BpAP1 directly regulates BpDEF to promote male inflorescence formation in Betula platyphylla × B. pendula

Transcriptomic landscape of staminate catkins development during overwintering process in Betula platyphylla

Betula platyphylla, belonging to the cold-specialized lineage Betulaceae, exhibits a unique reproductive strategy where staminate catkins emerge in the first summer and undergo an overwintering process, culminating in flowering in the following year. However, the underlying regulatory mechanism remains unclear. In this study, we investigated the male germline development of B. platyphylla in four distinct stages: microsporocytes in Oct. (S1), uninuclear microspores from Dec. (S2) to Mar. of the following year (S3), and bicellular microspores in Apr. (S4). We performed RNA sequencing on mature pollen and the four stages of staminate catkins. Using weighted gene co-expression network analysis (WGCNA), we identified five highly correlated gene modules with distinct expression profiles. These modules exhibited strong correlations with sugar metabolism, cell cycle, flowering, and cell wall dynamics, highlighting their dynamic roles during male germline developmental stages. During the overwintering process, we observed that the expression of transcription factors such as BpDUO1 and BpAMS at the appropriate developmental stages, suggests their significant roles in male germline development. The expression patterns of BpFLC and BpFT suggest their potential involvement in temperature perception during male reproductive development. These findings offer valuable insights into the reproductive success of plants adapting to cold environments.

Functional study of BpCOI1 reveals its role in affecting disease resistance in birch

Plants interact with biotic and abiotic environments. Some of these interactions are detrimental including herbivory consumption and infections by microbial pathogens. The COI1 (coronatine insensitive 1) protein is the master controller of JA-regulated plant responses and plays a regulatory role in the plant defense response. However, there is little information on COI1 function in birch (Betula platyphylla × Betula pendula). Herein, we studied the F-box protein BpCOI1 which is located in the nucleus. To validate the function of this protein, we developed transgenic birch plants with overexpression or repression of BpCOI1 gene. Growth traits, such as tree height, ground diameter, number of lateral branches, did not change significantly among transgenic lines. Alternaria alternata treatment experiments indicated that low expression of BpCOI1 reduced disease resistance in birch. Furthermore, our results showed that low expression of BpCOI1 significantly reduced the sensitivity of plants to exogenous MeJA. Co-expression analysis showed gene expression patterns with similar characteristics. These genes may be closely related in function, or members involved in the same signaling pathway or physiological process with BpCOI 1. The results of transcriptome sequencing and co-expression analysis showed that BpCOI1 affects plant defense against Alternaria alternata by regulating jasmonates. This study reveals the role of BpCOI1 in disease resistance and proposes the possibility of controlling diseases through molecular breeding in birch.

Role of lncRNAs in cis- and trans-regulatory responses to salt in Populus trichocarpa

Long non-coding RNAs (lncRNAs) are emerging as versatile regulators in diverse biological processes. However, little is known about their cis- and trans-regulatory contributions in gene expression under salt stress. Using 27 RNA-seq data sets from Populus trichocarpa leaves, stems and roots, we identified 2988 high-confidence lncRNAs, including 1183 salt-induced differentially expressed lncRNAs. Among them, 301 lncRNAs have potential for positively affecting their neighboring genes, predominantly in a cis-regulatory manner rather than by co-transcription. Additionally, a co-expression network identified six striking salt-associated modules with a total of 5639 genes, including 426 lncRNAs, and in these lncRNA sequences, the DNA/RNA binding motifs are enriched. This suggests that lncRNAs might contribute to distant gene expression of the salt-associated modules in a trans-regulatory manner. Moreover, we found 30 lncRNAs that have potential to simultaneously cis- and trans-regulate salt-responsive homologous genes, and Ptlinc-NAC72, significantly induced under long-term salt stress, was selected for validating its regulation of the expression and functional roles of the homologs PtNAC72.A and PtNAC72.B (PtNAC72.A/B). The transient transformation of Ptlinc-NAC72 and a dual-luciferase assay of Ptlinc-NAC72 and PtNAC72.A/B promoters confirmed that Ptlinc-NAC72 can directly upregulate PtNAC72.A/B expression, and a presence/absence assay was further conducted to show that the regulation is probably mediated by Ptlinc-NAC72 recognizing the tandem elements (GAAAAA) in the PtNAC72.A/B 5' untranslated region (5'-UTR). Finally, the overexpression of Ptlinc-NAC72 produces a hypersensitive phenotype under salt stress. Altogether, our results shed light on the cis- and trans-regulation of gene expression by lncRNAs in Populus and provides an example of long-term salt-induced Ptlinc-NAC72 that could be used to mitigate growth costs by conferring plant resilience to salt stress.

