Tissue-specific Expression Patterns Research Articles

Tissue-specific transcriptome analyses unveils candidate genes for flavonoid biosynthesis, regulation and transport in the medicinal plant Ilex asprella

It is not clear that the genes involved with flavonoids synthesis, regulation and transport in Ilex asprella. Transcriptome analysis of leaf, stem and root has uncovered 28,478 differentially expressed genes (DEGs) that are involved in various biological processes. Among these, the expression of 31 candidate synthetase genes, 19 transcription factors, and 5 transporters associated with flavonoid biosynthesis varies across tissues, encompassing seven complete biosynthetic pathways (stilbene, aurone, flavone, isoflavone, flavonol, phlobaphene, and anthocyanin) and one partial pathway (proanthocyanidin). Tissue-specific expression patterns suggest that the stilbenes, aurones, flavones and anthocyanin branches are more prominent in roots, as indicated by key genes such as STS(Ilex_044726), CH4ʹGT(Ilex_047989), FNS(Ilex_043640) and UFGT(Ilex_014720). In leaves, the phlobaphenes and flavonols branches are dominant, determined by CHI(Ilex_005941), FNR(Ilex_039777) and FLS(Ilex_046424). The isoflavone pathway appears to be more active in stems due to the presence of IFS(Ilex_029360), mirroring the accumulation of the intermediate metabolite chalcone, which is regulated by CHS(Ilex_047537). The absence of LAR genes implies that gallocatechin, and catechin liked proanthocyanidins cannot be synthesized in I. asprella. Meanwhile, the general phenylpropanoid pathway is more active in roots, stems than in leaves, as evidenced by the expression of PAL(Ilex_042231, Ilex_014816), C4H(Ilex_017598), and 4CL(Ilex_042033). Flavanone, dihydroflavonol and leucoanthocyanidin, key intermediates, accumulate more rapidly in stem, stem and root, respectively, regulated by CHI(Ilex_005941), F3H(Ilex_004635) and DFR(Ilex_004771). Correlation and network analyses reveal that candidate regulators and transporters are closely associated with the synthesis genes. The study provides profound snoop into flavonoids metabolism in I. asprella and offers valuable refer for medicinal plant.

Evolutionary Insights and Expression Dynamics of the Glutathione Peroxidase (GPX) Gene Family in Water lily (Nymphaea colorata) in Response to Multiple Abiotic Stresses

The glutathione peroxidase (GPX) family in plants contains various isoenzymes, each with distinct subcellular localizations, tissue-specific expression patterns, and responses to environmental stress. In current study, we conducted genome-wide bioinformatics analyses of the GPX gene family in Nymphaea colorata, identifying five putative NcGPX genes dispersed across five of the fourteen chromosomes. Examination of the protein sequences revealed that NcGPXs comprehend three conserved cysteine residues, with predicted in-silico subcellular localizations in chloroplast, extracellular, or cytoplasm. We reported that NcGPX genes protein lengths and molecular weight (MW) ranged from 171-248 amino acids (aa) and 18.798-27.076 kDa, respectively. A comparative neighbor-joining phylogenetic study revealed that GPX genes were clustered into four main groups (Group A– D) from water lily and two closely related plant species, alongside with Arabidopsis thaliana. The universal analysis showed that segmental duplications occurred within the NcGPX gene family. Investigation of gene structure and motifs suggested that most NcGPX genes have relatively conserved exon-intron structures and motif arrangements. Promoter region exploration of NcGPX genes revealed numerous cis-acting regulatory elements associated with development, stress, and hormone responses. The identified 3D protein structures showed that water lily GPXs form conserved dimeric protein signatures. Finally, gene expression and enzymes accumulation of NcGPXs in response to different abiotic stresses, in leaves of N. colorata were analysed using real-time RT-qPCR and spectrophotometry. The results indicate that different members of the GPX gene family are co-ordinately regulated under specific environmental stress conditions, establishing a foundation for studying their gene functions and improving abiotic stress tolerance in water lily genetic breeding.

