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Recent genome duplications facilitate the phenotypic diversity of Hb repertoire in the Cyprinidae

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Science China(Life Sciences) 2021年第7期64卷 1149-1164页

作者： Yi Lei Liandong Yang Haifeng Jiang Juan Chen Ning Sun Wenqi lv Shunping He The Key Laboratory ofAquatic Biodiversity and Conservation of Chinese Academy of Sciences Institute of HydrobiologyChinese Academy of SciencesWuhan 430072China University of Chinese Academy of Sciences Beijing 100049China Center for Excellence in Animal Evolution and Genetics Chinese Academy of SciencesKunming 650223China

Whole-genome duplications(WGDs)are an important contributor to phenotypic innovations in evolutionary history.The diversity of blood oxygen transport traits is the perfect reflection of physiological versatility for evolutionary success among vertebrates.In this study,the evolutionary changes of hemoglobin(Hb)repertoire driven by the recent genome duplications were detected in representative Cyprinidae fish,including eight diploid and four tetraploid species.Comparative genomic analysis revealed a substantial variation in both membership composition and intragenomic organization of Hb genes in these species.Phylogenetic reconstruction analyses were conducted to characterize the evolutionary history of these genes.Data were integrated with the expression profiles of the genes during ontogeny.Our results indicated that genome duplications facilitated the phenotypic diversity of the Hb gene family;each was associated with species-specific changes in gene content via gene loss and fusion after genome duplications.This led to repeated evolutionary transitions in the ontogenic regulation of Hb gene expression.Our results revealed that genome duplications helped to generate phenotypic changes in Cyprinidae Hb systems.

关键词： genome duplication gene duplication hemoglobin gene family genomic organization gene family evolution

The Pathology of Primary Familial Brain Calcification:Implications for Treatment

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Neuroscience Bulletin 2023年第4期39卷 659-674页

作者： Xuan Xu Hao Sun Junyu Luo Xuewen Cheng Wenqi lv Wei Luo Wan-Jin Chen Zhi-Qi Xiong Jing-Yu Liu Institute of Neuroscience State Key Laboratory of NeuroscienceCenter for Excellence in Brain Science and Intelligence TechnologyChinese Academy of SciencesShanghai200031China College of Life Science and Technology Huazhong University of Science and TechnologyWuhan430074China Department of Neurology and Institute of Neurology of First Affiliated Hospital Institute of Neuroscienceand Fujian Key Laboratory of Molecular NeurologyFujian Medical UniversityFuzhou350005China Department of Neurology The Second Affiliated HospitalZhejiang University School of MedicineHangzhou310009China

Primary familial brain calcification(PFBC)is an inherited neurodegenerative disorder mainly characterized by progressive calcium deposition bilaterally in the brain,accompanied by various symptoms,such as dystonia,ataxia,parkinsonism,dementia,depression,headaches,and epilepsy.Currently,the etiology of PFBC is largely unknown,and no specific prevention or treatment is available.During the past 10 years,six causative genes(SLC20A2,PDGFRB,PDGFB,XPR1,MYORG,and JAM2)have been identified in PFBC.In this review,considering mechanistic studies of these genes at the cellular level and in animals,we summarize the pathogenesis and potential preventive and therapeutic strategies for PFBC patients.Our systematic analysis suggests a classification for PFBC genetic etiology based on several characteristics,provides a summary of the known composition of brain calcification,and identifies some potential therapeutic targets for PFBC.

关键词： Primary familial brain calcification Causative gene Pathogenesis Preventive and therapeutic strategy

Pseudo-chromosome–length genome assembly for a deep-sea eel Ilyophis brunneus sheds light on the deep-sea adaptation

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Science China(Life Sciences) 2023年第6期66卷 1379-1391页

作者： Jie Chen Honghui Zeng Wenqi lv Ning Sun Cheng Wang Wenjie Xu Mingliang Hu Xiaoni Gan Lisheng He Shunping He Chengchi Fang Institute of Deep-Sea Science and Engineering Chinese Academy of SciencesSanya572000China State Key Laboratory of Freshwater Ecology and Biotechnology Institute of HydrobiologyChinese Academy of SciencesWuhan430072China University of Chinese Academy of Sciences Beijing100049China School for Ecological and Environmental Sciences Northwestern Polytechnical UniversityXi’an710072China

