A5025272563- RNA and protein synthesis mechanisms
- Genetic Mapping and Diversity in Plants and Animals
- Chromosomal and Genetic Variations
- Plant Molecular Biology Research
- Plant Genetic and Mutation Studies
- Plant Disease Resistance and Genetics
- Genomics and Phylogenetic Studies
- DNA and Nucleic Acid Chemistry
- Advanced biosensing and bioanalysis techniques
- Genetics and Plant Breeding
- Genetic and phenotypic traits in livestock
- Plant Stress Responses and Tolerance
- Bioenergy crop production and management
- Plant Reproductive Biology
- Plant Gene Expression Analysis
- Photosynthetic Processes and Mechanisms
- Plant Pathogens and Fungal Diseases
- Genetic diversity and population structure
- Wheat and Barley Genetics and Pathology
- Machine Learning in Bioinformatics
- RNA modifications and cancer
- Plant nutrient uptake and metabolism
- Single-cell and spatial transcriptomics
- Irrigation Practices and Water Management
- Genomics and Chromatin Dynamics
Nanjing Agricultural University
2020-2025
Nanjing Forestry University
2016-2023
As one of the most ancient tree species, codon usage pattern analysis Ginkgo biloba is a useful way to understand its evolutionary and genetic mechanisms. Several studies have been conducted on angiosperms, but seldom gymnosperms. Based RNA-Seq data G. transcriptome, amount 17,579 unigenes longer than 300 bp were selected analyzed from 68,547 candidates. The tended towards more frequently use A/U-ending codons, which showed an obvious gradient progressing gymnosperms dicots monocots....
I-motifs (iMs) are four-stranded non-B DNA structures containing C-rich sequences. The formation of iMs is sensitive to pH conditions and methylation, although the extent which still unknown in both humans plants. To investigate this, we here conducted iMab antibody-based immunoprecipitation sequencing (iM-IP-seq) along with bisulfite using CK (original genomic without methylation-related treatments) hypermethylated or demethylated at 5.5 7.0 rice, establishing a link between pH, methylation...
Abstract I-motifs (iMs) are non-canonical DNA secondary structures that fold from cytosine (C)-rich genomic regions termed putative i-motif forming sequences (PiMFSs). The structure of iMs is stabilized by hemiprotonated C-C base pairs, and their functions now suspected in key cellular processes human cells such as genome stability regulation gene transcription. In plants, biological relevance still largely unknown. Here, we characterized PiMFSs with high potential for formation the rice...
Background: Maize mesophyll (M) cells play important roles in various biological processes such as photosynthesis II and secondary metabolism. Functional differentiation occurs during M-cell development, but the underlying mechanisms for regulating development are largely unknown. Results: We conducted single-cell RNA sequencing (scRNA-seq) to profile transcripts maize leaves. then identified coregulated modules by analyzing resulting pseudo-time-series data through gene regulatory network...
Transposons significantly contribute to genome fractions in many plants. Although numerous transposon-related mutations have been identified, the evidence regarding transposon-derived genes regulating crop yield and other agronomic traits is very limited. In this study, we characterized a rice Harbinger gene called PANICLE NUMBER AND GRAIN SIZE (PANDA), which epigenetically coordinates panicle number grain size. Mutation of PANDA caused reduced but increased size rice, while transgenic...
G-quadruplexes (G4s) are challenging targets for chemical biology interventions, notably because of their dynamic topological polymorphism. We found that the antibiotic small- molecule colistin (COL) interacts specifically with a single subtype G4 structures, so-called parallel G4s. This interaction triggers aggregation G4/COL complexes in structure-specific manner, which can thus be separated from bulk solution by centrifugation. unprecedented mode affinity-precipitation was exploited here...
Restriction site associated DNA sequencing (RAD-seq), a next-generation technology, has greatly facilitated genetic linkage mapping studies in outbred species. RAD-seq is capable of discovering thousands markers for across many individuals, and can be applied species with or without reference genome. Although several analytical tools are available data, alternative strategies necessary improving the marker quality hence accuracy. We demonstrate strategy constructing dense maps hybrid forest...
A DNA G-quadruplex (G4) is a non-canonical four-stranded nucleic acid structure involved in many biological processes mammals. The current knowledge on plant G4s, however, limited; whether and how G4s impact gene expression plants still largely unknown. Here, we applied protocol referred to as BG4-DNA-IP-seq followed by comprehensive characterization of rice (Oryza sativa L.); next integrated dG4s (experimentally detectable G4s) with existing omics data found that exhibited differential...
Abstract Background Cold is one of the main abiotic stresses that severely affect plant growth and development, crop productivity as well. Transcriptional changes during cold stress have already been intensively studied in various species. However, gene networks involved regulation differential tolerance between tobacco varieties with contrasting resistance are quite limited. Results Here, we conducted multiple time-point transcriptomic analyses using Tai (TT, susceptibility) Yan (YT,...
Long noncoding RNAs (lncRNAs) have emerged as pivotal regulators in plant immune responses, yet their roles rice resistance against Magnaporthe oryzae (M. oryzae) remain inadequately explored. In this study, we integrated translatome data with conventional genome annotations to construct an optimized protein-coding dataset. Subsequently, developed a robust pipeline (“RiceLncRNA”) for the accurate identification of lncRNAs. Using strand-specific RNA sequencing (ssRNA-seq) from resistant...
Abstract Single-stranded DNA (ssDNA) is essential for various DNA-templated processes in both eukaryotes and prokaryotes. However, comprehensive characterizations of ssDNA still lag plants compared to nonplant systems. Here, we conducted situ S1-sequencing, with starting gDNA ranging from 5 µg 250 ng, followed by rice (Oryza sativa L.). We found that loci were substantially associated a subset non-B structures functional genomic loci. Subtypes had distinct epigenetic features. Importantly,...
With the plummeting cost of next-generation sequencing technologies, high-density genetic linkage maps could be constructed in a forest hybrid F1 population. However, based on such maps, quantitative trait loci (QTL) mapping cannot directly conducted with traditional statistical methods or tools because phase and segregation pattern molecular markers are not always fixed as inbred lines.We implemented composite interval (CIM) method to multivariate data trees developed corresponding...
Meiotic recombination events include crossovers and non-crossovers or gene conversions. Although the rate of is often used for genetic mapping, conversion are not well studied especially in outbred species, which could produce distorted markers thus affect precision maps.We proposed a strategy identifying Populus with next-generation sequencing (NGS) data from two parents their progeny an F1 hybrid population. The first involved phasing heterozygous SNPs to obtain parental haplotype blocks...
Single nucleotide polymorphism (SNP) is one of the most widely used molecular markers to help researchers understand relationship between phenotypes and genotypes. SNP calling mainly consists two steps, including read alignment locus identification based on statistical models, various software have been developed applied in this issue. Meanwhile, our study, very low agreement (<25%) was found among prediction results generated by different software, which much less consistent than...
Bundle sheath (BS) cells exhibit dramatically structural differences and functional variations at physiological, biochemical epigenetic levels as compared to mesophyll (M) in maize. The regulatory mechanisms controlling divergences between M BS have been extensively investigated. However, cell-related networks are still not completely characterized. To address this, we herein conducted WGCNA-related co-expression assays using bulk cell RNA-seq data sets identified a module containing 384...