Tissue-specific, temporal, and core gene-dependent expression patterns of Hsp70s reveal functional allocation in Chlamys farreri under heat stress

Heat shock proteins 70 KDa (Hsp70s) engage in a broad spectrum of cellular functions in response to various stressors. Marine bivalves face substantial threats from the rising seawater temperature attributed to global warming. In the present study, expression patterns of Hsp70s in Zhikong scallop Chlamys farreri (CfHsp70s) were determined in embryos and larvae at all developmental stages, in healthy adult tissues, and across four various tissues exposed to high temperature for acute and chronic periods through in silico analysis. Spatiotemporal expressions suggested CfHsp70s performed specific functional differentiations in scallop's development and growth. Regulatory expression patterns of CfHsp70s, characterized by predominant down-regulation in the mantle, gill and hemocytes, as well as contrasting up-regulation in the heart, suggest differential functional allocation of CfHsp70s among tissues in response to heat stress. Particularly, a core set of 14 CfHsp70s, especially the nine members of the Hsp70B2s, characterized by gene expansion, intron-less structure, shorter gene length, preference for hydrophilic amino acids, and coordinated expression profiles, was predominantly responsible for the inducible up-regulations observed across all four tissue types. Collectively, the tissue-specific, temporal and core gene-dependent expression patterns of CfHsp70s illustrate the functional allocation and molecular evolution of Hsp70 family members in Zhikong scallops.

Genome-Wide Identification and Characterization of bHLH Gene Family in Hevea brasiliensis

The basic helix-loop-helix (bHLH) transcription factors play crucial roles in plant growth, development, and stress responses. However, their identification and insights into the understanding of their role in rubber trees remain largely uncovered. In this study, the bHLH gene family was explored and characterized in rubber trees using systematic bioinformatics approaches. In total, 180 bHLH genes were identified in the rubber tree genome, distributed unevenly across 18 chromosomes, and phylogenetic analysis classified these genes into 23 distinct subfamilies. Promoter regions revealed a high density of cis-elements responsive to light and hormones. Enrichment analysis indicated involvement in numerous biological processes, including growth, development, hormone responses, abiotic stress resistance, and secondary metabolite biosynthesis. Protein interaction network analysis identified extensive interactions between HbbHLH genes and other functional genes, forming key clusters related to iron homeostasis, plant growth, and stomatal development. Expression profiling of HbbHLH genes have demonstrated varied responses to endogenous and environmental changes. RT-qPCR of eleven HbbHLH genes in different tissues and under ethylene, jasmonic acid, and cold treatments revealed tissue-specific expression patterns and significant responses to these stimuli, highlighting the roles of these genes in hormone and cold stress responses. These findings establish a framework for exploring the molecular functions of bHLH transcription factors in rubber trees.

Identification of the NAC Family and a Functional Analysis of NoNAC36a Under Flooding Stress in Watercress (Nasturtium officinale R.Br.)

Watercress (Nasturtium officinale R.Br.) is a cruciferous aquatic vegetable that possesses significant nutritional value. The NAC family is a transcription factor family specific to plants that play an important role in regulating plant responses to abiotic stress. In order to investigate the response of NAC genes to flooding stress in watercress, we conducted a study on the NoNAC family. In this study, a total of 119 NoNAC genes were obtained through genome-wide identification. Phylogenetic analysis indicated that the NoNAC family members can be categorized into ten subgroups. The results of gene structure analysis revealed that each branch within the subgroups exhibited similar motif composition and gene structure. The heatmap analysis showed that several NoNAC genes demonstrated tissue-specific expression patterns, suggesting their potential as regulators of associated tissue development. As an aquatic plant, watercress serves as a valuable material for investigating plant resistance to flooding stress. This study found that flooding can significantly increase the watercress plant height, which is a typical escape strategy under flooding. The analysis of the expression of NoNAC genes in the stem transcriptome after flooding indicated that only NoNAC36a consistently exhibited significant differential changes and down-regulated expression at the three time points of flooding treatment. This suggests that NoNAC36a may be involved in regulating watercress plant height increases under flooding stress. The utilization of a virus-induced gene silencing assay to investigate the biological function of NoNAC36a revealed that NoNAC36a silencing caused cell elongation and expansion, thus increasing watercress plant height. The yeast one-hybrid and dual luciferase assays demonstrated that NoNAC36a binds the promoter of NoXTH33 and inhibits its expression. Subsequently, the results of yeast two-hybrid, luciferase complementary, and pull-down assays revealed the interaction between NoMOB1A and NoNAC36a in vivo and in vitro. Sequence alignment indicated that NoMOB1A and AtMOB1A share an identical amino acid sequence. RT-qPCR analysis indicated that flooding prompted the expression of NoMOB1A in stems. Thus, it is speculated that NoMOB1A may exhibit functions similar to AtMOB1A and that the up-regulation of NoMOB1A expression in stems may facilitate an increase in plant height under flooding. In summary, the NoNAC family was analyzed, and revealed a regulatory network centered on NoNAC36a that facilitates watercress resistance to flooding stress. This study enhanced the understanding of the NoNAC genes and established a theoretical foundation for investigating plant flooding tolerance.