High hydrostatic pressure,low temperature,and scarce food supply are the major factors that limit the survival of vertebrates in extreme deep-sea environments.Here,we constructed a high-quality genome of the deep-sea Muddy arrowtooth eel(MAE,Ilyophis brunneus,captured below a depth of 3,500 m)by using Illumina,Pac Bio,and Hi-C sequencing.We compare it against those of shallow-water eel and other outgroups to explore the genetic basis that underlies the adaptive evolution to deep-sea biomes.The MAE genome was estimated to be 1.47 Gb and assembled into 14 pseudo-chromosomes.Phylogenetic analyses indicated that MAE diverged from its closely related shallow-sea species,European eel,~111.9 Mya and experienced a rapid evolution.The genome evolutionary analyses primarily revealed the following:(i)under high hydrostatic pressure,the positively selected gene TUBGCP3 and the expanded family MLC1 may improve the cytoskeleton stability;ACOX1 may enhance the fluidity of cell membrane and maintain transport activity;the expansion of ABCC12 gene family may enhance the integrity of DNA;(ii)positively selected HARS likely maintain the transcription ability at low temperatures;and(iii)energy metabolism under a food-limited environment may be increased by expanded and positively selected genes in AMPK and m TOR signaling pathways.

关键词： Ilyophis brunneus genome evolution deep sea adaption high hydrostatic pressure

Enlarged fins of Tibetan catfish provide new evidence of adaptation to high plateau

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Science China(Life Sciences) 2023年第7期66卷 1554-1568页

作者： Liandong Yang Ning Sun Honghui Zeng Ying Wang Wenjun Chen Zufa Ding Yang Liu Jing Wang Minghui Meng Yanjun Shen Jingliang Kang Xiuhui Ma Wenqi lv Juan Chen Axel Meyer Baocheng Guo Shunping He State Key Laboratory of Freshwater Ecology and Biotechnology Institute of HydrobiologyChinese Academy of SciencesWuhan430072China Key Laboratory of Zoological Systematics and Evolution Institute of ZoologyChinese Academy of SciencesBeijing100101China Academy of Plateau Science and Sustainability Qinghai Normal UniversityXining810016China Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin School of Life SciencesJianghan UniversityWuhan430056China State Key Laboratory of Genetic Resources and Evolution Kunming Institute of ZoologyChinese Academy of SciencesKunming650223China University of Chinese Academy of Sciences Beijing100049China Department of Biology University of Konstanz78457KonstanzGermany Center for Excellence in Animal Evolution and Genetics Chinese Academy of SciencesKunming650223China

The uplift of the Tibetan Plateau significantly altered the geomorphology and climate of the Euroasia by creating large mountains and rivers.Fishes are more likely to be affected relative to other organisms,as they are largely restricted to river systems.Faced with the rapidly flowing water in the Tibetan Plateau,a group of catfish has evolved greatly enlarged pectoral fins with more numbers of fin-rays to form an adhesive apparatus.However,the genetic basis of these adaptations in Tibetan catfishes remains elusive.In this study,we performed comparative genomic analyses based on the chromosome-level genome of Glyptosternum maculatum in family Sisoridae and detected some proteins with conspicuously high evolutionary rates in particular in genes involved in skeleton development,energy metabolism,and hypoxia response.We found that the hoxd12a gene evolved faster and a loss-of-function assay of hoxd12a supports a potential role for this gene in shaping the enlarged fins of these Tibetan catfishes.Other genes with amino acid replacements and signatures of positive selection included proteins involved in low temperature(TRMU)and hypoxia(VHL)responses.Functional assays reveal that the G.maculatum TRMU allele generates more mitochondrial ATP than the ancestral allele found in low-altitude fishes.Functional assays of VHL alleles suggest that the G.maculatum allele has lower transactivation activity than the low-altitude forms.These findings provide a window into the genomic underpinnings of physiological adaptations that permit G.maculatum to survive in the harsh environment of the Tibetan Himalayas that mirror those that are convergently found in other vertebrates such as humans.

