A5039103139- Plant Molecular Biology Research
- Plant Reproductive Biology
- Gene expression and cancer classification
- Bioinformatics and Genomic Networks
- Chromosomal and Genetic Variations
- Genomics and Chromatin Dynamics
- RNA modifications and cancer
- Plant Stress Responses and Tolerance
- Single-cell and spatial transcriptomics
- Photosynthetic Processes and Mechanisms
- Plant nutrient uptake and metabolism
- Plant-Microbe Interactions and Immunity
- Powdery Mildew Fungal Diseases
- Polysaccharides and Plant Cell Walls
- Traditional Chinese Medicine Analysis
- Plant Ecology and Taxonomy Studies
- Protist diversity and phylogeny
- Bryophyte Studies and Records
- Plant Virus Research Studies
- Natural product bioactivities and synthesis
- Plant biochemistry and biosynthesis
- RNA and protein synthesis mechanisms
- Plant tissue culture and regeneration
- Plant and Fungal Interactions Research
- Genomics and Phylogenetic Studies
Center for Excellence in Molecular Plant Sciences
2019-2024
Chinese Academy of Sciences
2019-2024
University of Chinese Academy of Sciences
2019-2023
Abstract The life cycle of genome builds spans interlocking pillars assembly, annotation, and comparative genomics to drive biological insights. While tools exist address each pillar separately, there is a growing need for integrate different project holistically. For example, approaches can provide quality control assembly or annotation; in turn, help identify artifacts that may complicate the interpretation comparisons. JCVI library versatile Python‐based offers suite excel across these...
Age and wounding are two major determinants for regeneration. In plants, the root regeneration is triggered by wound-induced auxin biosynthesis. As plants age, regenerative capacity gradually decreases. How leads to burst how age wound signals collaboratively regulate poorly understood. Here, we show that increased levels of three closely-related miR156-targeted Arabidopsis (Arabidopsis thaliana) SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) transcription factors, SPL2, SPL10, SPL11, suppress...
Highlights•The dynamic chromatin state landscape during shoot regeneration is revealed•Collapse of pluripotency in the absence cytokinin signaling•Generation a catalog regulatory sequences regeneration•A cohort transcription factors involved outlinedSummaryShoot mediated by sequential action two phytohormones, auxin and cytokinin. However, landscapes underlying this response have not yet been studied. In study, we jointly profiled accessibility, histone modifications, transcriptomes to...
Abstract Plants undergo extended morphogenesis. The shoot apical meristem (SAM) allows for reiterative development and the formation of new structures throughout life plant. Intriguingly, SAM produces morphologically different leaves in an age-dependent manner, a phenomenon known as heteroblasty. In Arabidopsis thaliana, small orbicular juvenile phase, but gives rise to large elliptical adult phase. Previous studies have established that developmental decline microRNA156 (miR156) is...
The phytohormone cytokinin has various roles in plant development, including meristem maintenance, vascular differentiation, leaf senescence, and regeneration. Prior investigations have revealed that acts via a phosphorelay similar to the two-component system by which bacteria sense respond external stimuli. eventual targets of this are type-B ARABIDOPSIS RESPONSE REGULATORS (B-ARRs), containing conserved N-terminal receiver domain (RD), middle DNA binding (DBD), C-terminal transactivation...
Gene knock-out/down methods are commonly used to explore the functions of genes interest, but a database that systematically collects perturbed data is not available currently. Manual curation all human cell line RNA-seq datasets enabled us develop comprehensive perturbation (GPSAdb, https://www.gpsadb.com/). The current version GPSAdb collected 3048 associated with 1458 genes, which were knocked out/down by siRNA, shRNA, CRISPR/Cas9, or CRISPRi. provides full exploration these and generated...
The development of perennial crops holds great promise for sustainable agriculture and food security. However, the evolution transition between perenniality annuality is poorly understood. Here, using two Brassicaceae species, Crucihimalaya himalaica Erysimum nevadense, as polycarpic models, we reveal that from to biennial annual flowering behavior a continuum determined by dosage three closely related MADS-box genes. Diversification expression patterns, functional strengths, combinations...
DNA methylation affects gene expression and maintains genome integrity. The DNA-dependent RNA polymerase IV (Pol IV), together with the RNA-dependent RDR2, produces double-stranded small interfering precursors essential for establishing maintaining in plants. We determined cryo–electron microscopy structures of Pol IV–RDR2 holoenzyme backtracked transcription elongation complex. These reveal that RDR2 form a complex their active sites connected by an interpolymerase channel, through which...
Bryophytes represents a sister to the rest of land plants. Despite their evolutionary importance and relatively simple body plan, comprehensive understanding cell types transcriptional states that underpin temporal development bryophytes has not been achieved. Using time-resolved single-cell RNA sequencing, we define cellular taxonomy Marchantia polymorpha across asexual reproduction phases. We identify two maturation aging trajectories main plant M. at resolution: gradual tissues organs...
Significance Why the developmental transitions of multicellular organisms are unidirectional and how rate these is determined biological mysteries. Earlier reports have shown that both animals plants utilize microRNA (miRNA) as a timer in regulating their transitions. However, age temporally regulates abundance miRNAs poorly understood. In plants, progressive decline miR156 triggers appearance adult traits. Here, we show cell division apical meristem trigger for decline. The transcriptional...
Abstract Weed species are detrimental to crop yield. An understanding of how weeds originate and adapt field environments is needed for successful management reduction herbicide use. Although early flowering one the weed trait syndromes that enable ruderal overcome frequent disturbances, underlying genetic basis poorly understood. Here, we establish Cardamine occulta as a model study ruderality. By genome assembly QTL mapping, identify impairment vernalization response regulator gene FLC...
Open or accessible regions of the genome are primary positions binding sites for transcription factors and chromatin regulators. Transposase-accessible sequencing (ATAC-seq) can probe accessibility in intact nucleus. Here, we describe a protocol to generate ATAC-seq libraries from fresh Arabidopsis thaliana tissues establish an easy-to-use bioinformatic analysis pipeline. Our method could be applied other plants allows reliable detection changes throughout plant growth development. For...
Abstract Background Transcription factors (TFs) play central roles in regulating gene expression. With the rapid growth use of high-throughput sequencing methods, there is a need to develop comprehensive data processing and analyzing framework for inferring influential TFs based on ChIP-seq/ATAC-seq datasets. Results Here, we introduce FindIT2 (Find Influential Targets), an R/Bioconductor package annotating multi-omics data. supports complete peaks, identifying TF targets by combination...