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Background Intermuscular bones (IBs) are segmental intramembranous ossifications located within myosepta. They share similarities with tendon ossification, a form of heterotopic ossification (HO). The mechanisms underlying IB formation remain incompletely understood. Results In this study, we systematically analyzed transcriptome data across multiple tissues, species, time points, and resolutions in teleosts. First, we identified IB-specific expression genes using the tau index method. Through cross-species comparisons of the tendon development process, we discovered that candidate genes were primarily enriched in extracellular matrix organization, ossification, regulation of angiogenesis, and other related processes. We also revealed that some of these candidate genes are abnormally expressed in runx2b −/− zebrafish, which lack IBs. To clarify the trajectory of cell differentiation during IB formation, we demonstrated that myoseptal stem cells differentiate into osteoblasts, fibroblasts, and tenocytes in runx2b +/+ zebrafish. However, in runx2b −/− zebrafish, the differentiation of myoseptal stem cell into osteoblast was inhibited, while differentiation into clec3bb  + tenocyte and fibroblast was enhanced. Additionally, runx2b deficiency led to the upregulation of clec3bb expression in the clec3bb  + tenocyte cluster. Notably, a compensatory effect was observed in cell differentiation and gene expression in runx2b −/− zebrafish, suggesting that runx2b and the candidate genes, such as clec3bb , were involved in the gene network of IB development. Conclusions The results elucidate cell differentiation process during tendon ossification in teleosts and identify the key factor clec3bb involved in this process. These findings provide a foundation for understanding tendon ossification in teleosts and for further research on tendon ossification in mammals.

Erythritol has been widely used in the food industry, which predominantly synthesizes it via microbial fermentation, in which Yarrowia lipolytica serves as the preferred candidate chassis strain. However, the wild-type strain of Y. lipolytica exhibits several limitations, including suboptimal industrial performance and elevated levels of by-products, which pose significant challenges in biomanufacturing processes. It is significant to understand the synthesis mechanism of erythritol for improving the capacity of erythritol production by Y. lipolytica. In this study, a mutant exhibiting high erythritol production and stable genetic performance was obtained via a combination of UV and atmospheric and room-temperature plasma mutagenesis. Some key genes related to erythritol production were identified through comparative transcriptome analysis of the mutant strain, revealing significant changes in their expression levels. Individual overexpression of the genes encoding ribose-5-phosphate isomerase, glucose-6-phosphate-1-epimerase, adenylate kinase, and alcohol dehydrogenase in Y. lipolytica Po1g enhanced erythritol production, demonstrating the critical role of each gene in erythritol production. This finding elucidates the molecular mechanism underlying the improved erythritol yield in the mutant strain. The Y. lipolytica mutant C1 produced 194.47 g/L erythritol in a 10 L fermenter with a productivity of 1.68 g/L/h during batch fermentation, surpassing the wild-type strain and reducing the cultivation time by 21 h. It is significant to understand the mechanism of erythritol synthesis for improving erythritol production and its application in industrial-scale production.

Summary Verticillium dahliae is a widespread and destructive soilborne vascular pathogenic fungus that causes serious diseases in dicot plants. Here, comparative transcriptome analysis showed that the number of genes upregulated in defoliating pathotype V991 was significantly higher than in the non‐defoliating pathotype 1cd3‐2 during the early response of cotton. Combined with analysis of the secretome during the V991–cotton interaction, an elicitor VP2 was identified, which was highly upregulated at the early stage of V991 invasion, but was barely expressed during the 1cd3‐2‐cotton interaction. Full‐length VP2 could induce cell death in several plant species, and which was dependent on NbBAK1 but not on NbSOBIR1 in N. benthamiana. Knock‐out of VP2 attenuated the pathogenicity of V991. Furthermore, overexpression of VP2 in cotton enhanced resistance to V. dahliae without causing abnormal plant growth and development. Several genes involved in JA, SA and lignin synthesis were significantly upregulated in VP2‐overexpressing cotton. The contents of JA, SA, and lignin were also significantly higher than in the wild‐type control. In summary, the identified elicitor VP2, recognized by the receptor in the plant membrane, triggers the cotton immune response and enhances disease resistance.

