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Exploring Splicing Variants and Novel Genes in Sacred Lotus Based on RNA-seq Data

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Phyton-International Journal of Experimental Botany 2023年第6期92卷 1665-1679页

作者： Xinyi Zhang Zimeng Yu pingfang yang State Key Laboratory of Biocatalysis and Enzyme Engineering School of Life SciencesHubei UniversityWuhan430026China

Sacred lotus(Nelumbo nucifera)is a typical aquatic plant,belonging to basal eudicot plant,which is ideal for genome and genetic evolutionary *** lotus gene diversity is important for the study of molecular genetics and *** this research,public RNA-seq data and the annotated reference genome were used to identify the genes in lotus.A total of 26,819 consensus and 1,081 novel genes were ***,a comprehensive analysis of gene alternative splicing events was conducted,and a total of 19,983“internal”alternative splicing(AS)events and 14,070“complete”AS events were detected in 5,878 and 5,881 multi-exon expression genes,*** made from the AS events show the predominance of intron retention(IR)subtype of AS events representing 33%.IR is followed by alternative acceptor(AltA),alternative donor(AltD)and exon skipping(ES),highlighting the universality of the intron definition model in *** addition,functional annotations of the gene with AS indicated its relationship to a number of biological processes such as cellular process and metabolic process,showing the key role for alternative splicing in influencing the growth and development of *** results contribute to a better understanding of the current gene diversity in lotus,and provide an abundant resource for future functional genome analysis in lotus.

关键词： Novel genes alternative splicing intron retention ontology

Comparative Analysis of the Endosperm Proteins Separated by 2-D Electrophoresis for Two Cultivars of Hybrid Rice （Oryza sativa L,）

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Journal of Integrative Plant Biology 2006年第9期48卷 1028-1033页

作者： pingfang yang Shihua Shen Tingyun Kuang Key Laboratory of Photosynthesis and Environmental Molecular Physiology Institute of Botany the Chinese Academy of Sciences Beijing 100093 China Graduate School of the Chinese Academy of Sciences Beijing 100039 China

Liangyoupeijiu is a two-parental-line, and Shanyou63 is a three-parental-line hybrid rice （Oryza sativa L.）. Although both belong to the indica subspecies, they have obvious differences with respect to morphology, physiology and grain quality. Variations in endosperm protein compositions were studied by comparing the 2-D electrophoresis （2-DE） maps for these two cultivars of hybrid rice. After matrix-assisted laser desorption/ionization time of flight mass spectrometry （MALDI-TOF/MS） analysis, a 21-kDa precursor of 19- kDa globulin was identified as the major storage protein for both cultivars. Some isoforms of peroxiredoxin and seed maturation protein were found to only exist in Shanyou63, whereas aldose reductase and starch granule-bound starch synthase were only detected in Liangyoupeijiu. These data might provide a foundation for further comparative studies of these two cultivars of hybrid rice.

关键词： endosperm hybrid rice mass spectrometry matrix assisted laser desorption/ionization time of flight 2-D electrophoresis

Whole genome re-sequencing reveals evolutionary patterns of sacred lotus (Nelumbo nucifera)

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Journal of Integrative Plant Biology 2018年第1期60卷 2-15页

作者： Longyu Huang Mei yang Ling Li Hui Li Dong yang Tao Shi pingfang yang Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture Wuhan Botanical Garden of Chinese Academy of SciencesWuhan 43oo74 China University of Chinese Academy of Sciences Beijing 100049 China Sino-African Joint Research Center Chinese Academy of Sciences Wuhan 430074 China Hubei Collaborative Innovation Center for Grain Industry Jingzhou 434025 China

Sacred lotus(Nelumbo nucifera or lotus) is an important aquatic plant in horticulture and ecosystems. As a foundation for exploring genomic variation and evolution among different germplasms, we re-sequenced 19 individuals from three cultivated temperate lotus subgroups(rhizome,seed and flower lotus), one wild temperate lotus subgroup(wild lotus), one tropical lotus group(Thai lotus) and an outgroup(Nelumbo lutea). Through genetic diversity and polymorphism analysis by non-missing SNP sites widely distributed in the whole genome, we confirmed that wild and Thai lotus exhibited greater differentiation with a higher genomic diversity compared to cultivated lotus. Rhizome lotus had the lowest genomic diversity and a closer relationship to wild lotus, whereas the genomes of seed and flower lotus were admixed. Genes in energy metabolism process and plant immunity evolved rapidly in lotus, reflecting local *** established that candidate genes in genomic regions with significant differentiation associated with temperate and tropical lotus divergence always exhibited highly divergent expression pattern. Together, this study comprehensive and credible interpretates important patterns of genetic diversity and relationships, gene evolution, and genomic signature from ecotypic differentiation of sacred lotus.

