Ground Tissue Research Articles

The bundle sheath in Zea mays leaves functions as a protective barrier against the toxic effect of lead

Lead is a highly toxic metal. It impairs the metabolism of living organisms. Plants show different sensitivity to the action of this element. One of the plants with relatively high lead tolerance is Zea mays, where even in detached leaves treated with Pb2+ ions, the photosynthesis rate remains very high compared to other plant species. This study set out to determine the mechanism responsible for the high resistance of maize photosynthetic tissue to the toxic effect of this metal. For this purpose, the cut leaves of Z. mays were incubated in Pb(NO3)2 solutions at different concentrations. Regions of lead accumulation in tissues and cells were located using histochemical methods and transmission electron microscopy. The experiments showed a diverse distribution of lead ions in the leaf blade of Z. mays. Most of the accumulated Pb2+ ions were observed in the vascular bundle and the bundle sheath, while minimal traces of metal were transferred to the mesophyll. In Pisum sativum leaves, although Pb(NO3)2 concentration in the solution was two-fold lower, lead accumulated in all the leaf tissues – mainly in the vascular bundle, epidermis, sclerenchyma, and mesophyll. Thus, bundle sheath cells in maize leaves were able to inhibit the flow of Pb2+ ions to the ground tissue. Therefore, the influence of the toxic metal on photosynthesis in mesophyll cells remained minimal. These experiments show that the structure of Z. mays leaf, with a layer of bundle sheath cells (characteristic of C4 plants), contributes to the protecting photosynthetic tissue against the toxic effect of lead.

Anatomical and Transcriptome Analyses of Moso Bamboo Culm Neck Growth: Unveiling Key Insights.

The Moso bamboo culm neck, connected with the rhizome and the shoot bud, is an important hub for connecting and transporting the aboveground and belowground systems of bamboo for the shoot bud development and rapid growth. Our previous study revealed that the culm neck generally undergoes six different developmental stages (CNS1-CNS6), according to the primary thickening growth of the underground shoot bud. However, the molecular mechanism of the culm neck development remains unknown. The present study focused on the developmental process of the CNS3-CNS5 stages, representing the early, middle, and late elongation stages, respectively. These stages are densely packed with vascular tissues and consist of epidermis, hypodermis, cortex, and ground tissue. Unlike the hollow structure of the culms, the culm necks are solid structures. As the culm neck continues to grow, the lignin deposition increases noticeably, contributing to its progressive strengthening. For the transcriptome analysis, a total of 161,160 transcripts with an average length of 2373 were obtained from these stages using both PacBio and Illumina sequencing. A total of 92.2% of the reads mapped to the Moso bamboo reference genome. Further analysis identified a total of 5524 novel genes and revealed a dynamic transcriptome. Secondary-metabolism- and transport-related genes were upregulated particularly with the growth of the culm neck. Further analysis revealed the molecular processes of lignin accumulation in the culm neck, which include differentially expressed genes (DEGs) related to cell wall loosening and remodeling and secondary metabolism. Moreover, the upregulations of transcription factors such as MYBH and RSM in the MYB family play crucial roles during critical transitions in the culm neck development, such as changes in the angle between the rhizome and the culm neck. Our new findings provide essential insights into the cellular roadmaps, transcriptional networks, and key genes involved in the culm neck development.

Distinct ADP-ribosylation factor-GTP exchange factors govern the opposite polarity of 2 receptor kinases.

Polarity of plasma membrane proteins is essential for cell morphogenesis and control of cell division and, thus, influences organ and whole plant development. In Arabidopsis (Arabidopsis thaliana) root endodermal cells, 2 transmembrane kinases, INFLORESCENCE AND ROOT APICES RECEPTOR KINASE (IRK) and KINASE ON THE INSIDE (KOIN), accumulate at opposite lateral domains. Their polarization is tightly linked to their activities regulating cell division and ground tissue patterning. The polarization of IRK and KOIN relies solely on the secretion of newly synthesized protein. However, the secretion machinery by which their opposite, lateral polarity is achieved remains largely unknown. Here, we show that different sets of ADP-ribosylation factor (ARF)-guanine-nucleotide exchange factors (ARF-GEFs) mediate their secretion. ARF-GEF GNOM-like-1 (GNL1) regulates KOIN secretion to the inner polar domain, thereby directing KOIN sorting early in the secretion pathway. For IRK, combined chemical and genetic analyses showed that the ARG-GEF GNL1, GNOM, and the BREFELDIN A-INHIBITED-GUANINE NUCLEOTIDE-EXCHANGE FACTORs 1 to 4 (BIG1-BIG4) collectively regulate its polar secretion. The ARF-GEF-dependent mechanisms guiding IRK or KOIN lateral polarity were active across different root cell types and functioned regardless of the protein's inner/outer polarity in those cells. Therefore, we propose that specific polar trafficking of IRK and KOIN occurs via distinct mechanisms that are not constrained by cell identity or polar axis and likely rely on individual protein recognition.

