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Evidence that Natural Selection is the Primary Cause of the Guanine-cytosine Content Variation in Rice Genes

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Journal of Integrative Plant Biology 2007年第9期49卷 1393-1399页

作者： Xiaoli Shi xiyin wang Zhe Li Qihui Zhu Ji Yang Song Ge Jingchu Luo State Key Laboratory of Systematic and Evolutionary Botany Institute of Botany the Chinese Academy of Sciences Beijing 100093 China College of Life Sciences National Laboratory of Plant Genetic Engineering and Protein Engineering Center of Bioinformatics Peking University Beijing 100871 China College of Mathematics Hebei Polytechnic University Tangshan 063009 China Center for Evolutionary Biology School of Life Sciences Fudan University Shanghai 200433 China

Cereal genes are classified into two distinct classes according to the guanine-cytosine （GC） content at the third codon sites （GC3）. Natural selection and mutation bias have been proposed to affect the GC content. However, there has been controversy about the cause of GC variation. Here, we characterized the GC content of 1 092 paralogs and other single-copy genes in the duplicated chromosomal regions of the rice genome （ssp. indica） and classified the paralogs into GC3-rich and GC3-poor groups. By referring to out-group sequences from Arabidopsis and maize, we confirmed that the average synonymous substitution rate of the GC3-rich genes is significantly lower than that of the GC3-poor genes. Furthermore, we explored the other possible factors corresponding to the GC variation including the length of coding sequences, the number of exons in each gene, the number of genes in each family, the location of genes on chromosomes and the protein functions. Consequently, we propose that natural selection rather than mutation bias was the primary cause of the GC variation.

关键词： guanine-cytosine content mutation bias natural selection paralogs synonymous substitution rate two gene classes

WGDI:A user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes

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Molecular Plant 2022年第12期15卷 1841-1851页

作者： Pengchuan Sun Beibei Jiao Yongzhi Yang Lanxing Shan Ting Li Xiaonan Li Zhenxiang Xi xiyin wang Jianquan Liu Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education and State Key Laboratory of Hydraulics and Mountain River Engineering College of Life SciencesSichuan UniversityChengduChina Center for Genomics and Bio-computing North China University of Science and TechnologyTangshanHebeiChina State Key Laboratory of Grassland Agro-Ecosystem College of EcologyLanzhou UniversityLanzhouChina

Evidence of whole-genome duplications(WGDs)and subsequent karyotype changes has been detected in most major lineages of living organisms on *** clarify the complex resulting multi-layered patterns of gene collinearity in genome analyses,there is a need for convenient and accurate *** meet this need,we developed WGDI(Whole-Genome Duplication Integrated analysis),a Python-based command-line tool that facilitates comprehensive analysis of recursive polyploidization events and cross-species genome *** supports three main workflows(polyploid inference,hierarchical inference of genomic homology,and ancestral chromosome karyotyping)that can improve the detection of WGD and characterization of WGD-related events based on high-quality chromosome-level ***,it can extract complete synteny blocks and facilitate reconstruction of detailed karyotype *** toolkit is freely available at GitHub(https://***/SunPengChuan/wgdi).As an example of its application,WGDI convincingly clarified karyotype evolution in Aquilegia coerulea and Vitis vinifera following WGDs and rejected the hypothesis that Aquilegia contributed as a parental lineage to the allopolyploid origin of core dicots.

关键词： WGDI polyploidy collinearity inference of hierarchical and event-related gene collinearity ancestral chromosome karyotype

Integrated network analyses identify MYB4R1 neofunctionalization in the UV-B adaptation of Tartary buckwheat

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Plant Communications 2022年第6期3卷 267-281页

作者： Moyang Liu Wenjun Sun Zhaotang Ma Chaocheng Guo Jiahao Chen Qi Wu xiyin wang Hui Chen College of Life Science Sichuan Agricultural UniversityYa’an 625014China Joint Center for Single Cell Biology School of Agriculture and BiologyShanghai Jiao Tong UniversityShanghai 200240China Shanghai Collaborative Innovation Center of Agri-Seeds/School of Agriculture and Biology Shanghai Jiao Tong UniversityShanghai 200240China School of Life Science North China University of Science and TechnologyTangshan 063210China State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China Key Laboratory of Major Crop Diseases and Rice Research InstituteSichuan Agricultural UniversityChengdu 611130China

A hallmark of adaptive evolution is innovation in gene function,which is associated with the development of distinct roles for genes during plant evolution;however,assessing functional innovation over long periods of time is not *** buckwheat(Fagopyrum tataricum)originated in the Himalayan region and has been exposed to intense UV-B radiation for a long time,making it an ideal species for studying novel UV-B response mechanisms in ***,we developed a workflow to obtain a co-functional network of UV-B responses using data from more than 10,000 samples in more than 80 projects with multi-species and multiomics *** the entire network revealed that flavonoid biosynthesis was most significantly related to the UV-B ***,we found that the regulatory factor MYB4R1,which resides at the core of the network,has undergone *** vitro and in vivo experiments demonstrated that MYB4R1 regulates flavonoid and anthocyanin accumulation in response to UV-B in buckwheat by binding to L-box motifs in the FtCHS,FtFLS,and FtUFGT *** used deep learning to develop a visual discrimination model of buckwheat flavonoid content based on natural populations exposed to global UV-B *** study highlights the critical role of gene neofunctionalization in UV-B adaptation.

