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[PMID]: 29497059
[Au] Autor:Park JY; Kim H; Lee I
[Ad] Address:Laboratory of Plant Developmental Genetics, School of Biological Sciences, Plant Genomics & Breeding Institute, Seoul National University, Seoul, 08826, Korea.
[Ti] Title:Author Correction: Comparative analysis of molecular and physiological traits between perennial Arabis alpina Pajares and annual Arabidopsis thaliana Sy-0.
[So] Source:Sci Rep;8(1):4052, 2018 Mar 01.
[Is] ISSN:2045-2322
[Cp] Country of publication:England
[La] Language:eng
[Ab] Abstract:A correction to this article has been published and is linked from the HTML and PDFversions of this paper. The error hasnot been fixed in the paper.
[Pt] Publication type:PUBLISHED ERRATUM
[Em] Entry month:1803
[Cu] Class update date: 180307
[Lr] Last revision date:180307
[St] Status:In-Data-Review
[do] DOI:10.1038/s41598-018-21281-5

  2 / 184 MEDLINE  
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[PMID]: 29467177
[Au] Autor:Lazaro A; Obeng-Hinneh E; Albani MC
[Ad] Address:Univeristy of Cologne CITY: Cologne Germany [DE].
[Ti] Title:Extended vernalization regulates inflorescence fate in Arabis alpina by stably silencing PERPETUAL FLOWERING 1.
[So] Source:Plant Physiol;, 2018 Feb 21.
[Is] ISSN:1532-2548
[Cp] Country of publication:United States
[La] Language:eng
[Ab] Abstract:The alpine perennial Arabis alpina initiates flower buds during prolonged exposure to cold. In the accession Pajares we demonstrate that the length of vernalization influences flowering time and inflorescence fate, but does not affect the axillary branches that maintain vegetative growth. The expression of floral organ identity genes gradually increases in the main shoot apex during vernalization, correlating with an increase in floral commitment. In northern Arabidopsis thaliana accessions, the length of vernalization modulates the stable silencing of the floral repressor FLOWERING LOCUS C (FLC). We demonstrate that expression of PERPETUAL FLOWERING 1 (PEP1), the orthologue of FLC in A. alpina, is similarly influenced by the duration of the exposure to cold. Extended vernalization results in stable silencing of PEP1 in the inflorescence. In contrast, insufficient vernalization leads to PEP1 reactivation after cold treatment, which correlates with delayed flowering and the appearance of floral reversion phenotypes such as bracts and vegetative inflorescence branches. Floral reversion is reduced in the pep1-1 mutant, suggesting that PEP1 regulates the fate of the inflorescence after vernalization. The effect of vernalization duration on stable silencing of PEP1 is specific to meristems that initiate flowering during cold treatment. Extended vernalization fails to silence PEP1 in young seedlings and axillary branches that arise from buds initiated during cold treatment, which remain vegetative. We conclude that the duration of vernalization in A. alpina differentially regulates PEP1 in the inflorescence and axillary branches. PEP1 has a dual role regulating meristem fate; it prevents meristems from flowering and antagonizes inflorescence development after vernalization.
[Pt] Publication type:JOURNAL ARTICLE
[Em] Entry month:1802
[Cu] Class update date: 180222
[Lr] Last revision date:180222
[St] Status:Publisher

  3 / 184 MEDLINE  
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[PMID]: 29463014
[Au] Autor:Kawabe A; Nukii H; Furihata HY
[Ad] Address:Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Kyoto 603-8555, Japan. akiraka@cc.kyoto-su.ac.jp.
[Ti] Title:Exploring the History of Chloroplast Capture in Arabis Using Whole Chloroplast Genome Sequencing.
[So] Source:Int J Mol Sci;19(2), 2018 Feb 18.
[Is] ISSN:1422-0067
[Cp] Country of publication:Switzerland
[La] Language:eng
[Ab] Abstract:Chloroplast capture occurs when the chloroplast of one plant species is introgressed into another plant species. The phylogenies of nuclear and chloroplast markers from East Asian species are incongruent, which indicates hybrid origin and shows chloroplast capture. In the present study, the complete chloroplast genomes of , and were sequenced in order to analyze their divergence and their relationships. The chloroplast genomes of and were similar, which indicates chloroplast replacement. If hybridization causing chloroplast capture occurred once, divergence between recipient species would be lower than between donor species. However, the chloroplast genomes of species with possible hybrid origins, and differ at similar levels to possible maternal donor species which suggests that multiple hybridization events have occurred in their respective histories. The mitochondrial genomes exhibited similar patterns, while and were more similar to each other than to . This suggests that the two organellar genomes were co-transferred during the hybridization history of the East Asian species.
[Pt] Publication type:JOURNAL ARTICLE
[Em] Entry month:1802
[Cu] Class update date: 180221
[Lr] Last revision date:180221
[St] Status:In-Process