Morpho-anatomical adaptations of dominantly grown wild Datura inoxia to wastewater resource: Productivity and ecological issues

With the increasing global water scarcity, wastewater irrigation has become widespread, but it can have detrimental ecological consequences. Although wastewater contains valuable nutrients for plants, improper treatment or the use of untreated wastewater in irrigation can negatively impact soil fertility and plant growth. This study is divided into two parts: firstly, a phytosociological survey was conducted to identify plant species with the highest importance value index (IVI) in the vicinity of wastewater-irrigated areas. Secondly, a comparative morpho-anatomical analysis was carried out to investigate the morpho-anatomical adaptations of the species with the highest IVI under wastewater irrigation compared to normal water irrigation. The results of the phytosociological survey revealed the presence of 51 plant species in the vicinity of the wastewater-irrigated areas, with varying relative densities and coverage. Datura inoxia exhibited the highest IVI (28.79), followed by Xanthium strumarium (24.34), while Lippia nodiflora showed the lowest IVI (1.86). The morphological growth of D. inoxia was superior under normal water irrigation, but the average root length was greater under wastewater irrigation. Regarding cell anatomy, cell thickness and cell area characteristics in the dermal, ground, and vascular tissues of the stem and root tended to be greater under wastewater treatment. However, the opposite trend was observed in leaf anatomical analysis, possibly due to the combined effect of wastewater and climatic conditions. Stem and root xylem thickness were greater under wastewater irrigation, whereas phloem thickness was higher under normal water irrigation. The number of vascular bundles in the stem, root, and leaf was higher under wastewater treatment compared to normal water irrigation, but their arrangement was circular in the latter and scattered under wastewater irrigation. Datura inoxia demonstrated strong adaptive potential under wastewater irrigation, as indicated by its highest relative density, coverage, and IVI, suggesting its suitability for phytoremediation. However, due to the low relative density, coverage, and IVI of many other species, the use of untreated wastewater for irrigation cannot be appreciated.

N6-adenosine methylation of mRNA integrates multilevel auxin response and ground tissue development in Arabidopsis.

N6-methyl adenosine (m6A) is a widespread internal mRNA modification impacting the expression of numerous genes. Here we characterize the auxin-related defects among the pleiotropic phenotypes of the hypomorphic Arabidopsis thaliana mutants with the impaired status of m6A and present that they show strong resistance to exogenously applied auxin. By compiling major published m6A datasets, we propose that among the high-confidence target transcripts emerge those encoding the main components required for auxin signaling, including the auxin receptors TIR1/AFBs and ARF transcriptional regulators. We also observe subtle changes in endogenous levels of indole-3-acetic acid (IAA) metabolites in these hypomorphic lines, which correlate with the methylation status of the IAA amidohydrolase transcripts. In addition, we reveal that the reduced m6A levels lead to defects in the endodermal patterning in the primary root arising from the impaired timing of the periclinal cell divisions. These defects can be reverted by inhibition of auxin signaling. Together, our data underline that m6A likely affects the auxin-dependent processes at multiple levels.

Influence of Shading and Anatomical Structure of the Stem Cutting on Rooting Performance of Fig (Ficus Sp.)

