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Genomic analysis of Nypa fruticans elucidates its intertidal adaptations and early palm evolution

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Journal of Integrative Plant Biology 2024年第4期66卷 824-843页

作者： Weihong Wu Xiao Feng Nan Wang Shao Shao Min Liu Fa Si Linhao Chen Chuanfeng Jin Shaohua Xu Zixiao Guo Cairong Zhong Suhua Shi Ziwen He state key laboratory of biocontrol and Guangdong Provincial key laboratory of Plant Resources School of Life SciencesSun Yat-sen UniversityGuangzhou 510275China Greater Bay Area Institute of Precision Medicine School of Life SciencesFudan UniversityGuangzhou 511462China Hainan Academy of Forestry(Hainan Academy of Mangrove) Haikou 571100China

Nypa fruticans(Wurmb),a mangrove palm species with origins dating back to the Late Cretaceous period,is a unique species for investigating long-term adaptation strategies to intertidal environments and the early evolution of palms.Here,we present a chromosome-level genome sequence and assembly for N.fruticans.We integrated the genomes of N.fruticans and other palm family members for a comparative genomic analysis,which confirmed that the common ancestor of all palms experienced a whole-genome duplication event around 89 million years ago,shaping the distinctive characteristics observed in this clade.We also inferred a low mutation rate for the N.fruticans genome,which underwent strong purifying selection and evolved slowly,thus contributing to its stability over a long evolutionary period.Moreover,ancient duplicates were preferentially retained,with critical genes having experienced positive selection,enhancing waterlogging tolerance in N.fruticans.Furthermore,we discovered that the pseudogenization of Early Methionine-labelled 1(EM1)and EM6 in N.fruticans underly its crypto-vivipary characteristics,reflecting its intertidal adaptation.Our study provides valuable genomic insights into the evolutionary history,genome stability,and adaptive evolution of the mangrove palm.Our results also shed light on the long-term adaptation of this species and contribute to our understanding of the evolutionary dynamics in the palm family.

关键词： crypto-vivipary genome stability long-term adaptation mangrove Nypa fruticans palm

Tributyltin causes generational neurodevelopmental toxicity and the protective effect of folic acid in zebrafish

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Journal of Environmental sciences 2024年第3期137卷 615-625页

作者： Haoxing Cai Naying Zheng Chen Tang Yuxuan Zhang Zhenghong Zuo Chengyong He state key laboratory of Cellular Stress Biology School of Life SciencesFaculty of Medicine and Life SciencesXiang’an Hospital of Xiamen UniversityXiamen UniversityXiamen 361005China

Tributyltin(TBT),a common organotin environmental pollutant,may pose a threat to human development during critical early-life periods.We aimed to assess the neurodevelopmental intergenerational toxicity of early-life exposure to TBT and the protective effect of DNA methyl donor folic acid(FA).Specifically,after early-life exposure(1–21 days postfertilization,dpf)to TBT(0,1,10 and 100 ng/L),zebrafish(Danio rerio)were cultured in clean medium until sexual maturity.The exposed females were mated with unexposed males to produce embryos(F1).The F1 generation were cultured(4–120 hours post-fertilization,hpf)with and without 1 mmol/L FA.The neurotoxic effects of early-life TBT exposure for zebrafish and their offspring(F1)were significantly enhanced anxiety and reduced aggression,decreased gene expression of DNA methyltransferase in the brain and increased serotonin levels in the body.Moreover,the intergenerational neurodevelopmental toxicity,as manifested in the F1 generation,was attenuated by FA supplementation.In summary,early-life TBT exposure led to intergenerational neurodevelopmental deficits in zebrafish,and DNA methyl donors had a protective effect on F1 neurodevelopment,which can inform the prevention and treatment of intergenerational neurotoxicity due to organotin pollutants.

关键词： Tributyltin Neurodevelopment Intergeneration DNA methylation Folic acid Zebrafish

A twist in the tale:global insights into archaeal box C/D RNA-guided 2′-O-methylation

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Science China(life sciences) 2024年第4期67卷 849-850页

作者： Bin Li Jianhua Yang MOE key laboratory of Gene Function and Regulation State Key Laboratory of BiocontrolSchool of Life SciencesSun Yat-sen UniversityGuangzhou 510275China The Fifth Affiliated Hospital Sun Yat-sen UniversityZhuhai 519000China

The 2′-O-methylation of RNA stands as a dynamic and multifaceted modification,wielding significant influence over the regulation of RNA function,stability,and interactions within the cellular context(Sun et al.,2023)... 详细信息

关键词： twist insight

Gibberellin promotes cambium reestablishment during secondary vascular tissue regeneration after girdling in an auxin-dependent manner in Populus

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Journal of Integrative Plant Biology 2024年第1期66卷 86-102页

作者： Yufei Zhang Lingyan Wang Yuexin Wu Donghui Wang Xin‐Qiang He state key laboratory of Protein and Plant Gene Research School of Life SciencesPeking UniversityBeijing 100871China

