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The Features and Regulation of Co-transcriptional Splicing in Arabidopsis

Molecular Plant 2020年第2期13卷 278-294页

作者： Danling Zhu Fei Mao Yuanchun Tian Xiaoya Lin lianfeng gu Hongya gu Li-jia Qu Yufeng Wu Zhe Wu SUSTech-PKU Institute of Plant and Food Science Department of BiologySouthern University of Science and TechnologyShenzhen 518055China State Key Laboratory for Crop Genetics and Germplasm Enhancement Bioinformatics CenterNanjing Agriculture UniversityNanjingJiangsu 210095China State Key Laboratory of Protein and Plant Gene Research Peking-Tsinghua Center for Life SciencesCollege of Life SciencesPeking UniversityBeijing 100871China Basic Forestry and Proteomics Research Center College of ForestryFujian Agriculture and Forestry UniversityFuzhou 350002China Present address:School of Life Sciences Guangzhou UniversityGuangzhou 510006China

Precursor mRNA(pre-mRNA)splicing is essential for gene expression in most eukaryotic *** studies from mammals,Drosophila,and yeast show that the majority of splicing events occurs *** plants,however,the features of co-transcriptional splicing(CTS)and its regulation still remain largely ***,we used chromatin-bound RNA sequencing to study CTS in Arabidopsis *** found that CTS is widespread in Arabidopsis seedlings,with a large proportion of alternative splicing events determined *** efficiency correlated with gene expression level,the chromatin landscape and,most surprisingly,the number of introns and exons of individual genes,but is independent of gene *** combination with enhanced crosslinking and immunoprecipitation sequencing analysis,we further showed that the hnRNP-like proteins RZ-1B and RZ-1C promote efficient CTS globally through direct binding,frequently to exonic ***,this general effect of RZ-1B/1C on splicing promotion is mainly observed at the chromatin level,not at the mRNA ***-1C promotes CTS of multiple-exon genes in association with its binding to regions both proximal and distal to the regulated *** propose that RZ-1C promotes efficient CTS of genes with multiple exons through cooperative interactions with many exons,introns,and splicing *** work thus reveals important features of CTS in plants and provides methodologies for the investigation of CTS and RNA-binding proteins in plants.

关键词： co-transcriptional splicing CB-RNA-seq eClip-seq RNA binding protein chromatin transcription

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Phytophthora Effectors Modulate Genome-wide Alternative Splicing of Host mRNAs to Reprogram Plant Immunity

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Molecular Plant 2020年第10期13卷 1470-1484页

作者： Jie Huang Xinyu Lu Hongwei Wu Yuchen Xie Qian Peng lianfeng gu Juyou Wu Yuanchao Wang Anireddy SNReddy Suomeng Dong Department of Plant Pathology Nanjing Agricultural UniversityNanjing 210095China Basic Forestry and Proteomics Research Center College of ForestryFujian Agriculture and Forestry UniversityFuzhou 350002China State Key Laboratory of Crop Genetics and Germplasm Enhancement College of HorticultureNanjing Agricultural UniversityNanjing 210095China Colorado State University Program in Cell and Molecular BiologyFort CollinsCO 80523USA Key Laboratory of Integrated Management of Crop Diseases and Pests(Ministry of Education) Nanjing 210095China The Key Laboratory of Plant Immunity Nanjing Agricultural UniversityNanjing 210095China

Alternative splicing(AS)of pre-mRNAs increases transcriptome and proteome diversity,regulates gene expression through multiple mechanisms,and plays important roles in plant development and stress ***,the prevalence of genome-wide plant AS changes during infection and the mechanisms by which pathogens modulate AS remain poorly ***,we examined the global AS changes in tomato leaves infected with Phytophthora infestans,the infamous Irish famine *** show that more than 2000 genes exhibiting significant changes in AS are not differentially expressed,indicating that AS is a distinct layer of transcriptome reprogramming during plant-pathogen ***,our results show that *** subverts host immunity by repressing the AS of positive regulators of plant immunity and promoting the AS of susceptibility *** study the underlying mechanism,we established a luminescence-based AS reporter system in Nicotiana benthamiana to screen pathogen effectors modulating plant *** identified nine splicing regulatory effectors(SREs)from 87 *** *** studies revealed that SRE3 physically binds U1-70K to manipulate the plant AS machinery and subsequently modulates AS-mediated plant *** study not only unveils genome-wide plant AS reprogramming during infection but also establishes a novel AS screening tool to identify SREs from a wide range of plant pathogens,providing opportunities to understand the splicing regulatory mechanisms through which pathogens subvert plant immunity.