Fig (Ficus sp.) belongs to tropical and subtropical climates which have great potential for the commercial cultivation. Cutting is the most common and effective method of propagation for figs which is influenced by different exogenous and endogenous factors. In this light, a study was conducted to observe the responses of stem cutting of fig (Ficus sp.) of one exotic and two indigenous varieties (Teen- Ficus carica; wild fig- Ficus hispida and joggo fig- Ficus racemosa) in respect of duration of shade and anatomical status of stem. The study was laid in Completely Randomized Design (CRD) with two factors (duration of shade and cultivars) and three replications of the treatments. The four different treatments of shade duration were as T1= open or control, T2=3 days of shading, T3= 6 days of shading and T4= 9 days of shading. Data were collected on root and sprout growth of the cuttings at weekly interval from two weeks of planting the cuttings in sand filled plastic cups. When the duration of shading increased, the teen (Ficus carica) showed the longest sprout (1.59 mm) and root (2 mm) as well as maximum number of root (5.67) and sprout (2.33). Better rooting performance was found in teen and it was very low in wild fig. A relationship between rooting performance and anatomical structure was clearly observed in this study. Long period of shading has positive effect on number and length of sprout in teen and wild fig. On the other hand, short period of shading minimized the days required for sprouting in teen Presence of thin cuticle, thin trichome and the absence of druses crystal in ground tissue and medulla also enhanced the performance of stem cutting of teen.

Visualization of the frequency effect of pulsed electric field on enzymatic browning of peel ground tissue

The enzymatic browning behavior of a model ground tissue, banana peel, influenced by the frequency variable of pulsed electric field (PEF), has been visualized and studied. The tissue was PEF-treated with 15 µs pulse at 3.3 kV/cm using trains of 5, 15, and 30 pulses, each varying from 0.1 Hz to 10 Hz; images and electrical conductivity were recorded intermittently throughout the incubation. The degree of browning was quantified with a browning index (BI) term, and the uniformity of browning was visually assessed by inspecting the pattern of pigment distribution. Moreover, the degree of tissue disintegration was calculated using a conductivity-based tissue disintegration index (DI) and compared to the BI and specific energy input. Browning uniformity was found to be significantly affected and increased with decreasing frequency. The effect was most noticeable up to disintegration degree of about 63, DI, or when the frequency of 5 or 15 pulses was reduced from 1 Hz to 0.1 Hz. Remarkably, the decrease at 5 pulses resulted in a significant increase in BI without a substantial increase in DI. The observed effect has been attributed to increased electrophoretic mobility of browning agents along the extracellular path during 0.1 Hz pulsation. Furthermore, lowering the frequency to 0.1 Hz reduced the energy required for a browning level close to saturation by about 57% compared to 10 Hz.

Spatial transcriptomics of a lycophyte root sheds light on root evolution

Plant roots originated independently in lycophytes and euphyllophytes, whereas early vascular plants were rootless. The organization of the root apical meristem in euphyllophytes is well documented, especially in the model plant Arabidopsis. However, little is known about lycophyte roots and their molecular innovations during evolution. In this study, spatial transcriptomics was used to detect 97 root-related genes in the roots of the lycophyte Selaginella moellendorffii. A high number of genes showed expression patterns similar to what has been reported for seed plants, supporting the idea of a highly convergent evolution of mechanisms to control root development. Interaction and complementation data of SHORTROOT (SHR) and SCARECROW (SCR) homologs, furthermore, support a comparable regulation of the ground tissue (GT) between euphyllophytes and lycophytes. Root cap formation, in contrast, appears to be differently regulated. Several experiments indicated an important role of the WUSCHEL-RELATED HOMEOBOX13 gene SmWOX13a in Selaginella root cap formation. In contrast to multiple Arabidopsis WOX paralogs, SmWOX13a is able to induce root cap cells in Arabidopsis and has functionally conserved homologs in the fern Ceratopteris richardii. Lycophytes and a part of the euphyllophytes, therefore, may share a common mechanism regulating root cap formation, which was diversified or lost during seed plant evolution. In summary, we here provide a new spatial data resource for the Selaginella root, which in general advocates for conserved mechanisms to regulate root development but shows a clear divergence in the control of root cap formation, with a novel putative role of WOX genes in root cap formation in non-seed plants.

