Search

In the ovules of most sexually reproducing plants, one hypodermal cell differentiates into a megaspore mother cell (MMC), which gives rise to the female germline. Trans-acting small interfering RNAs known as tasiR-ARFs have been suggested to act non-cell-autonomously to prevent the formation of multiple MMCs by repressing AUXIN RESPONSE FACTOR3 (ARF3) expression in Arabidopsis (Arabidopsis thaliana), but the underlying mechanisms are unknown. Here, we examined tasiR-ARF-related intercellular regulatory mechanisms. Expression analysis revealed that components of the tasiR-ARF biogenesis pathway are restricted to distinct ovule cell types, thus limiting tasiR-ARF production to the nucellar epidermis. We also provide data suggesting tasiR-ARF movement along the mediolateral axis into the hypodermal cells and basipetally into the chalaza. Furthermore, we used cell type-specific promoters to express ARF3m, which is resistant to tasiR-ARF regulation, in different ovule cell layers. ARF3m expression in hypodermal cells surrounding the MMC, but not in epidermal cells, led to a multiple-MMC phenotype, suggesting that tasiR-ARFs repress ARF3 in these hypodermal cells to suppress ectopic MMC fate. RNA sequencing analyses in plants with hypodermally expressed ARF3m showed that ARF3 potentially regulates MMC specification through phytohormone pathways. Our findings uncover intricate spatial restriction of tasiR-ARF biogenesis, which together with tasiR-ARF mobility enables cell-cell communication in MMC differentiation.

Female germline cells in flowering plants differentiate from somatic cells to produce specialized reproductive organs, called ovules, embedded deep inside the flowers. We investigated the molecular basis of this distinctive developmental program by performing single-cell RNA sequencing (scRNA-seq) of 16,872 single cells of Arabidopsis thaliana ovule primordia at three developmental time points during female germline differentiation. This allowed us to identify the characteristic expression patterns of the main cell types, including the female germline and its surrounding nucellus. We then reconstructed the continuous trajectory of female germline differentiation and observed dynamic waves of gene expression along the developmental trajectory. A focused analysis revealed transcriptional cascades and identified key transcriptional factors that showed distinct expression patterns along the germline differentiation trajectory. Our study provides a valuable reference dataset of the transcriptional process during female germline differentiation at single-cell resolution, shedding light on the mechanisms underlying germline cell fate determination., Zhimin Hou, Yanhui Liu et al. used single cell RNA-seq to analyze the model organism, Arabidopsis thaliana, at three stages during female germline differentiation. They reconstructed the continuous trajectory of female germline differentiation, providing a valuable reference for future investigation of germline cell fate determination in A. thaliana.

Background Sugarcane (Saccharum spontaneum L.), the major sugar and biofuel feedstock crop, is cultivated mainly by vegetative propagation worldwide due to the infertility of female reproductive organs resulting in the reduction of quality and output of sugar. Deciphering the gene expression profile during ovule development will improve our understanding of the complications underlying sexual reproduction in sugarcane. Optimal reference genes are essential for elucidating the expression pattern of a given gene by quantitative real-time PCR (qRT-PCR). Method In this study, based on transcriptome data obtained from sugarcane ovule, eighteen candidate reference genes were identified, cloned, and their expression levels were evaluated across five developmental stages ovule (AC, MMC, Meiosis, Mitosis, and Mature). Results Our results indicated that FAB2 and MOR1 were the most stably expressed genes during sugarcane female gametophyte development. Moreover, two genes, cell cycle-related genes REC8 and CDK, were selected, and their feasibility was validated. This study provides important insights into the female gametophyte development of sugarcane and reports novel reference genes for gene expression research on sugarcane sexual reproduction.

RNA-dependent RNA polymerases (RDRs), involved in the production of various small interfering RNA (siRNA), play critical roles in plant growth, development process, and abiotic/biotic stresses. In this study, 5 RDR genes (AcRDRs) were identified from the pineapple genome. Phylogenetic analysis showed that AcRDRs could be divided into 4 subgroups. Gene structure analysis showed that the number of introns varied from 2 to 18. Furthermore, we analyzed AcRDR expression patterns in vegetative organs and in sexual organs, namely ovules and stamens, at different developmental stages respectively. AcRDR2, AcRDR3 and AcRDR6b showed higher expressions in the male and female reproductive organs, while AcRDR3 also was accumulated highly in sepal and fruit. AcRDR6a exhibited the highest expression levels at the mature ovule and stamen. AcRDR1 had an expression peak in the root. Furthermore, we checked the responses of AcRDRs to abiotic stresses and phytohormones. The results of this study provided basic genomic information for AcRDRs and insights into the probable roles of these genes in plant growth and development.