  4 / 184 MEDLINE  
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[PMID]: 29429846
[Au] Autor:Sun W; Xiong Z; Chu L; Li W; Soares MA; White JF; Li H
[Ad] Address:Medical School, Kunming University of Science and Technology, Kunming 650500,China.
[Ti] Title:Bacterial communities of three plant species from Pb-Zn contaminated sites and plant-growth promotional benefits of endophytic Microbacterium sp. (strain BXGe71).
[So] Source:J Hazard Mater;, 2018 Feb 06.
[Is] ISSN:1873-3336
[Cp] Country of publication:Netherlands
[La] Language:eng
[Ab] Abstract:The endophytic bacterial community of two hyperaccumulators (Arabis alpine, Dysphania ambrosioides) and Veronica ciliate was investigated by Illumina sequencing technology. In addition, the culturable endophytic bacteria (EB) were isolated and their plant-growth promotion capabilities were studied. A dataset consisting of 221,075 filtered high-quality and classifiable unique 16S rDNA gene tags, and an average of 36,846 tags with a mean length of 464-bp for each sample was generated. In total, 10801 different operational taxonomic units (OTUs) were detected, belonging to 18 bacterial phyla, 41 classes, 91 orders, 135 families, and 215 genera. Pseudomonas was the most dominant genus in both shoots and roots of the two hyperaccumulators, making up 81.56% and 81.13%, 41.60% and 77.06% of the total number of OTUs, respectively. However, both Chao 1 and Shannon indices of EB of the two hyperaccumulators were significantly lower than those of V. ciliate (P <. 05), except the Shannon index of D. ambrosioides shoots. The endophytic bacterial community of roots and shoots of A. alpine showed greater similarity with that of D. ambrosioides roots (12 km away), and clustered to one group in dendrogram, in clear contrast to that of V. ciliate, which grew closer to A. alpine (60 m away). Combining results of soil and plant analyses, we suggest that the soil properties, especially heavy metal concentration, may influence the plants endophytic bacterial community composition. Pot experiments showed that the strain BXGe71 (Microbacterium sp.) from A. alpine significantly enhanced host plants' growth under multi-heavy metal (HM) stress (P < .05, t-test).
[Pt] Publication type:JOURNAL ARTICLE
[Em] Entry month:1802
[Cu] Class update date: 180212
[Lr] Last revision date:180212
[St] Status:Publisher

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[PMID]: 29203652
[Au] Autor:Mateos JL; Tilmes V; Madrigal P; Severing E; Richter R; Rijkenberg CWM; Krajewski P; Coupland G
[Ad] Address:Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany.
[Ti] Title:Divergence of regulatory networks governed by the orthologous transcription factors FLC and PEP1 in Brassicaceae species.
[So] Source:Proc Natl Acad Sci U S A;114(51):E11037-E11046, 2017 Dec 19.
[Is] ISSN:1091-6490
[Cp] Country of publication:United States
[La] Language:eng
[Ab] Abstract:Genome-wide landscapes of transcription factor (TF) binding sites (BSs) diverge during evolution, conferring species-specific transcriptional patterns. The rate of divergence varies in different metazoan lineages but has not been widely studied in plants. We identified the BSs and assessed the effects on transcription of FLOWERING LOCUS C (FLC) and PERPETUAL FLOWERING 1 (PEP1), two orthologous MADS-box TFs that repress flowering and confer vernalization requirement in the Brassicaceae species and , respectively. We found that only 14% of their BSs were conserved in both species and that these contained a CArG-box that is recognized by MADS-box TFs. The CArG-box consensus at conserved BSs was extended compared with the core motif. By contrast, species-specific BSs usually lacked the CArG-box in the other species. Flowering-time genes were highly overrepresented among conserved targets, and their CArG-boxes were widely conserved among Brassicaceae species. Cold-regulated (COR) genes were also overrepresented among targets, but the cognate BSs and the identity of the regulated genes were usually different in each species. In cold, COR gene transcript levels were increased in and mutants compared with WT, and this correlated with reduced growth in Therefore, FLC orthologs regulate a set of conserved target genes mainly involved in reproductive development and were later independently recruited to modulate stress responses in different Brassicaceae lineages. Analysis of TF BSs in these lineages thus distinguishes widely conserved targets representing the core function of the TF from those that were recruited later in evolution.
[Pt] Publication type:JOURNAL ARTICLE
[Em] Entry month:1712
[Cu] Class update date: 180109
[Lr] Last revision date:180109
[St] Status:In-Data-Review
[do] DOI:10.1073/pnas.1618075114

