogen recognition. Additionally, Varroa mites, like ticks, lack homologs of crucial immune signaling components, such as the unpaired ligand (JAK/STAT), Eiger (JNK), and multiple elements of the IMD pathway. They also do not encode canonical antimicrobial peptides (AMPs) like defensins but possess putative homologs of ctenidins, AMPs previously identified in spiders and ticks, which may be adopted as a novel genetic readout for immune response in mites. Our findings lay the groundwork for future functional studies on mite immunity and open new avenues for RNAi-based biocontrol strategies targeting immune pathways to enhance Varroa management. Full article

Acrossocheilus parallens has become an important commercial aquaculture species in southern China due to its high nutritional content and ornamental value. However, at present, there is very little research on its gonad development and reproductive regulation, which has restricted the development of its aquaculture industry. In this research, the gonadal transcriptome sequencing data of female and male A. parallens were first analyzed and compared. A total of 67,251 unigenes were successfully assembled and a total of 34,069 unigenes were annotated. After the comparative transcriptome analysis, a sum of 14,514 differentially expressed genes (DEGs) were identified between the male and female gonads, with 9111 having significantly high expression in the testes and 5403 having high expression in the ovaries. Additionally, 82 DEGs related to reproduction, gonad development and differentiation in the gonads were identified and the differential expression profiles of partial genes were further validated using real-time fluorescence quantitative PCR. These results provide basic data for further research on the functions of the genes and pathways related to sex differentiation and gonad development in A. parallens. Full article

Agropyron michnoi is a perennial grass with rhizomes in the genus Agropyron. It has a strong tolerance to drought and low temperature, and it is an established species in sandy flat and hilly slope lands, which constitute sandy grassland. So, it is an important forage species in dry grassland and desert steppes. Rhizomes not only enable asexual reproducibility but also confer strong resilience to stresses in A. michnoi. However, during production and utilization, it has been found that there are significant differences in the development of rhizomes among individuals of A. michnoi, yet the regulatory mechanism remains unclear. Therefore, in this study, the A. michnoi ‘Baiyinxile’ was used as the material, and the anatomical structures of the rhizomes, roots, and stems were analyzed using the paraffin sectioning technique. The results showed that the anatomical structure composition of the cross-section of the rhizome was similar to that of the root, while the arrangement of the vascular bundles in the stele was different from that of the root but similar to that of the stem. Subsequently, the Agropyron michnoi plants were classified into two types: plants with rhizomes and plants without rhizomes. Root, stem, and rhizome samples were collected from each type, and RNA sequencing was conducted. De novo transcriptomic analysis was performed to identify the candidate genes involved in rhizome development. From the RNA sequencing, a total of 103.73 Gb clean bases were obtained, from which 215,282 unigenes with an average length of 905.67 bp were assembled. Among these unigenes, 161,175 (74.87%) were functionally annotated based on seven common public databases. From pairwise comparisons of differentially expressed genes between the five samples, 129 candidate genes that are potentially specifically expressed in rhizomes were selected. Pathway enrichment analysis revealed that the rhizome-expressed genes are highly enriched in pathways of phenylpropanoid biosynthesis and starch and sucrose metabolism. The rhizome-specific expression pattern of 10 of the 129 candidate genes was further validated using qRT-PCR. Through the analysis of metabolites, 11 metabolites closely related to rhizome development, such as choline and betaine, were successfully identified. CYP family genes were selected for functional verification, and phylogenetic analysis revealed that CYP86B1 was grouped with CYP 86B1 of species such as Triticum aestivum and Lolium rigidum and was named AmrCYP86B1. The cloning results showed that its size was 1599 bp, and its subcellular localization was in the endoplasmic reticulum. Through stable genetic transformation, the study found that AmrCYP86B1 can promote the development of plant roots and stems and increase the dry matter content of the roots. Hormone detection showed that overexpression of AmrCYP 86B1 decreased the content of ABA hormone and increased the content of GA3 hormone in the plants. Combined with previous studies, it was determined that AmrCYP 86B1 promoted rhizome elongation by regulating ABA and GA3 hormones. The selected candidate genes involved in rhizome development, along with the preliminary functional verification, provide a preliminary mechanistic interpretation of rhizome development. This will contribute to in-depth research on the molecular mechanism of rhizome development in A. Michnoi. Full article