Secondary vascular tissue(SVT)development and regeneration are regulated by phytohormones.In this study,we used an in vitro SVT regeneration system to demonstrate that gibberellin(GA)treatment significantly promotes auxin-induced cambium reestablishment.Altering GA content by overexpressing or knocking down ent-kaurene synthase(KS)affected secondary growth and SVT regeneration in poplar.The poplar DELLA gene GIBBERELLIC ACID INSENSITIVE(PtoGAI)is expressed in a specific pattern during secondary growth and cambium regeneration after girdling.Overexpression of PtoGAI disrupted poplar growth and inhibited cambium regeneration,and the inhibition of cambium regeneration could be partially restored by GA application.Further analysis of the PtaDR5:GUS transgenic plants,the localization of PIN-FORMED 1(PIN1)and the expression of auxin-related genes found that an additional GA treatment could enhance the auxin response as well as the expression of PIN1,which mediates auxin transport during SVT regeneration.Taken together,these findings suggest that GA promotes cambium regeneration by stimulating auxin signal transduction.

关键词： auxin cambium gibberellin Populus secondary vascular tissue regeneration

Evolution and conservation genetics of pangolins

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Integrative Zoology 2024年第3期19卷 426-441页

作者： Tongtong GU Jingyang HU Li YU state key laboratory for Conservation and Utilization of Bio-Resource in Yunnan School of Life SciencesYunnan UniversityKunmingChina

Pangolins(Pholidota,Manidae)are classified as an evolutionarily distinct and globally endangered mammal due to their unique morphology(nail-like scales and a myrmecophagous diet)and being the victim of heavy poaching and worldwide trafficking.As such,pangolins serve as a textbook example for studying the special phenotypic evolutionary adaptations and conservation genetics of an endangered species.Recent years have demonstrated significant advancements in the fields of molecular genetics and genomics,which have translated to a series of important research achievements and breakthroughs concerning the evolution and conservation genetics of pangolins.This review comprehensively presents the hitherto advances in phylogeny,adaptive evolution,conservation genetics,and conservation genomics that are related to pangolins,which will provide an ample understanding of their diversity,molecular adaptation mechanisms,and evolutionary potentials.In addition,we highlight the priority of investigating species/population diversity among pangolins and suggest several avenues of research that are highly relevant for future pangolin conservation.

关键词： adaptive evolution conservation genetics conservation genomics pangolins phylogeny

Correction of a CADASIL point mutation using adenine base editors in hiPsCsandbloodvessel organoids

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Journal of Genetics and Genomics 2024年第2期51卷 197-207页

作者： Jingwen Wang Lei Zhang Guanglan Wu Jinni Wu Xinyao Zhou Xiaolin Chen Yongxia Niu Yiren Jiao Qianyi Liu Puping Liang Guang Shi Xueqing Wu Junjiu Huang MOE key laboratory of Gene Function and Regulation State Key Laboratory of BiocontrolSchool of Life SciencesSun Yat-sen UniversityGuangzhouGuangdong 510275China key laboratory of Reproductive Medicine of Guangdong Province The First Affiliated Hospital and School of Life SciencesSun Yat-sen UniversityGuangzhouGuangdong 510275China Center of Reproductive Medicine Children's Hospital of Shanxi and Women Health Center of ShanxiTaiyuanShanxi 030013China

Cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL) is a monogenic small vessel disease caused by mutations in the NOTCH3 gene. However, the pathogenesis of CADASIL remains unclear, and patients have limited treatment options. Here, we use human induced pluripotent stem cells (hiPSCs) generated from the peripheral blood mononuclear cells of a patient with CADASIL carrying a heterozygous NOTCH3 mutation (c.1261C>T, p.R421C) to develop a disease model. The correction efficiency of different adenine base editors (ABEs) is tested using the HEK293T-NOTCH3 reporter cell line. ABEmax is selected based on its higher efficiency and minimization of predicted off-target effects. Vascular smooth muscle cells (VSMCs) differentiated from CADASIL hiPSCs show NOTCH3 deposition and abnormal actin cytoskeleton structure, and the abnormalities are recovered in corrected hiPSC-derived VSMCs. Furthermore, CADASIL blood vessel organoids generated for in vivo modeling show altered expression of genes related to disease phenotypes, including the downregulation of cell adhesion, extracellular matrix organization, and vessel development. The dual adeno-associated virus (AAV) split-ABEmax system is applied to the genome editing of vascular organoids with an average editing efficiency of 8.82%. Collectively, we present potential genetic therapeutic strategies for patients with CADASIL using blood vessel organoids and the dual AAV split-ABEmax system.

