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[PMID]:29202710
[Au] Autor:Parvathaneni RK; DeLeo VL; Spiekerman JJ; Chakraborty D; Devos KM
[Ad] Endereço:Institute of Plant Breeding, Genetics and Genomics, University of Georgia, 30602, Athens, Georgia, United States.
[Ti] Título:Parallel loss of introns in the ABCB1 gene in angiosperms.
[So] Source:BMC Evol Biol;17(1):238, 2017 Dec 04.
[Is] ISSN:1471-2148
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: The presence of non-coding introns is a characteristic feature of most eukaryotic genes. While the size of the introns, number of introns per gene and the number of intron-containing genes can vary greatly between sequenced eukaryotic genomes, the structure of a gene with reference to intron presence and positions is typically conserved in closely related species. Unexpectedly, the ABCB1 (ATP-Binding Cassette Subfamily B Member 1) gene which encodes a P-glycoprotein and underlies dwarfing traits in maize (br2), sorghum (dw3) and pearl millet (d2) displayed considerable variation in intron composition. RESULTS: An analysis of the ABCB1 gene structure in 80 angiosperms revealed that the number of introns ranged from one to nine. All introns in ABCB1 underwent either a one-time loss (single loss in one lineage/species) or multiple independent losses (parallel loss in two or more lineages/species) with the majority of losses occurring within the grass family. In contrast, the structure of the closest homolog to ABCB1, ABCB19, remained constant in the majority of angiosperms analyzed. Using known phylogenetic relationships within the grasses, we determined the ancestral branch-points where the losses occurred. Intron 7, the longest intron, was lost in only a single species, Mimulus guttatus, following duplication of ABCB1. Semiquantitative PCR showed that the M. guttatus ABCB1 gene copy without intron 7 had significantly lower transcript levels than the gene copy with intron 7. We further demonstrated that intron 7 carried two motifs that were highly conserved across the monocot-dicot divide. CONCLUSIONS: The ABCB1 gene structure is highly dynamic, while the structure of ABCB19 remained largely conserved through evolution. Precise removal of introns, preferential removal of smaller introns and presence of at least 2 bp of microhomology flanking most introns indicated that intron loss may have predominantly occurred through non-homologous end-joining (NHEJ) repair of double strand breaks. Lack of microhomology in the exon upstream of lost phase I introns was likely due to release of the selective constraint on the penultimate base (3rd base in codon) of the terminal codon by the splicing machinery. In addition to size, the presence of regulatory motifs will make introns recalcitrant to loss.
[Mh] Termos MeSH primário: Genes de Plantas
Íntrons/genética
Magnoliopsida/genética
Proteínas de Plantas/genética
[Mh] Termos MeSH secundário: Arabidopsis/genética
Sequência de Bases
Sequência Conservada/genética
DNA Complementar/genética
Evolução Molecular
Regulação da Expressão Gênica de Plantas
Mimulus/genética
Motivos de Nucleotídeos/genética
Oryza/genética
Filogenia
Reação em Cadeia da Polimerase
Polimorfismo Genético
RNA Mensageiro/genética
RNA Mensageiro/metabolismo
Reprodutibilidade dos Testes
Análise de Sequência de DNA
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (DNA, Complementary); 0 (Plant Proteins); 0 (RNA, Messenger)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180309
[Lr] Data última revisão:
180309
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171206
[St] Status:MEDLINE
[do] DOI:10.1186/s12862-017-1077-x


  2 / 8530 MEDLINE  
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[PMID]:28923723
[Au] Autor:Borah R; Kumari D; Gogoi A; Biswas S; Goswami R; Shim J; Begum NA; Kumar M
[Ad] Endereço:Department of Environmental Science, Tezpur University, Napaam 784028, Assam, India.
[Ti] Título:Efficacy and field applicability of Burmese grape leaf extract (BGLE) for cadmium removal: An implication of metal removal from natural water.
[So] Source:Ecotoxicol Environ Saf;147:585-593, 2018 Jan.