In the Philippines, Bombyx mori parental strains Lat21 and B221 are crossed to yield NC144 and CN144, which demonstrate hybrid vigor. The molecular basis of the observed vigor in the hybrids is warranted, as it may assist in improving local sericulture programs. This study, therefore, aims to investigate the basis of hybrid vigor and generate molecular resources through whole-silkworm larvae transcriptome sequencing, assembly, and analysis. Differential gene expression was also conducted among the parental strains and hybrids. Assembly of the pre-processed reads was also performed using de novo and reference-based protocols. As expected, the reference-based assembly was better than de novo, based on E90N50, N50, and BUSCO assembly completeness metrics. The Analysis of the differentially expressed genes (DEGs) revealed 202 upregulated and 182 downregulated genes in the hybrids (with the parents as the reference) and 66 upregulated and 753 downregulated genes in NC144 (with CN144 as the reference). Among these were genes encoding heat shock proteins and antimicrobial peptides, which may serve as markers for marker-assisted breeding. The genes were further validated using quantitative real-time PCR. Moreover, the inducible nature of these genes under stressors like extreme temperature and bacterial exposure suggests their potential as diagnostic tools for stress assessment. Full article

Coast Live Oak (Quercus agrifolia) is a native keystone hardwood species of the California coastal and semi-arid forest environment. Q. agrifolia is threatened by pathogens such as the oomycete Phytophthora ramorum, which is known to cause Sudden Oak Death in environments from Southern California to Oregon. This study considers oaks and their rootzone microbes recovering from moderate and low-intensity fires in rapid succession, compared to high- and low-intensity fires with a large time gap between them. cDNA libraries from nine oak leaf tissue samples were sequenced on DNBseq. Soil samples were sent out for shotgun metagenomics and for 16S community profiling. The de novo Q. agrifolia assembly yielded 521,817 transcripts with an average length of 805.2 bp. Among identified DEGs (differentially expressed genes) between the trail areas, several candidate genes were identified including shikimate dehydrogenase and myrcene synthase. The MegaBLAST results showed a high degree of similarity to WGS sequences from Q. agrifolia that had been previously annotated in other closely related Quercus species. There was a differential abundance of microbial genera associated with the different burn areas, including Pedobacter, Filimonas, Cohnella, and Sorangium. The data embody the first Q. agrifolia transcriptome that with further development could be used to screen oak seedlings for resistance; beneficial microbial populations have been identified that are associated with fire recovery under varied conditions. Full article

Rhododendron decorum, a widely distributed Rhododendron species in southwestern China, is recognized not only for its significant ornamental value but also as a culinary resource for local tribes. However, the defense mechanisms underlying the ecological adaptations of R. decorum remain to be elucidated. In this study, we conducted comparative transcriptomic analyses of various organs (corolla, androecium/gynoecium and leaves) of R. decorum collected from two distinct two regions. Approximately 186.98 Gb of clean data were generated from three organs of R. decorum across these regions. Through de novo assembly, a total of 92,025 unigenes were obtained and nearly half of them (43,515 unigenes) were successfully annotated. Enrichment analysis of differentially expressed genes (DEGs) within three comparative groups of different organs (HQI/LFI, HQO/LFO and HQL/LFL, respectively) revealed that the distribution of R. decorum in the Heqing region exhibited an increased requirement for plant immunity, including resistance to diseases, insects, and herbivores across various plant organs. Conversely, R. decorum in the Lijiang region showed a greater reliance on environmental factors, such as cold tolerance, aromatic compounds production, and the attraction of pollinating insects. Notably, the validation of 21 pivotal genes identified from significantly regulated enrichment pathways across different organs showed functional consistency in the KEGG enrichment analysis among different organs in these two regions. The functional disparities observed in the transcriptome of R. decorum across distinct regions provide valuable insight into the understanding of its adaptive defense mechanism. Full article

Daldinia carpinicola is a newly identified species of wood-rotting fungi, with substantial aspects of its biology and ecological function yet to be clarified. A Nanopore third-generation sequencer was employed for de novo genome assembly to examine the genetic characteristics. The genome consisted of 35.93 Mb in 46 contigs with a scaffold N50 of 4.384 Mb. Glycoside hydrolases and activities enzymes accounted for a large proportion of the 522 identified carbohydrate-active enzymes (CAZymes), suggesting a strong wood degradation ability. Phylogenetic and comparative analysis revealed a close evolutionary relationship between D. carpinicola and D. bambusicola. D. carpinicola and Hypoxylon fragiforme exhibited significant collinear inter-species genome alignment. Based on transcriptome and metabolomic analyses, D. carpinicola showed a greater ability to utilize sucrose over sawdust as a carbon source, enhancing its growth by activating glycolysis/gluconeogenesis and the citrate cycle. However, compared with sucrose, sawdust as a carbon source activated D. carpinicola amino acid biosynthesis and the production of various secondary metabolites, including diterpenoid, indole alkaloid, folate, porphyrin, and biotin metabolism. The study establishes a theoretical basis for research and applications in biological processes, demonstrating a strategy to modulate the production of secondary metabolites by altering its carbon sources in D. carpinicola. Full article