关键词： late blight Phytophthora infestans alternative splicing splicing regulatory effectors plant immunity tomato

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Degradome sequencing reveals endogenous small RNA targets in rice (Oryza sativa L. ssp. indica)

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Frontiers in Biology 2010年第1期5卷 67-90页

作者： Ming ZHOU lianfeng gu Pingchuan LI Xianwei SONG Liya WEI Zhiyu CHEN Xiaofeng CAO State Key Laboratory of Plant Genomics and National Center for Plant Gene Research Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing 100101China Graduate School of the Chinese Academy of Sciences Yuquan RoadBeijing 100039China

MicroRNAs(miRNAs)and small interfering RNAs(siRNAs)regulate gene expression in *** miRNAs modulate their targets mainly via messenger RNA(mRNA)*** RNA(sRNA)targets have been extensively investigated in Arabidopsis using computational prediction,experimental validation,and degradome ***,small RNA targets are largely unknown in rice(Oryza sativa).Here,we report global identification of small RNA targets using high throughput degradome sequencing in the rice indica cultivar 93-11(Oryza sativa ***).One hundred and seventy-seven transcripts targeted by a total of 87 unique miRNAs were *** targets for the conserved miRNAs between Arabidopsis and rice,transcription factors comprise around 70%(58 in 82),indicating that these miRNAs act as masters of gene regulatory nodes in *** contrast,non-conserved miRNAs targeted diverse genes which provide more complex regulatory *** addition,5 AUXIN RESPONSE FACTORs(ARFs)cleaved by the TAS3 derived ta-siRNAs were also detected.A total of 40 sRNA targets were further validated via RNA ligasemediated 5′rapid amplification of cDNA ends(RLM 5′-RACE).Our degradome results present a detailed sRNAtarget interaction atlas,which provides a guide for the study of the roles of sRNAs and their targets in rice.

关键词： Degradome miRNA ta-siRNA small RNA targets rice

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Chromosomal-level genome and metabolome analyses of highly heterozygous allohexaploid Dendrocalamus brandisii elucidate shoot quality and developmental characteristics

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Journal of Integrative Plant Biology 2024年第6期66卷 1087-1105页

作者： Jutang Jiang Zeyu Zhang Yucong Bai Xiaojing Wang Yuping Dou Ruiman Geng Chongyang Wu Hangxiao Zhang Cunfu Lu lianfeng gu Jian Gao Key Laboratory of National Forestry and Grassland Administration Beijing for Bamboo&Rattan Science and TechnologyInstitute of Gene Science and Industrialization for Bamboo and Rattan ResourcesInternational Center for Bamboo and RattanBeijing 100102China College of Forestry Basic Forestry and Proteomics Research CenterFujian Agriculture and Forestry UniversityFuzhou 350002China School of Life Science Peking UniversityBeijing 100871China College of Biological Sciences and Biotechnology Beijing Forestry UniversityBeijing 100083China

Dendrocalamus brandisii(Munro)Kurz is a sympodial bamboo species with inimitable taste and flavorful *** rapid growth and use as high-quality material make this bamboo species highly valued for both food processing and wood ***,genome information for *** is lacking,primarily due to its polyploidy and large genome ***,we assembled a high-quality genome for hexaploid ***,which comprises 70chromosomes with a total size of 2,756 Mb,using long-read Hi Fi ***,we accurately separated the genome into its three constituent *** used Oxford Nanopore Technologies long reads to construct a transcriptomic dataset covering 15 tissues for gene annotation to complement our genome assembly,revealing differential gene expression and post-transcriptional *** integrating metabolome analysis,we unveiled that well-balanced lignin formation,as well as abundant flavonoid and fructose contents,contribute to the superior quality of *** *** genomic,transcriptomic,and metabolomic datasets provided a solid foundation for enhancing bamboo shoot quality and developing efficient gene-editing *** study should facilitate research on *** and enhance its use as a food source and wood material by providing crucial genomic resources.

