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| 1 | Whole genome re-sequencing reveals evolutionary patterns of sacred lotus (Nelumbo nucifera)显示文摘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 adaptation.We 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. | Longyu Huang Mei Yang Ling Li Hui Li Dong Yang Tao Shi Pingfang Yang | 2018 | Journal of Integrative Plant Biology2018，60，1： | 8 |
| 2 | A comparative study of the characteristics of two Coxsackie A virus type 16 strains (genotype B)显示文摘Coxsackie A virus is one of the major pathogens associated with hand, foot and mouth disease (HFMD). The etiological characteristics of Coxsackie A virus type 16 (CA16) are thought to correlate with the pathological process of its infection. Two CA16 strains that were isolated from a severe HFMD patient presented with different plaque forms. This observation, along with biological analysis, indicated that the differences in the strains' biological characteristics, such as proliferation kinetics and immunogenicity, correlate with differences in their pathogenicity toward neonatal mice. Furthermore, these differences are thought to be associated with the sequence of the 5′ non-coding region of the viral genome and the VP1 structural region sequence. The results suggest that the biological and genetic characteristics of the CA16 viral strains are relevant to their pathogenicity. | YANG ErXia ZHAO Heng ZHANG Ying LIU JianSheng LIAO Yun WANG LiChun CUI PingFang YANG LiXian LIU LongDing DONG ChengHong DONG ShaoZhong SHAO CongWen JIANG Li SUN Le LI QiHan | 2012 | Science China(Life Sciences)2012，55，4： | 5 |
| 3 | Gene Expression Profile Changes in Germinating Rice显示文摘Water absorption is a prerequisite for seed germination.During imbibition,water influx causes the resumption of many physiological and metabolic processes in growing seed.In order to obtain more complete knowledge about the mechanism of seed germination,two-dimensional gel electrophoresis was applied to investigate the protein profile changes of rice seed during the first 48 h of imbibition.Thirtynine differentially expressed proteins were identified,including 19 down-regulated and 20 up-regulated proteins.Storage proteins and some seed development-and desiccation-associated proteins were down regulated.The changed patterns of these proteins indicated extensive mobilization of seed reserves.By contrast,catabolism-associated proteins were up regulated upon imbibition.Semi-quantitative real time polymerase chain reaction analysis showed that most of the genes encoding the down-or upregulated proteins were also down or up regulated at mRNA level.The expression of these genes was largely consistent at mRNA and protein levels.In providing additional information concerning gene regulation in early plant life,this study will facilitate understanding of the molecular mechanisms of seed germination. | Dongli He Chao Han Pingfang Yang | 2011 | Journal of Integrative Plant Biology2011，53，10： | 3 |
| 4 | Comparative Analysis of the Endosperm Proteins Separated by 2-D Electrophoresis for Two Cultivars of Hybrid Rice (Oryza sativa L,)显示文摘Liangyoupeijiu 是 two-parental-line,并且 Shanyou63 是 three-parental-line 混血儿米饭(Oryza sativa L.) 。尽管两个属于 indica 亚种,他们关于形态学,生理学和谷物质量有明显的差别。在内乳蛋白质作文的变化被比较电气泳动(2-DE ) 为混合米饭的这二栽培变种印射的 2-D 学习。在飞行团 spectrometry (MALDI-TOF/MS ) 的帮助矩阵的激光解吸附作用 / 电离时间以后分析, 19-kDa 血球素的一位 21-kDa 先锋为两栽培变种作为主要存储蛋白质被识别。peroxiredoxin 和种子成熟蛋白质的某 isoforms 被发现仅仅在 Shanyou63 存在,而 aldose reductase 和淀粉小粒界限淀粉 synthase 仅仅在 Liangyoupeijiu 被检测。这些数据可能为混合米饭的这二栽培变种的进一步比较的研究提供一个基础。 | Pingfang Yang Shihua Shen Tingyun Kuang | 2006 | Journal of Integrative Plant Biology2006，48，9： | 3 |
