Shanghai Key Laboratory of Plant Functional Genomics and Resources

Shanghai, China

Shanghai Key Laboratory of Plant Functional Genomics and Resources

Shanghai, China

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An M.,Shanghai Key Laboratory of Plant Functional Genomics and Resources | An M.,Chinese Academy of Sciences | Deng M.,Shanghai Key Laboratory of Plant Functional Genomics and Resources | Deng M.,Chinese Academy of Sciences | And 6 more authors.
Frontiers in Plant Science | Year: 2017

Natural introgression can cause negative effects where rare species experience genetic assimilation and invade by their abundant congeners. Quercus austrocochinchinensis and Q. kerrii (subgenus Cyclobalanopsis) are a pair of closely related species in the Indo-China area. Morphological intermediates of the two species have been reported in this region. In this study, we used AFLP, SSR and two key leaf morphological diagnostic traits to study the two Q. austrocochinchinensis populations, two pure Q. kerrii and two putative hybrid populations in China. Rates of individual admixture were examined using the Bayesian clustering programs STRUCTURE and NewHybrids, with no a priori species assignment. In total, we obtained 151 SSR alleles and 781 polymorphic loci of AFLP markers. Population differentiation inferred by SSR and AFLP was incoherent with recognized species boundaries. Bayesian admixture analyses and principal coordinate analysis identified more hybrids and backcrossed individuals than morphological intermediates in the populations. SSR inferred a wide genetic assimilation in Q. austrocochinchinensis, except for subpopulation D2 in the core area of Xi-Shuang-Ban-Na Nature Reserve (XSBN). However, AFLP recognized more Q. austrocochinchinensis purebreds than SSR. Analysis using NewHybrids on AFLP data indicated that these hybridized individuals were few F2 and predominantly backcrosses with both parental species. All these evidences indicate the formation of a hybrid swarm at XSBN where the two species co-exist. Both AFLP and SSR recognized that the core protected area of XSBN (D2) has a high percentage of Q. austrocochinchinensis purebreds and a unique germplasm. The Hainan population and the other subpopulations of XSBN of the species might have lost their genetic integrity. Our results revealed a clear genetic differentiation in the populations and subpopulations of Q. austrocochinchinensis and ongoing introgression between Q. austrocochinchinensis and Q. kerrii at the disturbed contact areas. Combining the results from genetic and morphological analyses, the conservation of subpopulation D2 should be prioritized. Conservation and restoration of the integrity of tropical ravine rainforest is an important long-termgoal for the successful conservation of Q. austrocochinchinensis. The fine-scale landscape might play an essential role in shaping the spatial patterns of hybridization. Further studies are needed to evaluate these patterns and dynamics. © 2017 An, Deng, Zheng, Jiang and Song.


Hsieh T.-Y.,CAS Shanghai Institutes for Biological Sciences | Hsieh T.-Y.,Chinese Academy of Sciences | Hsieh T.-Y.,Shanghai Key Laboratory of Plant Functional Genomics and Resources
Taiwan Journal of Forest Science | Year: 2016

Since the industrial revolution, human activities have influenced climate, causing a severe threat to species and ecosystems on Earth. To improve people's understanding of the impacts of climate change and enhance their ability to resolve threats of climate change, the author combined his expertise and a literature review to assess the recent adverse effects of climate change on species and ecosystems. The study considered the following: (1) the impacts of climate change on species, (2) the impacts of climate change on ecosystems, (3) how climate change affects organisms and ecosystems in tropical and subtropical East Asia, and (4) management strategies to protect species and ecosystems from climate change.


Ono N.N.,University of California at Davis | Qin X.,University of California at Davis | Wilson A.E.,University of California at Davis | Li G.,University of California at Davis | And 4 more authors.
PLoS ONE | Year: 2016