关键词： bamboo shoots Dendrocalamus brandisii(Munro)Kurz flavonoid genome lignin

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Allele-aware chromosome-scale assembly of the allopolyploid genome of hexaploid Ma bamboo(Dendrocalamus latiflorus Munro)

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Journal of Integrative Plant Biology 2022年第3期64卷 649-670页

作者： Yushan Zheng Deming Yang Jundong Rong Liguang Chen Qiang Zhu Tianyou He Lingyan Chen Jing Ye Lili Fan Yubang Gao Hangxiao Zhang lianfeng gu College of Forestry Fujian Agriculture and Forestry UniversityFuzhou 350002China College of Landscape Architecture Fujian Agriculture and Forestry UniversityFuzhou 350002China Basic Forestry and Proteomics Research Center College of ForestryFujian Provincial Key Laboratory of Haixia Applied PlantSystems BiologyFujian Agriculture and Forestry UniversityFuzhou 350002China

Dendrocalamus latiflorus Munro is a woody clumping bamboo with rapid shoot *** genetic transformation and clustered regularly interspaced short palindromic repeats(CRISPR)/CRISPR-associated protein 9(Cas9)gene editing techniques are available for ***,enabling reverse genetic ***,*** has the potential to be a model bamboo ***,the genome sequence of *** has remained unreported due to its polyploidy and large genome ***,we sequenced the *** genome and assembled it into three allele-aware subgenomes(AABBCC),representingthe largest genome of a major bamboo *** assembled 70 allelic chromosomes(2,737 Mb)for hexaploid *** using both singlemolecule sequencing from the Pacific Biosciences(Pac Bio)Sequel platform and chromosome conformation capture sequencing(Hi-C).Repetitive sequences comprised 52.65%of the *** *** annotated 135231 protein-coding genes in the genome based on transcriptomes from eight different *** sequencing using RNA-Seq and Pac Bio singlemolecule real-time long-read isoform sequencing revealed highly differential alternative splicing(AS)between non-abortive and abortive shoots,suggesting that AS regulates the abortion rate of bamboo *** high-quality hexaploid genome and comprehensive strand-specific transcriptome datasets for this Poaceae family member will pave the way for bamboo research using *** as a model species.

关键词： alternative splicing bamboo shoots chromosome conformation capture sequencing D.latiflorus genome assembly single-molecular sequencing

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Development of an efficient expression system with large cargo capacity for interrogation of gene function in bamboo based on bamboo mosaic virus

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Journal of Integrative Plant Biology 2023年第6期65卷 1369-1382页

作者： Yandong Jin Baijie Wang Mingchuan Bao Yujie Li Shengwu Xiao Yuhua Wang Jun Zhang Liangzhen Zhao Hangxiao Zhang Yau-Heiu Hsu Mingjie Li lianfeng gu College of Forestry Fujian Agriculture and Forestry UniversityFuzhou 350002China Basic Forestry and Proteomics Research Center School of Future TechnologyCollege of ForestryFujian Agriculture and Forestry UniversityFuzhou 350002China Graduate Institute of Biotechnology Chung Hsing UniversityTaichung 40227China College of crop science Fujian Agriculture and Forestry UniversityFuzhou 350002China

Bamboo is one of the fastest growing plants among monocotyledonous species and is grown extensively in subtropical *** bamboo has high economic value and produces much biomass quickly,gene functional research is hindered by the low efficiency of genetic transformation in this *** therefore explored the potential of a bamboo mosaic virus(BaMV)-mediated expression system to investigate genotype-phenotype *** determined that the sites between the triple gene block proteins(TGBps)and the coat protein(CP)of BaMV are the most efficient insertion sites for the expression of exogenous genes in both monopodial and sympodial bamboo ***,we validated this system by individually overexpressing the two endogenous genes ACE1 and DEC1,which resulted in the promotion and suppression of intemode elongation,*** particular,this system was able to drive the expression of three 2A-linked betalain biosynthesis genes(more than 4 kb in length)to produce betalain,indicating that it has high cargo capacity and may provide the prerequisite basis for the development of a DNA-free bamboo genome editing platform in the *** BaMV can infect multiple bamboo species,we anticipate that the system described in this study will greatly contribute to gene function research and further promote the molecular breeding of bamboo.

