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Association of daily sitting time and leisure-time physical activity with body fat among ***

Journal of Sport and Health Science 2024年第2期13卷 195-203页

作者： Jingwen Liao Min Hu Kellie Imm Clifton J.Holmes Jie Zhu Chao Cao Lin Yang Guangdong Provincial Key Laboratory of Physical Activity and Health Promotion Guangzhou Sport UniversityGuangzhou 510500China Scientific Research Center Guangzhou Sport UniversityGuangzhou 510500China Division of Epidemiology&Genetics Department of Population and Public Health SciencesKeck School of Medicine of the University of Southern CaliforniaLos AngelesCA 90033USA Program in Physical Therapy Washington University School of MedicineSt.LouisMO 63110USA Center for Human Nutrition Washington University School of MedicineSt.LouisMO 63110USA Department of Plastic and Reconstructive Surgery Shanghai East HospitalTongji UniversityShanghai 200070China Department of Cancer Epidemiology and Prevention Research Alberta Health ServicesCalgary T2S 3C3Canada Department of Oncology and Community Health sciences University of CalgaryCalgary T2N 1N4Canada

Background:Prolonged sitting and reduced physical activity lead to low energy ***,little is known about the joint impact of daily sitting time and physical activity on body fat *** investigated the independent and joint associations of daily sitting time and physical activity with body fat among ***:This was a cross-sectional analysis of *** representative data from the National Health and Nutrition Examination Survey2011-2018 among adults aged 20 years or *** sitting time and leisure-time physical activity(LTPA)were self-reported using the Global Physical Activity *** fat(total and trunk fat percentage)was determined via dual X-ray ***:Among 10,808 adults,about 54.6%spent 6 h/day or more sitting;more than one-half reported no LTPA(inactive)or less than 150 min/week LTPA(insufficiently active)with only 43.3%reported 150 min/week or more LTPA(active)in the past *** fully adjusting for sociodemographic data,lifestyle behaviors,and chronic conditions,prolonged sitting time and low levels of LTPA were associated with higher total and trunk fat percentages in both *** stratifying by LTPA,the association between daily sitting time and body fat appeared to be stronger in those who were inactive/insuufficiently *** the joint analyses,inactive/insuufficiently active adults who reported sitting more than 8 h/day had the highest total(female:3.99%(95%confidence interval(95%CI):3.09%-4.88%);male:3.79%(95%CI:2.75%-4.82%))and trunk body fat percentages(female:4.21%(95%CI:3.09%-5.32%);male:4.07%(95%CI:2.95%-5.19%))when compared with those who were active and sitting less than 4 h/***:Prolonged daily sitting time was associated with increased body fat among *** higher body fat associated with 6 h/day sitting may not be offset by achieving recommended levels of physical activity.

关键词： Adults Body fat distribution Physical activity Sitting time

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Recombination and repeat-induced point mutation landscapes reveal trade-offs between the sexual and asexual cycles of Magnaporthe oryzae

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Journal of Genetics and Genomics 2024年第7期51卷 723-734页

作者： Xifang Zong Yaxin Lou Mengshuang Xia Kunyang Zhao Jingxuan Chen Ju Huang Sihai Yang Long Wang State Key Laboratory of Pharmaceutical Biotechnology School of Life SciencesNanjing UniversityNanjingJiangsu 210000China State Key Laboratory for Crop Genetics and Germplasm Enhancement Bioinformatics CenterAcademy for Advanced Interdisciplinary StudiesNanjing Agricultural UniversityNanjingJiangsu 210000China Co-Innovation Center for Sustainable Forestry in southern China Nanjing Forestry UniversityNanjingJiangsu 210000China

The fungal disease caused by Magnaporthe oryzae is one of the most devastating diseases that endanger many crops *** shows that sexual reproduction can be advantageous for fungal diseases as hybridization facilitates ***,the pervasive clonal lineages of *** observed in natural fields contradict this expectation.A better understanding of the roles of recombination and the fungi-specific repeat-induced point mutation(RIP)in shaping its evolutionary trajectory is essential to bridge this knowledge *** we systematically investigate the RIP and recombination landscapes in *** using a whole genome sequencing data from 252 population samples and 92 cross *** data reveal that the RIP can robustly capture the population history of ***,and we provide accurate estimations of the recombination and RIP rates across different *** ***,our results highlight a parent-of-origin bias in both recombination and RIP rates,tightly associating with their sexual potential and variations of effector *** bias suggests a critical trade-off between generating novel allelic combinations in the sexual cycle to facilitate host-jumping and stimulating transposon-associated diversification of effectors in the asexual cycle to facilitate host *** findings provide unique insights into understanding the evolution of blast fungus.