[Is] ISSN:1090-2414
[Cp] País de publicação:Netherlands
[La] Idioma:eng
[Ab] Resumo:Burmese Grape Leaf Extract (BGLE), a low cost adsorbent was studied for cadmium (Cd(II)) removal from metal solutions and natural water samples. Batch adsorption studies were carried out to examine the influence of contact time and initial metal concentration after characterization under scanning electron microscopy (SEM). Cd(II)adsorptiononto BGLE was best explained by pseudo-second order kinetics (R = 0.99) and best fitted with Langmuir isotherm model (R = 0.76). Beside the selective adsorption activity of BGLE towards Cd(II), only 0.1g of BGLE have shown effective adsorption of these ions with a maximum adsorption capacity (q ) of 44.72mgg . This study was a unique combination of laboratory experiments and field implication. Study indicates that same efficacy cannot be obtained in natural water samples as obtained in the case of laboratory due to the interference of major ions in water.
[Mh] Termos MeSH primário: Cádmio/análise
Magnoliopsida/química
Extratos Vegetais/química
Folhas de Planta/química
Poluentes Químicos da Água/análise
Purificação da Água/métodos
[Mh] Termos MeSH secundário: Adsorção
Concentração de Íons de Hidrogênio
Íons
Cinética
Modelos Teóricos
Soluções
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Ions); 0 (Plant Extracts); 0 (Solutions); 0 (Water Pollutants, Chemical); 00BH33GNGH (Cadmium)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180223
[Lr] Data última revisão:
180223
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170920
[St] Status:MEDLINE


  3 / 8530 MEDLINE  
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[PMID]:29233877
[Au] Autor:Batoko H; Dagdas Y; Baluska F; Sirko A
[Ad] Endereço:Université catholique de Louvain, Institut des Sciences de la Vie, Croix du Sud 4, L7.07.14, 1348 Louvain-la-Neuve, Belgium Henri.batoko@uclouvain.be.
[Ti] Título:Understanding and exploiting autophagy signaling in plants.
[So] Source:Essays Biochem;61(6):675-685, 2017 12 12.
[Is] ISSN:1744-1358
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Autophagy is an essential catabolic pathway and is activated by various endogenous and exogenous stimuli. In particular, autophagy is required to allow sessile organisms such as plants to cope with biotic or abiotic stress conditions. It is thought that these various environmental signaling pathways are somehow integrated with autophagy signaling. However, the molecular mechanisms of plant autophagy signaling are not well understood, leaving a big gap of knowledge as a barrier to being able to manipulate this important pathway to improve plant growth and development. In this review, we discuss possible regulatory mechanisms at the core of plant autophagy signaling.
[Mh] Termos MeSH primário: Autofagia/fisiologia
Magnoliopsida/metabolismo
Plantas/metabolismo
[Mh] Termos MeSH secundário: Autofagia/genética
Magnoliopsida/genética
Plantas/genética
Transdução de Sinais/genética
Transdução de Sinais/fisiologia
[Pt] Tipo de publicação:JOURNAL ARTICLE; REVIEW; RESEARCH SUPPORT, NON-U.S. GOV'T
[Em] Mês de entrada:1801
[Cu] Atualização por classe:180220
[Lr] Data última revisão:
180220
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171214
[St] Status:MEDLINE
[do] DOI:10.1042/EBC20170034


  4 / 8530 MEDLINE  
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[PMID]:29293597
[Au] Autor:Silva SR; Michael TP; Meer EJ; Pinheiro DG; Varani AM; Miranda VFO
[Ad] Endereço:Universidade Estadual Paulista (Unesp), Botucatu, Instituto de Biociências, São Paulo, Brazil.
[Ti] Título:Comparative genomic analysis of Genlisea (corkscrew plants-Lentibulariaceae) chloroplast genomes reveals an increasing loss of the ndh genes.