关键词： Nelumbo nucifera Whole genome re-sequencing reveals evolutionary patterns of sacred lotus Figure

Comparative Proteomic Analysis of Rice Shoots Exposed to High Arsenate

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Journal of Integrative Plant Biology 2013年第10期55卷 965-978页

作者： Yanli Liu Ming Li Chao Han Fengxia Wu Bingkun Tu pingfang yang College of Horticulture and Forestry Sciences Huazhong Agricultural University Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture Wuhan Botanical Garden the Chinese Academy of Sciences

Consumption of arsenic contaminated water and cereals is a serious threat to humans all over the world. Rice （Oryza sativa ＂Nipponbare＂）, as a main cereal crop, can accumulate arsenic more than 10-fold that of in other cereals. To gain a comprehensive understanding of the response of rice subjected to 100 μM arsenate stress, a comparative proteomic analysis of rice shoots in combination with morphological and biochemical investigations have been performed in this study. The results demonstrated that arsenate suppressed the growth of rice seedlings, destroyed the cellular ultra-structure and changed the homeostasis of reactive oxygen species. Moreover, a total of 38 differentially displayed proteins, which were mainly involved in metabolism, redox and protein-metabolism, were identified. The data suggest the arsenic can inhibit rice growth through negatively affecting chloroplast structure and photosynthesis. In addition, upregulation of the proteins involved in redox and protein metabolism might help the rice to be resistant or tolerant to arsenic toxicity. In general, this study improves our understanding about the rice arsenic responsive mechanism.

关键词： Arsenate metabolism proteomics rice ultra-structure.

The high-quality genome of lotus reveals tandem duplicate genes involved in stress response and secondary metabolites biosynthesis

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Horticulture Research 2023年第5期10卷 271-274页

作者： Huanhuan Qi Feng Yu Jiao Deng Liangsheng Zhang pingfang yang State Key Laboratory of Biocatalysis and Enzyme Engineering School of Life SciencesHubei UniversityWuhan 430026China Research Center of Buckwheat Industry Technology Guizhou Normal UniversityGuiyang 550001China College of Agriculture&Biotechnology Zhejiang UniversityHangzhou 310058China

Dear Editor,Lotus(Nelumbo nucifera Gaertn.),which has been domesticated and cultivated for several thousands of years and endowed with religious and cultural symbolism[1],belongs to the Nelumbo genus Nelumbonaceae *** an early eudicot,it is not only essential for plant phylogeny but also widely used as a vegetable,a medic-inal herb,and for ornamental *** contains abundant func-tional compounds,such as f lavonoids and benzylisoquinoline alkaloids(BIAs),which are used to treat diverse diseases.

关键词： Lotus religious symbol

Identifying RNA Modifications by Direct RNA Sequencing Reveals Complexity of Epitranscriptomic Dynamics in Rice

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Genomics, Proteomics & Bioinformatics 2023年第4期21卷 788-804页

作者： Feng Yu Huanhuan Qi Li Gao Sen Luo Rebecca Njeri Damaris Yinggen Ke Wenhua Wu pingfang yang State Key Laboratory of Biocatalysis and Enzyme Engineering School of Life SciencesHubei UniversityWuhan 430062China

Transcriptome analysis based on high-throughput sequencing of a cDNA library has been widely applied to functional genomic ***,the cDNA dependence of most RNA sequencing techniques constrains their ability to detect base modifications on RNA,which is an important element for the post-transcriptional regulation of gene *** comprehensively profile the N^(6)-methyladenosine(m^(6)A)and N^(5)-methylcytosine(m5 C)modifications on RNA,direct RNA sequencing(DRS)using the latest Oxford Nanopore Technology was applied to analyze the transcriptome of six tissues in *** 94 million reads were generated,with an average length ranging from 619 nt to 1013 nt,and a total of 45,707 transcripts across 34,763 genes were *** profiles of transcripts at the isoform level were quantified among ***-wide mapping of m^(6)A and m5 C demonstrated that both modifications exhibited tissue-specific *** transcripts with m^(6)A modifications tended to be modified by m5 C,and the transcripts with modifications presented higher expression levels along with shorter poly(A)tails than transcripts without modifications,suggesting the complexity of gene expression *** Ontology analysis demonstrated that m^(6)A-and m5 C-modified transcripts were involved in central metabolic pathways related to the life cycle,with modifications on the target genes selected in a tissue-specific ***,most modified sites were located within quantitative trait loci that control important agronomic traits,highlighting the value of cloning functional *** results provide new insights into the expression regulation complexity and data resource of the transcriptome and epitranscriptome,improving our understanding of the rice genome.