关键词： Magnaporthe oryzae Crossover Repeat-induced point mutation(RiP) Effectors Sexual reproduction

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Deciphering the population structure and genetic basis of growth traits from whole-genome resequencing of the leopard coral grouper(Plectropomus leopardus)

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Zoological Research 2024年第2期45卷 329-340页

作者： Shao-Xuan Wu Qi-Fan Zeng Wen-Tao Han Meng-Ya Wang Hui Ding Ming-Xuan Teng Ming-Yi Wang Pei-Yu Li Xin Gao Zhen-Min Bao Bo Wang Jing-Jie Hu MOE Key Laboratory of Marine Genetics and Breeding College of Marine Life Sciences/Key Laboratory of Tropical Aquatic Germplasm of Hainan ProvinceSanya Oceanographic InstitutionOcean University of ChinaQingdaoShandong/SanyaHainan 266100/572025China Hainan Seed Industry Laboratory SanyaHainan 572025China southern Marine Science and Engineer Guangdong Laboratory GuangzhouGuangdong 511458China

The leopard coral grouper(Plectropomus leopardus)is a species of significant economic *** artificial cultivation of *** has thrived in recent decades,the advancement of selective breeding has been hindered by the lack of comprehensive population genomic *** this study,we identified over 8.73 million single nucleotide polymorphisms(SNPs)through whole-genome resequencing of 326 individuals spanning six distinct ***,we categorized 226 individuals with high-coverage sequencing depth(≥14×)into eight clusters based on their genetic profiles and phylogenetic ***,four of these clusters exhibited pronounced genetic differentiation compared with the other *** identify potentially advantageous loci for ***,we examined genomic regions exhibiting selective sweeps by analyzing the nucleotide diversity(θπ)and fixation index(FST)in these four *** these high-coverage resequencing data,we successfully constructed the first haplotype reference panel specific to *** achievement holds promise for enabling high-quality,***,we combined low-coverage sequencing data with imputation techniques for a genome-wide association study,aiming to identify candidate SNP loci and genes associated with growth traits.A significant concentration of these genes was observed on chromosome 17,which is primarily involved in skeletal muscle and embryonic development and cell ***,our detailed investigation of growth-related SNPs across the eight clusters revealed that cluster 5 harbored the most promising candidate SNPs,showing potential for genetic selective breeding *** findings provide a robust toolkit and valuable insights into the management of germplasm resources and genome-driven breeding initiatives targeting ***.

关键词： Plectropomus leopardus Whole-genome resequencing Growth Haplotype reference panel Single nucleotide polymorphisms

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Transcriptomic analysis reveals key regulators of mammogenesis and the pregnancy-lactation cycle

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Science China(Life sciences) 2014年第3期57卷 340-355页

作者： ZHOU YuanYuan GONG Wei XIAO JingFa WU JiaYan PAN LinLin LI XiaoNuan WANG XuMin WANG WeiWei HU SongNian YU Jun Beijing Key Laboratory of genome and Precision Medicine Technologies CAS Key Laboratory of Genome Sciences and InformationBeijing Institute of GenomicsChinese Academy of Sciences University of Chinese Academy of sciences Division of Gastroenterology Department of MedicineUniversity of Alberta