Transcriptional dynamics and tissue-specific expression patterns of transposable elements in orthopteran insects

Transposable elements (TEs) are prevalent in the genomes of orthopteran insects, contributing significantly to their genome evolution and diversity. In light of the existing gap in our understanding of TEs transcript dynamics in orthopteran insects, we recognize the critical need to undertake comprehensive analyses in this area. Therefore, we have decided to delve into the characterization of TE transcripts, their abundance profiles, and the formation of chimeric transcripts using RNA-seq data and genome assemblies. The transcript analysis of TEs across various species revealed significant differences in TE abundance and expression patterns. In particular, Schistocerca americana exhibited twice the number of transcripts within the genus Schistocerca compared to the average of other species, while Gryllus bimaculatus displayed the lowest number of transcripts. Despite this, all Schistocerca species shared similar fractions of TE transcripts at the clade level, with DNA transposons (45%) being the most abundant, followed by LINE (19%) and LTR elements (18%). Interestingly, Acrida cinerea displayed different TE abundance patterns compared to Schistocerca species, particularly with an increased proportion of LTR transcripts, accounting for 31% of the total transcripts. Further analysis revealed tissue-specific transcriptional activity of TE clades, with notable differences between male and female specimens. In Gryllus bimaculatus, TEs were highly transcribed across ovaries and gut tissues in females compared to male testes and gut. Conversely, Gastrimargus marmoratus displayed higher TE transcription in male tissues compared to females, indicating species-specific expression patterns. A similar pattern has been observed in Acrida cinerea, except in female gonads, where 4618 TEs were transcribed compared to 3757 in male gonads. Despite these variations, no correlation was found between genome size and TE transcript abundance. Additionally, highly conserved TEs were involved in the formation of chimeric transcripts, indicating potential regulatory roles in gene expression. The expression quantification analysis of chimeric TEs and genes revealed tissue-specific expression patterns, and TEs do not control the overall expression of all genes except some, suggesting regulatory roles of TEs in gene expression. Overall, our study underscores tissue-specific variations in TE expression and transcript abundance among different species. Additionally, our findings suggest the involvement of highly conserved TEs in the formation of chimeric transcripts across different species.

Comparative analysis of IRE1s in plants: insights into heat stress adaptation in Triticum aestivum

BackgroundThe unfolded protein response (UPR) pathway serves as a crucial mechanism enabling plants to perceive, respond to, and shield themselves from adverse environmental conditions. Inositol-requiring enzyme 1 (IRE1) is one of the key players of the UPR, and resides in the endoplasmic reticulum (ER) within the cell. This study provides a comprehensive analysis of 195 IRE1 genes across 90 diverse plant species, with a focus on their identification and characterization.ResultsTo decipher the functions of IRE1 family members, we investigated the evolution and spread of IREs in plants and analysed their structural and localization characteristics. Our detailed cis-element analysis revealed unique IRE1 regulation patterns in different plant species. Furthermore, gene expression analysis revealed tissue-specific and heat stress-responsive expression patterns of TaIRE1s, which were subsequently confirmed via quantitative gene expression analysis. TaIRE1-6A was upregulated in response to dithiothreitol (DTT) treatment as well as heat stress. This finding suggests that IRE1 might play a role in linking the UPR pathway and the heat stress response (HSR).ConclusionsOur findings provide a comprehensive understanding of the evolution and expansion of IRE1 genes in different plant species. These findings provide a foundation for further in-depth research on the functional diversity of IREs in nutritious crops following polyploidization. By linking the UPR with HSR, IRE1 could be a key contributor to wheat's resilience against heat stress. Additionally, this connection offers important insights for future functional studies in other crops. Thus, this knowledge could be used for engineering climate resilience in crops such as wheat.

Gastroesophageal reflux disease increases predisposition to severe COVID-19: Insights from integrated Mendelian randomization and genetic analysis.

