A5101998663- Genetic Mapping and Diversity in Plants and Animals
- VLSI and FPGA Design Techniques
- VLSI and Analog Circuit Testing
- Genomics and Phylogenetic Studies
- Genetic and phenotypic traits in livestock
- Chromosomal and Genetic Variations
- Low-power high-performance VLSI design
- Metallurgy and Material Forming
- GABA and Rice Research
- Genetics and Plant Breeding
- Rice Cultivation and Yield Improvement
- Machine Learning in Bioinformatics
- Aquatic Ecosystems and Phytoplankton Dynamics
- Advanced Computing and Algorithms
- Microstructure and mechanical properties
- Plant Molecular Biology Research
- Wastewater Treatment and Nitrogen Removal
- Microstructure and Mechanical Properties of Steels
- Plant Virus Research Studies
- Microbial infections and disease research
- 3D IC and TSV technologies
- Plant tissue culture and regeneration
- MicroRNA in disease regulation
- Computational Geometry and Mesh Generation
- Advancements in Photolithography Techniques
Center for Excellence in Molecular Plant Sciences
2013-2025
Chinese Academy of Sciences
2015-2025
National Center for Gene Research
2013-2025
Qinghai Normal University
2024
Anhui Agricultural University
2024
National Institute for Viral Disease Control and Prevention
2023
DuPont (United States)
2023
Chinese University of Hong Kong
2010-2023
Qingdao University
2023
Affiliated Hospital of Qingdao University
2023
Crop domestications are long-term selection experiments that have greatly advanced human civilization. The domestication of cultivated rice (Oryza sativa L.) ranks as one the most important developments in history. However, its origins and processes controversial long been debated. Here we generate genome sequences from 446 geographically diverse accessions wild species Oryza rufipogon, immediate ancestral progenitor rice, 1,083 indica japonica varieties to construct a comprehensive map...
The next-generation sequencing technology coupled with the growing number of genome sequences opens opportunity to redesign genotyping strategies for more effective genetic mapping and analysis. We have developed a high-throughput method recombinant populations utilizing whole-genome resequencing data generated by Illumina Genome Analyzer. A sliding window approach is designed collectively examine genome-wide single nucleotide polymorphisms genotype calling recombination breakpoint...
The rich genetic diversity in Oryza sativa and rufipogon serves as the main sources rice breeding. Large-scale resequencing has been undertaken to discover allelic variants rice, but much of information for variation is often lost by direct mapping short sequence reads onto O. japonica Nipponbare reference genome. Here we constructed a pan-genome dataset sativa-O. species complex through deep sequencing de novo assembly 66 divergent accessions. Intergenomic comparisons identified 23 million...
Bin Han and colleagues report the draft genome of moso bamboo, an important non-timber forest product. RNA sequencing analysis bamboo flowering tissues suggests a connection between drought-responsive genes potential genes. Bamboo represents only major lineage grasses that is native to forests one most products in world. However, no species Bambusoideae subfamily has been sequenced. Here, we high-quality sequence (P. heterocycla var. pubescens). The 2.05-Gb assembly covers 95% genomic...
Bin Han and colleagues report the draft genome sequence of grass carp Ctenopharyngodon idellus, a major commercially farmed species freshwater fish. Analyses identify lineage-specific duplications that may have contributed to adaptation this vegetarian diet. The is an important fish, accounting for ∼16% global aquaculture, has Here we 0.9-Gb gynogenetic female adult 1.07-Gb wild male adult. Genome annotation identified 27,263 protein-coding gene models in genome. A total 114 scaffolds...
Various stable circular RNAs (circRNAs) are newly identified to be the abundance of noncoding in Archaea, Caenorhabditis elegans , mice, and humans through high-throughput deep sequencing coupled with analysis massive transcriptional data. CircRNAs play important roles miRNA function controlling by acting as competing endogenous or positive regulators on their parent coding genes. However, little is known regarding circRNAs plants. Here, we report 2354 rice that were computational ssRNA-seq...
Abstract Exploitation of heterosis is one the most important applications genetics in agriculture. However, genetic mechanisms are only partly understood, and a global view from representative number hybrid combinations lacking. Here we develop an integrated genomic approach to construct genome map for 1,495 elite rice varieties their inbred parental lines. We investigate 38 agronomic traits identify 130 associated loci. In-depth analyses effects heterozygous genotypes reveal that there few...
Expression, genetic variation, and tissues Human genomes show extensive variation across individuals, but we have only just started documenting the effects of this on regulation gene expression. Furthermore, a few been examined per variant. In order to examine how expression varies among within Genotype-Tissue Expression (GTEx) Consortium collected 1641 postmortem samples covering 54 body sites from 175 individuals. They identified quantitative traits that affect determined which these...