关键词： neofunctionalization deep learning MYB UV-B radiation Tartary buckwheat

Universal RNA editing in a human liver at the fetal stage

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Open Journal of Genetics 2012年第3期2卷 163-166页

作者： Dong Liu Cong Liu xiyin wang Sigurdur Ingvarsson Huiping Chen Department of Medical Genetics Tongji Medical College Huazhong University of Science and Technology Wuhan China Institute for Experimental Pathology and Faculty of Medicine University of Iceland Keldur Iceland

It is known that RNA editing occurs in human cells, which can change the information transmission from DNA to RNA and proteins. Most previous studies have focused on editing of the mRNAs. Here we reported that several kinds of RNAs, including miRNA, rRNA, mRNA, miscRNA and unknown RNA, exhibited base editing in a human fetal liver. Several editing types are displayed. Our data reveals that RNA editing may occur in different species of RNAs.

关键词： RNA Editing miRNA rRNA mRNA miscRNA Fetal Liver

Coriander Genomics Database:a genomic,transcriptomic,and metabolic database for coriander

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Horticulture Research 2020年第1期7卷 2082-2091页

作者： Xiaoming Song Fulei Nie Wei Chen Xiao Ma Ke Gong Qihang Yang Jinpeng wang Nan Li Pengchuan Sun Qiaoying Pei Tong Yu Jingjing Hu Xinyu Li Tong Wu Shuyan Feng Xiu-Qing Li xiyin wang Center for Genomics and Biocomputing/College of Life Sciences North China University of Science and TechnologyTangshanHebei 063210China School of Genomics and Bio-Big-Data Chengdu University of Traditional Chinese MedicineChengdu 610075China Library North China University of Science and TechnologyTangshanHebei 063210China Fredericton Research and Development Centre Agriculture and Agri-Food CanadaFrederictonNew Brunswick E3B 4Z7Canada

Coriander(Coriandrum sativum L.),also known as cilantro,is a globally important vegetable and spice *** genome and that of carrot are models for studying the evolution of the Apiaceae ***,we developed the Coriander Genomics Database(CGDB,http://***/)to collect,store,and integrate the genomic,transcriptomic,metabolic,functional annotation,and repeat sequence data of coriander and carrot to serve as a central online platform for Apiaceae and other related *** these data sets in the CGDB,we intriguingly found that seven transcription factor(TF)families showed significantly greater numbers of members in the coriander genome than in the carrot *** highest ratio of the numbers of MADS TFs between coriander and carrot reached 3.15,followed by those for tubby protein(TUB)and heat shock *** a demonstration of CGDB applications,we identified 17 TUB family genes and conducted systematic comparative and evolutionary ***-seq data deposited in the CGDB also suggest dose compensation effects of gene expression in *** allows bulk downloading,significance searches,genome browser analyses,and BLAST searches for comparisons between coriander and other plants regarding genomics,gene families,gene collinearity,gene expression,and the metabolome.A detailed user manual and contact information are also available to provide support to the scientific research community and address scientific *** will be continuously updated,and new data will be integrated for comparative and functional genomic analysis in Apiaceae and other related plants.

关键词： cor Cor globally

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关于德彪西钢琴作品演奏中的几个要点

音乐探索 2008年第4期 79-84页

作者：王溪音四川音乐学院管弦系四川成都610021

德彪西是印象主义音乐的代表。他的音乐风格深受象征主义和印象画派影响,色彩缤纷、迷离恍惚,开创了音乐史上的印象主义时期。学习德彪西钢琴音乐就应该严格地把握他的音乐风格、和声与调性的特点、触键与踏板的运用、节奏的变化,这样... 详细信息

德彪西是印象主义音乐的代表。他的音乐风格深受象征主义和印象画派影响,色彩缤纷、迷离恍惚,开创了音乐史上的印象主义时期。学习德彪西钢琴音乐就应该严格地把握他的音乐风格、和声与调性的特点、触键与踏板的运用、节奏的变化,这样才能表现出德彪西钢琴音乐中的印象主义风格。

关键词：德彪西调性和声触键踏板节奏

Paleo-polyploidization in Lycophytes

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Genomics, Proteomics & Bioinformatics 2020年第3期18卷 333-340页