This study aims to investigate the potential causal relationship, shared genomic loci, as well as potential molecular pathways and tissue-specific expression patterns between gastroesophageal reflux disease (GERD) and the risk of hospitalized/severe 2019 coronavirus disease (COVID-19). We employed linkage disequilibrium score regression and bidirectional Mendelian randomization (MR) analysis to explore potential genetic associations between GERD (N=602,604) and hospitalized COVID-19 (N=2095,324) as well as severe COVID-19 (N=1086,211). Additionally, shared genomic loci were extracted from common pivotal regions, further confirmed through corresponding colocalization analyses. GERD-driven molecular pathway network was constructed using extensive literature data mining to understand the molecular-level impacts of GERD on COVID-19. Our results revealed a significant positive genetic correlation between GERD and both hospitalized (rg = 0.418) and severe COVID-19 (rg = 0.314). Furthermore, the MR analysis demonstrated a unidirectional causal effect of genetic predisposition to GERD on COVID-19 outcomes, including hospitalized COVID-19 (odds ratio [OR]: 1.33, 95% confidence interval [CI]: 1.27-1.44, p=9.17e-12) and severe COVID-19 (OR: 1.27, 95% CI: 1.18-1.37, p=1.20e-05). Additionally, GERD and both COVID-19 conditions shared one genomic locus with lead-SNPs rs1011407 and rs1123573, corresponding to the transcription factor BCL11A. Colocalization analysis further demonstrated a significant positive correlation between genome-wide association study and expression quantitative trait locus (eQTL) abnormalities, including rs1011407 (eQTL_p=2.35e-07) and rs1123573 (eQTL_p=2.74e-05). Molecular pathway analysis indicated that GERD might promote the progression of COVID-19 by inducting immune-activated and inflammation-related pathways. These findings confirm that genetically determined GERD may increase the susceptibility to hospitalized/severe COVID-19. The shared genetic loci and the potential molecular pathways offer valuable insights into causal connections between GERD and COVID-19.

Delineating Notch1 and Notch2: Receptor-Specific Significance and Therapeutic Importance of Pinpoint Targeting Strategies for Hematological Malignancies.

Notch1 and Notch2, transmembrane receptors belonging to the Notch family, are pivotal mediators of intercellular communication and have profound implications including cell fate determination, embryonic development, and tissue homeostasis in various cellular processes. Despite their structural homology, Notch1 and Notch2 exhibit discrete phenotypic characteristics and functional nuances that necessitate their individualized targeting in specific medical scenarios. Aberrant Notch signaling, often driven by the dysregulated activity of one receptor over the other, is implicated under various pathological conditions. Notch1 dysregulation is frequently associated with T-cell acute lymphoblastic leukemia, whereas Notch2 perturbations are linked to B-cell malignancies and solid tumors, including breast cancer. Hence, tailored therapeutic interventions that selectively inhibit the relevant Notch receptor need to be devised to disrupt the signaling pathways driving the specific disease phenotype. In this review, we emphasize the importance of distinct tissue-specific expression patterns, functional divergence, disease-specific considerations, and the necessity to minimize off-target effects that collectively underscore the significance of "individualized" targeting for Notch1 and Notch2. This comprehensive review sheds light on the receptor-specific characteristics of Notch1 and Notch2, providing insights into their roles in cellular processes and offering opportunities for developing tailored therapeutic interventions in the fields of biomedical research and clinical practice.

Genome-wide characterization of the DIR gene family in sesame reveals the function of SiDIR21 in lignan biosynthesis

Furofuran-type lignans, mainly sesamin and sesamolin, are the most representative functional active ingredients in sesame (Sesamum indicum L.). Their exceptional antioxidant properties, medicinal benefits, and health-promoting functions have garnered significant attention. Dirigent (DIR) proteins, found in vascular plants, are crucial for the biosynthesis of secondary metabolites, like lignans, and essential for responding to abiotic and biotic stresses. Despite their importance, they have yet to be systematically analyzed, especially those involved in lignan synthesis in sesame. This study unveiled 44 DIR genes in sesame. Phylogenetic analysis categorized these SiDIRs into five subgroups (DIR-a, DIR-b/d, DIR-e, DIR-f, and DIR-g), aligning with conserved motifs and gene structures analyses. Expression analysis unveiled distinct tissue-specific and hormone-responsive expression patterns among the SiDIR gene family members. Particularly, SiDIR21, a member of the DIR-a subgroup, exhibited robust expression in lignan-accumulating tissues and consistently high expression levels in germplasm during seed development with high sesamin content. Furthermore, SiDIR21 overexpression in hairy roots significantly increased sesamin and sesamolin contents, confirming its role in lignan synthesis. Overall, our study offers a valuable resource for exploring SiDIRs’ functions and the lignan biosynthesis pathway in sesame.