  6 / 184 MEDLINE  
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[PMID]: 29084582
[Au] Autor:Chica C; Louis A; Roest Crollius H; Colot V; Roudier F
[Ad] Address:Institut de Biologie de l'Ecole Normale Suprieure (IBENS), Ecole Normale Suprieure, Centre National de la Recherche Scientifique (CNRS), Institut National de la Sant et de la Recherche Mdicale (INSERM), Paris, F-75005, France.
[Ti] Title:Comparative epigenomics in the Brassicaceae reveals two evolutionarily conserved modes of PRC2-mediated gene regulation.
[So] Source:Genome Biol;18(1):207, 2017 Oct 31.
[Is] ISSN:1474-760X
[Cp] Country of publication:England
[La] Language:eng
[Ab] Abstract:BACKGROUND: Polycomb Repressive Complexes 2 (PRC2) are multi-protein chromatin modifiers that are evolutionarily conserved among eukaryotes and play key roles in the regulation of gene expression, notably through the trimethylation of lysine 27 of histone H3 (H3K27me3). Although PRC2-mediated gene regulation has been studied in many organisms, few studies have explored in depth the evolutionary conservation of PRC2 targets. RESULTS: Here, we compare the H3K27me3 epigenomic profiles for the two closely related species Arabidopsis thaliana and Arabidopsis lyrata and the more distant species Arabis alpina, three Brassicaceae that diverged from each other within the past 24 million years. Using a robust set of gene orthologs present in the three species, we identify two classes of evolutionarily conserved PRC2 targets, which are characterized by either developmentally plastic or developmentally constrained H3K27me3 marking across species. Constrained H3K27me3 marking is associated with higher conservation of promoter sequence information content and higher nucleosome occupancy compared to plastic H3K27me3 marking. Moreover, gene orthologs with constrained H3K27me3 marking exhibit a higher degree of tissue specificity and tend to be involved in developmental functions, whereas gene orthologs with plastic H3K27me3 marking preferentially encode proteins associated with metabolism and stress responses. In addition, gene orthologs with constrained H3K27me3 marking are the predominant contributors to higher-order chromosome organization. CONCLUSIONS: Our findings indicate that developmentally plastic and constrained H3K27me3 marking define two evolutionarily conserved modes of PRC2-mediated gene regulation that are associated with distinct selective pressures operating at multiple scales, from DNA sequence to gene function and chromosome architecture.
[Pt] Publication type:JOURNAL ARTICLE
[Em] Entry month:1711
[Cu] Class update date: 171102
[Lr] Last revision date:171102
[St] Status:In-Process
[do] DOI:10.1186/s13059-017-1333-9

