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Comparative analysis of long noncoding RNAs in angiosperms and characterization of long noncoding RNAs in response to heat stress in Chinese cabbage

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Horticulture Research 2021年第1期8卷 693-713页

作者： Xiaoming Song Jingjing Hu Tong Wu Qihang Yang Xuehuan Feng Hao Lin Shuyan Feng Chunlin Cui Ying Yu Rong Zhou Ke Gong Tong Yu qiaoying pei Nan Li College of Life Sciences/Center for Genomics and Bio-computing North China University of Science and TechnologyTangshanHebeiChina Food Science and Technology Department University of Nebraska-LincolnLincolnNEUSA School of Life Science and Technology and Center for Informational Biology University of Electronic Science and Technology of ChinaChengduChina Department of Food Science Aarhus UniversityAarhusDenmark

Long noncoding RNAs(lncRNAs)are widely present in different species and play critical roles in response to abiotic ***,the functions of lncRNAs in Chinese cabbage under heat stress remain ***,we first conducted a global comparative analysis of 247,242 lncRNAs among 37 *** results indicated that lncRNAs were poorly conserved among different species,and only 960 lncRNAs were homologous to 524 miRNA *** then carried out lncRNA sequencing for a genome-wide analysis of lncRNAs and their target genes in Chinese cabbage at different stages of heat *** total,18,253 lncRNAs were identified,of which 1229 differentially expressed(DE)lncRNAs were characterized as being *** ceRNA network revealed that 38 lncRNAs,16 miRNAs,and 167 mRNAs were involved in the heat response in Chinese *** analysis of the cis-and trans-regulated genes indicated that the targets of DE lncRNAs were significantly enriched in the“protein processing in endoplasmic reticulum”and“plant hormone signal transduction”***,the majority of HSP and PYL genes involved in these two pathways exhibited similar expression patterns and responded to heat stress *** on the networks of DE lncRNA-mRNAs,29 and 22 lncRNAs were found to interact with HSP and PYL genes,***,the expression of several critical lncRNAs and their targets was verified by ***,we conducted a comparative analysis of lncRNAs among 37 species and performed a comprehensive analysis of lncRNAs in Chinese *** findings expand the knowledge of lncRNAs involved in the heat stress response in Chinese cabbage,and the identified lncRNAs provide an abundance of resources for future comparative and functional studies.

关键词： stress analysis characterization

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

Comprehe nsive an alysis of SSRs and database construction using all complete gene-cod ing sequences in major horticultural and represe ntative plants

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Horticulture Research 2021年第1期8卷 1766-1782页

作者： Xiaoming Song Qihang Yang Yun Bai Ke Gong Tong Wu Tong Yu qiaoying pei Weike Duan Zhinan Huang Zhiyuan Wang Zhuo Liu Xi Kang Wei Zhao Xiao Ma School of Life Sciences/Library North China University of Science and TechnologyTangshanHebei 063210China School of Life Science and Technology and Center for Informational Biology University of Fleetronic Science and Technology of China610054 ChengduChina Food Science and Technology Department University of Nebraska-LincolnLincolnNE 68588USA College of Life Sciences and Food Engineering Huaiyin In stitute of Technology223003 Huai'anChina

Simple sequence repeats(SSRs)are one of the most important genetic markers and widely exist in most ***,we identified 249,822 SSRs from 3,951,919 genes in 112 ***,we conducted a comprehensive analysis of these SSRs and constructed a plant SSR database(PSSRD).Interestingly,more SSRs were found in lower plants than in higher plants,showing that lower plants needed to adapt to early extreme *** specific enriched functional terms in the lower plant Chlam^tdomonas reinhardtii were detected when it was compared with seven other higher *** addition,Guanylate_cyc existed in more genes of lower plants than of higher *** our PSSRD,we constructed an interactive plotting function in the chart interface,and users can easily view the detailed information of *** SSR information,including sequences,primers,and annotations,can be downloaded from our ***,we developed Web SSR Finder and Batch SSR Finder tools,which can be easily used for identifying *** database was developed using PHP,HTML,J avaScript,and MySQL,which are freely available at http://***/.We conducted an analysis of the Myb gene families and flowering genes as two applications of the *** analysis indicated that whole-genome duplication and whole-genome triplication played a major role in the expansion of the Myb gene *** SSR markers in our database will greatly facilitate comparative genomics and functional genomics studies in the future.