关键词： CADASIL Induced pluripotent stem cells Adenine base editors AAV Blood vessel Organoid

Genetic mechanism of body size variation in groupers:Insights from phylotranscriptomics

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Zoological Research 2024年第2期45卷 314-328页

作者： Wei-Wei Zhang Zhuo-Ying Weng Xi Wang Yang Yang Duo Li Le Wang Xiao-Chun Liu Zi-Ning Meng state key laboratory of biocontrol Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory of Aquatic Economic AnimalsSchool of Life SciencesSun Yat-sen UniversityGuangzhouGuangdong 510275China Southern laboratory of Ocean Science and Engineering(Zhuhai) ZhuhaiGuangdong 519000China Area of Ecology and Biodiversity School of Biological SciencesUniversity of Hong KongHong Kong SAR 999077China Molecular Population Genetics Group Temasek Life Sciences LaboratorySingapore City 117604Singapore

Animal body size variation is of particular interest in evolutionary biology,but the genetic basis remains largely unknown.Previous studies have shown the presence of two parallel evolutionary genetic clusters within the fish genus Epinephelus with evident divergence in body size,providing an excellent opportunity to investigate the genetic basis of body size variation in vertebrates.Herein,we performed phylotranscriptomic analysis and reconstructed the phylogeny of 13 epinephelids originating from the South China Sea.Two genetic clades with an estimated divergence time of approximately 15.4 million years ago were correlated with large and small body size,respectively.A total of 180 rapidly evolving genes and two positively selected genes were identified between the two groups.Functional enrichment analyses of these candidate genes revealed distinct enrichment categories between the two groups.These pathways and genes may play important roles in body size variation in groupers through complex regulatory networks.Based on our results,we speculate that the ancestors of the two divergent groups of groupers may have adapted to different environments through habitat selection,leading to genetic variations in metabolic patterns,organ development,and lifespan,resulting in body size divergence between the two locally adapted populations.These findings provide important insights into the genetic mechanisms underlying body size variation in groupers and species differentiation.

关键词： Phylotranscriptomics Grouper Body size Rapidly evolving genes(REGs) Positively selected genes(PSGs)

Ultrafast micro/nano-manufacturing of metastable materials for energy

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National Science Review 2024年第4期11卷 283-298页

作者： Xiaoya Cui Yanchang Liu Yanan Chen school of Materials Science and Engineering Key Laboratory of Advanced Ceramics and Machining Technology(Ministry of Education) and Tianjin Key Laboratory of Composite and Functional MaterialsTianjin University Ministry of Education key laboratory of Protein sciences School of Life SciencesTsinghua University

The structural engineering of metastable nanomaterials with abundant defects has attracted much attention in energy-related fields. The high-temperature shock(HTS) technique, as a rapidly developing and advanced synthesis strategy, offers significant potential for the rational design and fabrication of high-quality nanocatalysts in an ultrafast, scalable, controllable and eco-friendly way. In this review, we provide an overview of various metastable micro-and nanomaterials synthesized via HTS, including single metallic and bimetallic nanostructures, high entropy alloys, metal compounds(e.g. metal oxides) and carbon nanomaterials. Note that HTS provides a new research dimension for nanostructures, i.e. kinetic modulation. Furthermore, we summarize the application of HTS—as supporting films for transmission electron microscopy grids—in the structural engineering of 2D materials, which is vital for the direct imaging of metastable materials. Finally, we discuss the potential future applications of high-throughput and liquid-phase HTS strategies for non-equilibrium micro/nano-manufacturing beyond energy-related fields.It is believed that this emerging research field will bring new opportunities to the development of nanoscience and nanotechnology in both fundamental and practical aspects.

关键词： high-temperature shock technique defect engineering metastable phase kinetic modulation non-equilibrium micro/nano-manufacturing

Current therapies for osteoarthritis and prospects of CRISPR-based genome,epigenome,and RNA editing in osteoarthritis treatment

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Journal of Genetics and Genomics 2024年第2期51卷 159-183页

作者： Yuxi Chen Xiao Luo Rui Kang Kaixin Cui Jianping Ou Xiya Zhang Puping Liang MOE key laboratory of Gene Function and Regulation State Key Laboratory of BiocontrolSchool of Life SciencesSun Yat-sen UniversityGuangzhouGuangdong 510275China Center for Reproductive Medicine The Third Affiliated Hospital of Sun Yat-sen UniversitySun Yat-sen UniversityGuangzhouGuangdong 510630China

Osteoarthritis(OA)is one of the most common degenerative joint diseases worldwide,causing pain,disability,and decreased quality of life.The balance between regeneration and inflammation-induced degradation results in multiple etiologies and complex pathogenesis of OA.Currently,there is a lack of effective therapeutic strategies for OA treatment.With the development of CRISPR-based genome,epigenome,and RNA editing tools,OA treatment has been improved by targeting genetic risk factors,activating chondrogenic elements,and modulating inflammatory regulators.Supported by cell therapy and in vivo delivery vectors,genome,epigenome,and RNA editing tools may provide a promising approach for personalized OA therapy.This review summarizes CRISPR-based genome,epigenome,and RNA editing tools that can be applied to the treatment of OA and provides insights into the development of CRISPR-based therapeutics for OA treatment.Moreover,in-depth evaluations of the efficacy and safety of these tools in human OA treatment are needed.

关键词： Osteoarthritis Genome editing Epigenone editing RNA editing