A5028404995- Fungal and yeast genetics research
- Genomics and Phylogenetic Studies
- Chromosomal and Genetic Variations
- CRISPR and Genetic Engineering
- Evolution and Genetic Dynamics
- Fermentation and Sensory Analysis
- Mitochondrial Function and Pathology
- Telomeres, Telomerase, and Senescence
- Genetics, Aging, and Longevity in Model Organisms
- Yeasts and Rust Fungi Studies
- DNA Repair Mechanisms
- RNA and protein synthesis mechanisms
- RNA Research and Splicing
- Epigenetics and DNA Methylation
- Genomics and Chromatin Dynamics
- Cancer Genomics and Diagnostics
- Cancer-related gene regulation
- Horticultural and Viticultural Research
- Protist diversity and phylogeny
- Genetic Mapping and Diversity in Plants and Animals
- Plant Pathogenic Bacteria Studies
- Cervical Cancer and HPV Research
- Genetic Neurodegenerative Diseases
- Plant-Microbe Interactions and Immunity
- Marine Ecology and Invasive Species
Sun Yat-sen University
2020-2025
Sun Yat-sen University Cancer Center
2020-2025
First Affiliated Hospital of Zhengzhou University
2024
Institut de Recherche sur le Cancer et le Vieillissement de Nice
2015-2023
Inserm
2015-2023
Centre National de la Recherche Scientifique
2015-2023
Université Côte d'Azur
2017-2023
Southwest University
2023
Fondation ARC pour la Recherche sur le Cancer
2019-2021
Rice University
2010-2016
Large-scale population genomic surveys are essential to explore the phenotypic diversity of natural populations. Here we report whole-genome sequencing and phenotyping 1,011 Saccharomyces cerevisiae isolates, which together provide an accurate evolutionary picture variants that shape species-wide landscape this yeast. Genomic analyses support a single ‘out-of-China’ origin for species, followed by several independent domestication events. Although domesticated isolates exhibit high variation...
Structural rearrangements have long been recognized as an important source of genetic variation, with implications in phenotypic diversity and disease, yet their detailed evolutionary dynamics remain elusive. Here we use long-read sequencing to generate end-to-end genome assemblies for 12 strains representing major subpopulations the partially domesticated yeast Saccharomyces cerevisiae its wild relative paradoxus. These population-level high-quality genomes comprehensive annotation enable...
Abstract Although it is widely believed that early vertebrate evolution was shaped by ancient whole-genome duplications, the number, timing and mechanism of these events remain elusive. Here, we infer history vertebrates through genomic comparisons with a new chromosome-scale sequence invertebrate chordate amphioxus. We show how karyotypes amphioxus diverse are derived from 17 ancestral linkage groups (and 19 bilaterian groups) fusion, rearrangement duplication. resolve two distinct...
Acorn worms, also known as enteropneust (literally, 'gut-breathing') hemichordates, are marine invertebrates that share features with echinoderms and chordates. Together, these three phyla comprise the deuterostomes. Here we report draft genome sequences of two acorn Saccoglossus kowalevskii Ptychodera flava. By comparing them diverse bilaterian genomes, identify shared traits were probably inherited from last common deuterostome ancestor, then explore evolutionary trajectories leading this...
Plant immunity is activated upon pathogen perception and often affects growth yield when it constitutively active. How plants fine-tune immune homeostasis in their natural habitats remains elusive. Here, we discover a conserved suppression network cereals that orchestrates homeostasis, centering on Ca2+-sensor, RESISTANCE OF RICE TO DISEASES1 (ROD1). ROD1 promotes reactive oxygen species (ROS) scavenging by stimulating catalase activity, its protein stability regulated ubiquitination....
Pangenomes provide access to an accurate representation of the genetic diversity species, both in terms sequence polymorphisms and structural variants (SVs). Here we generated Saccharomyces cerevisiae Reference Assembly Panel (ScRAP) comprising reference-quality genomes for 142 strains representing species' phylogenetic ecological diversity. The ScRAP includes phased haplotype assemblies several heterozygous diploid polyploid isolates. We identified circa (ca.) 4,800 nonredundant SVs that a...
• Plant disease resistance genes (R genes) encode proteins that function to monitor signals indicating pathogenic infection, thus playing a critical role in the plant's defense system. Although many studies have been performed explore functional details of these important genes, their origin and evolutionary history remain unclear. In this study, focusing on largest group R nucleotide-binding site–leucine-rich repeat (NBS-LRR) we conducted an extensive genome-wide survey 38 representative...
Long-read sequencing technologies such as Pacific Biosciences and Oxford Nanopore MinION are capable of producing long reads with average fragment lengths over 10,000 base-pairs maximum reaching 100,000 base- pairs. Compared short reads, the assemblies obtained from long-read platforms have much higher contig continuity genome completeness fragments able to extend paths into problematic or repetitive regions. Many successful assembly applications technology been reported ranging small...
Horseshoe crabs are marine arthropods with a fossil record extending back approximately 450 million years. They exhibit remarkable morphological stability over their long evolutionary history, retaining number of ancestral arthropod traits, and often cited as examples "living fossils." As arthropods, they belong to the Ecdysozoa, an ancient super-phylum whose sequenced genomes (including insects nematodes) have thus far shown more divergence from pattern eumetazoan genome organization than...