关键词： Glyptosternum maculatum enlarged fins adaptation Tibetan Plateau

Sympatric or micro-allopatric speciation in a glacial lake?Genomic islands support neither

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National Science Review 2022年第12期9卷 37-49页

作者： Ning Sun Liandong Yang Fei Tian Honghui Zeng Ziwen He Kai Zhao Cheng Wang Minghui Meng Chenguang Feng Chengchi Fang Wenqi lv Jing Bo Yongtao Tang Xiaoni Gan Zuogang Peng Yiyu Chen Shunping He State Key Laboratory of Freshwater Ecology and Biotechnology Institute of Hydrobiology Chinese Academy of Sciences University of Chinese Academy of Sciences Key Laboratory of Adaptation and Evolution of Plateau Biota Northwest Institute of Plateau Biology Chinese Academy of Sciences State Key Laboratory of Biocontrol Guangdong Key Lab of Plant Resources School of Life Sciences Sun Yat-sen University School of Ecology and Environment Northwestern Polytechnical University Institute of Deep-Sea Science and Engineering Chinese Academy of Sciences Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education) Southwest University School of Life Sciences National Natural Science Foundation of China Center for Excellence in Animal Evolution and Genetics Chinese Academy of Sciences

Apparent cases of sympatric speciation may actually be due to micro-allopatric or micro-parapatric speciation.One way to distinguish between these models is to examine the existence and nature of genomic islands of divergence,wherein divergent DNA segments are interspersed with low-divergence segments.Such islands should be rare or absent under micro-allopatric speciation but common in cases of speciation with gene flow.Sympatric divergence of endemic fishes is known from isolated saline,crater,postglacial,and ancient lakes.Two morphologically distinct cyprinid fishes,Gymnocypris eckloni scoliostomus(GS) and G.eckloni eckloni(GE),in a small glacial lake on the Qinghai-Tibet Plateau,Lake Sunmcuo,match the biogeographic criteria of sympatric speciation.In this study,we examined genome-wide variation in 46individuals from these two groups.The divergence time between the GS and GE lineages was estimated to be 20-60 Kya.We identified 54 large genomic islands(≥100 kb) of speciation,which accounted for 89.4%of the total length of all genomic islands.These islands harboured divergent genes related to olfactory receptors and olfaction signals that may play important roles in food selection and assortative mating in fishes.Although the genomic islands clearly indicated speciation with gene flow and rejected micro-allopatric speciation,they were too large to support the hypothesis of sympatric speciation.Theoretical and recent empirical studies suggested that continual gene flow in sympatry should give rise to many small genomic islands(as small as a few kilobases in size).Thus,the observed pattern is consistent with the extensive evidence on parapatric speciation,in which adjacent habitats facilitate divergent selection but also permit gene flow during speciation.We suggest that many,if not most,of the reported cases of sympatric speciation are likely to be micro-parapatric speciation.

关键词： sympatric speciation gene flow genomic islands micro-parapatric speciation selection olfaction

Temperature acclimation in hot-spring snakes and the convergence of cold response

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The Innovation 2022年第5期3卷 97-106页

作者： Chaochao Yan Wei Wu wenqi Dong Bicheng Zhu Jiang Chang Yunyun lv Shilong Yang Jia-Tang Li CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization and Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province Chengdu Institute of BiologyChinese Academy of SciencesChengdu 610041China University of Chinese Academy of Sciences Beijing 100049China College of Wildlife and Protected Area Northeast Forestry UniversityHarbin 660223China State Key Laboratory of Environmental Criteria and Risk Assessment Chinese Research Academy of Environmental SciencesBeijing 100085China College of Life Science Neijiang Normal UniversityNeijiangSichuan 641100China Center for Excellence in Animal Evolution and Genetics Chinese Academy of SciencesKunming 650223China