Farmyard manure, a potential organic additive to reclaim copper and Macrophomina phaseolina stress responses in mash bean plants

In the era of global warming, stress combinations instead of individual stress are realistic threats faced by plants that can alter or trigger a wide range of plant responses. In the current study, the cumulative effect of charcoal rot disease caused by notorious fungal pathogen viz., Macrophomina phaseolina was investigated under toxic levels of copper (Cu) in mash bean, and farmyard manure (FYM) was employed to manage stress. Therefore, Cu-spiked soil (50 and 100 mg/kg) was inoculated with the pathogen, and amended with 2% FYM, to assess the effect of intricate interactions on mash bean plants through pot experiments. Results demonstrated that the individual stress of the pathogen or Cu was more severe for morpho-growth, physio-biochemical, and expression profiles of stress-related genes and total protein in mash bean plants as compared to stress combinations. Under single Cu stress, a significant amount of Cu accumulated in plant tissues, particularly in roots than in upper ground tissues, while, under stress combination less Cu accumulated in the plants. Nonetheless, 2% FYM in soil encountered the negative effect of stress responses provoked by the pathogen, Cu, or both by improving health markers (photosynthetic pigments, reducing sugar, total phenolics) and oxidative stress markers (catalase, peroxidase, and polyphenol oxidase), together with regulating the expression of stress-related genes (catalase, ascorbate peroxidase, and cytokinin-resistant genes), and proteins, besides decreasing Cu uptake in the plants. FYM worked better at lower concentrations (50 mg/kg) of Cu than at higher ones (100 mg/kg), hence could be used as a suitable option for better growth, yield, and crop performance under charcoal rot disease stress in Cu-contaminated soils.

Transcriptional control of hydrogen peroxide homeostasis regulates ground tissue patterning in the Arabidopsis root.

In multicellular organisms, including higher plants, asymmetric cell divisions (ACDs) play a crucial role in generating distinct cell types. The Arabidopsis root ground tissue initially has two layers: endodermis (inside) and cortex (outside). In the mature root, the endodermis undergoes additional ACDs to produce the endodermis itself and the middle cortex (MC), located between the endodermis and the pre-existing cortex. In the Arabidopsis root, gibberellic acid (GA) deficiency and hydrogen peroxide (H2O2) precociously induced more frequent ACDs in the endodermis for MC formation. Thus, these findings suggest that GA and H2O2 play roles in regulating the timing and extent of MC formation. However, details of the molecular interaction between GA signaling and H2O2 homeostasis remain elusive. In this study, we identified the PEROXIDASE 34 (PRX34) gene, which encodes a class III peroxidase, as a molecular link to elucidate the interconnected regulatory network involved in H2O2- and GA-mediated MC formation. Under normal conditions, prx34 showed a reduced frequency of MC formation, whereas the occurrence of MC in prx34 was restored to nearly WT levels in the presence of H2O2. Our results suggest that PRX34 plays a role in H2O2-mediated MC production. Furthermore, we provide evidence that SCARECROW-LIKE 3 (SCL3) regulates H2O2 homeostasis by controlling transcription of PRX34 during root ground tissue maturation. Taken together, our findings provide new insights into how H2O2 homeostasis is achieved by SCL3 to ensure correct radial tissue patterning in the Arabidopsis root.

DNA-free high-quality RNA extraction from 39 difficult-to-extract plant species (representing seasonal tissues and tissue types) of 32 families, and its validation for downstream molecular applications

