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1.
Cell Mol Life Sci ; 2019 Jun 27.
Artigo em Inglês | MEDLINE | ID: mdl-31250033

RESUMO

Oxidative stress can lead to plant growth retardation, yield loss, and death. The atr7 mutant of Arabidopsis thaliana exhibits pronounced tolerance to oxidative stress. Using positional cloning, confirmed by knockout and RNA interference (RNAi) lines, we identified the atr7 mutation and revealed that ATR7 is a previously uncharacterized gene with orthologs in other seed plants but with no homology to genes in lower plants, fungi or animals. Expression of ATR7-GFP fusion shows that ATR7 is a nuclear-localized protein. RNA-seq analysis reveals that transcript levels of genes encoding abiotic- and oxidative stress-related transcription factors (DREB19, HSFA2, ZAT10), chromatin remodelers (CHR34), and unknown or uncharacterized proteins (AT5G59390, AT1G30170, AT1G21520) are elevated in atr7. This indicates that atr7 is primed for an upcoming oxidative stress via pathways involving genes of unknown functions. Collectively, the data reveal ATR7 as a novel seed plants-specific nuclear regulator of oxidative stress response.

2.
Plant Physiol ; 180(1): 185-197, 2019 05.
Artigo em Inglês | MEDLINE | ID: mdl-30837347

RESUMO

Thiamin pyrophosphate (TPP) is the active form of vitamin B1 and works as an essential cofactor for enzymes in key metabolic pathways, such as the tricarboxylic acid (TCA) cycle and the pentose phosphate pathway. Although its action as a coenzyme has been well documented, the roles of TPP in plant metabolism are still not fully understood. Here, we investigated the functions of TPP in the regulation of the metabolic networks during photoperiod transition using previously described Arabidopsis (Arabidopsis thaliana) riboswitch mutant plants, which accumulate thiamin vitamers. The results show that photosynthetic and metabolic phenotypes of TPP riboswitch mutants are photoperiod dependent. Additionally, the mutants are more distinct from control plants when plants are transferred from a short-day to a long-day photoperiod, suggesting that TPP also plays a role in metabolic acclimation to the photoperiod. Control plants showed changes in the amplitude of diurnal oscillation in the levels of metabolites, including glycine, maltose, and fumarate, following the photoperiod transition. Interestingly, many of these changes are not present in TPP riboswitch mutant plants, demonstrating their lack of metabolic flexibility. Our results also indicate a close relationship between photorespiration and the TCA cycle, as TPP riboswitch mutants accumulate less photorespiratory intermediates. This study shows the potential role of vitamin B1 in the diurnal regulation of central carbon metabolism in plants and the importance of maintaining appropriate cellular levels of thiamin vitamers for the plant's metabolic flexibility and ability to acclimate to an altered photoperiod.

3.
Plant Reprod ; 32(1): 15-27, 2019 03.
Artigo em Inglês | MEDLINE | ID: mdl-30707279

RESUMO

KEY MESSAGE: A protocol for the isolation of egg apparatus cells from the basal angiosperm Amborella trichopoda to generate RNA-seq data for evolutionary studies of fertilization-associated genes. Sexual reproduction is particularly complex in flowering plants (angiosperms). Studies in eudicot and monocot model species have significantly contributed to our knowledge on cell fate specification of gametophytic cells and on the numerous cellular communication events necessary to deliver the two sperm cells into the embryo sac and to accomplish double fertilization. However, for a deeper understanding of the evolution of these processes, morphological, genomic and gene expression studies in extant basal angiosperms are inevitable. The basal angiosperm Amborella trichopoda is of special importance for evolutionary studies, as it is likely sister to all other living angiosperms. Here, we report about a method to isolate Amborella egg apparatus cells and on genome-wide gene expression profiles in these cells. Our transcriptomics data revealed Amborella-specific genes and genes conserved in eudicots and monocots. Gene products include secreted proteins, such as small cysteine-rich proteins previously reported to act as extracellular signaling molecules with important roles during double fertilization. The detection of transcripts encoding EGG CELL 1 (EC1) and related prolamin-like family proteins in Amborella egg cells demonstrates the potential of the generated data set to study conserved molecular mechanisms and the evolution of fertilization-related genes and their encoded proteins.