Cotton has been cultivated and used to make fabrics for at least 7000 years. Two allotetraploid species of great commercial importance, Gossypium hirsutum barbadense, were domesticated after polyploidization are worldwide. Although the overall genetic diversity between these two studied with limited accessions, their population structure variations remain largely unknown. We resequence genomes 147 cotton including diverse wild relatives, landraces, modern cultivars, construct a comprehensive...
Abstract Non-random gene organization in eukaryotes plays a significant role genome evolution. Here, we investigate the origin of biosynthetic cluster for production defence compounds oat—the avenacin cluster. We elucidate structure and organisation this 12-gene cluster, characterise last two missing pathway steps, reconstitute entire tobacco by transient expression. show that has formed de novo since divergence oats subtelomeric region lacks homology with other grasses, order is...
Abstract Exploitation of crop heterosis is crucial for increasing global agriculture production. However, the quantitative genomic analysis was lacking, and there currently no effective prediction tool to optimize cross-combinations. Here 2,839 rice hybrid cultivars 9,839 segregation individuals were resequenced phenotyped. Our findings demonstrated that indica – hybrid-improving breeding a process broadened genetic resources, pyramided breeding-favorable alleles through combinatorial...
THP-1 monocyte, which can be differentiated into macrophages by PMA, is widely used in researches on pathogen infection and host innate immunity, but reports the induction methods of PMA are different lack a unified standard, transcriptome characteristics macrophage compared with cells remains unclear. In this research, we examined differentiation effect three factors including time, cell seeding density concentration detecting positive rate CD14 expression. The 80ng/ml time 24h, 5×10 5...
Abstract The genome’s dynamic nature, exemplified by elements like extrachromosomal circular DNA (eccDNA), is crucial for biodiversity and adaptation. Yet, the role of eccDNA in plants, particularly rice, remains underexplored. Here, we identify 25,598 eccDNAs, unveiling widespread presence across six rice tissues revealing its formation as a universal random process. Interestingly, discover that direct repeats play pivotal formation, pointing to unique origin mechanism. Despite eccDNA’s...
Total anomalous pulmonary venous connection (TAPVC) is recognized as a rare congenital heart defect (CHD). With high mortality rate of approximately 80%, the survival and outcomes TAPVC patients are not satisfactory. However, genetic aetiology mechanism remain elusive. This study aimed to investigate underlying genomic risks through next-generation sequencing (NGS).Rare variants were identified whole exome (WES) 78 sporadic cases 100 healthy controls using Fisher's exact test gene-based...
Surgical robot automation has attracted increasing research interest over the past decade, expecting its potential to benefit surgeons, nurses and patients. Recently, learning paradigm of embodied intelligence demonstrated promising ability learn good control policies for various complex tasks, where AI simulators play an essential role facilitate relevant research. However, existing open-sourced surgical are still not sufficiently supporting human interactions through physical input...
Abstract Heading date (flowering time), which greatly influences regional and seasonal adaptability in rice (Oryza sativa), is regulated by many genes different photoperiod pathways. Here, we characterized a heading gene, Early 5 (Ehd5), using modified bulked segregant analysis method. The ehd5 mutant showed late flowering under both short-day long-day conditions, as well reduced yield, compared to the wild type. Ehd5, encodes WD40 domain-containing protein, induced light follows circadian...
Miscanthus, a rhizomatous perennial plant, has great potential for bioenergy production its high biomass and stress tolerance. We report chromosome-scale assembly of Miscanthus lutarioriparius genome by combining Oxford Nanopore sequencing Hi-C technologies. The 2.07-Gb covers 96.64% the genome, with contig N50 1.71 Mb. centromere telomere sequences are assembled all 19 chromosomes chromosome 10, respectively. Allotetraploid origin M. is confirmed using centromeric satellite repeats....
Phages widely exist in numerous environments from wastewater to deep ocean, representing a huge virus diversity, yet remain poorly characterized. Among them, jumbo phages are of particular interests due their large genome (>200 kb) and unusual biology. To date, only six strains infecting Klebsiella pneumoniae have been described. Here, we report the isolation characterization two hospital sixth genus: φKp5130 φKp9438. Both showed lytic activity against broad range clinical...
In this paper, we describe a routability-driven placer called Ripple. Two major techniques cell inflation and net-based movement are used in global placement followed by rough legalization step to reduce congestion. Cell is performed the horizontal vertical directions alternatively. We propose new method movement, which target position calculated for each considering of net as whole instead working on individually. detailed placement, use combination two kinds strategy: traditional...
Due to a significant mismatch between the objectives of wirelength and routing congestion, routability issue is becoming more important in VLSI design. In this paper, we present high quality placer Ripple 2.0 solve routability-driven placement problem. We will study how make use path information cell spreading relieve congestion with tangled logic detail. Several techniques are proposed, including (1) lookahead analysis pin density consideration, (2) path-based inflation (3) robust...