BackgroundHigh-purity RNA serves as the basic requirement for downstream molecular analysis of plant species, especially the differential expression of genes to various biotic and abiotic stimuli. But, the extraction of high-quality RNA is usually difficult from plants rich in polysaccharides and polyphenols, and their presence usually interferes with the downstream applications. The aim of the study is to optimize the extraction of high-quality RNA from diverse plant species/tissues useful for downstream molecular applications.ResultsExtraction of RNA using commercially available RNA extraction kits and routine hexadecyltrimethylammonium bromide (CTAB) methods did not yield good quality DNA-free RNA from Prosopis cineraria, Conocarpus erectus, and Phoenix dactylifera. A reliable protocol for the extraction of high-quality RNA from mature leaves of these difficult-to-extract trees was optimized after screening nine different methods. The DNase I-, and proteinase K treatment-free modified method, consisting of extraction with CTAB method followed by TRIzol, yielded high-quality DNA-free RNA with an A260/A280 and A260/A230 ratios > 2.0. Extraction of RNA from Conocarpus, the most difficult one, was successful by avoiding the heat incubation of ground tissue in a buffer at 65 oC. Pre-warming of the buffer for 5–10 min was sufficient to extract good-quality RNA. RNA integrity number of the extracted RNA samples ranged between 7 and 9.1, and the gel electrophoresis displayed intact bands of 28S and 18S RNA. A cDNA library constructed from the RNA of P. cineraria was used for the downstream applications. Real-time qPCR analysis using the cDNA from P. cineraria RNA confirmed the quality. The extraction of good quality RNA from samples of the desert-growing P. cineraria (> 20-years-old) collected in alternate months of the year 2021 (January to December covering winter, spring, autumn, and the very dry and hot summer) proved the efficacy of the protocol. The protocol’s broad applicability was further validated by extracting good-quality RNA from 36 difficult-to-extract plant species, including tissues such as roots, flowers, floral organs, fruits, and seeds.ConclusionsThe modified DNase I and Proteinase K treatment-free protocol enables to extract DNA-free, high-quality, intact RNA from a total of 39 difficult-to-extract plant species belonging to 32 angiosperm families is useful to extract good-quality RNA from dicots and monocots irrespective of tissue types and growing seasons.

Single-cell transcriptome atlas reveals spatiotemporal developmental trajectories in the basal roots of moso bamboo (Phyllostachys edulis).

Roots are essential for plant growth and development. Bamboo is a large Poaceae perennial with 1642 species worldwide. However, little is known about the transcriptional atlas that underpins root cell-type differentiation. Here, we set up a modified protocol for protoplast preparation and report single-cell transcriptomes of 14 279 filtered single cells derived from the basal root tips of moso bamboo. We identified four cell types and defined new cell-type-specific marker genes for the basal root. We reconstructed the developmental trajectories of the root cap, epidermis, and ground tissues and elucidated critical factors regulating cell fate determination. According to in situ hybridization and pseudotime trajectory analysis, the root cap and epidermis originated from a common initial cell lineage, revealing the particularity of bamboo basal root development. We further identified key regulatory factors for the differentiation of these cells and indicated divergent root developmental pathways between moso bamboo and rice. Additionally, PheWOX13a and PheWOX13b ectopically expressed in Arabidopsis inhibited primary root and lateral root growth and regulated the growth and development of the root cap, which was different from WOX13 orthologs in Arabidopsis. Taken together, our results offer an important resource for investigating the mechanism of root cell differentiation and root system architecture in perennial woody species of Bambusoideae.

Morphology, Taxonomy, Culm Internode and Leaf Anatomy, and Palynology of the Giant Reed (Arundo donax L.), Poaceae, Growing in Thailand.

In this paper, we present the morphology, taxonomy, anatomy, and palynology of Arundo donax. A detailed morphological description and illustrations of the species are provided, along with information about the identification, distribution, the specimens examined, habitat and ecology, the International Union for Conservation of Nature (IUCN) conservation assessment, phenology, etymology, vernacular name, and uses. The species can be distinguished by its large, tall rhizomatous perennial reed; cauline leaves; an open, large, plumose panicle inflorescence; subequal glumes as long as the spikelets; glabrous rachilla; all bisexual florets; and a lemma with a straight awn and with long white hairs outside below the middle part. In this study, two names were lectotypified: Arundo bifaria and A. bengalensis, which are synonyms of A. donax. The culm internodes in the transverse section have numerous vascular bundles scattered in the ground tissue, and the parenchyma cells have significantly lignified cell walls. Vascular bundles are composed of phloem and xylem and are enclosed in a continuous sclerenchymatous bundle sheath. The chloroplasts in the transverse section of the leaf blades are found only in the mesophyll cells but are absent in the bundle sheath cells, which indicates that it is a C3 grass. The leaves have stomata on both surfaces and are confined to the intercostal zones. The stomata are typically paracytic, with two lateral subsidiary cells placed parallel to the guard cells. The stomatal density is higher on the abaxial surface [450-839/mm2 (606.83 ± 72.71)] relative to the adaxial surface [286-587/mm2 (441.27 ± 50.72)]. The pollen grains are spheroidal or subspheroidal [polar axis length/equatorial axis length ratio (P/E ratio) = 0.89-1.16 (1.02 ± 0.07)] with a single pore surrounded by a faint annulus, and the exine sculpturing is granular.