[So] Source:PLoS One;13(1):e0190321, 2018.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:In the carnivorous plant family Lentibulariaceae, all three genome compartments (nuclear, chloroplast, and mitochondria) have some of the highest rates of nucleotide substitutions across angiosperms. While the genera Genlisea and Utricularia have the smallest known flowering plant nuclear genomes, the chloroplast genomes (cpDNA) are mostly structurally conserved except for deletion and/or pseudogenization of the NAD(P)H-dehydrogenase complex (ndh) genes known to be involved in stress conditions of low light or CO2 concentrations. In order to determine how the cpDNA are changing, and to better understand the evolutionary history within the Genlisea genus, we sequenced, assembled and analyzed complete cpDNA from six species (G. aurea, G. filiformis, G. pygmaea, G. repens, G. tuberosa and G. violacea) together with the publicly available G. margaretae cpDNA. In general, the cpDNA structure among the analyzed Genlisea species is highly similar. However, we found that the plastidial ndh genes underwent a progressive process of degradation similar to the other terrestrial Lentibulariaceae cpDNA analyzed to date, but in contrast to the aquatic species. Contrary to current thinking that the terrestrial environment is a more stressful environment and thus requiring the ndh genes, we provide evidence that in the Lentibulariaceae the terrestrial forms have progressive loss while the aquatic forms have the eleven plastidial ndh genes intact. Therefore, the Lentibulariaceae system provides an important opportunity to understand the evolutionary forces that govern the transition to an aquatic environment and may provide insight into how plants manage water stress at a genome scale.
[Mh] Termos MeSH primário: Cloroplastos/genética
Genoma de Cloroplastos
Magnoliopsida/genética
NADPH Desidrogenase/genética
[Mh] Termos MeSH secundário: Magnoliopsida/classificação
Filogenia
[Pt] Tipo de publicação:COMPARATIVE STUDY; JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
EC 1.6.99.1 (NADPH Dehydrogenase)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180215
[Lr] Data última revisão:
180215
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180103
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0190321


  5 / 8530 MEDLINE  
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[PMID]:29270891
[Au] Autor:Rather GA; Sharma A; Pandith SA; Kaul V; Nandi U; Misra P; Lattoo SK
[Ad] Endereço:Plant Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, 180001, India.
[Ti] Título:De novo transcriptome analyses reveals putative pathway genes involved in biosynthesis and regulation of camptothecin in Nothapodytes nimmoniana (Graham) Mabb.
[So] Source:Plant Mol Biol;96(1-2):197-215, 2018 Jan.
[Is] ISSN:1573-5028
[Cp] País de publicação:Netherlands
[La] Idioma:eng
[Ab] Resumo:KEY MESSAGE: Comprehensive transcriptome analysis of leaf and root tissues of Nothapodytes nimmoniana unravels several putative pathway genes, transcription factors and CYPs related to camptothecin (CPT) biosynthesis. Additionally, post-transcriptional suppression by artificial microRNA (aMIR) of NnCYP76B6 (geraniol 10-hydroxylase) suggests its role in CPT biosynthesis. Tissue-specific LC-MS/MS analysis revealed the presence of secologanin as the central intermediate of MIA pathway in N. nimmoniana. Nothapodytes nimmoniana is a rich source of potent anticancer drug camptothecin (CPT) whose biosynthetic pathway is unresolved due to the lack of genomic and transcriptomic information. Present investigation entails deep transcriptome analysis of N. nimmoniana which led to identification of putative pathway genes and regulatory components involved in CPT biosynthesis. Using Illumina HiSeq 2500 sequencing platform a total of 31,172,889 (6.23 Gb) and 31,218,626 (6.24 Gb) raw reads were generated from leaf and root wood, respectively. These were assembled de novo into 138,183 unique contigs. Additionally, 16 cytochrome P450 transcripts related to secondary metabolism were also identified. Further, transcriptome data pool presented 1683 putative transcription factors of which transcripts corresponding to WRKY TFs were the most abundant (14.14%). A total of 2741 transcripts were differentially expressed out of which 478 contigs showed downregulation in root wood and 2263 contigs were up-regulated. Further, comparative analyses of 17 genes involved in CPT biosynthetic pathway were validated by qRT-PCR. On basis of intermediates, two distinct seco-iridoid pathways are involved in the biosynthesis of monoterpene indole alkaloids either through multiple isomers of strictosidinic acid or strictosidine. Tissue-specific LC-MS/MS analysis revealed the presence of secologanin as the central intermediate of MIA pathway in N. nimmoniana. Geraniol-10 hydroxylase (NnCYP76B6) an important enzyme in CPT biosynthesis which specifically shunts geraniol into the secologanin pathway was also cloned from the trancriptome resource. In planta transient expression of NnCYP76B6 showed a significant enhancement in mRNA transcript levels coincident with enhanced CPT accumulation. Further, artificial microRNA (aMIR) mediated downregulation of NnCYP76B6 resulted in reduction of mRNA transcript levels as well as CPT content in comparison to control. These empirical results suggest a plausible regulatory role for NnCYP76B6 in CPT biosynthesis and also establish a valuable repository for deciphering various structural, rate limiting and regulatory genes of CPT biosynthetic pathway.