关键词： ACE1 bamboo BaMV-mediated overexpression DEC1 expression virus-mediated genome editing

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Genome-wide profiling of circular RNAs,alternative splicing,and R-loops in stem-differentiating xylem of Populus trichocarpa

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Journal of Integrative Plant Biology 2021年第7期63卷 1294-1308页

作者： Xuqing Liu Yubang Gao Jiakai Liao Miao Miao Kai Chen Feihu Xi Wentao Wei Huihui Wang Yongsheng Wang XiXu Anireddy S.N.Reddy lianfeng gu Basic Forestry and Proteomics Research Center College of ForestryFujian Provincial Key Laboratory of Haixia Applied Plant Systems BiologyFujian Agriculture and Forestry UniversityFuzhou 350002China Basic Forestry and Proteomics Research Center College of Life ScienceFujian Agriculture and Forestry UniversityFuzhou 350002China Department of Biology and Program in Cell and Molecular Biology Colorado State UniversityFort CollinsColorado 80523USA

Circular RNAs(circRNAs)are a recently dis-covered type of non‐coding RNA derived from pre‐mRNAs.R‐loops consist of a DNA:RNA hybrid andthe associated single‐stranded ***-dopsis thaliana,circRNA:DNA R‐loops regulatealternative splicing(AS)ofSEPALLATA3(SEP3).However,the occurrence and functions ofcircRNAs and R‐loops inPopulus trichocarpaarelargely ***,we performed circRNA‐enriched sequencing in the stem‐differentiatingxylem(SDX)*** identified 2,742distinct circRNAs,including circ‐CESA4,circ‐IRX7,and circ‐guX1,which are generated from genesinvolved in cellulose,and hemicellulose biosyn-thesis,*** investigate the roles ofcircRNAs in modulating alternative splicing(AS),we detected 7,836 AS events using PacBio Iso‐Seq and identified 634 circRNAs that overlappedwith 699 AS ***,using DNA:RNAhybrid immunoprecipitation followed by se-quencing(DRIP‐seq),we identified 8,932 R‐looppeaks that overlapped with 181 circRNAs and 672AS ***,several SDX‐related circRNAsoverlapped with R‐loop peaks,pointing to theirpossible roles in modulating AS in ***,overexpressing circ‐IRX7increased the levels ofR‐loop structures and decreased the frequency ofintron retention in *** provides a valuable R‐loop atlas resourceand uncovers the interplay between circRNAs andAS in SDX ***.

关键词： alternative splicing circular RNA R‐loop Populustrichocarpa stem‐differentiating xylem

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Profiling of circular RNA N^(6)-methyladenosine in moso bamboo(Phyllostachys edulis)using nanopore-based direct RNA sequencing

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Journal of Integrative Plant Biology 2020年第12期62卷 1823-1838页

作者： Yongsheng Wang Huihui Wang Feihu Xi Huiyuan Wang Ximei Han Wentao Wei Hangxiao Zhang Qianyue Zhang Yushan Zheng Qiang Zhu Markus V.Kohnen Anireddy S.N.Reddy lianfeng gu Basic Forestry and Proteomics Research Center College of life scienceFujian Agriculture and Forestry UniversityFuzhou 350002China Basic Forestry and Proteomics Research Center College of ForestryFujian Agriculture and Forestry UniversityFuzhou 350002China College of Forestry Fujian Agriculture and Forestry UniversityFuzhou 350002China Department of Biology and Program in Cell and Molecular Biology Colorado State UniversityFort CollinsColoradoUSA

N6-methyladenosine(m^(6)A)is a prevalent modification in messenger RNAs and circular RNAs that play important roles in regulating various aspects of RNA ***,the occurrence of the m^(6)A modification in plant circular RNAs has not been reported.A widely used method to identify m^(6)A modifications relies on m^(6)A-specific antibodies followed by next-generation sequencing of precipitated RNAs(MeRIP-Seq).However,one limitation of MeRIP-Seq is that it does not provide the precise location of m^(6)A at single-nucleotide *** more recent sequencing techniques such as Nanopore-based direct RNA sequencing(DRS)can overcome such limitations,the technology does not allow sequencing of circular RNAs,as these molecules lack a poly(A)***,we developed a novel method to detect the precise location of m^(6)A modifications in circular RNAs using Nanopore *** first enriched our samples for circular RNAs,which we then fragmented and sequenced on the Nanopore platform with a customized *** this method,we identified 470 unique circular RNAs from DRS reads based on the back-spliced junction *** exonic circular RNAs,about 10%contained m^(6)A sites,which mainly occurred around acceptor and donor splice *** study demonstrates the utility of our antibody-independent method in identifying total and methylated circular RNAs using Nanopore *** method has the additional advantage of providing the exact location of m^(6)A sites at single-base resolution in circular RNAs or linear transcripts from non-coding RNA without poly(A)tails.