An organ unique to mammals, the mammary gland develops 90% of its mass after birth and experiences the pregnancy-lactation-involution cycle （PL cycle） during reproduction. To understand mammogenesis at the transcriptomic level and using a ribo-minus RNA-seq protocol, we acquired greater than 50 million reads each for the mouse mammary gland during pregnancy （day 12 of pregnancy）, lactation （day 14 of lactation）, and involution （day 7 of involution）. The pregnancy-, lacta- tion- and involution-related sequencing reads were assembled into 17344, 10160, and 13739 protein-coding transcripts and 1803, 828, and 1288 non-coding RNAs （ncRNAs）, respectively. Differentially expressed genes （DEGs） were defined in the three samples, which comprised 4843 DEGs （749 up-regulated and 4094 down-regulated） from pregnancy to lactation and 4926 DEGs （4706 up-regulated and 220 down-regulated） from lactation to involution. Besides the obvious and substantive up- and down-regulation of the DEGs, we observe that lysosomal enzymes were highly expressed and that their expression coin- cided with milk secretion. Further analysis of transcription factors such as Trpsl, Gtf2i, Tcf712, Nuprl, Vdr, Rbl, and Aebpl, and ncRNAs such as mir-125b, Let7, mir-146a, and mir-15 has enabled us to identify key regulators in mammary gland de- velopment and the PL cycle.

关键词： mouse mammary gland mammogenesis transcriptome rmRNA-seq miRNAs transcription factors

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Genomic divergence and mutation load in the Begonia masoniana complex from limestone karsts

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Plant Diversity 2024年第5期46卷 575-584页

作者： Yiqing Chen Lina Dong Huiqin Yi Catherine Kidner Ming Kang Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in southern China Guangzhou 510650China University of Chinese Academy of sciences Beijing 100049China Guangxi Key Laboratory of Conservation and Restoration Ecology in Karst Terrain Guangxi Institute of BotanyGuangxi Zhang Autonomous Region and the Chinese Academy of SciencesGuilin 541006China Institute of Molecular Plant sciences University of EdinburghDaniel Rutherford Building Max Born CrescentThe King's BuildingsEdinburgh EH93BFUK Royal Botanic Garden Edinburgh 20a Inverleith RowEdinburgh EH35LRUK State Key Laboratory of Plant Diversity and Specialty Crops South China Botanical GardenChinese Academy of SciencesGuangzhou 510650China

Understanding genome-wide diversity,inbreeding,and the burden of accumulated deleterious mutations in small and isolated populations is essential for predicting and enhancing population persistence and ***,these effects are rarely studied in limestone karst ***,we re-sequenced the nuclear genomes of 62 individuals of the Begonia masoniana complex(***,***,*** and ***)and investigated genomic divergence and genetic load for these four *** analyses revealed four distinct clusters corresponding to each species within the ***,there was only limited admixture between *** and *** occurring in overlapping geographic *** species experienced historical bottlenecks during the Pleistocene,which were likely caused by glacial climate *** detected an asymmetric historical gene flow between group pairs within this timeframe,highlighting a distinctive pattern of interspecific divergence attributable to karst geographic *** found that isolated populations of *** have limited gene flow,the smallest recent population size,the highest inbreeding coefficients,and the greatest accumulation of recessive deleterious *** findings underscore the urgency to prioritize conservation efforts for these isolated *** study is among the first to disentangle the genetic differentiation and specific demographic history of karst Begonia plants at the whole-genome level,shedding light on the potential risks associated with the accumulation of deleterious mutations over generations of ***,our findings may facilitate conservation planning by providing critical baseline genetic data and a better understanding of the historical events that have shaped current population structure of rare and endangered karst plants.

关键词： Conservation genomics Karst landscape Demographic history Inbreeding Isolated populations Mutation load

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亚热带森林植物的叶片和根系功能性状部分耦合但具有不同的群落性状分布格局

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Journal of Plant Ecology 2024年第1期17卷 94-110页

作者： Wenqi Luo Oscar J Valverde-Barrantes Monique Weemstra James F Cahill Jr Zi Wang Dong He Yongfa Chen Chengjin Chu Youshi Wang State Key Laboratory of Biocontrol School of Life Sciences/School of EcologySun Yat-sen UniversityGuangzhou 510275China International Center for Tropical Botany Department of Biological SciencesFlorida International UniversityMiamiFL 33199USA Department of Biological sciences University of AlbertaEdmontonABT6G 2E9Canada School of Ecology and the Environment Xinjiang UniversityUrumqi 830046China

植物的生态过程依赖于叶片和根系的功能运行,但少有研究同时关注这两类性状在群落中的分布格局(CTD)。本文测定了广东亚热带森林44种共生木本植物的16个叶片和根系性状,旨在检验类比的叶片和根系性状是否耦合,是否沿类似的功能性状谱变... 详细信息