Assuntos
Separação Celular/métodos , Genoma de Planta , Magnoliopsida/citologia , Magnoliopsida/genética , Óvulo Vegetal/genética , Óvulo Vegetal/citologia , RNA de Plantas , Transcriptoma
4.
Nat Commun ; 10(1): 737, 2019 02 13.
Artigo em Inglês | MEDLINE | ID: mdl-30760717

RESUMO

Plants have adapted to the diurnal light-dark cycle by establishing elaborate transcriptional programs that coordinate many metabolic, physiological, and developmental responses to the external environment. These transcriptional programs have been studied in only a few species, and their function and conservation across algae and plants is currently unknown. We performed a comparative transcriptome analysis of the diurnal cycle of nine members of Archaeplastida, and we observed that, despite large phylogenetic distances and dramatic differences in morphology and lifestyle, diurnal transcriptional programs of these organisms are similar. Expression of genes related to cell division and the majority of biological pathways depends on the time of day in unicellular algae but we did not observe such patterns at the tissue level in multicellular land plants. Hence, our study provides evidence for the universality of diurnal gene expression and elucidates its evolutionary history among different photosynthetic eukaryotes.


Assuntos
Ritmo Circadiano , Eucariotos/genética , Evolução Molecular , Perfilação da Expressão Gênica/métodos , Transcriptoma/genética , Clorófitas/genética , Embriófitas/genética , Eucariotos/classificação , Fotossíntese/genética , Filogenia , Rodófitas/genética
5.
Plant Reprod ; 32(2): 229, 2019 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-30805714

RESUMO

The article Transcriptomics of manually isolated Amborella trichopoda egg apparatus cells, written by María Flores-Tornero, Sebastian Proost, Marek Mutwil, Charles P. Scutt, Thomas Dresselhaus, Stefanie Sprunck, was originally published electronically on the publisher's internet portal (currently SpringerLink) on 1 February 2019 without open access.

6.
Plant J ; 97(6): 1132-1153, 2019 03.
Artigo em Inglês | MEDLINE | ID: mdl-30480348

RESUMO

Common bean (Phaseolus vulgaris L.) is an important legume species with a rich natural diversity of landraces that originated from the wild forms following multiple independent domestication events. After the publication of its genome, several resources for this relevant crop have been made available. A comprehensive characterization of specialized metabolism in P. vulgaris, however, is still lacking. In this study, we used a metabolomics approach based on liquid chromatography-mass spectrometry to dissect the chemical composition at a tissue-specific level in several accessions of common bean belonging to different gene pools. Using a combination of literature search, mass spectral interpretation, 13 C-labeling, and correlation analyses, we were able to assign chemical classes and/or putative structures for approximately 39% of all measured metabolites. Additionally, we integrated this information with transcriptomics data and phylogenetic inference from multiple legume species to reconstruct the possible metabolic pathways and identify sets of candidate genes involved in the biosynthesis of specialized metabolites. A particular focus was given to flavonoids, triterpenoid saponins and hydroxycinnamates, as they represent metabolites involved in important ecological interactions and they are also associated with several health-promoting benefits when integrated into the human diet. The data are presented here in the form of an accessible resource that we hope will set grounds for further studies on specialized metabolism in legumes.

7.
Plant J ; 96(2): 404-420, 2018 10.
Artigo em Inglês | MEDLINE | ID: mdl-30044525

RESUMO

Plastid ribosomes are very similar in structure and function to the ribosomes of their bacterial ancestors. Since ribosome biogenesis is not thermodynamically favorable under biological conditions it requires the activity of many assembly factors. Here we have characterized a homolog of bacterial RsgA in Arabidopsis thaliana and show that it can complement the bacterial homolog. Functional characterization of a strong mutant in Arabidopsis revealed that the protein is essential for plant viability, while a weak mutant produced dwarf, chlorotic plants that incorporated immature pre-16S ribosomal RNA into translating ribosomes. Physiological analysis of the mutant plants revealed smaller, but more numerous, chloroplasts in the mesophyll cells, reduction of chlorophyll a and b, depletion of proplastids from the rib meristem and decreased photosynthetic electron transport rate and efficiency. Comparative RNA sequencing and proteomic analysis of the weak mutant and wild-type plants revealed that various biotic stress-related, transcriptional regulation and post-transcriptional modification pathways were repressed in the mutant. Intriguingly, while nuclear- and chloroplast-encoded photosynthesis-related proteins were less abundant in the mutant, the corresponding transcripts were increased, suggesting an elaborate compensatory mechanism, potentially via differentially active retrograde signaling pathways. To conclude, this study reveals a chloroplast ribosome assembly factor and outlines the transcriptomic and proteomic responses of the compensatory mechanism activated during decreased chloroplast function.