Background Hollow heart is a kind of physiological defect that seriously affects the yield, quality, and economic value of cucumber. However, the formation of hollow hearts may relate to multiple factors in cucumber, and it is necessary to conduct analysis. Results In this study, hollow and non-hollow fruits of cucumber K07 were used for comparative transcriptome sequencing and analysis. 253 differentially expressed genes and 139 transcription factors were identified as being associated with the formation of hollow hearts. Hormone (auxin) signaling and cell wall biosynthesis were mainly enriched in GO and KEGG pathways. Expression levels of key genes involved in indole-3-acetic acid biosynthesis in carpel were lower in the hollow fruits than non-hollow fruits, while there was no difference in the flesh. The concentration of indole-3-acetic also showed lower in the carpel than flesh. The biosynthetic pathway and content analysis of the main components of the cell wall found that lignin biosynthesis had obvious regularity with hollow heart, followed by hemicellulose and cellulose. Correlation analysis showed that there may be an interaction between auxin and cell wall biosynthesis, and they collectively participate in the formation of hollow hearts in cucumber. Among the differentially expressed transcription factors, MYB members were the most abundant, followed by NAC, ERF, and bHLH. Conclusions The results and analyses showed that the low content of auxin in the carpel affected the activity of enzymes related to cell wall biosynthesis at the early stage of fruit development, resulting in incomplete development of carpel cells, thus forming a hollow heart in cucumber. Some transcription factors may play regulatory roles in this progress. The results may enrich the theory of the formation of hollow hearts and provide a basis for future research.

Carotenoids play a significant role in the growth, development, color, and aroma quality of tea plants. The molecular mechanism underlying carotenoid metabolism in tea plants remain to be elucidated. In this study, we determined the carotenoid contents in three tea cultivars (‘Suchazao’, ‘Huangjinya’, and ‘Zhongbai 4’) and conducted transcriptome sequencing on the new shoots and mature leaves of these cultivars. Our results indicated that lutein was the predominant carotenoid in ‘Suchazao’ and ‘Zhongbai 4’, whereas β-carotene was the predominant carotenoid in ‘Huangjinya’. The mature leaves of all three tea cultivars contained higher carotenoids levels compared to the new shoots. In the transcriptome analysis, we identified 24 and 20 key DEGs involved in carotenoid biosynthesis and degradation, respectively. Expression analysis and correlation analysis indicated that CsPSY , CsPDS , CsZDS , CsLCYE , CsLCYB , CsBCH , CsCYP97A3 , CsZEP , CsOR , CsCCD1.2 , and CsCCD4 play crucial roles in the carotenoid metabolism in tea plants. Furthermore, several transcription factors, including CsMYB59-LOC114278066 and CsNAC56-LOC114260089, were identified in pairwise comparisons, implying their potential role in carotenoid accumulation. These results elucidated carotenoid accumulation patterns in new shoots and mature leaves of three tea cultivars with different leaf colors. It also provided insights into the molecular mechanism that regulate carotenoid accumulation in tea plants.

Regulatory RNAs play versatile roles in bacteria in the coordination of gene expression during various physiological processes, especially during stress adaptation. Photosynthetic bacteria use sunlight as their major energy source. Therefore, they are particularly vulnerable to the damaging effects of excess light or UV irradiation. In addition, like all bacteria, photosynthetic bacteria must adapt to limiting nutrient concentrations and abiotic and biotic stress factors. Transcriptome analyses have identified hundreds of potential regulatory small RNAs (sRNAs) in model cyanobacteria such as Synechocystis sp. PCC 6803 or Anabaena sp. PCC 7120, and in environmentally relevant genera such as Trichodesmium, Synechococcus and Prochlorococcus. Some sRNAs have been shown to actually contain μORFs and encode short proteins. Examples include the 40-amino-acid product of the sml0013 gene, which encodes the NdhP subunit of the NDH1 complex. In contrast, the functional characterization of the non-coding sRNA PsrR1 revealed that the 131 nt long sRNA controls photosynthetic functions by targeting multiple mRNAs, providing a paradigm for sRNA functions in photosynthetic bacteria. We suggest that actuatons comprise a new class of genetic elements in which an sRNA gene is inserted upstream of a coding region to modify or enable transcription of that region. Hundreds of potentially regulatory small RNAs (sRNAs) have been identified in model cyanobacteria and, despite recent significant progress, their functional characterization is substantial work and continues to provide surprising insights of general interest.

Coleoid cephalopods are excellent models for evolutionary and developmental studies due to their centralized nervous system, short life span, and sophisticated sense organs. Arm suckers, essential for predation, manipulation, and locomotion, have been studied in Decapodiformes, but little is known at the cellular and molecular levels. Here, we investigated sucker development in from the embryo to the juvenile stage using morphological, histological, immunostaining, scanning electron microscopy (SEM), in situ hybridization, and transcriptomic analyses. SEM revealed that suckers initially form symmetrically and later become asymmetrical through an embedding process. Histology showed progressive structural differentiation, while immunostaining with acetylated α-tubulin and phalloidin visualized nerve fiber and muscle development. Transcriptome profiling of embryonic stages 12, 14, and 20 identified 2,349 differentially expressed genes (DEGs) linked to arm and muscle development. Among them, , , and WNT signaling molecules ( , , ) exhibited increased expression in arms and developing suckers, consistent with in situ hybridization results. These findings suggest that WNT signaling contributes to sucker muscle development in , paralleling its conserved role in vertebrates. This study provides new insights into the embryonic morphogenesis of arms and suckers, highlighting the molecular and cellular mechanisms that shape cephalopod appendages.