植物的生态过程依赖于叶片和根系的功能运行,但少有研究同时关注这两类性状在群落中的分布格局(CTD)。本文测定了广东亚热带森林44种共生木本植物的16个叶片和根系性状,旨在检验类比的叶片和根系性状是否耦合,是否沿类似的功能性状谱变异,是否表现出类似的CTD,其CTD和群落加权平均性状值(CWM)是否沿环境梯度表现出类似的响应。研究结果表明,叶片和根系性状变异的第一轴均呈显出由资源获取向资源保守变异的经济学谱,但叶片变异的第二轴主要由叶片碳含量表征,而根系变异的第二轴主要由反映菌根协作程度的根系粗细表征。类比的叶片和根系化学性状整体正相关,但形态性状的耦合程度较低。在群落水平上,叶片和根系性状第一轴的CWM均随海拔升高而变得更保守,而第二轴的变化则不一致。随土壤磷含量的降低或钾含量的升高,根系变得更细和在养分性状上更保守,而叶片性状无显著变化。当整合多维性状轴时,叶片性状呈发散格局,且随海拔、土壤磷和钾含量的增加呈收敛趋势;而根系性状呈收敛格局,但沿上述环境梯度呈发散趋势。该研究强调,叶片和根系性状与环境互作的差异可能导致不同的性状分布格局;植物可通过多样的地上和地下功能设计应对环境异质性。

关键词：性状维度群落构建叶片性状根系性状植物经济谱群落性状结构亚热带森林

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Genetic diversity of food-medicinal Lycium *** China:Insights from chloroplast genome

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Chinese Herbal Medicines 2024年第3期16卷 401-411页

作者： Ruyu Yao Bin Wang Michael Heinrich Qiuling Wang Peigen Xiao Institute of Medicinal Plant Development Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing 100193China Hainan Provincial Key Laboratory of Resources Conservation and Development of southern Medicine Hainan Branch of the Institute of Medicinal Plant DevelopmentChinese Academy of Medical Sciences and Peking Union Medical CollegeHaikou 570311China Research Group‘Pharmacognosy and Phytotherapy’ UCL School of PharmacyUniversity of LondonLondon WC1N1AXUnited Kingdom Kunming Institute of Botany Chinese Academy of SciencesKunming 650201China

Objective:Goji(fruits of Lycium spp.)is commonly consumed as food and *** increasing market demand for goji has led to its wide cultivation and broad breeding,which might cause loss of genetic *** study aims to uncover the genetic diversity of the cultivated and wild ***:The chloroplast genome(CPG)of 34 accessions of Chinese food-medicinal Lycium spp.,including the popular cultivars and their wild relatives,was re-sequenced and assembled,based on which the genetic diversity was ***:Sequence structural comparison shows that CPG is comparatively conserved within *** analysis indicates that CPG is sufficient for the discrimination of Lycium species;combined with nuclear ribosomal internal transcribed spacer(Nr ITS)sequences,materials with mixed genetic backgrounds can be *** diversity analysis reveals that the modern cultivars are probably with a common maternal parent,while the wild accessions are with higher level of genetic ***:For the first time this study reveals the intraspecies genetic diversity of Lycium *** CPG,highlighting the urgent conservation demand of wild genetic resources of *** study also demonstrates that CPG provides crucial evidence for identification of Lycium species with mixed genetic backgrounds and highlights the importance of the wild relatives in genetic diversity *** CPG-based technology will contribute to the sustainable development of medicinal plants broadly.

关键词： chloroplast genome cultivar food-medicine genetic diversity goji wild relative

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Mitochondrial genome sequences of Artemia tibetiana and Artemia urmiana:assessing molecular changes for high plateau adaptation

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Science China Life sciences 2013年第5期56卷 440-452页

作者： ZHANG HangXiao LUO QiBin SUN Jing LIU Fei WU Gang YU Jun WANG WeiWei CAS Key Laboratory of genome sciences and Information Beijing Institute of GenomicsChinese Academy of Sciences University of Chinese Academy of sciences Department of genome Oriented Bioinformatics Technische Universit t MünchenWissenschaftszentrum WeihenstephanFreising 85350Germany Division of Gastroenterology Department of MedicineUniversity of AlbertaEdmonton T6G 2V2AlbertaCanada

