Whole-transcriptome sequencing reveals a vernalization-related ceRNA regulatory network in chinese cabbage (Brassica campestris L. ssp. pekinensis)

Background The transition from vegetative growth to reproductive growth involves various pathways. Vernalization is a crucial process for floral organ formation and regulation of flowering time that is widely utilized in plant breeding. In this study, we aimed to identify the global landscape of mRNAs, microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs) related to vernalization in Chinese cabbage. These data were then used to construct a competitive endogenous RNA (ceRNA) network that provides valuable information to better understand the vernalization response. Results In this study, seeds sampled from the Chinese cabbage doubled haploid (DH) line ‘FT’ with or without vernalization treatment were used for whole-transcriptome sequencing. A total of 2702 differentially expressed (DE) mRNAs, 151 DE lncRNAs, 16 DE circRNAs, and 233 DE miRNAs were identified in the vernalization-treated seeds. Various transcription factors, such as WRKY, MYB, NAC, bHLH, MADS-box, zinc finger protein CONSTANS-like gene, and B3 domain protein, and regulatory proteins that play important roles in the vernalization pathway were identified. Additionally, we constructed a vernalization-related ceRNA–miRNA–target gene network and obtained 199 pairs of ceRNA relationships, including 108 DEmiRNA‒DEmRNA, 67 DEmiRNA‒DElncRNA, and 12 DEmiRNA‒DEcircRNA interactions, in Chinese cabbage. Furthermore, several important vernalization-related genes and their interacting lncRNAs, circRNAs, and miRNAs, which are involved in the regulation of flowering time, floral organ formation, bolting, and flowering, were identified. Conclusions Our results reveal the potential mRNA and non-coding RNAs involved in vernalization, providing a foundation for further studies on the molecular mechanisms underlying vernalization in Chinese cabbage.

Dynamic Hormone Gradients Regulate Wound-Induced de novo Organ Formation in Tomato Hypocotyl Explants

Plants have a remarkable regenerative capacity, which allows them to survive tissue damage after biotic and abiotic stresses. In this study, we use Solanum lycopersicum ‘Micro-Tom’ explants as a model to investigate wound-induced de novo organ formation, as these explants can regenerate the missing structures without the exogenous application of plant hormones. Here, we performed simultaneous targeted profiling of 22 phytohormone-related metabolites during de novo organ formation and found that endogenous hormone levels dynamically changed after root and shoot excision, according to region-specific patterns. Our results indicate that a defined temporal window of high auxin-to-cytokinin accumulation in the basal region of the explants was required for adventitious root formation and that was dependent on a concerted regulation of polar auxin transport through the hypocotyl, of local induction of auxin biosynthesis, and of local inhibition of auxin degradation. In the apical region, though, a minimum of auxin-to-cytokinin ratio is established shortly after wounding both by decreasing active auxin levels and by draining auxin via its basipetal transport and internalization. Cross-validation with transcriptomic data highlighted the main hormonal gradients involved in wound-induced de novo organ formation in tomato hypocotyl explants.

Developmental mechanisms of sex differences: from cells to organisms

ABSTRACT Male-female differences in many developmental mechanisms lead to the formation of two morphologically and physiologically distinct sexes. Although this is expected for traits with prominent differences between the sexes, such as the gonads, sex-specific processes also contribute to traits without obvious male-female differences, such as the intestine. Here, we review sex differences in developmental mechanisms that operate at several levels of biological complexity – molecular, cellular, organ and organismal – and discuss how these differences influence organ formation, function and whole-body physiology. Together, the examples we highlight show that one simple way to gain a more accurate and comprehensive understanding of animal development is to include both sexes.

Tissue-Specific Metabolic Reprogramming during Wound-Induced Organ Formation in Tomato Hypocotyl Explants

Plants have remarkable regenerative capacity, which allows them to survive tissue damage after exposure to biotic and abiotic stresses. Some of the key transcription factors and hormone crosstalk mechanisms involved in wound-induced organ regeneration have been extensively studied in the model plant Arabidopsis thaliana. However, little is known about the role of metabolism in wound-induced organ formation. Here, we performed detailed transcriptome analysis and used a targeted metabolomics approach to study de novo organ formation in tomato hypocotyl explants and found tissue-specific metabolic differences and divergent developmental pathways. Our results indicate that successful regeneration in the apical region of the hypocotyl depends on a specific metabolic switch involving the upregulation of photorespiratory pathway components and the differential regulation of photosynthesis-related gene expression and gluconeogenesis pathway activation. These findings provide a useful resource for further investigation of the molecular mechanisms involved in wound-induced organ formation in crop species such as tomato.

