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| 1 | Integration of Metabolomics and Subcellular Organelle Expression Microarray to Increase Understanding the Organic Acid Changes in Post-harvest Citrus Fruit显示文摘Citric acid plays an important role in fresh fruit favor and its adaptability to post-harvest storage conditions.In order to explore organic acid regulatory mechanisms in post-harvest citrus fruit,systematic biological analyses were conducted on stored Hirado Buntan Pummelo(HBP;Citrus grandis)fruits.High-performance capillary electrophoresis,subcellular organelle expression microarray,real-time quantitative reverse transcription polymerase chain reaction,gas chromatography mass spectrometry(GC-MS),and conventional physiological and biochemical analyses were undertaken.The results showed that the concentration of organic acids in HBP underwent a regular fuctuation.GC-MS-based metabolic profling indicated that succinic acid,g-aminobutyric acid(GABA),and glutamine contents increased,but 2-oxoglutaric acid content declined,which further confrmed that the GABA shunt may have some regulatory roles in organic acid catabolism processes.In addition,the concentration of organic acids was signifcantly correlated with senescence-related physiological processes,such as hydrogen peroxide content as well as superoxide dismutase and peroxidase activities,which showed that organic acids could be regarded as important parameters for measuring citrus fruit post-harvest senescence processes. | Xiaohua Sun Andan Zhu Shuzhen Liu Ling Sheng Qiaoli Ma Li Zhang Elsayed Mohamed Elsayed Nishawy Yunliu Zeng Juan Xu Zhaocheng Ma Yunjiang Cheng Xiuxin Deng | 2013 | Journal of Integrative Plant Biology2013，55，11： | 14 |
| 2 | Microarray Expression Profiling of Postharvest Ponkan Mandarin (Citrus reticulata) Fruit under Cold Storage Reveals Regulatory Gene Candidates and Implications on Soluble Sugars Metabolism显示文摘Low temperature storage is widely applied to maintain citrus postharvest fruit quality.In this study,the transcriptional and metabolic changes in the pulp tissue of Citrus reticulata Blanco cv.'Ponkan' were studied for three successive months under cold storage by Affymetrix Citrus GeneChip and gas chromatography,respectively.As many as 2 161 differentially expressed transcripts were identified based on the bayesian hierarchical model.The statistical analysis of gene ontology revealed that defense/stress-related genes were induced quickly,while autophagy-related genes were overrepresented in the late sampling stages,suggesting that the functional shift may coincide with the subsequent steps of chilling development.We further classified the potential regulatory components and concluded that ethylene may play the crucial role in chilling development in this non-climacteric fruit.To cope with complex events,53 upregulated transcription factors represented regulatory candidates.Within these,the AP2-EREBP,C2H2 and AS2 gene family were overrepresented.Cold storage also causes alterations in various metabolic pathways;a keen interest is paid in deciphering expression changes of soluble sugar genes as increased evidence that soluble sugars act as both osmolytes and metabolite signal molecules.Our results will likely facilitate further studies in this field with promising genetic candidates during chilling. | Andan Zhu Wenyun Li Junli Ye Xiaohua Sun Yuduan Ding Yunjiang Cheng Xiuxin Deng | 2011 | Journal of Integrative Plant Biology2011，53，5： | 3 |
| 3 | Complete loss of RNA editing from the plastid genome and most highly expressed mitochondrial genes of Welwitschia mirabilis显示文摘Comparative genomics among gymnosperms suggested extensive loss of mitochondrial RNA editing sites from Welwitschia mirabilis based on predictive analysis. However, empirical or transcriptome data to confirm this massive loss event are lacking,and the potential mechanisms of RNA site loss are unclear. By comparing genomic sequences with transcriptomic and reversetranscription PCR sequencing data, we performed a comprehensive analysis of the pattern of RNA editing in the mitochondrial and plastid genomes(mitogenome and plastome, respectively) of W. mirabilis and a second gymnosperm, Ginkgo biloba. For W.mirabilis, we found only 99 editing sites located in 13 protein-coding genes in the mitogenome and a complete loss of RNA editing from the plastome. The few genes having high editing frequency in the Welwitschia mitogenome showed a strong negative correlation with gene expression level. Comparative analyses with G. biloba, containing 1,405 mitochondrial and 345 plastid editing sites, revealed that the editing loss from W. mirabilis is mainly due to the substitution of editable cytidines to thymidines at the genomic level, which could be caused by retroprocessing. Our result is the first study to uncover massive editing loss from both the mitogenome and plastome in a single genus. Furthermore, our results suggest that gene expression level and retroprocessing both contributed to the evolution of RNA editing in plant organellar genomes. | Weishu Fan Wenhu Guo Lexis Funk Jeffrey P.Mower Andan Zhu | 2019 | Science China(Life Sciences)2019，62，4： | 2 |