关键词： circular precise overcome

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Classification of Rice Yield Using UAV-Based Hyperspectral Imagery and Lodging Feature

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Plant Phenomics 2021年第1期3卷 115-128页

作者： Jian Wang Bizhi Wu Markus VKohnen Daqi Lin Changcai Yang Xiaowei Wang Ailing Qiang Wei Liu Jianbin Kang Hua Li Jing Shen Tianhao Yao Jun Su Bangyu Li lianfeng gu Institute of Crop Sciences Ningxia Academy of Agriculture and Forestry ScienceYinchuanNingxia 750105China Basic Forestry and Proteomics Research Center College of ForestryFujian Agriculture and Forestry UniversityFuzhou 350002China State Key Laboratory of Marine Environmental Science Xiamen UniversityChina Digital Fujian Institute of Big Data for Agriculture and Forestry Key Laboratory of Smart Agriculture and ForestryFujian Agriculture and Forestry UniversityFuzhou 350002China Seed Workstations of the Ningxia Hui Autonomous Region YinchuanNingxia 750004China Aerospace Information Research Center Institute of AutomationChinese Academic ScienceBeijing 100190China

High-yield rice cultivation is an effective way to address the increasing food demand *** classification of high-yield rice is a key step of ***,manual measurements within breeding programs are time consuming and have high cost and low throughput,which limit the application in large-scale field *** this study,we developed an accurate large-scale approach and presented the potential usage of hyperspectral data for rice yield measurement using the XGBoost algorithm to speed up the rice breeding process for many *** total,13 japonica rice lines in regional trials in northern China were divided into different categories according to the manual measurement of *** an Unmanned Aerial Vehicle(UAV)platform equipped with a hyperspectral camera to capture images over multiple time series,a rice yield classification model based on the XGBoost algorithm was *** comparison experiments were carried out through the intraline test and the interline test considering lodging characteristics at the midmature stage or *** result revealed that the degree of lodging in the midmature stage was an important feature affecting the classification accuracy of ***,we developed a low-cost,high-throughput phenotyping and nondestructive method by combining UAV-based hyperspectral measurements and machine learning for estimation of rice yield to improve rice breeding efficiency.

关键词： breeding equipped consuming

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Genome-wide Detection and Analysis of Alternative Splicing for Nucleotide Binding Site-Leucine-Rich Repeats Sequences in Rice

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Journal of Genetics and Genomics 2007年第3期34卷 247-257页

作者：顾连峰郭荣发广东海洋大学农学院湛江524088

Alternative splicing is a major contributor to genomic complexity and proteome diversity, yet the analysis of alternative splicing for the sequence containing nucleotide binding site and leucine-rich repeats （NBS-LRR） domain has not been explored in rice （Oryza sativa L.）. Hidden Markov model （HMM） searches were performed for NBS-LRR domain. 875 NBS-LRR-encoding sequences were obtained from the Institute for Genomic Research （TIGR）. All of them were used to blast Knowledge-based Oryza Molecular Biological Encyclopaedia （KOME）, TIGR rice gene index （TGI）, and Universal Protein Resource （UniProt） to obtain homologous full-length cDNAs （FL-cDNAs）, tentative consensus sequences, and protein sequences. Alternative splicing events were detected from genomic alignment of FL-cDNAs, tentative consensus sequences, and protein sequences, which provide valuable information on splice variants of genes. These sequences were aligned to the corresponding BAC sequences using the Spidey and Sim4 programs and each of the proteins was aligned by tBLASTn. Of the 875 NBS-LRR sequences, 119 （13.6%） sequences had alternative splicing where multiple FL-cDNAs, TGI sequences and proteins corresponded to the same gene. 71 intron retention events, 20 exon skipping events, 16 alternative termination events, 25 alternative initiation events, 12 alternative 5＇ splicing events, and 16 alternative 3＇ splicing events were identified. Most of these alternative splices were supported by two or more transcripts. The data sets are available at http：//***. Furthermore, the bioinformatics analysis of splice boundaries showed that exon skipping and intron retention did not exhibit strong consensus. This implies a different regulation mechanism that guides the expression of splice isoforms. This article also presents the analysis of the effects of intron retention on proteins. The C-terminal regions of alternative proteins turned out to be more variable than the N-terminal regions. Finally, tiss

关键词： alternative splicing bioinformatics NBS-LRR homologous sequence rice

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