关键词： Direct RNA sequencing Polyadenylated transcriptome N6-methyladenosine N5-methylcytosine Rice

Comparative Metabolomics Analysis between Red- and White-Flowered Common Buckwheat Cultivars

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Phyton-International Journal of Experimental Botany 2021年第3期90卷 859-870页

作者： Jiao Deng Fen Dong Chaoxin Wu Jiali Zhao Hongyou Li Juan Huang Taoxiong Shi Ziye Meng Fang Cai Qingfu Chen pingfang yang Research Center of Buckwheat Industry Technology School of Life SciencesGuizhou Normal UniversityGuiyang550001China State Key Laboratory of Biocatalysis and Enzyme Engineering School of Life SciencesHubei UniversityWuhan430026China Affiliated Hospital of Jianghan University Wuhan430015China

Common buckwheat(Fagopyrum esculentum),a specialty crop in southwest China,is not only used as a supplement to primary grain crops but also to produce beverages,such as tea and *** fully exploit the products made from common buckwheat flower,ultra-performance liquid chromatography–electrospray ionization–tandem mass spectrometry(UPLC–ESI–MS/MS)was conducted to analyze the metabolites in red-(‘Guihong 2’)and white-flowered(‘Fengtian 1’)buckwheat cultivars.A total of 784 metabolites were identified of which flavonoids were the largest group with 191 components,followed by organic acids and derivatives(126),and amino acids and derivatives(95).Besides,dozens of phenylpropanoids,nucleotides and derivates,lipids,alkaloids as well as several kinds of indole derivatives and sterides were *** these rich varieties of metabolites,24 metabolites were only detected in the red flower that mainly included 8 anthocyanins and 6 flavones,while 22 metabolites were only detected in the white flower,which mainly contained 5 lipids,5 flavonoids,and 5 organic acids and *** results enrich the metabolites’information of buckwheat and may be helpful for the exploitation of products from common buckwheat flowers.

关键词： Common buckwheat flowers metabolites flavonoid metabolites anthocyanins

Transcriptomic and Proteomic Analyses of Rice Pistils during Pollination

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Transcriptomic and Proteomic Analyses of Rice Pistils during...

Comparative DNA-methylome and transcriptome analysis reveals heterosis-and polyploidy-associated epigenetic changes in rice

第十届全国植物结构与生殖生物学学术研讨会

作者： Kun Wang Ming Li pingfang yang Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture Wuhan Botanical GardenChinese Academy of Sciences Graduate University of Chinese Academy of Sciences

Pollination is a critical step that can determine the rate of seed *** with those of the self-incompatibility (SI),the mechanisms of compatible pollination are still largely *** studies mainly focused on the gene expressional profile of stigma or pistil rather than its dynamic changes during the pollen-pistil *** this study,the deep-sequencing based transcriptomic technique,iTRAQ and two-dimensional gel electrophoresis based quantitative proteomic techniques were combined to analyze the dynamic changes of gene expressional profile in rice pistil during the *** bioinformatics analysis,RNA-Seq results yielded a total of 963 genes that exhibited significant (FDR2 or <0.5) *** and 2D-MS separately yielded 145 and 41 differentially expressed *** those,we found that fine-tuning of the biochemical and physiological cellular environment is crucial for reproductive *** study provides a temporal and spatial gene expressional profile of pollen-pistil interactions,which will help us to obtain a more comprehensive view into the gene expression networks and biochemical pathways during the plant sexual reproductive process.

关键词： rice Pollination Transcriptomic Proteomic

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The Crop Journal 2023年第2期11卷 427-437页

作者： Xiaolan Rao Jun Ren Wei Wang Rongrong Chen Qian Xie Yanqing Xu Dongmei Li Zhaojian Song Yuchi He Detian Cai pingfang yang Shiyou Lyu Li Li Wei Liu Xianhua Zhang School of Life Sciences Hubei UniversityWuhan 430062HubeiChina Wuhan Polyploid Bio-Technology Limited Company Wuhan 430345HubeiChina State Key Laboratory of Hybrid Rice Hunan Hybrid Rice Research CenterChangsha 410125HunanChina Institute for Regenerative Medicine Shanghai East HospitalSchool of Life Sciences and TechnologyTongji UniversityShanghai 200123China

Heterosis and polyploidy have an overwhelming influence on plant ***,polyploid rice hybrids have been used to breed new rice varieties because they combine the advantages of both heterosis and *** this study,we generated six rice lines:autotetraploid rice hybrids and their autotetraploid parents,diploid donors,and hybrids of the diploid *** investigate the molecular mechanism controlling the effects of both hybridization and polyploidization,we performed bisulfite and RNA sequencing on young panicles at the pollen meiosis stage to compare the DNA metabolomes and transcriptomes among the six rice *** hybrids lines were hypermethylated compared to their corresponding parents and the autotetraploid lines showed globally increased DNA methylation of their transposable elements compared to the diploid *** alteration in DNA methylation level corresponded to the differential gene expressions among the rice genotypes,suggesting that methylation changes induced by polyploidization and hybridization may affect gene *** of gene candidates were identified that may be associated with heterosis and *** results provide DNA information that can be used to investigate epigenetic modification during heterosis and polyploidy in rice.

关键词： Oryza sativa Neotetraploid rice Heterosis Whole genome duplication Epigenetic changes