[Mh] Termos MeSH primário: Camptotecina/metabolismo
Magnoliopsida/metabolismo
Transcriptoma/genética
[Mh] Termos MeSH secundário: Sistema Enzimático do Citocromo P-450/genética
Sistema Enzimático do Citocromo P-450/metabolismo
Perfilação da Expressão Gênica
Magnoliopsida/genética
MicroRNAs/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (MicroRNAs); 9035-51-2 (Cytochrome P-450 Enzyme System); EC 1.14.- (geraniol 10-hydroxylase); XT3Z54Z28A (Camptothecin)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180212
[Lr] Data última revisão:
180212
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171223
[St] Status:MEDLINE
[do] DOI:10.1007/s11103-017-0690-9


  6 / 8530 MEDLINE  
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[PMID]:29247025
[Au] Autor:Bukhari G; Zhang J; Stevens PF; Zhang W
[Ad] Endereço:Department of Biology, Virginia Commonwealth University, 1000 West Cary Street, Richmond, Virginia 23284 USA.
[Ti] Título:Evolution of the process underlying floral zygomorphy development in pentapetalous angiosperms.
[So] Source:Am J Bot;104(12):1846-1856, 2017 Dec.
[Is] ISSN:1537-2197
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:PREMISE OF THE STUDY: Observations of floral ontogeny indicated that floral organ initiation in pentapetalous flowers most commonly results in a median-abaxial (MAB) petal during early development, a median-adaxial (MAD) petal being less common. Such different patterns of floral organ initiation might be linked with different morphologies of floral zygomorphy that have evolved in Asteridae. Here, we provide the first study of zygomorphy in pentapetalous angiosperms placed in a phylogenetic framework, the goal being to find if the different patterns of floral organ initiation are connected with particular patterns of zygomorphy. METHODS: We analyzed patterns of floral organ initiation and displays of zygomorphy, extracted from floral diagrams representing 405 taxa in 330 genera, covering 83% of orders (30 out of 36) and 37% of families (116 out of 313) in core eudicots in the context of a phylogeny using ancestral state reconstructions. KEY RESULTS: The MAB petal initiation is the ancestral state of the pattern of floral organ initiation in pentapetalous angiosperms. Taxa with MAD petal initiation represent ∼30 independent origins from the ancestral MAB initiation. There are distinct developmental processes that give rise to zygomorphy in different lineages of pentapetalous angiosperms, closely related lineages being likely to share similar developmental processes. CONCLUSIONS: We have demonstrated that development indeed constrains the processes that give rise to floral zygomorphy, while phylogenetic distance allows relaxation of these constraints, which provides novel insights on the role that development plays in the evolution of floral zygomorphy.
[Mh] Termos MeSH primário: Evolução Biológica
Flores/crescimento & desenvolvimento
Magnoliopsida/genética
Magnoliopsida/fisiologia
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180207
[Lr] Data última revisão:
180207
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171217
[St] Status:MEDLINE
[do] DOI:10.3732/ajb.1700229


  7 / 8530 MEDLINE  
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[PMID]:29217673
[Au] Autor:Prieu C; Sauquet H; Gouyon PH; Albert B
[Ad] Endereço:Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay 91405 Orsay cedex, France prieu@mnhn.fr.
[Ti] Título:More than sixty origins of pantoporate pollen in angiosperms.
[So] Source:Am J Bot;104(12):1837-1845, 2017 Dec.