Genome-wide identification and analysis of ERF transcription factors related to abiotic stress responses in Nelumbo nucifera

BackgroundEthylene-responsive factor (ERF) transcription factors belong to the APETALA2/ERF (AP2/ERF) superfamily, and play crucial roles in plant development process and stress responses. However, the function of ERF proteins (especially for their role in response to abiotic stresses) remains scarce in Nelumbo nucifera, which is an important aquatic plant with high ornamental, economic, and ecological values.ResultsA total of 107 ERF genes were identified from the N. nucifera genome, and phylogenetic analysis classified these genes into 11 groups. The NnERF genes in the same group exhibited similar gene structure and conserved motifs, and they were unevenly distributed across the 8 chromosomes, with three pairs of tandem duplications and 21 pairs of segmental duplications. Synteny analysis revealed 44 and 39 of NnERF genes were orthologous to those in Arabidopsis thaliana and Oryza sativa, respectively. Tissue-specific expression patterns analysis of NnERF showed that 26 NnERF genes were expressed in all tested tissues, in which five genes exhibited high expression levels. Furthermore, 16 NnERF genes were selected for exploring their responses to different abiotic stresses, including cold, salt, drought, and Cd stresses. qRT-PCR analysis revealed that all these 16 investigated genes were regulated by at least one stress treatment, and 12 genes responded to all the stress treatments with different expression patterns or levels, suggesting their potential roles in diverse abiotic stress tolerance of N. nucifera. Additionally, two representative stress-related NnERFs (Nn3g19628 and Nn1g06033) were confirmed to be nuclear-localized proteins and displayed transcriptional activation.ConclusionsIn this study, we conducted a genome-wide identification and analysis of NnERF gene family related to abiotic stress responses in N. nucifera, which provides valuable information for further functional validation of these genes in stress responses, and forms a foundation for stress tolerance breeding in N. nucifera and other aquatic ornamental plants.

TORC1 Regulates Thermotolerance via Modulating Metabolic Rate and Antioxidant Capacity in Scallop Argopecten irradians irradians.

Target of rapamycin complex 1 (TORC1) is a key regulator of metabolism in eukaryotes across multiple pathways. Although TORC1 has been extensively studied in vertebrates and some invertebrates, research on this complex in scallops is limited. In this study, we identified the genes encoding TORC1 complex subunits in the scallop Argopecten irradians irradians through genome-wide in silico scanning. Five genes, including TOR, RAPTOR, LST8, DEPTOR, and PRAS40, that encode the subunits of TORC1 complex were identified in the bay scallop. We then conducted structural characterization and phylogenetic analysis of the A. i. irradians TORC1 (AiTORC1) subunits to determine their structural features and evolutionary relationships. Next, we analyzed the spatiotemporal expressions of AiTORC1-coding genes during various embryo/larvae developmental stages and across different tissues in healthy adult scallops. The results revealed stage- and tissue-specific expression patterns, suggesting diverse roles in development and growth. Furthermore, the regulation of AiTORC1-coding genes was examined in temperature-sensitive tissues (the mantle, gill, hemocyte, and heart) of bay scallops exposed to high-temperature (32 °C) stress over different durations (0 h, 6 h, 12 h, 24 h, 3 d, 6 d, and 10 d). The expression of AiTORC1-coding genes was predominantly suppressed in the hemocyte but was generally activated in the mantle, gill, and heart, indicating a tissue-specific response to heat stress. Finally, functional validation was performed using the TOR inhibitor rapamycin to suppress AiTORC1, leading to an enhanced catabolism, a decreased antioxidant capacity, and a significant reduction in thermotolerance in bay scallops. Collectively, this study elucidates the presence, structural features, evolutional relationships, expression profiles, and roles in antioxidant capacity and metabolism regulation of AiTORC1 in the bay scallop, providing a preliminary understanding of its versatile functions in response to high-temperature challenges in marine mollusks.