Hydrolyzable tannins (HTs) play important roles in plant herbivore deterrence and promotion of human health. A critical step in HT production is the formation of 1-O-galloyl-β-D-glucopyranoside (β-glucogallin, ester-linked gallic acid and glucose) by a UDP-glucosyltransferase (UGT) activity. We cloned and biochemically characterized four candidate UGTs from pomegranate (Punica granatum), of which only UGT84A23 and UGT84A24 exhibited β-glucogallin forming activities in enzyme assays. Although overexpression and single RNAi knockdown pomegranate hairy root lines of UGT84A23 or UGT84A24 did not lead to obvious alterations in punicalagin (the prevalent HT in pomegranate) accumulation, double knockdown lines of the two UGTs resulted in largely reduced levels of punicalagins and bis-hexahydroxydiphenyl glucose isomers. An unexpected accumulation of galloyl glucosides (ether-linked gallic acid and glucose) was also detected in the double knockdown lines, suggesting that gallic acid was utilized by an unidentified UGT activity for glucoside formation. Transient expression in Nicotiana benthamiana leaves and immunogold labeling in roots of pomegranate seedlings collectively indicated cytosolic localization of UGT84A23 and UGT84A24. Overall, functional characterization and localization of UGT84A23 and UGT84A24 open up opportunities for further understanding the regulatory control of HT metabolism in plants and its coordination with other biochemical pathways in the metabolic network. © 2016 Ono et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.


Qin X.,University of California at Davis | Fischer K.,University of California at Davis | Fischer K.,University of California at Merced | Yu S.,University of California at Davis | And 5 more authors.
BMC Plant Biology | Year: 2016

Background: β-carotene, the most active provitamin A molecule produced by plants, plays important roles in human nutrition and health. β-carotene does not usually accumulate in the endosperm (i.e. flour) of mature wheat grains, which is a major food source of calories for humans. Therefore, enriching β-carotene accumulation in wheat grain endosperm will enable a sustainable dietary supplementation of provitamin A. Several metabolic genes affecting β-carotene accumulation have already been isolated from wheat, including phytoene synthase 1 (PSY1), lycopene ε-cyclase (LCYe) and carotenoid β-ring hydroxylase1/2 (HYD1/2). Results: In this work, we cloned and biochemically characterized two carotenoid cleavage dioxygenases (CCDs), CCD1 and CCD4, from wheat. While CCD1 homoeologs cleaved β-apo-8'-carotenal, β-carotene, lutein and zeaxanthin into apocarotenoid products, CCD4 homoeologs were inactive towards these substrates in in vitro assays. When analyzed by real-time qPCR, PSY1, LCYe, HYD1/2 and CCD1/4 homoeologs showed distinct expression patterns in vegetative tissues and sections of developing tetraploid and hexaploid wheat grains, suggesting that carotenoid metabolic genes and homoeologs are differentially regulated at the transcriptional level in wheat. Conclusions: The CCD1/4 enzyme activity and the spatial-temporal gene expression data provide critical insights into the specific carotenoid metabolic gene homoeologs that control β-carotene accumulation in wheat grain endosperm, thus establishing the knowledge base for generation of wheat varieties with enhanced β-carotene in the endosperm through breeding and genome editing approaches. © 2016 The Author(s).


Wilson A.E.,University of California at Davis | Matel H.D.,Cavite State University | Tian L.,University of California at Davis | Tian L.,Shanghai Key Laboratory of Plant Functional Genomics and Resources | Tian L.,Chinese Academy of Sciences
Phytochemistry Reviews | Year: 2016

Acylation of core compound skeletons, together with other modifications, plays a significant role in producing the incredible diversity of plant specialized metabolites. Two major classes of acyltransferases, the BAHD and serine carboxypeptidase-like (SCPL) acyltransferases, can bring together through acylation compounds from the same or divergent metabolic pathways. BAHD acyltransferases (BAHD-ATs) employ CoA thioesters as the activated substrate, SCPL acyltransferases (SCPL-ATs), on the other hand, utilize β-acetal esters, typically glucose esters formed by UDP glycosyltransferases (UGTs). While the general trend of high energy glucose ester enabled acyltransfers is seen throughout the spermatophytes (seed plants), the specific metabolites that are conjugated appear to be lineage specific. In this review, we examine the reaction mechanism, biochemical property and evolutionary relationship of SCPL-ATs that utilize various glucose ester donors and acceptors from the same or different plant specialized metabolic pathways. The occurrence and taxonomic distribution of galloylated flavan-3-ols, hydrolyzable tannins and galloylated flavonols are also evaluated. Furthermore, glucose ester (acyl donor)-forming UGT activities and the subcellular localization of the UGT and SCPL-AT catalyzed reactions are discussed. © 2016 Springer Science+Business Media Dordrecht


Jiang X.-L.,Shanghai Key Laboratory of Plant Functional Genomics and Resources | Jiang X.-L.,Chinese Academy of Sciences | Deng M.,Shanghai Key Laboratory of Plant Functional Genomics and Resources | Deng M.,Chinese Academy of Sciences | And 3 more authors.
Tree Genetics and Genomes | Year: 2016