Background Transcription factors (TFs) are essential regulators of growth and development in eukaryotes. Basic-helix-loop-helix (bHLHs) is one of the most significant TFs families involved in several critical regulatory functions. Cryptochrome-interacting bHLH (CIB) and cryptochromes form an extensive regulatory network to mediate a plethora of pathways. Although bHLHs regulate critical biological processes in plants, the information about pineapple bHLHs remains unexplored. Results Here, we identified a total of 121 bHLH proteins in the pineapple genome. The identified genes were renamed based on the ascending order of their gene ID and classified into 18 subgroups by phylogenetic analysis. We found that bHLH genes are expressed in different organs and stages of pineapple development. Furthermore, by the ectopic expression of AcCIB2 in Arabidopsis and complementation of Atcib2 mutant, we verified the involvement of AcCIB2 in photomorphogenesis and abiotic stress response. Conclusions Our findings revealed that AcCIB2 plays an essential role in flowering time regulation and abiotic stress response. The present study provides additional insights into the current knowledge of bHLH genes and suggests their potential role in various biological processes during pineapple development.

The coordinated development of sporophytic and gametophytic tissues is essential for proper ovule patterning and fertility. However, the mechanisms regulating their integrated development remain poorly understood. Here, we report that the Swi2/Snf2-Related1 (SWR1) chromatin-remodeling complex acts with the ERECTA receptor kinase-signaling pathway to control female gametophyte and integument growth in Arabidopsis thaliana by inhibiting transcription of the microRNA gene MIR398c in early-stage megagametogenesis. Moreover, pri-miR398c is transcribed in the female gametophyte but is then translocated to and processed in the ovule sporophytic tissues. Together, SWR1 and ERECTA also activate ARGONAUTE10 (AGO10) expression in the chalaza; AGO10 sequesters miR398, thereby ensuring the expression of three AGAMOUS-LIKE (AGL) genes (AGL51, AGL52, and AGL78) in the female gametophyte. In the context of sexual organ morphogenesis, these findings suggest that the spatiotemporal control of miRNA biogenesis, resulting from coordination between chromatin remodeling and cell signaling, is essential for proper ovule development in Arabidopsis.

Additional file 8: Table S8. Protein sequences analysed in the present study.

This study identified 57 basic leucine zipper (bZIP) genes from the pineapple genome, and the analysis of these bZIP genes was focused on the evolution and divergence after multiple duplication events in relation to the pineapple genome fusion. According to bioinformatics analysis of a phylogenetic tree, the bZIP gene family was divided into 11 subgroups in pineapple, Arabidopsis, and rice; gene structure and conserved motif analyses showed that bZIP genes within the same subgroup shared similar intron-exon organizations and motif composition. Further synteny analysis showed 17 segmental duplication events with 27 bZIP genes. The study also analyzed the pineapple gene expression of bZIP genes in different tissues, organs, and developmental stages, as well as in abiotic stress responses. The RNA-sequencing data showed that AcobZIP57 was upregulated in all tissues, including vegetative and reproductive tissues. AcobZIP28 and AcobZIP43 together with the other 25 bZIP genes did not show high expression levels in any tissue. Six bZIP genes were exposed to abiotic stress, and the relative expression levels were detected by quantitative real-time PCR. A significant response was observed for AcobZIP24 against all kinds of abiotic stresses at 24 and 48 h in pineapple root tissues. Our study provides a perspective for the evolutionary history and general biological involvement of the bZIP gene family of pineapple, which laid the foundation for future functional characterization of the bZIP genes in pineapple.

Additional file 9: Table S9. DNA sequences analysed in the present study.

Additional file 1: Table S1. The properties of bHLH genes in pineapple.