| 4 | High-quality Cymbidium mannii genome and multifaceted regulation of crassulacean acid metabolism in epiphytes显示文摘Epiphytes with crassulacean acid metabolism(CAM)photosynthesis are widespread among vascular plants,and repeated evolution of CAM photosynthesis is a key innovation for micro-ecosystem adaptation.However,we lack a complete understanding of the molecular regulation of CAM photosynthesis in epiphytes.Here,we report a high-quality chromosome-level genome assembly of a CAM epiphyte,Cymbidium mannii(Orchidaceae).The 2.88-Gb orchid genome with a contig N50 of 22.7 Mb and 27192 annotated genes was organized into 20 pseudochromosomes,82.8%of which consisted of repetitive elements.Recent expansions of long terminal repeat retrotransposon families have made a major contribution to the evolution of genome size in Cymbidium orchids.We reveal a holistic scenario of molecular regulation of metabolic physiology using high-resolution transcriptomics,proteomics,and metabolomics data collected across a CAM diel cycle.Patterns of rhythmically oscillating metabolites,especially CAM-related products,reveal circadian rhythmicity in metabolite accumulation in epiphytes.Genomewide analysis of transcript and protein level regulation revealed phase shifts during the multifaceted regulation of circadian metabolism.Notably,we observed diurnal expression of several core CAM genes(especially bCA and PPC)that may be involved in temporal fixation of carbon sources.Our study provides a valuable resource for investigating post-transcription and translation scenarios in C.mannii,an Orchidaceae model for understanding the evolution of innovative traits in epiphytes. | Weishu Fan Zheng-Shan He Mengqing Zhe Jing-Qiu Feng Le Zhang Yiwei Huang Fang Liu Jia-Lin Huang Ji-Dong Ya Shi-Bao Zhang Jun-Bo Yang Andan Zhu De-Zhu Li | 2023 | Plant Communications2023，4，5： | 1 |
| 5 | Rapid evolution of T2/S-RNase genes in Fragaria linked to multiple transitions from self-incompatibility to self-compatibility显示文摘The T2/RNase gene family is widespread in eukaryotes,and particular members of this family play critical roles in the gametophytic self-incompatibility(GSI) system in plants.Wild diploid strawberry(Fragaria)species have diversified their sexual systems via self-incompatible and self-compatible traits,yet how these traits evolved in Fragaria remains elusive.By integrating the published and de novo assembled genomes and the newly generated RNA-seq data,members of the RNase T2 gene family were systematically identified in six Fragaria species,including three self-incompatible species(Fragaria nipponica,Fragaria nubicola,and Fragaria viridis) and three self-compatible species(Fragaria nilgerrensis,Fragaria vesca,and Fragaria iinumae).In total,115 RNase T2 genes were identified in the six Fragaria genomes and can be classified into three classes(Ⅰ-Ⅲ) according to phylogenetic analysis.The identified RNase T2 genes could be divided into 22 homologous gene sets according to amino acid sequence similarity and phylogenetic and syntenic relationships.We found that extensive gene loss and pseudogenization coupled with small-scale duplications mainly accounted for variations in the RNase T2 gene numbers in Fragaria.Multiple copies of homologous genes were mainly generated from tandem and segmental duplication events.Furthermore,we newly identified five S-RNase genes in three self-incompatible Fragaria genomes,including two in F.nipponica,two in F.viridis,and one in F.nubicola,which fit for typical features of a pistil determinant,including highly pistil-specific expression,highly polymorphic proteins and alkaline isoelectric point(pI),while no S-RNase genes were found in all three selfcompatible Fragaria species.Surprisingly,these T2/S-RNase genes contain at least one large intron(>10 kb).This study revealed that the rapid evolution of T2/S-RNase genes within the Fragaria genus could be associated with its sexual mode,and repeated evolution of the self-compatible traits in Fragaria was convergent via losses of S-RNase. | Wu Chen Hong Wan Fang Liu Haiyuan Du Chengjun Zhang Weishu Fan Andan Zhu | 2023 | Plant Diversity2023，45，2： | 1 |
| 6 | Comparative transcript profiling of gene expression between seedless Ponkan mandarin and its seedy wild type during floral organ development by suppression subtractive hybridization and cDNA microarray显示文摘 | QIU Wenming ZHU Andan WANG Yao | 2012 | BMC Genomics2012，13，1： | 1 |
| 7 | Plastid RNA editing reduction accompanied with genetic variations in Cymbidium,a genus with diverse lifestyle modes显示文摘Recent sequencing efforts have broadly uncovered the evolutionary trajectory of plastid genomes(plastomes)of flowering plants in diverse habitats,yet our knowledge of the evolution of plastid posttranscriptional modifications is limited.In this study,we generated 11 complete plastomes and performed ultra-deep transcriptome sequencing to investigate the co-evolution of plastid RNA editing and genetic variation in Cymbidium,a genus with diverse trophic lifestyles.Genome size and gene content is reduced in terrestrial and green mycoheterotrophic orchids relative to their epiphytic relatives.This could be partly due to extensive losses and pseudogenization of ndh genes for the plastid NADH dehydrogenase-like complex,but independent pseudogenization of ndh genes has also occurred in the epiphyte C.mannii,which was reported to use strong crassulacean acid metabolism photosynthesis.RNA editing sites are abundant but variable in number among Cymbidium plastomes.The nearly twofold variation in editing abundance is mainly due to extensive reduction of ancestral editing sites in ndh transcripts of terrestrial,mycoheterotrophic,and C.mannii plastomes.The co-occurrence of editing reduction and pseudogenization in ndh genes suggests functional constraints on editing machinery may be relaxed,leading to nonrandom loss of ancestral edited sites via reduced editing efficiency.This study represents the first systematic examination of RNA editing evolution linked to plastid genome variation in a single genus.We also propose an explanation for how genomic and posttranscriptional variations might be affected by lifestyle-associated ecological adaptation strategies in Cymbidium. | Mengqing Zhe Le Zhang Fang Liu Yiwei Huang Weishu Fan Junbo Yang Andan Zhu | 2022 | Plant Diversity2022，44，3： | 0 |
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