Genome-Wide Identification and Analysis of Cell Cycle Genes in Birch

Research Highlights: This study identified the cell cycle genes in birch that likely play important roles during the plant’s growth and development. This analysis provides a basis for understanding the regulatory mechanism of various cell cycles in Betula pendula Roth. Background and Objectives: The cell cycle factors not only influence cell cycles progression together, but also regulate accretion, division, and differentiation of cells, and then regulate growth and development of the plant. In this study, we identified the putative cell cycle genes in the B. pendula genome, based on the annotated cell cycle genes in Arabidopsis thaliana (L.) Heynh. It can be used as a basis for further functional research. Materials and Methods: RNA-seq technology was used to determine the transcription abundance of all cell cycle genes in xylem, roots, leaves, and floral tissues. Results: We identified 59 cell cycle gene models in the genome of B. pendula, with 17 highly expression genes among them. These genes were BpCDKA.1, BpCDKB1.1, BpCDKB2.1, BpCKS1.2, BpCYCB1.1, BpCYCB1.2, BpCYCB2.1, BpCYCD3.1, BpCYCD3.5, BpDEL1, BpDpa2, BpE2Fa, BpE2Fb, BpKRP1, BpKRP2, BpRb1, and BpWEE1. Conclusions: By combining phylogenetic analysis and tissue-specific expression data, we identified 17 core cell cycle genes in the Betulapendula genome.

Transcriptome sequencing and gene expression profiling of Pinus sibirica under different cold stresses

Cold stress is a major abiotic factor that affects plant growth and geographical distribution. Pinus sibirica is extremely frigostable tree species. To understand the molecular mechanisms of cold tolerance by P. sibirica, physiological responses were analyzed and transcriptome profiling was conducted to the plants treated by cold stress. The physiological data showed that membrane permeability relative conductivity (REC), reactive oxygen species (ROS), malonaldehyde (MDA) content, peroxidase (POD) and catalase (CAT) activity, soluble sugar, soluble protein and proline contents were increased significantly (p < 0.05) in response to cold stress. Transcriptome analysis identified a total of 871, 1397 and 872 differentially expressed genes (DEGs) after cold treatment for 6 h, 24 h and 48 h at -20°C, respectively. The signaling pathway mediated by Ca²⁺ as a signaling molecule and abscisic acid pathways were the main cold signal transduction pathways in P. sibirica. The APETALA2/Ethylene-Responsive Factor (AP2/ERF) and MYB transcription factor families also play an important role in the transcriptional regulation of P. sibirica. In addition, many genes related to photosynthesis were differentially expressed under cold stress. We also validated the reliability of transcriptome data with quantitative real-time PCR. This study lays the foundation for understanding the molecular mechanisms related to cold responses in P. sibirica.

Genome-wide analysis and expression profile of the bZIP gene family in poplar

BACKGROUND

The bZIP gene family, which is widely present in plants, participates in varied biological processes including growth and development and stress responses. How do the genes regulate such biological processes? Systems biology is powerful for mechanistic understanding of gene functions. However, such studies have not yet been reported in poplar.

RESULTS

In this study, we identified 86 poplar bZIP transcription factors and described their conserved domains. According to the results of phylogenetic tree, we divided these members into 12 groups with specific gene structures and motif compositions. The corresponding genes that harbor a large number of segmental duplication events are unevenly distributed on the 17 poplar chromosomes. In addition, we further examined collinearity between these genes and the related genes from six other species. Evidence from transcriptomic data indicated that the bZIP genes in poplar displayed different expression patterns in roots, stems, and leaves. Furthermore, we identified 45 bZIP genes that respond to salt stress in the three tissues. We performed co-expression analysis on the representative genes, followed by gene set enrichment analysis. The results demonstrated that tissue differentially expressed genes, especially the co-expressing genes, are mainly involved in secondary metabolic and secondary metabolite biosynthetic processes. However, salt stress responsive genes and their co-expressing genes mainly participate in the regulation of metal ion transport, and methionine biosynthetic.