Yunnan Plateau and its adjacent areas (YPA) with typical subtropical evergreen broad-leaved forests (SEBF) have a rich number of vascular plants and high endemism. However, how ancient geological and climatic events in YPA have shaped the SEBF remains poorly understood. In this study, we integrated multilocus phylogeography, species distribution models (SDMs), and regression analysis to investigate the effects of paleoenvironmental changes on the contemporary genetic patterns of Quercus schottkyana, an endemic and dominant evergreen oak in the YPA. A total of 380 samples were taken from 29 populations, covering the natural geographical distribution of Q. schottkyana. Molecular dating indicated that haplotype divergence began at late Miocene; this finding supported the hypothesis that major uplifting of YPA occurred after late Miocene, which led to the speciation and divergence of Q. schottkyana. Unlike previous biome reconstruction studies based on palynology data, our SDM analysis indicated that the distribution ranges of Q. schottkyana was comparatively stable after the Last Glacial Maximum (LGM) and experienced only a slight northward expansion afterward. Species genetic diversity showed a significant negative correlation to the habitat stability using regression analysis. These analyses suggested the admixture of individuals from genetically differentiated populations in the unstable habitats, which in turn increased the genetic diversity of Q. schottkyana. We also found that climate gradient along the latitude cline influenced the genetic structure of Q. schottkyana. This study provides new insights into the understanding of the evolutionary history of SEBF in YPA. © 2016, Springer-Verlag Berlin Heidelberg.


Zhu Z.,Fudan University | Zhou C.,Fudan University | Yang J.,Fudan University | Yang J.,Shanghai Key Laboratory of Plant Functional Genomics and Resources
Frontiers in Plant Science | Year: 2015

Alternanthera philoxeroides is a perennial amphibious weed native to South America but has now spread to diverse parts of the world. A. philoxeroides reproduces both sexually and asexually in its native range, but propagates solely through vegetative means in its introduced range. Traits associated with sexual reproduction become degraded for sexual dysfunction, with flowers possessing either pistillate stamens or male-sterile anthers. Degradations of sexual characters for loss of sexuality commonly take place in clonal plants. The underlying molecular-genetic processes remain largely unknown. We compared the gene expression profiles of abnormal stamens with that of normal stamens by RNA-Seq analysis, and identified a large number of differentially expressed genes between abnormal and normal stamens. In accordance with flower morphology, the expression of B-class MADS-box genes (ApAP3, ApTM6, and ApPI) was markedly reduced in pistillate stamens. However, most of the genes involved in meiosis were expressed normally in stamens with male-sterile anthers. In addition to verifying the expression patterns of genes previously known to be related to stamen and pollen grain development, we also identified previously unknown molecular phenotypes associated with sexual dysfunction in A. philoxeroides, that is helpful for dissecting the molecular mechanisms underpinning various male-sterile phenotypes and the molecular processes underlying the transition from sexuality to asexuality in clonal plants. © 2015 Zhu, Zhou and Yang. All rights reserved.


Zhang L.-Y.,Fudan University | Zhu Z.,Fudan University | Yang J.,Fudan University | Yang J.,Shanghai Key Laboratory of Plant Functional Genomics and Resources
Journal of Systematics and Evolution | Year: 2015

HORMA domain-containing proteins play important roles in cell cycle regulation and DNA repair, acting as adaptors to recruit other proteins. Although containing the conserved HORMA domain in structure, different types of HORMA proteins have diverged significantly in function. The mechanisms underlying the evolution and functional diversification of HORMA proteins remain unclear. Here we conduct an integrative approach, combining sequence, structural, gene coexpression and protein–protein interaction data, to trace the structural and functional evolution of HORMA proteins. Comparative sequence and structure analysis revealed that variations in both amino acid sequence and domain composition contributed to the functional diversification of different HORMA domain-containing proteins. Multiple amino acid substitutions at the C-terminal region promoted the functional divergence between MAD2 and REV7 by facilitating interaction with different partners. The emergence of the HOP1CTD domain contributed to the function of HOP1 as a meiosis-specific structural component of the lateral elements of the synaptonemal complex. Additionally, different types of HORMA proteins were recruited into different functional modules in the genetic network while functioning distinctly. © 2015 Institute of Botany, Chinese Academy of Sciences


Cao J.,Shanghai Key Laboratory of Plant Functional Genomics and Resources | Jiang M.,Shanghai Key Laboratory of Plant Functional Genomics and Resources | Li P.,Shanghai Key Laboratory of Plant Functional Genomics and Resources | Chu Z.,Shanghai Key Laboratory of Plant Functional Genomics and Resources | Chu Z.,Chinese Academy of Sciences
BMC Genomics | Year: 2016