Bioactive Glass Applications in Different Periodontal Lesions: A Narrative Review

Tissue engineering in the orofacial region with bioactive components by the activation of immune complexes or other proteins is the current focus of biomaterials research. Consequently, natural ground materials and tissue components are being created. Bioactive glass is one of the most promising biomaterials and has bioactive properties making it suited for a range of different clinical dental applications, including the regeneration of hard tissues in the craniofacial region. This narrative review provides a summary of the favorable properties and recent applications of bioactive glass materials for the management of periodontal lesions. Bioactive glass mimics natural calcified tissues in terms of composition and has a bioactive role in bone regeneration. The present review concluded that bioactive glass materials have a promising potential for various periodontal applications including the repair of infrabony defects, gingival recession, furcation defects, and guided tissue regeneration. However, further in vivo studies and clinical trials are warranted to advance and validate the potential of bioactive glass for periodontal applications and translate its usage in dental clinics for periodontology.

Structure and histochemistry of the stem of Dracaena cambodiana Pierre ex Gagnep.

Dracaena cambodiana Pierre ex Gagnep is an important plant resource for producing dragon's blood and one of most popular ornamental trees in China. For a better understanding of the physiological function of the stem, the structural characteristics and main substance histological location of the stems of D. cambodiana were studied. The structural characteristics of the different developmental stages of stems of D. cambodiana were observed and described detailly. And then a schematic diagram of the mature stem was created. Histochemical staining showed that two kinds of polysaccharides distributed in parenchymal cells. Saponins distributed mainly in ground tissue and phenolic compounds distributed mainly in the thick cell walls. An abundant of calcium oxalate raphide bundles were identified in cortex and primary tissue. Finally, the role of the above results in the taxonomy of Dracaena species and in their strong adaptability was discussed.

Microbiome diversity, composition and assembly in a California citrus orchard.

The citrus root and rhizosphere microbiomes have been relatively well described in the literature, especially in the context of Huanglonbing disease. Yet questions addressing the assembly of root microbial endophytes have remained unanswered. In the above ground tree tissues, leaves and stems have been the research focus point, while flush and flower microbiomes, two important tissues in the vegetative and reproductive cycles of the tree, are not well described. In this study, the fungal and bacterial taxa in five biocompartments (bulk soil, rhizosphere, root endosphere, flower and flush) of citrus trees grown in a single California orchard were profiled using an amplicon-based metagenomic Illumina sequencing approach. Trees with no observable signs of abiotic or biotic stresses were sampled for two consecutive years during the floral development phase. The rhizosphere was the most biodiverse compartment compared to bulk soil, root endosphere, flower and flush microbiomes. In addition, the belowground bacteriome was more diverse than the mycobiome. Microbial richness decreased significantly from the root exosphere to the endosphere and was overall low in the above ground tissues. Root endophytic microbial community composition shared strong similarities to the rhizosphere but also contained few taxa from above ground tissues. Our data indicated compartmentalization of the microbiome with distinct profiles between above and below ground microbial communities. However, several taxa were present across all compartments suggesting the existence of a core citrus microbiota. These findings highlight key microbial taxa that could be engineered as biopesticides and biofertilizers for citriculture.

NAC1 regulates root ground tissue maturation by coordinating with the SCR/SHR–CYCD6;1 module in Arabidopsis

Precise spatiotemporal control of the timing and extent of asymmetric cell divisions (ACDs) is essential for plant development. In the Arabidopsis root, ground tissue maturation involves an additional ACD of the endodermis that maintains the inner cell layer as the endodermis and generates the middle cortex to the outside. Through regulation of the cell cycle regulator CYCLIND6;1 (CYCD6;1), the transcription factors SCARECROW (SCR) and SHORT-ROOT (SHR) play critical roles in this process. In the present study, we found that loss of function of NAC1, a NAC transcription factor family gene, causes markedly increased periclinal cell divisions in the root endodermis. Importantly, NAC1 directly represses the transcription of CYCD6;1 by recruiting the co-repressor TOPLESS (TPL), creating a fine-tuned mechanism to maintain proper root ground tissue patterning by limiting production of middle cortex cells. Biochemical and genetic analyses further showed that NAC1 physically interacts with SCR and SHR to restrict excessive periclinal cell divisions in the endodermis during root middle cortex formation. Although NAC1–TPL is recruited to the CYCD6;1 promoter and represses its transcription in an SCR-dependent manner, NAC1 and SHR antagonize each other to regulate the expression of CYCD6;1. Collectively, our study provides mechanistic insights into how the NAC1–TPL module integrates with the master transcriptional regulators SCR and SHR to control root ground tissue patterning by fine-tuning spatiotemporal expression of CYCD6;1 in Arabidopsis.