[Is] ISSN:1537-2197
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:PREMISE OF THE STUDY: Apertures in pollen grains are key structures of the wall, involved in pollen tube germination and exchanges with the environment. Aperture types in angiosperms are diverse, but pollen with one and three apertures (including monosulcate and tricolpate, respectively) are the two most common types. Here, we investigate the phylogenetic distribution in angiosperms of pollen with many round, scattered apertures called pantoporate pollen. METHODS: We constructed a morphological data set with species producing pantoporate pollen and representative angiosperm species with other pollen types, sampled from every angiosperm order, with a total of 1260 species distributed in 330 families. This data set was analyzed with parsimony to characterize the phylogenetic distribution of pantoporate pollen in angiosperms. KEY RESULTS: We show that pantoporate pollen is distributed throughout most of the angiosperm tree, including early diverging angiosperms, monocots, and eudicots. However, this pollen type is usually restricted to a few species in a given group, and is seldom fixed at large taxonomical scales, with a few notable exceptions. CONCLUSIONS: Pantoporate pollen evolved many times during angiosperm history, but the persistence of this morphology in the long term is infrequent. This distribution pattern could indicate conflicting short-term and long-term selective pressures, pantoporate pollen being selected in the short run, but eliminated in the long run. Biological hypotheses supporting this scenario are discussed, in the context of both theoretical and empirical data on pollen biology.
[Mh] Termos MeSH primário: Evolução Biológica
Magnoliopsida/genética
Magnoliopsida/fisiologia
Modelos Genéticos
Pólen/citologia
Pólen/genética
[Mh] Termos MeSH secundário: Pólen/fisiologia
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180207
[Lr] Data última revisão:
180207
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171209
[St] Status:MEDLINE
[do] DOI:10.3732/ajb.1700289


  8 / 8530 MEDLINE  
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[PMID]:29224354
[Au] Autor:Liang N; Cai P; Wu D; Pan Y; Curtis JM; Gänzle MG
[Ad] Endereço:Department of Agricultural, Food and Nutritional Science, University of Alberta , Edmonton T6G 2R3, Canada.
[Ti] Título:High-Speed Counter-Current Chromatography (HSCCC) Purification of Antifungal Hydroxy Unsaturated Fatty Acids from Plant-Seed Oil and Lactobacillus Cultures.
[So] Source:J Agric Food Chem;65(51):11229-11236, 2017 Dec 27.
[Is] ISSN:1520-5118
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Hydroxy unsaturated fatty acids (HUFA) can function as antifungal agents. To investigate the antifungal spectrum, that is, the scope of the in vitro fungal-inhibition activities of HUFA and their potential applications, three HUFA were produced by microbial transformation or extracted from plant-seed oils; these compounds included coriolic acid (13-hydroxy-9,11-octadecadienoic acid) from Coriaria seed oil, 10-hydroxy-12-octadecenoic acid from cultures of Lactobacillus hammesii, and 13-hydroxy-9-octadecenoic acid from cultures of Lactobacillus plantarum TMW1.460Δlah. HUFA were purified by high-speed counter-current chromatography (HSCCC), characterized by LC-MS and MS/MS, and their antifungal activities were evaluated with 15 indicator fungal strains. The HUFA had different antifungal spectra when compared with unsaturated fatty acids with comparable structures but without hydroxy groups. The inhibitory effects of HUFA specifically targeted filamentous fungi, including Aspergillus niger and Penicillium roqueforti, whereas yeasts, including Candida spp. and Saccharomyces spp., were resistant to HUFA. The findings here support the development of food applications for antifungal HUFA.
[Mh] Termos MeSH primário: Antifúngicos/isolamento & purificação
Ácidos Graxos Insaturados/farmacologia
Lactobacillus/química
Magnoliopsida/química
Óleos Vegetais/isolamento & purificação
Sementes/química
[Mh] Termos MeSH secundário: Antifúngicos/química
Antifúngicos/farmacologia
Distribuição Contracorrente
Ácidos Graxos Insaturados/química
Ácidos Graxos Insaturados/isolamento & purificação
Fungos/efeitos dos fármacos
Lactobacillus plantarum/química
Testes de Sensibilidade Microbiana
Óleos Vegetais/química
Óleos Vegetais/farmacologia
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Antifungal Agents); 0 (Fatty Acids, Unsaturated); 0 (Plant Oils)
[Em] Mês de entrada:1801
[Cu] Atualização por classe:180108
[Lr] Data última revisão:
180108
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171212
[St] Status:MEDLINE
[do] DOI:10.1021/acs.jafc.7b05658


  9 / 8530 MEDLINE  
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[PMID]:29244846
[Au] Autor:Alvarez-Quinto RA; Cornejo-Franco JF; Quito-Avila DF
[Ad] Endereço:Centro de Investigaciones Biotecnológicas del Ecuador, CIBE, Escuela Superior Politécnica del Litoral, ESPOL, Guayaquil, Ecuador.