Assuntos
Proteínas de Arabidopsis/metabolismo , Arabidopsis/genética , GTP Fosfo-Hidrolases/metabolismo , Ribossomos/metabolismo , Arabidopsis/metabolismo , Proteínas de Arabidopsis/genética , Clorofila/metabolismo , Cloroplastos/metabolismo , GTP Fosfo-Hidrolases/genética , Perfilação da Expressão Gênica , Fotossíntese , Proteômica , Ribossomos/genética
8.
Nucleic Acids Res ; 46(W1): W76-W83, 2018 07 02.
Artigo em Inglês | MEDLINE | ID: mdl-29718316

RESUMO

Phytoplankton consists of autotrophic, photosynthesizing microorganisms that are a crucial component of freshwater and ocean ecosystems. However, despite being the major primary producers of organic compounds, accounting for half of the photosynthetic activity worldwide and serving as the entry point to the food chain, functions of most of the genes of the model phytoplankton organisms remain unknown. To remedy this, we have gathered publicly available expression data for one chlorophyte, one rhodophyte, one haptophyte, two heterokonts and four cyanobacteria and integrated it into our PlaNet (Plant Networks) database, which now allows mining gene expression profiles and identification of co-expressed genes of 19 species. We exemplify how the co-expressed gene networks can be used to reveal functionally related genes and how the comparative features of PhytoNet allow detection of conserved transcriptional programs between cyanobacteria, green algae, and land plants. Additionally, we illustrate how the database allows detection of duplicated transcriptional programs within an organism, as exemplified by two putative DNA repair programs within Chlamydomonas reinhardtii. PhytoNet is available from www.gene2function.de.


Assuntos
Embriófitas/genética , Internet , Fitoplâncton/genética , Software , Cianobactérias/genética , Bases de Dados Genéticas , Embriófitas/fisiologia , Regulação da Expressão Gênica de Plantas/genética , Redes Reguladoras de Genes/genética , Fotossíntese/genética , Fitoplâncton/fisiologia , Transcriptoma
9.
Nucleic Acids Res ; 46(W1): W133-W140, 2018 07 02.
Artigo em Inglês | MEDLINE | ID: mdl-29718322

RESUMO

The recent accumulation of gene expression data in the form of RNA sequencing creates unprecedented opportunities to study gene regulation and function. Furthermore, comparative analysis of the expression data from multiple species can elucidate which functional gene modules are conserved across species, allowing the study of the evolution of these modules. However, performing such comparative analyses on raw data is not feasible for many biologists. Here, we present CoNekT (Co-expression Network Toolkit), an open source web server, that contains user-friendly tools and interactive visualizations for comparative analyses of gene expression data and co-expression networks. These tools allow analysis and cross-species comparison of (i) gene expression profiles; (ii) co-expression networks; (iii) co-expressed clusters involved in specific biological processes; (iv) tissue-specific gene expression; and (v) expression profiles of gene families. To demonstrate these features, we constructed CoNekT-Plants for green alga, seed plants and flowering plants (Picea abies, Chlamydomonas reinhardtii, Vitis vinifera, Arabidopsis thaliana, Oryza sativa, Zea mays and Solanum lycopersicum) and thus provide a web-tool with the broadest available collection of plant phyla. CoNekT-Plants is freely available from http://conekt.plant.tools, while the CoNekT source code and documentation can be found at https://github.molgen.mpg.de/proost/CoNekT/.