Background: The type-2C protein phosphatases (PP2Cs), negatively regulating ABA responses and MAPK cascade pathways, play important roles in stress signal transduction in plants. Brachypodium distachyon is a new model plant for exploring the functional genomics of temperate grasses, cereals and biofuel crops. To date, genome-wide identification and analysis of the PP2C gene family in B. distachyon have not been investigated. Results: In this study, 86 PP2C genes in B. distachyon were identified. Domain-based analyses of PP2C proteins showed that they all contained the phosphatase domains featured as 11 conserved signature motifs. Although not all phosphatase domains of BdPP2C members included all 11 motifs, tertiary structure analysis showed that four residues contributing to magnesium/manganese ions (Mg2+/Mn2+) coordination were conserved, except for two noncanonical members. The analysis of their chromosomal localizations showed that most of the BdPP2C genes were located within the low CpG density region. Phylogenetic tree and synteny blocks analyses among B. distachyon, Arabidopsis thaliana and Oryza sativa revealed that all PP2C members from the three species can be phylogenetically categorized into 13 subgroups (A-M) and BdPP2Cs were evolutionarily more closely related to OsPP2Cs than to AtPP2Cs. Segmental duplications contributed particularly to the expansion of the BdPP2C gene family and all duplicated BdPP2Cs evolved mainly from purifying selection. Real-time quantitative reverse transcription PCR (qRT-PCR) analysis showed that BdPP2Cs were broadly expressed in disparate tissues. We also found that almost all members displayed up-regulation in response to abiotic stresses such as cold, heat, PEG and NaCl treatments, but down-regulation to biotic stresses such as Ph14, Guy11 and F0968 infection. Conclusions: In the present study, a comprehensive analysis of genome-wide identification and characterization of protein domains, phylogenetic relationship, gene and protein structure, chromosome location and expression pattern of the PP2C gene family was carried out for the first time in a new model monocot, i.e., B. distachyon. Our results provide a reference for genome-wide identification of the PP2C gene family of other species and also provide a foundation for future functional research on PP2C genes in B. distachyon. © 2016 Cao et al.


PubMed | Shanghai Key Laboratory of Plant Functional Genomics and Resources
Type: | Journal: BMC genomics | Year: 2016

The type-2C protein phosphatases (PP2Cs), negatively regulating ABA responses and MAPK cascade pathways, play important roles in stress signal transduction in plants. Brachypodium distachyon is a new model plant for exploring the functional genomics of temperate grasses, cereals and biofuel crops. To date, genome-wide identification and analysis of the PP2C gene family in B. distachyon have not been investigated.In this study, 86 PP2C genes in B. distachyon were identified. Domain-based analyses of PP2C proteins showed that they all contained the phosphatase domains featured as 11 conserved signature motifs. Although not all phosphatase domains of BdPP2C members included all 11 motifs, tertiary structure analysis showed that four residues contributing to magnesium/manganese ions (Mg(2+)/Mn(2+)) coordination were conserved, except for two noncanonical members. The analysis of their chromosomal localizations showed that most of the BdPP2C genes were located within the low CpG density region. Phylogenetic tree and synteny blocks analyses among B. distachyon, Arabidopsis thaliana and Oryza sativa revealed that all PP2C members from the three species can be phylogenetically categorized into 13 subgroups (A-M) and BdPP2Cs were evolutionarily more closely related to OsPP2Cs than to AtPP2Cs. Segmental duplications contributed particularly to the expansion of the BdPP2C gene family and all duplicated BdPP2Cs evolved mainly from purifying selection. Real-time quantitative reverse transcription PCR (qRT-PCR) analysis showed that BdPP2Cs were broadly expressed in disparate tissues. We also found that almost all members displayed up-regulation in response to abiotic stresses such as cold, heat, PEG and NaCl treatments, but down-regulation to biotic stresses such as Ph14, Guy11 and F0968 infection.In the present study, a comprehensive analysis of genome-wide identification and characterization of protein domains, phylogenetic relationship, gene and protein structure, chromosome location and expression pattern of the PP2C gene family was carried out for the first time in a new model monocot, i.e., B. distachyon. Our results provide a reference for genome-wide identification of the PP2C gene family of other species and also provide a foundation for future functional research on PP2C genes in B. distachyon.

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