Auxin response factors (ARFs) are transcription factors that bind with auxin response elements to regulate the expression of auxin responsive genes. The ARF genes family is characterized by a large multigene family in plants and plays important roles in plant development. However, the ARF gene family has not yet been identified in pineapple, one of the most important tropical fruit in the world. In this study, a total of 20 ARF genes, named as AcoARF1 to AcoARF20, were identified in pineapple. Firstly, a comprehensive bioinformatics analysis of the AcoARF gene family was presented, including chromosomal locations, phylogenetic relationships, gene structures, conserved motifs. Furthermore, we analyzed AcoARF expression patterns in vegetative organs and in sexual organs, namely ovules and stamens, at 7 and 4 different developmental stages respectively. AcoARF1, AcoARF3, AcoARF7 and AcoARF8 showed higher expression in fruit. AcoARF9 and AcoARF11 exhibited higher expression in flower, leaf and fruit, but not in root. During female and male gametophyte developments, AcoARF1, AcoARF2 and AcoARF19 were expressed at high level in developing ovule and stamen, implying their critical roles in reproduction. While, some AcoARFs expressed in ovule or stamen at specific stages, indicating their potentially particular functions. Our study provides comprehensive information of ARF family in pineapple, which will be useful in directing of selection of candidate genes related to tissue development in pineapple and pave the way to further functional verification of these AcoARF genes.

Significance In flowering plants, the female germ line begins as a single cell known as the megaspore mother cell (MMC) in each ovule. The mechanisms that restrict MMC fate to a single cell remain largely unknown. We show that the Arabidopsis cytochrome P450 gene KLU acts through the chromatin remodeling complex SWR1 to promote WRKY28 expression in ovule primordia. We show that WRKY28 is expressed in a few somatic cells surrounding the MMC and is required to inhibit these cells from acquiring the MMC-like cell fate. Consistent with non–cell-autonomous KLU activity, KLU -expressing cells and WRKY28 -expressing cells are neither identical nor adjacently positioned. Our study demonstrates that cell–cell interactions involving only somatic cells in ovule primordia ensure the specification of a single MMC.

Flowering plants display a remarkable diversity in inflorescence architecture, and pedicel length is one of the key contributors to this diversity. In Arabidopsis thaliana, the receptor-like kinase ERECTA (ER) mediated signaling pathway plays important roles in regulating inflorescence architecture by promoting cell proliferation. However, the regulating mechanism remains elusive in the pedicel. Genetic interactions between ERECTA signaling and the chromatin remodeling complex SWR1 in the control of inflorescence architecture were studied. Comparative transcriptome analysis was applied to identify downstream components. Chromatin immunoprecipitation and nucleosome occupancy was further investigated. The results indicated that the chromatin remodeler SWR1 coordinates with ERECTA signaling in regulating inflorescence architecture by activating the expression of PRE1 family genes and promoting pedicel elongation. It was found that SWR1 is required for the incorporation of the H2A.Z histone variant into nucleosomes of the whole PRE1 gene family and the ERECTA controlled expression of PRE1 gene family through regulating nucleosome dynamics. We propose that utilization of a chromatin remodeling complex to regulate gene expression is a common theme in developmental control across kingdoms. These findings shed light on the mechanisms through which chromatin remodelers orchestrate complex transcriptional regulation of gene expression in coordination with a developmental cue.

Biofouling is an important factor that affects the bivalve farming industry. Fouling organisms may reduce growth and survival rate of the cultured species. Fouler are often filter feeders, so they are potential competitors for food resource with the cultured species. The present study was conducted to measure the impact of fouling on food uptake and nutrient release in April and June, 2006 in Daya Bay near Guangzhou, China. Results showed that fouling organisms had significant effect on food uptake and nutrient release. The chlorophyll a uptake rate of fouled scallops was 7.53Lh−1±1.416Lh−1 and 11.94Lh−1±2.497Lh−1 in April and June, respectively, significantly higher than those of cleaned scallops, i.e., 4.23Lh−1±2.744Lh−1 and 2.57Lh−1±1.832Lh−1 respectively. The consumption of total particulate matter by fouled scallops in April and June was 5.52Lh−1±0.818Lh−1 and 3.07Lh−1±0.971Lh−1, respectively; the corresponding results for cleaned scallops are 2.49Lh−1±0.614Lh−1 and 2.37±1.214Lh−1, respectively. Fouling increased ammonia release significantly. The ammonia release rate of fouled scallops was 33.81Lh−1±7.699Lh−1 and 76.39Lh−1±9.251Lh−1 in April and June, while cleaned scallops released 2.46Lh−1±0.511Lh−1 and 7.23Lh−1±1.026Lh−1 ammonia, respectively. Phosphate release of fouled scallops was 22.72Lh−1±9.978Lh−1 in June and cleaned scallops released phosphate 6.01Lh−1±0.876Lh−1 in April. Therefore, fouling contributed much to food reduction and concentration increase of ammonia and phosphate in water.