Animals have evolved sophisticated temperature-sensing systems and mechanisms to detect and respond to ambient temperature changes.As a relict species endemic to the Qinghai-Tibet Plateau,hot-spring snake(Thermophis baileyi)survived the dramatic changes in climate that occurred during plateau uplift and ice ages,providing an excellent opportunity to explore the evolution of temperature sensation in ectotherms.Based on distributional information and behavioral experiments,we found that T.baileyi prefer hotspring habitats and respond more quickly to warmth than other two snakes,suggesting that T.baileyi may evolve an efficient thermal-sensing system.Using high-quality chromosome-level assembly and comparative genomic analysis,we identified cold acclimation genes experiencing convergent acceleration in high-altitude lineages.We also discovered significant evolutionary changes in thermosensation-and thermoregulation-related genes,including the transient receptor potential(TRP)channels.Among these genes,TRPA1 exhibited three species-specific amino acid replacements,which differed from those found in infrared imaging snakes,implying different temperature-sensing molecular strategies.

关键词： habitat spring snake

中国文化创意产品出口增长的二元边际及其影响因素研究

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国际贸易问题 2018年第12期 67-81页

作者：蓝天吕文琦东北财经大学国际经济贸易学院

本文将中国文化创意产品出口分解为集约边际和扩展边际,探究了文化创意产品出口增长模式并对其影响因素进行分析。研究结果表明:中国文化创意产品出口仍然属于数量增长型扩张,其增长主要来自集约边际,而扩展边际的作用有限;进口国经济... 详细信息

本文将中国文化创意产品出口分解为集约边际和扩展边际,探究了文化创意产品出口增长模式并对其影响因素进行分析。研究结果表明:中国文化创意产品出口仍然属于数量增长型扩张,其增长主要来自集约边际,而扩展边际的作用有限;进口国经济规模、文化产业生产率水平对文化创意产品出口数量和种类的增长具有促进作用,文化距离和固定贸易成本则有明显阻碍作用,共同边界对集约边际的正向影响显著;权力距离、个人主义或集体主义、男性与女性气质、不确定性规避、长短期取向、放任或约束等不同维度文化距离对集约边际和扩展边际的影响程度和方式不同,大多具有显著负向影响;金融危机带来的外部冲击主要影响集约边际,对扩展边际无显著影响。

关键词：文化创意产品二元边际文化距离影响因素

A systems biology approach identifies a regulator,BplERF1,of cold tolerance in Betula platyphylla

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Forestry Research 2021年第1期1卷 96-105页

作者： Kaiwen lv wenqi Wu Hairong Wei Guifeng Liu State Key Laboratory of Tree Genetics and Breeding Northeast Forestry UniversityHarbin 150040China Beijing Advanced Innovation Center for Tree Breeding by Molecular Design Beijing Forestry UniversityBeijing 100083China College of Forest Resources and Environmental Science Michigan Technological UniversityHoughtonMI 49931United States of America

Cold is an abiotic stress that can greatly affect the growth and survival of plants.Here,we reported that an AP2/ERF family gene,BplERF1,isolated from Betula platyphylla played a contributing role in cold stress tolerance.Overexpression of BplERF1 in B.platyphylla transgenic lines enhanced cold stress tolerance by increasing the scavenging capability and reducing H_(2)O_(2) and malondialdehyde(MDA)content in transgenic plants.Construction of BplERF-mediated multilayered hierarchical gene regulatory network(ML-hGRN),using Top-down GGM algorithm and the transcriptomic data of BplERF1 overexpression lines,led to the identification of five candidate target genes of BplERF1 which include MPK20,ERF9,WRKY53,WRKY70,and GIA1.All of them were then verified to be the true target genes of BplERF1 by chromatin-immunoprecipitation PCR(ChIP-PCR)assay.Our results indicate that BplERF1 is a positive regulator of cold tolerance and is capable of exerting regulation on the expression of cold signaling and regulatory genes,causing mitigation of reactive oxygen species.

关键词： tolerance platyphylla verified

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建筑电气安装中防雷接地施工技术的应用研究

山西建筑 2018年第11期44卷 127-128页

作者：吕文岐北京鑫大禹水利建筑工程有限公司北京101300

介绍了建筑电气安装防雷接地施工的重要性,对防雷接地工程的施工技术进行了探讨,并总结了一些现场施工技术要点,从而保证建筑质量,确保防雷接地系统的高效运作。

关键词：建筑电气安装防雷接地施工技术