Genome-wide characterization of PEBP genes in Mung bean (Vigna radiata L.) with functional analysis of VrFT1 in relation to photoperiod

Mung bean (Vigna radiata L.), a widely cultivated legume, belongs to the Fabaceae family’s Papilionoideae subfamily. Although Phosphatidylethanolamine-binding protein (PEBP) genes have been identified in several plant species, their presence and function in mung bean remain largely unexplored. In this study, we identified seven VrPEBP genes from mung bean and classified them into four clades: FT, MFT, TFL and FT-like. Cis-regulatory element analysis revealed that VrPEBP genes may play a role in light, hormone, and stress responses. Quantitative real-time PCR (qRT-PCR) analysis indicated that VrPEBPs were constitutively expressed in various tissues. However, tissue-specific expression patterns were observed among VrPEBP genes. Under short-day (SD) conditions, VrFT1 and VrMFT1 exhibited significantly higher expression levels than under long-day (LD) conditions at 8 and 4 h, respectively. Conversely, VrTFL2 and VrTFL3 showed significantly higher expression levels under LD conditions compared to SD conditions at 8 and 12 h, respectively. The varied expression patterns of these genes under different photoperiod suggest their potential involvement in the photoperiodic regulation of flowering in mung bean. Additionally, phenotypic analysis of transgenic Arabidopsis plants overexpressing VrFT1 revealed higher expression levels under SD conditions and predicted its role in promoting flowering. These results provide valuable insights into the evolution and function of PEBP genes in mung bean and lay the foundation for further research on their regulatory mechanisms and potential applications in mung bean improvement.

INVESTIGATION OF THE EVOLUTION OF SABATH GENE FAMILY IN CASSAVA <i>(Manihot esculenta)</i> REVEALS ITS POTENTIAL ROLE IN GROWTH AND DEVELOPMENT

SABATH is one class of enzyme belonging to the class of methyltransferase, playing a crucial role in plant defense and stress response mechanisms. Despite its importance, no systematic analysis of the expansion of the SABATH gene family in cassava (Manihot esculenta) has been reported up to date. In this study, we investigated the SABATH gene family in cassava, revealing their random distribution across 18 chromosomes, with variable numbers of gene copies per chromosome. According to gene duplication analysis, five duplication events were identified, primarily segmental duplications, indicating their evolutionary significance. The Ka/Ks ratio analysis indicated that most duplicated genes are under negative selection, preserving their functions, while one pair showed signs of positive selection, suggesting adaptive benefits. Gene structure analysis showed diverse exon counts, primarily three or four. Expression profiling across 11 cassava tissues demonstrated tissue-specific expression patterns, with some genes highly or exclusively expressed in specific tissues such as root apical meristems, embryogenic calli, and fibrous roots, implying distinct functional roles in cassava growth and development. Overall, this study provides valuable insights into the evolution and functional diversity of the SABATH gene family in cassava and identifies candidate genes for further functional characterization.

Troponin I and Its Clinical Significance

Troponin I is one of the regulatory proteins of the troponin complex (troponin I, troponin C and troponin T) found in both cardiac and skeletal muscle. The letter I stands for its inhibitory character as binding is prevented between actin and myosin in relaxed muscle. It plays a significant role in holding actin-tropomyosin complex in place by binding actin in thin myofilaments. Binding of calcium to troponin C causes certain conformational changes, leading to troponin I dislocation and thus exposing binding site of myosin on actin, which leads to muscle contraction. It is frequently used in the diagnosis of acute coronary syndrome and myocardial infarction, and also serves as a prognostic marker in their management (1). There are three distinct forms of troponin I with tissue-specific expression patterns: 1. Slow-twitch skeletal muscle isoform troponin I, 2. Fast-twitch skeletal muscle isoform troponin I and 3. Cardiac troponin I.

The Potential Role of PeMAP65-18 in Secondary Cell Wall Formation in Moso Bamboo.