In the present study, the effect of various substrata on the settlement of a pearl oyster, Pinctada martensii, was evaluated. The settlement of the larvae in the experiments with four different color substrata was compared and showed that deep color plastic sheets (red and blue) attracted significantly more larvae (P < 0.05) than light color (green and yellow). In addition, the influence of biofilm substrata was compared with that of non-film substrata of smooth or rough texture. Number of settled larvae was highest on biofilmed plastic sheets, either rough or smooth, then rough plastic sheets without film, the least recorded was on smooth plastic sheets without biofilm. Substrates of plastic sheets coated with tissue extracts of the same species appeared to attract larval settlement. The number of settled larvae on substrates with tissue extracts was significantly greater (P < 0.05) than that on the control. (C) 2007 Elsevier B.V. All rights reserved.

In most sexually reproducing plants, a single somatic, sub-epidermal cell in an ovule is selected to differentiate into a megaspore mother cell, which is committed to giving rise to the female germline. However, it remains unclear how intercellular signaling among somatic cells results in only one cell in the sub-epidermal layer differentiating into the megaspore mother cell. Here we uncovered a role of the THO complex in restricting the megaspore mother cell fate to a single cell. Mutations in TEX1, HPR1, and THO6, components of the THO/TREX complex, led to the formation of multiple megaspore mother cells, which were able to initiate gametogenesis. We demonstrated that TEX1 repressed the megaspore mother cell fate by promoting the biogenesis of TAS3-derived trans-acting smallinterfering RNA (ta-siRNA), which represses ARF3 expression. The TEX1 protein was present in epidermal cells, but not in the germline, and, through TAS3-derived ta-siRNA, restricted ARF3 expression to the medio domain of ovule primordia. Expansion of ARF3 expression into lateral epidermal cells in aTAS3 ta-siRNA-insensitive mutant led to the formation of supernumerary megaspore mother cells, suggesting that TEX1- and TAS3-mediated restriction of ARF3 expression limits excessive megaspore mother cell formation non-cell-autonomously. Our findings reveal the role of a small-RNA pathway in the regulation of female germline specification in Arabidopsis.

In this study, in vitro antibacterial effect of 16 different types of Chinese herbal medicine against Aeromonas hydrophila was evaluated. The boiling method was used to extract the bioactive ingredients from the herbal plants. The agar diffusion method was used to measure the zone of inhibition of gall, coptis, rhubarb, terminalia and other Chinese herbal medicine against Aeromonas hydrophila. The double tube dilution method was used to determine the minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC). Our results showed that different types of Chinese herbal medicine had different antibacterial effect against Aeromonas hydrophila. The water extract from gall, coptis, terminalia, rhubarb had stronger antibacterial effect, with their MIC values being 7.81 mg/mL, 15.63mg/mL, 31.25 mg/mL, 62.50 mg/mL, respectively. The MBC values of gall, coptis, terminalia, rhubarb were 15.63 mg/mL, 62.50 mg/mL, 62.50 mg/mL, 125.00 mg/mL, respectively. Next, we mixed gall extract individually with either terminalia, coptis, or rhubarb, and tested the MIC and MBC of the mixed extract. The MIC values of galls+terminalia, galls+coptis, galls+rhubarb were 3.906 mg/mL, 7.813 mg/mL, 15.625 mg/mL, respectively. The MBC values of galls+terminalia, galls+coptis, galls+rhubarb were 3.906 mg/mL, 7.813 mg/mL, 15.625 mg/mL, respectively. The in vitro antibacterial and bactericidal effect of the mixed compound were stronger than the 16 individual Chinese herbal medicine that.