| 5 | Identifying RNA Modifications by Direct RNA Sequencing Reveals Complexity of Epitranscriptomic Dynamics in Rice显示文摘Transcriptome analysis based on high-throughput sequencing of a cDNA library has been widely applied to functional genomic studies.However,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 expression.To 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 rice.Approximately 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 detected.Expression profiles of transcripts at the isoform level were quantified among tissues.Transcriptome-wide mapping of m^(6)A and m5 C demonstrated that both modifications exhibited tissue-specific characteristics.The 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 regulation.Gene 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 manner.Furthermore,most modified sites were located within quantitative trait loci that control important agronomic traits,highlighting the value of cloning functional loci.The results provide new insights into the expression regulation complexity and data resource of the transcriptome and epitranscriptome,improving our understanding of the rice genome. | Feng Yu Huanhuan Qi Li Gao Sen Luo Rebecca Njeri Damaris Yinggen Ke Wenhua Wu Pingfang Yang | 2023 | Genomics, Proteomics & Bioinformatics2023，21，4： | 1 |
| 6 | Comparative Proteomic Analysis of Rice Shoots Exposed to High Arsenate显示文摘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 mM 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 identi ed.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. | Yanli Liu Ming Li Chao Han Fengxia Wu Bingkun Tu Pingfang Yang | 2013 | Journal of Integrative Plant Biology2013，55，10： | 0 |
| 7 | Comparative Metabolomics Analysis between Red- and White-Flowered Common Buckwheat Cultivars显示文摘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 wine.To 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 detected.Among 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 derivatives.Our results enrich the metabolites’information of buckwheat and may be helpful for the exploitation of products from common buckwheat flowers. | Jiao Deng Fen Dong Chaoxin Wu Jiali Zhao Hongyou Li Juan Huang Taoxiong Shi Ziye Meng Fang Cai Qingfu Chen Pingfang Yang | 2021 | Phyton-International Journal of Experimental Botany2021，90，3： | 0 |
| 8 | The high-quality genome of lotus reveals tandem duplicate genes involved in stress response and secondary metabolites biosynthesis显示文摘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 family.As 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 use.It contains abundant func-tional compounds,such as f lavonoids and benzylisoquinoline alkaloids(BIAs),which are used to treat diverse diseases. | Huanhuan Qi Feng Yu Jiao Deng Liangsheng Zhang Pingfang Yang | 2023 | Horticulture Research2023，10，5： | 0 |
| 9 | Comparative DNA-methylome and transcriptome analysis reveals heterosis-and polyploidy-associated epigenetic changes in rice显示文摘Heterosis and polyploidy have an overwhelming influence on plant evolution.Recently,polyploid rice hybrids have been used to breed new rice varieties because they combine the advantages of both heterosis and polyploidy.In this study,we generated six rice lines:autotetraploid rice hybrids and their autotetraploid parents,diploid donors,and hybrids of the diploid donors.To 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 lines.The 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 donors.The 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 expression.Groups of gene candidates were identified that may be associated with heterosis and polyploidy.Our results provide DNA information that can be used to investigate epigenetic modification during heterosis and polyploidy in rice. | 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 | 2023 | The Crop Journal2023，11，2： | 0 |
| 10 | Exploring Splicing Variants and Novel Genes in Sacred Lotus Based on RNA-seq Data显示文摘Sacred lotus(Nelumbo nucifera)is a typical aquatic plant,belonging to basal eudicot plant,which is ideal for genome and genetic evolutionary study.Understanding lotus gene diversity is important for the study of molecular genetics and breeding.In 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 identified.Meanwhile,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,respectively.Observations 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 plants.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 lotus.The 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. | Xinyi Zhang Zimeng Yu Pingfang Yang | 2023 | Phyton-International Journal of Experimental Botany2023，92，6： | 0 |
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