Gibberellic acid (GA3), one of the natural diterpenoids produced by Fusarium fujikuroi, serves as an important phytohormone in agriculture for promoting plant growth. Presently, the metabolic engineering strategies for increasing the production of GA3 are progressing slowly, which seriously restricted the advancing of the cost-effective industrial production of GA3. In this study, an industrial strain with high-yield GA3 of F. fujikuroi was constructed by metabolic modification, coupling with transcriptome analysis and promoter engineering. The over-expression of AreA and Lae1, two positive factors in the regulatory network, generated an initial producing strain with GA3 production of 2.78 g L−1. Compared with a large abundance of transcript enrichments in the GA3 synthetic gene cluster discovered by the comparative transcriptome analysis, geranylgeranyl pyrophosphate synthase 2 (Ggs2), and cytochrome P450-3 genes, two key genes that respectively participated in the initial and final step of biosynthesis, were identified to be downregulated when the highest GA3 productivity was obtained. Employing with a nitrogen-responsive bidirectional promoter, the two rate-limiting genes were dynamically upregulated, and therefore, the production of GA3 was increased to 3.02 g L−1. Furthermore, the top 20 upregulated genes were characterized in GA3 over-production, and their distributions in chromosomes suggested potential genomic regions with a high transcriptional level for further strain development. The construction of a GA3 high-yield-producing strain was successfully achieved, and insights into the enriched functional transcripts provided novel strain development targets of F. fujikuroi, offering an efficient microbial development platform for industrial GA3 production.Key points• Global regulatory modification was achieved in F. fujikuroi for GA3 overproduction.• Comparative transcriptome analysis revealed bottlenecks in GA specific-pathway.• A dynamically nitrogen-regulated bidirectional promoter was cloned and employed.

Clostridium tyrobutyricum has great potential for bio-based chemicals and biofuel production from mannitol; however, the mannitol metabolic pathway and its metabolic regulatory mechanism have not been elucidated. To this end, the RNA-seq analysis on the mid-log growth phase of C. tyrobutyricum grown on mannitol or xylose was performed. Comparative transcriptome analysis and co-transcription experiment indicated that mtlARFD, which encodes the mannitol-specific IIA component, transcription activator, mannitol-specific IIBC components, and mannitol-1-phosphate 5-dehydrogenase, respectively, formed a polycistronic operon and could be responsible for mannitol uptake and metabolism. In addition, comparative genomic analysis of the mtlARFD organization and the MtlR protein structural domain among various Firmicutes strains identified the putative cre (catabolite-responsive element) sites and conserved phosphorylation sites, but whether the expression of mannitol operon was affected by CcpA- and MtlR-mediated metabolic regulation during mixed substrate fermentation needs to be further verified experimentally. Based on the gene knockout and complementation results, the predicted mannitol operon mtlARFD was confirmed to be responsible for mannitol utilization in C. tyrobutyricum. The results of this study could be used to enhance the mannitol metabolic pathway and explore the potential metabolic regulation mechanism of mannitol during mixed substrate fermentation.

Ogura cytoplasmic male sterility (CMS) lines are widely used breeding materials in cruciferous crops and play important roles in heterosis utilization; however, the sterility mechanism remains unclear. To investigate the microspore development process and gene expression changes after the introduction of orf138 and Rfo, cytological observation and transcriptome analysis were performed using a maintainer line, an Ogura CMS line, and a restorer line. Semithin sections of microspores at different developmental stages showed that the degradation of tapetal cells began at the tetrad stage in the Ogura CMS line, while it occurred at the bicellular microspore stage to the tricellular microspore stage in the maintainer and restorer lines. Therefore, early degradation of tapetal cells may be the cause of pollen abortion. Transcriptome analysis results showed that a total of 1287 DEGs had consistent expression trends in the maintainer line and restorer line, but were significantly up- or down-regulated in the Ogura CMS line, indicating that they may be closely related to pollen abortion. Functional annotation showed that the 1287 core DEGs included a large number of genes related to pollen development, oxidative phosphorylation, carbohydrate, lipid, and protein metabolism. In addition, further verification elucidated that down-regulated expression of genes related to energy metabolism led to decreased ATP content and excessive ROS accumulation in the anthers of Ogura CMS. Based on these results, we propose a transcriptome-mediated induction and regulatory network for cabbage Ogura CMS. Our research provides new insights into the mechanism of pollen abortion and fertility restoration in Ogura CMS.