Assuntos
Perfilação da Expressão Gênica/métodos , Plantas/genética , Software , Genoma de Planta , Genômica , Internet , Filogenia , Plantas/classificação , Plantas/metabolismo
10.
BMC Bioinformatics ; 18(1): 444, 2017 Oct 10.
Artigo em Inglês | MEDLINE | ID: mdl-29017446

RESUMO

BACKGROUND: Since experimental elucidation of gene function is often laborious, various in silico methods have been developed to predict gene function of uncharacterized genes. Since functionally related genes are often expressed in the same tissues, conditions and developmental stages (co-expressed), functional annotation of characterized genes can be transferred to co-expressed genes lacking annotation. With genome-wide expression data available, the construction of co-expression networks, where genes are nodes and edges connect significantly co-expressed genes, provides unprecedented opportunities to predict gene function. However, the construction of such networks requires large volumes of high-quality data, multiple processing steps and a considerable amount of computation power. While efficient tools exist to process RNA-Seq data, pipelines which combine them to construct co-expression networks efficiently are currently lacking. RESULTS: LSTrAP (Large-Scale Transcriptome Analysis Pipeline), presented here, combines all essential tools to construct co-expression networks based on RNA-Seq data into a single, efficient workflow. By supporting parallel computing on computer cluster infrastructure, processing hundreds of samples becomes feasible as shown here for Arabidopsis thaliana and Sorghum bicolor, which comprised 876 and 215 samples respectively. The former was used here to show how the quality control, included in LSTrAP, can detect spurious or low-quality samples. The latter was used to show how co-expression networks are able to group known photosynthesis genes and imply a role in this process of several, currently uncharacterized, genes. CONCLUSIONS: LSTrAP combines the most popular and performant methods to construct co-expression networks from RNA-Seq data into a single workflow. This allows large amounts of expression data, required to construct co-expression networks, to be processed efficiently and consistently across hundreds of samples. LSTrAP is implemented in Python 3.4 (or higher) and available under MIT license from https://github.molgen.mpg.de/proost/LSTrAP.


Assuntos
Perfilação da Expressão Gênica , Redes Reguladoras de Genes , Análise de Sequência de RNA/métodos , Software , Estatística como Assunto , Arabidopsis/genética , Regulação da Expressão Gênica de Plantas , Análise de Componente Principal , Controle de Qualidade , Sorghum/genética
11.
New Phytol ; 215(3): 1009-1025, 2017 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-28617955

RESUMO

While Brachypodium distachyon (Brachypodium) is an emerging model for grasses, no expression atlas or gene coexpression network is available. Such tools are of high importance to provide insights into the function of Brachypodium genes. We present a detailed Brachypodium expression atlas, capturing gene expression in its major organs at different developmental stages. The data were integrated into a large-scale coexpression database ( www.gene2function.de), enabling identification of duplicated pathways and conserved processes across 10 plant species, thus allowing genome-wide inference of gene function. We highlight the importance of the atlas and the platform through the identification of duplicated cell wall modules, and show that a lignin biosynthesis module is conserved across angiosperms. We identified and functionally characterised a putative ferulate 5-hydroxylase gene through overexpression of it in Brachypodium, which resulted in an increase in lignin syringyl units and reduced lignin content of mature stems, and led to improved saccharification of the stem biomass. Our Brachypodium expression atlas thus provides a powerful resource to reveal functionally related genes, which may advance our understanding of important biological processes in grasses.


Assuntos
Brachypodium/citologia , Brachypodium/genética , Parede Celular/genética , Regulação da Expressão Gênica de Plantas , Redes Reguladoras de Genes , Genes de Plantas , Lignina/metabolismo , Arabidopsis/genética , Bases de Dados Genéticas , Oryza/genética , Caules de Planta/metabolismo , Plantas Geneticamente Modificadas , Transcriptoma/genética
12.
Plant J ; 90(3): 447-465, 2017 May.
Artigo em Inglês | MEDLINE | ID: mdl-28161902

RESUMO

Molecular evolutionary studies correlate genomic and phylogenetic information with the emergence of new traits of organisms. These traits are, however, the consequence of dynamic gene networks composed of functional modules, which might not be captured by genomic analyses. Here, we established a method that combines large-scale genomic and phylogenetic data with gene co-expression networks to extensively study the evolutionary make-up of modules in the moss Physcomitrella patens, and in the angiosperms Arabidopsis thaliana and Oryza sativa (rice). We first show that younger genes are less annotated than older genes. By mapping genomic data onto the co-expression networks, we found that genes from the same evolutionary period tend to be connected, whereas old and young genes tend to be disconnected. Consequently, the analysis revealed modules that emerged at a specific time in plant evolution. To uncover the evolutionary relationships of the modules that are conserved across the plant kingdom, we added phylogenetic information that revealed duplication and speciation events on the module level. This combined analysis revealed an independent duplication of cell wall modules in bryophytes and angiosperms, suggesting a parallel evolution of cell wall pathways in land plants. We provide an online tool allowing plant researchers to perform these analyses at http://www.gene2function.de.