Telomere shortening is a hallmark of aging and counteracted by telomerase. As in humans, the zebrafish gut one organs with fastest rate telomere decline, triggering early tissue dysfunction during normal prematurely aged telomerase mutants. However, whether telomere-dependent an individual organ, gut, causes systemic unknown. Here we show that tissue-specific expression can prevent rescues premature tert-/-. Induction senescence low cell proliferation, while restoring integrity, inflammation...
The genomes of hybrid organisms, such as lager yeast (Saccharomyces cerevisiae × Saccharomyces eubayanus), contain orthologous genes, the functionality and effect which may differ depending on their origin copy number. How parental subgenomes in contribute to important phenotypic traits fermentation performance, aroma production, stress tolerance remains poorly understood. Here, three de novo hybrids with different ploidy levels (allodiploid, allotriploid, allotetraploid) were generated...
Repressor/activator protein 1 (RAP1) is a highly evolutionarily conserved found at telomeres. Although yeast Rap1 key telomere capping preventing non-homologous end joining (NHEJ) and consequently fusions, its role mammalian telomeres in vivo still controversial. Here, we demonstrate that RAP1 required to protect replicative senescent human cells. Downregulation of these cells, but not young or dividing pre-senescent leads uncapping fusions. The anti-fusion effect was further explored HeLa...
Cephalochordates, the sister group of tunicates plus vertebrates, have been called "living fossils" due to their resemblance fossil chordates from Cambrian strata. The genome cephalochordate Branchiostoma floridae shares remarkable synteny with vertebrates and is free whole-genome duplication. We performed RNA sequencing larvae adults Asymmetron lucayanum, a distantly related B. floridae. Comparisons about 430 orthologous gene groups among both cephalochordates 10 using an echinoderm,...
Abstract Summary Simulated genomes with pre-defined and random genomic variants can be very useful for benchmarking bioinformatics analyses. Here we introduce simuG, a lightweight tool simulating the full-spectrum of (single nucleotide polymorphisms, Insertions/Deletions, copy number variants, inversions translocations) any organisms (including human). The simplicity versatility simuG make it unique general-purpose genome simulator wide-range simulation-based applications. Availability...
Deletion of mitochondrial DNA in eukaryotes is currently attributed to rare accidental events associated with replication or repair double-strand breaks. We report the discovery that yeast cells arrest harmful intramitochondrial superoxide production by shutting down respiration through genetically controlled deletion oxidative phosphorylation genes. show this process critically involves antioxidant enzyme dismutase 2 and two-way mitochondrial-nuclear communication Rtg2 Rtg3. While...
With the increasing availability of high-quality genome assemblies, pangenome graphs emerged as a new paradigm in genomics field for identifying, encoding, and presenting genomic variation at both population species levels. However, it remains challenging to truly dissect interpret via biologically informative visualization. To facilitate better exploration understanding towards novel biological insights, here we present web-based interactive Visualization interpretation framework...
Abstract Background The Ras/Raf/MEK/ERK signaling pathway is involved in essential cell processes and it abnormally activated ~30 % of cancers cognitive disorders. Two ERK isoforms have been described, ERK1 ERK2; ERK2 being regarded by many as due to the embryonic lethality knock-out mice, whereas mice lacking are viable fertile. controversial question why we two ERKs whether they differential functions or display functional redundancy has not yet resolved. Results To investigate this used a...
Histone lysine-to-methionine (K-to-M) mutations are associated with multiple cancers, and they function in a dominant fashion to block the methylation of corresponding lysines on wild type histones. However, their mechanisms controversial. Here we show that fission yeast, introducing K9M mutation into one three histone H3 genes dominantly blocks H3K9 across genome. In addition, H3K9M enhances interaction tail methyltransferase Clr4 SAM (S-adenosyl-methionine)-dependent manner, is trapped at...
Abstract Background Rates of molecular evolution vary widely among species. While significant deviations from clock have been found in many taxa, effects life histories on are not fully understood. In plants, annual/perennial history traits long suspected to influence the evolutionary rates at level. To date, however, number genes investigated this subject is limited and conclusions mixed. evaluate possible heterogeneity between annual perennial plants genomic level, we 85 nuclear...
Aging varies among individuals due to both genetics and environment, but the underlying molecular mechanisms remain largely unknown. Using a highly recombined Saccharomyces cerevisiae population, we found 30 distinct quantitative trait loci (QTLs) that control chronological life span (CLS) in calorie-rich calorie-restricted environments under rapamycin exposure. Calorie restriction extended virtually all genotypes through different genetic variants. We tracked two major QTLs cell wall...
Vegetation restoration has become a common practice in karst rocky desertification (KRD) areas of southwestern China. The bacteria, which have made connection between soil and plants, been an important role regulating the succession vegetation. However, it is still unclear how bacterial communities properties respond to natural vegetation processes areas. To address this gap, we investigated nutrients, enzyme activity, community among various plant communities, including farmland (FL), land...