Tissue-specific metabolic reprogramming during wound induced de novo organ formation in tomato hypocotyl explants

SUMMARYPlants have remarkable regenerative capacity, which allows them to survive tissue damaging after biotic and abiotic stress. Some of the key transcription factors and the hormone crosstalk involved in wound-induced organ regeneration have been extensively studied in the model plant Arabidopsis thaliana. However, little is known about the role of metabolism in wound-induced organ regeneration.Here, we performed detailed transcriptome analysis and targeted metabolomics approach during de novo organ formation in tomato hypocotyl explants and found tissue-specific metabolic differences and divergent developmental pathways after wounding.Our results indicate that callus growth in the apical region of the hypocotyl depends on a specific metabolic switch involving the upregulation of the photorespiratory pathway and the differential regulation of photosynthesis-related genes and of the gluconeogenesis pathway.The endogenous pattern of ROS accumulation in the apical and basal region of the hypocotyl during the time-course were dynamically regulated, and contributed to tissue-specific wound-induced regeneration.Our findings provide a useful resource for further investigation on the molecular mechanisms involved in wound-induced organ formation in a crop species such as tomato.One-sentence SummaryMetabolic switch during wound-induced regeneration

The Formation of Responsive Regional Regulations in Supporting Regional Autonomy in Pekanbaru City

This article aims to produce regional laws that are responsive in supporting the implementation of regional autonomy so that the implementation of regional autonomy does not create new problems that can hinder or damage economic development and growth in a region. In this study, several legal approaches used include the main approach of Law number 32 of 2004 concerning regional autonomy and Law number 12 of 2011 concerning the law on the establishment of legislation. Another approach approached in one case is a historical approach, a comparative approach, and a conceptual approach. Results illuminate how the drafting of Perda constitutes based on certain principals (i.e. clarity of objectives, appropriate institutional or organ formation, compatibility between types and material content) can accommodate local wisdom for the community and avoid potentially problematic regulations in the regions.

Regulation of Early Plant Development by Red and Blue Light: A Comparative Analysis Between Arabidopsis thaliana and Solanum lycopersicum

In vertical farming, plants are grown in multi-layered growth chambers supplied with energy-efficient LEDs that produce less heat and can thus be placed in close proximity to the plants. The spectral quality control allowed by LED lighting potentially enables steering plant development toward desired phenotypes. However, this requires detailed knowledge on how light quality affects different developmental processes per plant species or even cultivar, and how well information from model plants translates to horticultural crops. Here we have grown the model dicot Arabidopsis thaliana (Arabidopsis) and the crop plant Solanum lycopersicum (tomato) under white or monochromatic red or blue LED conditions. In addition, seedlings were grown in vitro in either light-grown roots (LGR) or dark-grown roots (DGR) LED conditions. Our results present an overview of phenotypic traits that are sensitive to red or blue light, which may be used as a basis for application by tomato nurseries. Our comparative analysis showed that young tomato plants were remarkably indifferent to the LED conditions, with red and blue light effects on primary growth, but not on organ formation or flowering. In contrast, Arabidopsis appeared to be highly sensitive to light quality, as dramatic differences in shoot and root elongation, organ formation, and developmental phase transitions were observed between red, blue, and white LED conditions. Our results highlight once more that growth responses to environmental conditions can differ significantly between model and crop species. Understanding the molecular basis for this difference will be important for designing lighting systems tailored for specific crops.

Evolutionary Emergence of First Animal Organisms Triggered by Environmental Mechano-Biochemical Marine Stimulation

The evolutionary emergence of the first animals is thought to have been intimately associated to the formation of a primitive endomesodermal gut (i.e gastrulation) from ancestral multi-cellular spheres, blastulae, more than 700 million years ago. However, the biochemical cues having been at the origin of endomesoderm formation remain a mystery.Here we find that hydrodynamic mechanical strains developed by sea wavelets on pre-bilaterian Nematostella vectensis and pre-metazoan Choanoeca flexa representatives, which common ancestor dates back to more than 700 million years ago, can trigger gastrulation in a Myo-II dependent mechanotransductive process. Gastrulation in turn induces endomesoderm first biochemical specification through the mechanical activation of the βcat pathway in pre-bilaterian Nematostella vectensis, like in Drosophila and zebrafish embryos, which common ancestor dates back to 600-700 million years ago.These observations converge to animal emergence that has been mechanotransductively triggered by wavelet mechanical strains on the sea-shore in multicellular choanoflagellates through Myo-II more than 700 million years ago, a process achieved in first metazoan through mechanosensitive Y654-containing βcat evolutionary emergence found as conserved in all metazoan.One sentence summaryMarine hydrodynamic strains have activated first gastric organ formation from ancestral pre-animal cell colonies.