作者： Jinpeng wang Jigao Yu Pengchuan Sun Chao Li Xiaoming Song Tianyu Lei Yuxian Li Jiaqing Yuan Sangrong Sun Hongling Ding Xueqian Duan Shaoqi Shen Yanshuang Shen Jing Li Fanbo Meng Yangqin Xie Jianyu wang Yue Hou Jin Zhang Xianchun Zhang Xiu-Qing Li Andrew HPaterson xiyin wang Center for Computational Biology and Genomics and School of Life SciencesNorth China University of Science and TechnologyTangshan 063200China National Key Laboratory for North China Crop Improvement and Regulation Agriculture University of HebeiBaoding 071001China State Key Laboratory of Systematic and Evolutionary Botany Institute of BotanyChinese Academy of ScienceBeijing 100093China Fredericton Research and Development Centre Agriculture and Agri-Food CanadaFrederictonNew BrunswickE3B 4Z7Canada Plant Genome Mapping Laboratory University of AthensAthensGA 30602USA Department of Plant Biology University of GeorgiaAthensGA 30602USA Department of Crop and Soil Science University of GeorgiaAthensGA 30602USA Department of Genetics University of GeorgiaAthensGA 30602USA

Lycophytes and seed plants constitute the typical vascular *** have been thought to have no paleo-polyploidization although the event is known to be critical for the fast expansion of seed ***,genomic analyses including the homologous gene dot plot analysis detected multiple paleo-polyploidization events,with one occurring approximately 13–15 million years ago(MYA)and another about 125–142 MYA,during the evolution of the genome of Selaginella moellendorffii,a model *** addition,comparative analysis of reconstructed ancestral genomes of lycophytes and angiosperms suggested that lycophytes were affected by more paleopolyploidization events than seed *** from the present genomic analyses indicate that paleo-polyploidization has contributed to the successful establishment of both lineages—lycophytes and seed plants—of vascular plants.

关键词： Vascular plant Lycophytes Genome Polyploidy Evolution

染色体数目减少及B染色体产生的进化基因组学模型

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中国科学：生命科学 2020年第5期50卷 524-537页

作者：王振怡王希胤华北理工大学生命科学学院基因组学与计算生物学研究中心唐山063210 成都中医药大学基因组学与生物大数据学院成都610075

在长期进化过程中,染色体数目展示出动态性变化.关于真核生物染色体进化仍有许多谜团,一个是如何维持染色体数目,另外一个是B染色体是如何产生的.全基因组测序工作的开展为认识染色体数目变化提供了新的机会,特别是反复的多倍化事件后... 详细信息

在长期进化过程中,染色体数目展示出动态性变化.关于真核生物染色体进化仍有许多谜团,一个是如何维持染色体数目,另外一个是B染色体是如何产生的.全基因组测序工作的开展为认识染色体数目变化提供了新的机会,特别是反复的多倍化事件后染色体的改变有助于人们理解相关生物学规律和机制.通过比较基因组学分析,本文提出了染色体数目变化与B染色体产生的模型,认为染色体数目的减少主要是由于染色体融合,并且端粒的丢失及B染色体的产生在基因组重新整合和染色体数目减少中起着重要作用.

关键词：进化基因组学 B染色体染色体数目减少多倍化全基因组加倍核型进化

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基于Ks分布的被子植物演化的时间尺度研究

广西植物 2022年第10期42卷 1684-1693页

作者：焦贝贝王希胤华北理工大学生命科学学院河北唐山063210

物种演化时间估算是生命演化研究的重要部分。近年来,许多研究发现由于不同基因和不同物种的进化速率差异显著,因此需要新的方法对进化事件发生时间进行重新估计。为了对被子植物演化时间的重新估计,该研究基于共享多倍化事件或共享分... 详细信息

物种演化时间估算是生命演化研究的重要部分。近年来,许多研究发现由于不同基因和不同物种的进化速率差异显著,因此需要新的方法对进化事件发生时间进行重新估计。为了对被子植物演化时间的重新估计,该研究基于共享多倍化事件或共享分歧事件应该有共同同义突变率(Ks)峰值的理念,建立了基于基因组数据的进化速率矫正模型。结果表明:(1)对获取Ks分布三种常见方式进行比较分析,明确了通过提取共线性区块上Ks值的中位数的方式最优。(2)模拟了Ks值随时间累积系数(v)变化过程下的Ks分布,当假设v服从正态分布时,Ks分布出现了长尾现象。(3)将矫正方法应用到被子植物中,发现不同谱系的被子植物具有同步的辐射进化和适应性进化现象。并且,被子植物的进化速率虽然差异显著,但不同分支间的进化速率仍具有部分一致性,如木兰类植物进化速率最慢,真双子叶植物次之,单子叶植物进化速率最快。最终得到了相对可靠的物种同义突变率演化时间轴,为植物研究提供了系统发育和演化的支撑。

关键词：同义突变率(Ks)分布被子植物时间矫正系统发育树进化速率