CONCLUSIONS

Using comparative genomics and systems biology approaches, we, for the first time, systematically explore the structures and functions of the bZIP gene family in poplar. It appears that the bZIP gene family plays significant roles in regulation of poplar development and growth and salt stress responses through differential gene networks or biological processes. These findings provide the foundation for genetic breeding by engineering target regulators and corresponding gene networks into poplar lines.

Extracting Gradual Rules to Reveal Regulation Between Genes

Background:

Gene regulation represents a very complex mechanism in the cell initiated to increase or decrease gene expression. This regulation of genes forms a Gene regulatory Network GRN composed of a collection of genes and products of genes in interaction. The high throughput technologies that generate a huge volume of gene expression data are useful for analyzing the GRN. The biologists are interested in the relevant genetic knowledge hidden in these data sources. Although, the knowledge extracted by the different data mining approaches of the literature is insufficient for inferring the GRN topology or does not give a good representation of the real genetic regulation in the cell.

Objective:

In this work, we are interested in the extraction of genetic interactions from the high throughput technologies, such as the microarrays or DNA chips.

Methods:

In this paper, in order to extract expressive and explicit knowledge about the interactions between genes, we used the method of gradual patterns and rules extraction applied on numerical data that extracts the frequent co-variations between gene expression values. Furthermore, we choose to integrate experimental biological data and biological knowledge in the process of knowledge extraction of genetic interactions.

Results:

The validation results on real gene expression data of the model plant Arabidopsis and human lung cancer shows the performance of this approach.

Conclusion:

The extracted gradual rules express the genetic interactions composed of a GRN. These rules help to understand complex systems and cellular functions.

Functional Study of BpPP2C1 Revealed Its Role in Salt Stress in Betula platyphylla

PP2C protein phosphatase family is one of the largest gene families in the plant genome. Many PP2C family members are involved in the regulation of abiotic stress. We found that BpPP2C1 gene has highly up-regulated in root under salt stress in Betula platyphylla. Thus, transgenic plants of Betula platyphylla with overexpression and knockout of BpPP2C1 gene were generated using a zygote transformation system. Under NaCl stress treatment, we measured the phenotypic traits of transgenic plants, chlorophyll-fluorescence parameters, peroxidase (POD) activity, superoxide dismutase (SOD) activity, and malondialdehyde (MDA) content. We found that BpPP2C1 overexpressed lines showed obvious salt tolerance, while BpPP2C1 knocked out plants were sensitive to salt stress. Transcriptome analysis identified significantly amount of differentially expressed genes associated with salt stress in BpPP2C1 transgenic lines, especially genes in abscisic acid signaling pathway, flavonoid biosynthetic pathway, oxidative stress and anion transport. Functional study of BpPP2C1 in Betula platyphylla revealed its role in salt stress.

Transcriptome analysis of salt stress responsiveness in the seedlings of wild and cultivated Ricinus communis L

Soil salinity is one of the major environmental factors, influencing agricultural productivity of crops. As a non-edible and ideal oilseed crop, castor (Ricinus communis L.) has great industrial value in biofuel, but molecular mechanisms of salt stress regulation are still unknown. In this study, the differentially expressed genes (DEGs) for differential salt tolerance in two castor cultivar (wild castor : Y, cultivated castor 'Tongbi 5': Z) were identified. 12 libraries were sampled for Illumina high-throughput sequencing to consider 132,426 nonredundant unigenes and 31,221 gene loci. Multiple phytohormones and transcription factors (TFs) were correlated with salt-tolerance and differently enriched in these two genotypes. The type 2C protein phosphatases (PP2C) homologs were all upregulated under salt stress. Importantly, IAA (1), DELLA (1) and Jasmonate zim domain (JAZ) (1) were also identified and found to be differentially expressed. Based on the co-expressed module by regulatory networks and heatmap analysis, ERF/AP2, WRKY and bHLH families were prominently participate in high salt stress response of wild and cultivated castor. Finally, these results highlight that the hub DEGs and families were more accumulated in cultivated castor than those in wild castor, providing novel insights into the salinity adaptive mechanisms and genetic improvement in castor.