关键词： PHP HTML Web

Comparative analysis of the TCP gene family in celery,coriander and carrot(family Apiaceae)

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Vegetable Research 2021年第1期1卷 36-47页

作者： qiaoying pei Nan Li Yun Bai Tong Wu Qihang Yang Tong Yu Zhiyuan Wang Zhuo Liu Qiang Li Hao Lin Xiaoming Song College of Life Sciences/Center for Genomics and Bio-computing North China University of Science and TechnologyTangshan 063210China School of Life Science and Technology University of Electronic Science and Technology of ChinaChengdu 610054China Food Science and Technology Department University of Nebraska-LincolnLincolnNE 68588USA Faculty of Life Science Tangshan Normal UniversityTangshan 063000China

Apiaceae is one of the most important families in Apiales and includes many economically important vegetables and medicinal *** TEOSINTE BRANCHED 1/CYCLOIDEA/PROLIFERATING CELL FACTOR 1/2(TCP)gene family plays an important role in regulating plant growth and development,but it has not been widely studied in *** the present study,we identified 215 TCP family genes in six species of plant,of which 122 genes were present in three Apiaceae including 29 in celery(Apium graveolens),43 in coriander(Coriandrum sativum),and 50 in carrot(Daucus carota).Whole-genome duplication likely contributed to TCP gene family expansion in *** were more paralogs in carrot than in coriander and celery,which was attributable to the greater number of tandem and proximal duplicated genes on chromosome *** microRNAs were found to regulate 20 TCP genes in the three Apiaceae species,with miR-319 having the most target *** TCP genes showed high expression in the root,petiole and leaf of celery and *** results provide a basis for comparative and functional genomic analyses of TCP genes in Apiaceae and other plants.

关键词： TCP IDEA Whole

在体细胞重编程早期瞬时激活的线粒体炫对Nanog的调控

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科学新闻 2016年第1期 72-72页

作者：应仲富 Keshi Chen Lingjun Zheng Yi Wu Linpeng Li Rui Wang Qi Long Liang Yang Jingyi Guo Deyang Yao Yong Li Feixiang Bao Ge Xiang Jinglei Liu qiaoying Huang Zhiming Wu Andrew Paul Hutchins Duanqing pei 刘兴国中国科学院广州生物医药与健康研究院

文章简介体细胞重编程的各种机理已经有很多的报道,但是线粒体信号的不同信号和功能还不清楚。线粒体炫是最近发现的,是线粒体呼吸链产生的通过通透性转换孔释放的离子瞬时爆发的信号。假设线粒体炫在重编程中有一定的功能,研究人员发现... 详细信息

文章简介体细胞重编程的各种机理已经有很多的报道,但是线粒体信号的不同信号和功能还不清楚。线粒体炫是最近发现的,是线粒体呼吸链产生的通过通透性转换孔释放的离子瞬时爆发的信号。假设线粒体炫在重编程中有一定的功能,研究人员发现,在重编程早期,线粒体炫频率出现瞬时升高,伴随着强度的瞬时降低。在重编程早期,瞬时的提高线粒体炫频率能促进重编程,但是持续提高线粒体炫会抑制重编程。进一步的研究发现,线粒体炫能增加TET2蛋白结

关键词：线粒体粒线体 Nanog 重编程

在体细胞重编程早期瞬时激活的线粒体炫对Nanog的调控

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科学新闻 2017年第4期 69-69页

作者： Zhongfu Ying Keshi Chen Lingjun Zheng Yi Wu Linpeng Li Rui Wang Qi Long Liang Yang Jingyi Guo Deyang Yao Yong Li Feixiang Bao Ge Xiang Jinglei Liu qiaoying Huang Zhiming Wu Andrew Paul Hutchins Duanqing pei 刘兴国中国科学院广州生物医药与健康研究院

关键词：体细胞重编程线粒体粒线体 Nanog 调控调节控制