Microtubule-associated proteins (MAPs) play a pivotal role in the assembly and stabilization of microtubules, which are essential for plant cell growth, development, and morphogenesis. A class of plant-specific MAPs, MAP65, plays largely unexplored roles in moso bamboo (Phyllostachys edulis). This study identified 19 PeMAP65 genes in moso bamboo, systematically examining their phylogenetic relationships, conserved motifs, gene structures, collinearity, and cis-acting elements. Analysis of gene expression indicated that PeMAP65s exhibit tissue-specific expression patterns. Functional differentiation was investigated among the members of different PeMAP65 subfamilies according to their expression patterns in different development stages of bamboo shoots. The expression of PeMAP65-18 was positively correlated with the expression of genes involved in secondary cell wall (SCW) biosynthesis. Y1H and Dual-LUC assays demonstrated that the transcription of PeMAP65-18 was upregulated by PeMYB46, a key transcription factor of SCW biosynthesis. The result of subcellular localization showed that PeMAP65-18 was located in cortical microtubules. We speculate that PeMAP65-18 may play a crucial role in the SCW deposition of moso bamboo. This comprehensive analysis of the MAP65 family offers novel insights into the roles of PeMAP65s in moso bamboo, particularly in relation to the formation of SCWs.

Terpene synthase gene family in Jasminum sambac var. Fuzhou bifoliatum: genome-wide analysis and expression pattern in response to methyl jasmonate

Terpene synthases (TPSs) play a crucial role in the synthesis of terpenoids that contribute to the scent profiles of flowers. However, few studies report the genome-wide analysis of TPSs gene in Jasminum sambac var. Fuzhou bifoliatum and their expression pattern in response to methyl jasmonate (MeJA). In this study, we employed bioinformatics tools for genome-wide analysis of the J. sambac TPS (DJTPS) gene family and determined the physical and chemical properties, subcellular location, protein-protein interactions, phylogenetic relationship, subfamily classification, chromosomal location and collinearity, gene structure, conserved motifs, and promoter cis-acting elements. The expression patterns of DJTPSs in different tissues and in response to MeJA treatment were analyzed based on the transcriptome data combined with quantitative real-time PCR (qRT-PCR). We identified 32 intact DJTPS genes in the genome of J. sambac, which presented uneven distribution across nine chromosomes. All the deduced proteins were hydrophilic, predominantly localized in the cytoplasm. The phylogenetic analysis classified the DJTPS genes into five subfamilies: TPS-a, TPS-b, TPS-c, TPS-e/f, and TPS-g. The results of the collinearity analysis showed a total of 10 sets of replication events in DJTPSs, most of which underwent purifying selection. A comparative analysis of TPS homologous gene pairs was performed among J. sambac var. Fuzhou bifoliatum and other six species, which revealed different number of homologous gene pairs. The number of exons and motifs was conserved within the same subfamily. DJTPS genes carried multiple elements that may be involved in the response to MeJA. In addition, the transcriptome and qRT-PCR data unveiled that several TPS genes exhibited tissue-specific expression patterns, and the genes with specific expression in flowers were the most. Upon exposure to MeJA, 14 TPS genes showcased upregulated expression 5 h or 6 h post-treatment, and DJTPS03, DJTPS04 and DJTPS21 showed significantly increased expression levels after MeJA treatment. This study provides preliminary evidence that MeJA possesses the ability to enhance the expression of DJTPS genes during the critical flowering stage, which will facilitate the synthesis of terpenoids and improve the quality of floral fragrance.

Genome-Wide Identification of the Cyclic Nucleotide-Gated Ion Channel Gene Family and Expression Profiles Under Low-Temperature Stress in Luffa cylindrica L.

Cyclic nucleotide-gated ion channels (CNGCs) are cell membrane channel proteins for calcium ions. They have been reported to play important roles in survival and in the responses to environmental factors in various plants. However, little is known about the CNGC family and its functions in luffa (Luffa cylindrica L.). In this study, a bioinformatics-based method was used to identify members of the CNGC gene family in L. cylindrica. In total, 20 LcCNGCs were detected, and they were grouped into five subfamilies (I, II, Ⅲ, IV-a, and IV-b) in a phylogenetic analysis with CNGCs from Arabidopsis thaliana (20 AtCNGCs) and Momordica charantia (17 McCNGCs). The 20 LcCNGC genes were unevenly distributed on 11 of the 13 chromosomes in luffa, with none on Chromosomes 1 and 5. The members of each subfamily encoded proteins with highly conserved functional domains. An evolutionary analysis of CNGCs in luffa revealed three gene losses and a motif deletion. An examination of gene replication events during evolution indicated that two tandemly duplicated gene pairs were the primary driving force behind the evolution of the LcCNGC gene family. PlantCARE analyses of the LcCNGC promoter regions revealed various cis-regulatory elements, including those responsive to plant hormones (abscisic acid, methyl jasmonate, and salicylic acid) and abiotic stresses (light, drought, and low temperature). The presence of these cis-acting elements suggested that the encoded CNGC proteins may be involved in stress responses, as well as growth and development. Transcriptome sequencing (RNA-seq) analyses revealed tissue-specific expression patterns of LcCNGCs in various plant parts (roots, stems, leaves, flowers, and fruit) and the upregulation of some LcCNGCs under low-temperature stress. To confirm the accuracy of the RNA-seq data, 10 cold-responsive LcCNGC genes were selected for verification by quantitative real-time polymerase chain reaction (RT-qPCR) analysis. Under cold conditions, LcCNGC4 was highly upregulated (>50-fold increase in its transcript levels), and LcCNGC3, LcCNGC6, and LcCNGC13 were upregulated approximately 10-fold. Our findings provide new information about the evolution of the CNGC family in L. cylindrica and provide insights into the functions of the encoded CNGC proteins.