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[PMID]: 29042663
[Au] Autor:Park JY; Kim H; Lee I
[Ad] Address:Laboratory of Plant Developmental Genetics, School of Biological Sciences, Plant Genomics & Breeding Institute, Seoul National University, Seoul, 08826, Korea.
[Ti] Title:Comparative analysis of molecular and physiological traits between perennial Arabis alpina Pajares and annual Arabidopsis thaliana Sy-0.
[So] Source:Sci Rep;7(1):13348, 2017 Oct 17.
[Is] ISSN:2045-2322
[Cp] Country of publication:England
[La] Language:eng
[Ab] Abstract:Annual plants complete life cycle in a year while perennial plants maintain growth for several years. Arabis alpina, a polycarpic perennial, is a close relative of monocarpic annual Arabidopsis. Pajares is an accession of A. alpina requiring vernalization, a long-term cold for flowering. Arabidopsis shows holistic flowering whereas Pajares shows idiographic flowering, producing axillary branches under variable developmental phases from juvenile, adult vegetative to reproductive phases. To understand the molecular mechanism behind diverse phases of axillary branches, we analyzed the levels of primary miR156 expressions because miR156-SPL module is a key regulator for developmental phase transition. We found that in Pajares, miR156 levels were highly variable among the axillary branches, which causes differential sensitivity to vernalization. Thus, the axillary branches expressing high levels of miR156 remain in juvenile phase even after vernalization, whereas the axillary branches expressing low levels of miR156 produce flowers after vernalization. In contrast, every axillary branches of Arabidopsis winter annual Sy-0 expressed similar levels of miR156 and synchronously responded to vernalization, which causes holistic flowering. Therefore, we suggest that variable miR156 expression levels and the resulting differential response to vernalization among axillary branches are distinctive features determining polycarpic perenniality of A. alpina Pajares.
[Pt] Publication type:JOURNAL ARTICLE
[Em] Entry month:1710
[Cu] Class update date: 171027
[Lr] Last revision date:171027
[St] Status:In-Data-Review
[do] DOI:10.1038/s41598-017-13606-7

  8 / 184 MEDLINE  
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[PMID]: 28809950
[Au] Autor:Raman G; Park V; Kwak M; Lee B; Park S
[Ad] Address:Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongsan-buk, Republic of Korea.
[Ti] Title:Characterization of the complete chloroplast genome of Arabis stellari and comparisons with related species.
[So] Source:PLoS One;12(8):e0183197, 2017.
[Is] ISSN:1932-6203
[Cp] Country of publication:United States
[La] Language:eng
[Ab] Abstract:Arabis stellari var. japonica is an ornamental plant of the Brassicaceae family, and is widely distributed in South Korea. However, no information is available about its molecular biology and no genomic study has been performed on A. stellari. In this paper, the authors report the complete chloroplast genome sequence of A. stellari. The plastome of A. stellari was 153,683 bp in length with 36.4% GC and included a pair of inverted repeats (IRs) of 26,423 bp that separated a large single-copy (LSC) region of 82,807 bp and a small single-copy (SSC) region of 18,030 bp. It was also found to contain 113 unique genes, of which 79 were protein-coding genes, 30 were transfer RNAs, and four were ribosomal RNAs. The gene content and organization of the A. stellari chloroplast genome were similar to those of other Brassicaceae genomes except for the absence of the rps16 protein-coding gene. A total of 991 SSRs were identified in the genome. The chloroplast genome of A. stellari was compared with closely related species of the Brassicaceae family. Comparative analysis showed a minor divergence occurred in the protein-coding matK, ycf1, ccsA, accD and rpl22 genes and that the KA/KS nucleotide substitution ratio of the ndhA genes of A. stellari and A. hirsuta was 1.35135. The genes infA and rps16 were absent in the Arabis genus and phylogenetic evolutionary studies revealed that these genes evolved independently. However, phylogenetic analysis showed that the positions of Brassicaceae species are highly conserved. The present study provides A. stellari genomic information that may be found useful in conservation and molecular phylogenetic studies on Brassicaceae.
[Mh] MeSH terms primary: Arabis/genetics
Genome, Chloroplast/genetics
[Mh] MeSH terms secundary: Brassicaceae/genetics
Evolution, Molecular
RNA, Ribosomal/genetics
Republic of Korea
Sequence Analysis, DNA
[Pt] Publication type:JOURNAL ARTICLE
[Nm] Name of substance:0 (RNA, Ribosomal)
[Em] Entry month:1710
[Cu] Class update date: 171011
[Lr] Last revision date:171011
[Js] Journal subset:IM
[Da] Date of entry for processing:170816
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0183197