Vacuolar membrane H+-ATPase c`` subunit gene (ThVHAc``1) from Tamarix hispida Willd improves salt stress tolerance

The plant vacuolar H⁺-ATPase (V-ATPase) is a multisubunit complex. In addition to performing basic housekeeping functions, this complex is also involved in abiotic stress resistance in plants. In this study, a V-ATPase c`` subunit gene (ThVHAc``1) from Tamarix hispida Willd was cloned with a 534-bp ORF. Sequence analysis showed that the ThVHAc``1 protein contains four transmembrane helices and lacks a signal peptide. qRT-PCR results showed that ThVHAc``1 was primarily induced by treatments of NaCl, NaHCO₃, PEG₆₀₀₀, CdCl₂ or ABA in roots, stems and leaves of T. hispida. The expression pattern of ThVHAc``1 was significantly different from that of ThVHAc1 (a V-ATPase c subunit in T. hispida). Furthermore, the cell survival rates and density (OD<sub>600</sub>) results showed that the transgenic yeast overexpressing ThVHAc``1 exhibited increased tolerance to the above-mentioned abiotic stresses. In addition, the overexpression of ThVHAc``1 confers salt tolerance to transgenic Arabidopsis plants by improving the ROS content and decreasing the accumulation of O<sup>2-</sup> and H<sub>2</sub>O<sub>2</sub>. Similarly, the homologous transformation of the ThVHAc``1 gene into T. hispida also improved salt tolerance. Our results suggest that the ThVHAc``1 gene plays an important role in plant stress tolerance.

Characterization of the Poplar R2R3-MYB Gene Family and Over-Expression of PsnMYB108 Confers Salt Tolerance in Transgenic Tobacco

The MYB, one of the largest transcription factor families in plants, is related to various biological processes. For an example, the R2R3-MYB family plays an important role in regulation of primary and secondary metabolism, plant growth and development, and responses to hormones and stresses. However, functional studies on the poplar R2R3-MYB genes are limited. In this study, we identified 207 poplar R2R3-MYB genes that are unevenly distributed on the 19 chromosomes of poplar, followed by characterization of their conserved domains. On the basis of phylogenetic analysis, these genes can be divided into 23 groups. Evidence from synteny analyses indicated that the poplar R2R3-MYB gene family is featured by tandem and segmental duplication events. On the basis of RNA-Seq data, we investigated salt responsive genes and explored their expression patterns. Furthermore, we cloned the PsnMYB108 gene from poplar, which is significantly up-regulated in roots and leaves in response to salt stress. To validate its function, we developed transgenic tobacco plants that over-express the PsnMYB108 gene. It appears that the transgenic lines are more tolerant to salt stress than the wild type does. Evidence from physiological analyses demonstrated that over-expression of PsnMYB108 may improve tobacco salt stress tolerance by increasing the reactive oxygen species scavenging ability and the accumulation of proline. These results laid the foundation for future analysis and functional studies of poplar R2R3-MYB family members, and revealed that PsnMYB108 plays an important role in improving plant salt stress tolerance.

Negative feedback loop between BpAP1 and BpPI/BpDEF heterodimer in Betula platyphylla × B. pendula

MADS-box genes encode transcription factors involved in the control of many important developmental processes, especially the flower development of angiosperms. Analysis on gene regulatory relationship between MADS-box genes is useful for understanding the molecular mechanism of flower development. In this study, we focused on the regulatory relationship between MADS-box transcription factors APETALA1 (AP1) and PISTILLATA(PI)/DEFICIENS (DEF) in birch. We found that BpPI was an authentic target gene of BpAP1, and BpAP1 activated the expression of BpPI via directly binding to the CArG box motif. Functional analysis of BpPI showed that overexpression of BpPI may delay flowering via restricting flowering activators, in which BpAP1 was significantly down-regulated. We further investigated the regulatory of BpAP1 by BpPI, and found that BpPI could directly bind to the promoter of BpAP1 to restrict BpAP1 expression. In addition, we also found that BpPI could interact with its hypothetical partner BpDEF to co-regulate BpAP1 in birch. Our results suggested that overexpression of BpPI may delay flowering via restricting flowering activators, and there is a negative feedback loop between BpAP1 and BpPI/BpDEF heterodimer in birch. Our results will bring new evidences for further analysis of the molecular mechanism of flower formation in plants that produced unisexual flowers.