Brine shrimps,Artemia(Crustacea,Anostraca),inhabit hypersaline environments and have a broad geographical distribution from sea level to high *** therefore possess significant genetic diversity,which gives them their outstanding *** understand this remarkable plasticity,we sequenced the mitochondrial genomes of two Artemia tibetiana isolates from the Tibetan Plateau in China and one Artemia urmiana isolate from Lake Urmia in Iran and compared them with the genome of a low-altitude Artemia,*** compared the ratio of the rate of nonsynonymous(Ka) and synonymous(Ks) substitutions(Ka/Ks ratio) in the mitochondrial protein-coding gene sequences and found that atp8 had the highest Ka/Ks ratios in comparisons of *** with either *** or *** and that atp6 had the highest Ka/Ks ratio between *** and ***6 may have experienced strong selective pressure for high-altitude adaptation because although *** and *** are closely related they live at different *** identified two extended termination-associated sequences and three conserved sequence blocks in the D-loop region of the mitochondrial *** propose that sequence variations in the D-loop region and in the subunits of the respiratory chain complexes independently or collectively contribute to the adaptation of Artemia to different altitudes.

关键词： mitochondrial genome Artemia tibetiana sequence variation high plateau species

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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 ***,we present a chromosome-level genome sequence and assembly for *** integrated the genomes of *** 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 *** also inferred a low mutation rate for the *** genome,which underwent strong purifying selection and evolved slowly,thus contributing to its stability over a long evolutionary ***,ancient duplicates were preferentially retained,with critical genes having experienced positive selection,enhancing waterlogging tolerance in ***,we discovered that the pseudogenization of Early Methionine-labelled 1(EM1)and EM6 in *** underly its crypto-vivipary characteristics,reflecting its intertidal *** study provides valuable genomic insights into the evolutionary history,genome stability,and adaptive evolution of the mangrove *** 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

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The Clausena lansium genome provides new insights into alkaloid diversity and the evolution of the methyltransferase family

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Journal of Integrative Agriculture 2024年第10期 3537-3553页

作者： Yongzan Wei Yi Wang Fuchu Hu Wei Wang Changbin Wei Bingqiang Xu Liqin Liu Huayang Li Can Wang Hongna Zhang Zhenchang Liang Jianghui Xie State Key Laboratory of Biological Breeding of Tropical Crops Institute of Tropical Bioscience and Biotechnology Chinese Academy of Tropical Agricultural Sciences Key Laboratory of Tropical Fruit Biology (Ministry of Agriculture and Rural Affairs) South Subtropical Crops Research Institute Chinese Academy of Tropical Agricultural Sciences Sanya Research Academy Chinese Academy of Tropical Agricultural Sciences Beijing Key Laboratory of Grape sciences and Enology CAS Key Laboratory of Plant Resources Institute of Botany Chinese Academy of Sciences Key Laboratory of Genetic Resources Evaluation and Utilization of Tropical Fruits and Vegetables (Co-construction by Ministry and Province) Ministry of Agriculture and Rural Affairs/Institute of Tropical Fruit Trees Hainan Academy of Agricultural Sciences Haikou Experimental Station Chinese Academy of Tropical Agricultural Sciences Sanya Institute of Breeding and Multiplication/School of Tropical Agriculture and Forestry Hainan University

Wampee(Clausena lansium) is an important evergreen fruit tree native to southern China that has a long history of use for medicinal purposes. Here, a chromosome-level genome of C. lansium was constructed with a genome size of 282.9 Mb and scaffold N50 of 30.75 Mb. The assembled genome contains 48.70% repetitive elements and 24,381 protein-coding genes. Comparative genomic analysis showed that C. lansium diverged from Aurantioideae 15.91–24.95 million years ago. Additionally, some expansive and specific gene families related to methyltransferase activity and S-adenosylmethionine-dependent methyltransferase activity were also *** analysis indicated that N-methyltransferase(NMT) is mainly involved in alkaloid biosynthesis and O-methyltransferase(OMT) participates in the regulation of coumarin accumulation in wampee. This suggested that wampee's richness in alkaloids and coumarins might be due to the gene expansions of NMT and OMT. The tandem repeat event was one of the major reasons for the NMT expansion. Hence, the reference genome of C. lansium will facilitate the identification of some useful medicinal compounds from wampee resources and reveal their biosynthetic pathways.

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