  9 / 184 MEDLINE  
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[PMID]: 28796912
[Au] Autor:Hemmer C; Djennane S; Ackerer L; Hleibieh K; Marmonier A; Gersch S; Garcia S; Vigne E; Komar V; Perrin M; Gertz C; Belval L; Berthold F; Monsion B; Schmitt-Keichinger C; Lemaire O; Lorber B; Gutirrez C; Muyldermans S; Demangeat G; Ritzenthaler C
[Ad] Address:Institut de biologie molculaire des plantes du CNRS, Universit de Strasbourg, Strasbourg, France.
[Ti] Title:Nanobody-mediated resistance to Grapevine fanleaf virus in plants.
[So] Source:Plant Biotechnol J;, 2017 Aug 10.
[Is] ISSN:1467-7652
[Cp] Country of publication:England
[La] Language:eng
[Ab] Abstract:Since their discovery, single-domain antigen-binding fragments of camelid-derived heavy-chain-only antibodies, also known as nanobodies (Nbs), have proven to be of outstanding interest as therapeutics against human diseases and pathogens including viruses, but their use against phytopathogens remains limited. Many plant viruses including Grapevine fanleaf virus (GFLV), a nematode-transmitted icosahedral virus and causal agent of fanleaf degenerative disease, have worldwide distribution and huge burden on crop yields representing billions of US dollars of losses annually, yet solutions to combat these viruses are often limited or inefficient. Here, we identified a Nb specific to GFLV that confers strong resistance to GFLV upon stable expression in the model plant Nicotiana benthamiana and also in grapevine rootstock, the natural host of the virus. We showed that resistance was effective against a broad range of GFLV isolates independently of the inoculation method including upon nematode transmission but not against its close relative, Arabis mosaic virus. We also demonstrated that virus neutralization occurs at an early step of the virus life cycle, prior to cell-to-cell movement. Our findings will not only be instrumental to confer resistance to GFLV in grapevine, but more generally they pave the way for the generation of novel antiviral strategies in plants based on Nbs.
[Pt] Publication type:JOURNAL ARTICLE
[Em] Entry month:1708
[Cu] Class update date: 171007
[Lr] Last revision date:171007
[St] Status:Publisher
[do] DOI:10.1111/pbi.12819

  10 / 184 MEDLINE  
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[PMID]: 28722132
[Au] Autor:Torng P; Vikstrm L; Wunder J; Wtzel S; Coupland G; gren J
[Ad] Address:Department of Plant Ecology and Evolution, Evolutionary Biology Centre, Uppsala University, Norbyvgen 18D, SE-752 36, Uppsala, Sweden.
[Ti] Title:Evolution of the selfing syndrome: Anther orientation and herkogamy together determine reproductive assurance in a self-compatible plant.
[So] Source:Evolution;71(9):2206-2218, 2017 Sep.
[Is] ISSN:1558-5646
[Cp] Country of publication:United States
[La] Language:eng
[Ab] Abstract:Capacity for autonomous self-fertilization provides reproductive assurance, has evolved repeatedly in the plant kingdom, and typically involves several changes in flower morphology and development (the selfing syndrome). Yet, the relative importance of different traits and trait combinations for efficient selfing and reproductive success in pollinator-poor environments is poorly known. In a series of experiments, we tested the importance of anther-stigma distance and the less studied trait anther orientation for efficiency of selfing in the perennial herb Arabis alpina. Variation in flower morphology among eight self-compatible European populations was correlated with efficiency of self-pollination and with pollen limitation in a common-garden experiment. To examine whether anther-stigma distance and anther orientation are subject to directional and/or correlational selection, and whether this is because these traits affect pollination success, we planted a segregating F2 population at two native field sites. Selection strongly favored a combination of introrse anthers and reduced anther-stigma distance at a site where pollinator activity was low, and supplemental hand-pollination demonstrated that this was largely because of their effect on securing self-pollination. The results suggest that concurrent shifts in more than one trait can be crucial for the evolution of efficient self-pollination and reproductive assurance in pollinator-poor habitats.
[Pt] Publication type:JOURNAL ARTICLE
[Em] Entry month:1707
[Cu] Class update date: 170907
[Lr] Last revision date:170907
[St] Status:In-Process
[do] DOI:10.1111/evo.13308


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