[Ti] Título:Characterization of a not so new potexvirus from babaco (Vasconcellea x heilbornii).
[So] Source:PLoS One;12(12):e0189519, 2017.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:A new member of the genus Potexvirus was fully sequenced and characterized. The virus was isolated from babaco (Vasconcellea x heilbornii), a natural hybrid native to Ecuador. The virus contains a 6,692 nt long genome organized in five open reading frames in an arrangement typical of other potexviruses. Sequence comparisons revealed close relatedness with Papaya mosaic virus (PapMV), Alternathera mosaic virus (AltMV) and Senna mosaic virus (SenMV), exhibiting nucleotide identities up to 67% for the polymerase (Pol) and 68% for the coat protein (CP), with deduced amino acid identities of 70% and 72% for the Pol and CP, respectively. The presence of an AlkB domain, in the polymerase region, was observed. Terminal nucleotide sequences were conserved across potexviruses with characteristic motifs and predicted secondary structures at the 3' UTR. Although serologically undistinguishable from PapMV and AltMV, the new virus showed differences in host range and symptom induction. The name babaco mosaic virus is proposed for this newly characterized Potexvirus. The complete genome sequence of the new virus has been deposited in NCBI GenBank under accession number MF978248.
[Mh] Termos MeSH primário: Magnoliopsida/virologia
Potexvirus/genética
[Mh] Termos MeSH secundário: Genes Virais
Especificidade de Hospedeiro
Filogenia
Potexvirus/isolamento & purificação
Análise de Sequência de DNA
Proteínas Virais/genética
Tropismo Viral
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Viral Proteins)
[Em] Mês de entrada:1801
[Cu] Atualização por classe:180105
[Lr] Data última revisão:
180105
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171216
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0189519


  10 / 8530 MEDLINE  
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[PMID]:28460034
[Au] Autor:Li Z; De La Torre AR; Sterck L; Cánovas FM; Avila C; Merino I; Cabezas JA; Cervera MT; Ingvarsson PK; Van de Peer Y
[Ad] Endereço:Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
[Ti] Título:Single-Copy Genes as Molecular Markers for Phylogenomic Studies in Seed Plants.
[So] Source:Genome Biol Evol;9(5):1130-1147, 2017 05 01.
[Is] ISSN:1759-6653
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Phylogenetic relationships among seed plant taxa, especially within the gymnosperms, remain contested. In contrast to angiosperms, for which several genomic, transcriptomic and phylogenetic resources are available, there are few, if any, molecular markers that allow broad comparisons among gymnosperm species. With few gymnosperm genomes available, recently obtained transcriptomes in gymnosperms are a great addition to identifying single-copy gene families as molecular markers for phylogenomic analysis in seed plants. Taking advantage of an increasing number of available genomes and transcriptomes, we identified single-copy genes in a broad collection of seed plants and used these to infer phylogenetic relationships between major seed plant taxa. This study aims at extending the current phylogenetic toolkit for seed plants, assessing its ability for resolving seed plant phylogeny, and discussing potential factors affecting phylogenetic reconstruction. In total, we identified 3,072 single-copy genes in 31 gymnosperms and 2,156 single-copy genes in 34 angiosperms. All studied seed plants shared 1,469 single-copy genes, which are generally involved in functions like DNA metabolism, cell cycle, and photosynthesis. A selected set of 106 single-copy genes provided good resolution for the seed plant phylogeny except for gnetophytes. Although some of our analyses support a sister relationship between gnetophytes and other gymnosperms, phylogenetic trees from concatenated alignments without 3rd codon positions and amino acid alignments under the CAT + GTR model, support gnetophytes as a sister group to Pinaceae. Our phylogenomic analyses demonstrate that, in general, single-copy genes can uncover both recent and deep divergences of seed plant phylogeny.
[Mh] Termos MeSH primário: Cycadopsida/genética
Magnoliopsida/genética
[Mh] Termos MeSH secundário: Evolução Biológica
Cycadopsida/classificação
Genes de Plantas
Magnoliopsida/classificação
Filogenia
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171206
[Lr] Data última revisão:
171206
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170502
[St] Status:MEDLINE
[do] DOI:10.1093/gbe/evx070



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