Differential expression of nuclear-derived mitochondrial succinate dehydrogenase genes in metabolically active buffalo tissues.

Buffaloes are crucial to agriculture, yet mitochondrial biology in these animals is less studied compared to humans and laboratory animals. This research examines tissue-specific variations in mitochondrial succinate dehydrogenase (SDH) gene expression across buffalo kidneys, hearts, brains, and ovaries. Understanding these variations sheds light on mitochondrial energy metabolism and its impact on buffalo health and productivity, revealing insights into enzyme regulation and potential improvements in livestock management. RNA-seq data from buffalo kidney, heart, brain, and ovary tissues were reanalyzed to explore mitochondrial SDH gene expression. The expression of SDH subunits (SDHA, SDHB, SDHC, SDHD) and assembly factors (SDHAF1, SDHAF2, SDHAF3, SDHAF4) was assessed using a log2 fold-change threshold of + 1 for up-regulated and - 1 for down-regulated transcripts, with significance set at p < 0.05. Hierarchical clustering and differential expression analyses were performed to identify tissue-specific expression patterns and regulatory mechanisms, while Gene Ontology and KEGG pathway analyses were conducted to uncover functional attributes and pathway enrichments across different tissues. Reanalysis of RNA-seq data from different tissues of healthy female buffaloes revealed distinct expression patterns for SDH subunits and assembly factors. While SDHA, SDHB, and SDHC showed variable expression across tissues, SDHAF2, SDHAF3, and SDHAF4 exhibited tissue-specific profiles. Significant up-regulation of SDHA, SDHB, and several assembly factors was observed in specific tissue comparisons, with fewer down-regulated transcripts. Gene ontology and KEGG pathway analyses linked the up-regulated transcripts to mitochondrial ATP synthesis and the respiratory electron transport chain. Notably, tissue-specific variations in mitochondrial function were particularly evident in the ovary. This study identifies distinct SDH gene expression patterns in buffalo tissues, highlighting significant down-regulation of SDHA, SDHB, SDHC, and assembly factors in the ovary. These findings underscore the critical role of mitochondria in tissue-specific energy production and metabolic regulation, suggest potential metabolic adaptations, and emphasize the importance of mitochondrial complex II. The insights gained offer valuable implications for improving feed efficiency and guiding future research and therapies for energy metabolism disorders.

Functional analysis of PagERF021 gene in salt stress tolerance in Populus alba × P.glandulosa.

Poplar trees are crucial for timber and greening, but high levels of salt in the soil have severely limited the yield of poplar. ETS2 repressor factor (ERF) transcription factors play an important role in growth, development, and stress response in eukaryotes. Our study focused on the PagERF021 gene from Populus alba × P. glandulosa, which was significantly upregulated in various tissues under salt stress. Both the tissue-specific expression pattern and β-glucuronidase (GUS) staining of proPagERF021-GUS plants indicated that this gene was predominantly expressed in the roots and stems. The subcellular localization showed that the protein was only localized in the nucleus. The yeast assay demonstrated that this protein had transcriptional activation activity at its C-terminal and could specifically binding to the MYB-core cis-element. The overexpression of PagERF021 gene could scavenge the accumulation of reactive oxygen species and reduce the degree of cellular membrane damage, indicating that this gene enhanced the salt tolerance of poplars. This finding will provide a feasible insight for future research into the regulatory mechanisms of ERF genes in resisting to abiotic stress and the development of new stress-resistant varieties in plants.