New Representative of <i>Pinus</i> L. from Jurassic Deposits of Belgorod Region, Russia

A new species of fossil pines, P. bukatkinii sp. nov., was found in the Middle Jurassic of Stoilensk open mine (the vicinity of Stary Oskol town, Belgorod Region). Seed cones of the new species possess four key diagnostic characters of representatives of the genus Pinus L.: thickened scale apices with apophyses and umbo; trace to the seed scale and bract represents a single unit; resin canals enter the seed scale base abaxially; adaxially concave vascular bundles in the seed scale. The distinctive feature of the new species is a strong sclerification of the seed scale ground tissue. Galleries, made by herbivores, were found in seed cones of P. bukatkinii sp. nov., that represents the oldest documented evidence of parasitism on pinaceous seed cones.

SHORT-ROOT and SCARECROW homologs regulate patterning of diverse cell types within and between species.

The roles of SHORT-ROOT (SHR) and SCARECROW (SCR) in ground tissue patterning and differentiation have been well established in the root of Arabidopsis thaliana. Recently, work in additional organs and species revealed the extensive functional diversification of these genes, including regulation of cortical divisions essential for nodule organogenesis in legume roots, bundle sheath specification in the Arabidopsis leaf, patterning of inner leaf cell layers in maize, and stomatal development in rice. The co-option of distinct functions and cell types is attributed to different mechanisms, including paralog retention, spatiotemporal changes in gene expression, and novel protein functions. Elaborating our knowledge of the SHR-SCR module further unravels the developmental regulation that controls diverse forms and functions within and between species.

Genome-wide identification and characterization of the NPF genes provide new insight into low nitrogen tolerance in Setaria.

Nitrogen (N) is essential for plant growth and yield production and can be taken up from soil in the form of nitrate or peptides. The NITRATE TRANSPORTER 1/PEPTIDE TRANSPORTER family (NPF) genes play important roles in the uptake and transportation of these two forms of N. Bioinformatic analysis was used to identify and characterize the NPF genes in Setaria. RNA-seq was employed to analyze time-series low nitrate stress response of the SiNPF genes. Yeast and Arabidopsis mutant complementation were used to test the nitrate transport ability of SiNRT1.1B1 and SiNRT1.1B2. We identified 92 and 88 putative NPF genes from foxtail millet (Setaria italica L.) and its wild ancestor green foxtail (Setaria viridis L.), respectively. These NPF genes were divided into eight groups according to their sequence characteristics and phylogenetic relationship, with similar intron-exon structure and motifs in the same subfamily. Twenty-six tandem duplication and 13 segmental duplication events promoted the expansion of SiNPF gene family. Interestingly, we found that the tandem duplication of the SiNRT1.1B gene might contribute to low nitrogen tolerance of foxtail millet. The gene expression atlas showed that the SiNPFs were divided into two major clusters, which were mainly expressed in root and the above ground tissues, respectively. Time series transcriptomic analysis further revealed the response of these SiNPF genes to short- and long- time low nitrate stress. To provide natural variation of gene information, we carried out a haplotype analysis of these SiNPFs and identified 2,924 SNPs and 400 InDels based on the re-sequence data of 398 foxtail millet accessions. We also predicted the three-dimensional structure of the 92 SiNPFs and found that the conserved proline 492 residues were not in the substrate binding pocket. The interactions of SiNPF proteins with were analyzed using molecular docking and the pockets were then identified. We found that the SiNPFs- binding energy ranged from -3.8 to -2.7 kcal/mol. Taken together, our study provides a comprehensive understanding of the NPF gene family in Setaria and will contribute to function dissection of these genes for crop breeding aimed at improving high nitrogen use efficiency.