Assuntos
Proteínas de Plantas/metabolismo , Arabidopsis/genética , Arabidopsis/metabolismo , Bryopsida/genética , Bryopsida/metabolismo , Evolução Molecular , Oryza/genética , Oryza/metabolismo , Filogenia , Proteínas de Plantas/genética
13.
Trends Plant Sci ; 22(4): 298-307, 2017 04.
Artigo em Inglês | MEDLINE | ID: mdl-28126286

RESUMO

Understanding how genomes change as organisms become more complex is a central question in evolution. Molecular evolutionary studies typically correlate the appearance of genes and gene families with the emergence of biological pathways and morphological features. While such approaches are of great importance to understand how organisms evolve, they are also limited, as functionally related genes work together in contexts of dynamic gene networks. Since functionally related genes are often transcriptionally coregulated, gene coexpression networks present a resource to study the evolution of biological pathways. In this opinion article, we discuss recent developments in this field and how coexpression analyses can be merged with existing genomic approaches to transfer functional knowledge between species to study the appearance or extension of pathways.


Assuntos
Redes Reguladoras de Genes/genética , Genômica/métodos , Evolução Biológica , Evolução Molecular , Redes Reguladoras de Genes/fisiologia , Filogenia
14.
New Phytol ; 213(2): 900-915, 2017 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-27588563

RESUMO

Hybrid necrosis is a common type of hybrid incompatibility in plants. This phenomenon is caused by deleterious epistatic interactions, resulting in spontaneous activation of plant defenses associated with leaf necrosis, stunted growth and reduced fertility in hybrids. Specific combinations of alleles of ACCELERATED CELL DEATH 6 (ACD6) have been shown to be a common cause of hybrid necrosis in Arabidopsis thaliana. Increased ACD6 activity confers broad-spectrum resistance against biotrophic pathogens but reduces biomass production. We generated 996 crosses among individuals derived from a single collection area around Tübingen (Germany) and screened them for hybrid necrosis. Necrotic hybrids were further investigated by genetic linkage, amiRNA silencing, genomic complementation and metabolic profiling. Restriction site associated DNA (RAD)-sequencing was used to understand genetic diversity in the collection sites containing necrosis-inducing alleles. Novel combinations of ACD6 alleles found in neighbouring stands were found to activate the A. thaliana immune system. In contrast to what we observed in controlled conditions, necrotic hybrids did not show reduced fitness in the field. Metabolic profiling revealed changes associated with the activation of the immune system in ACD6-dependent hybrid necrosis. This study expands our current understanding of the active role of ACD6 in mediating trade-offs between defense responses and growth in A.  thaliana.


Assuntos
Alelos , Anquirinas/genética , Proteínas de Arabidopsis/genética , Arabidopsis/genética , Doenças das Plantas/genética , Polimorfismo de Nucleotídeo Único/genética , Sequência de Aminoácidos , Anquirinas/química , Anquirinas/metabolismo , Arabidopsis/metabolismo , Proteínas de Arabidopsis/química , Proteínas de Arabidopsis/metabolismo , Cruzamentos Genéticos , Regulação da Expressão Gênica de Plantas , Loci Gênicos , Geografia , Alemanha , Hibridização Genética , Metaboloma , Análise de Componente Principal , Temperatura Ambiente
15.
Methods Mol Biol ; 1533: 213-227, 2017.
Artigo em Inglês | MEDLINE | ID: mdl-27987173

RESUMO

Functional relations between genes can be represented as networks. These networks have been successfully used to infer gene function and to mediate transfer of functional knowledge between species. Transcriptionally coordinated or co-expressed genes tend to be functionally related, which combined with availability of transcriptomic data for multiple plant species make the co-expression networks a useful resource for the plant community. In this chapter, we describe PlaNet ( www.gene2function.de ), a database that includes comparative analyses for co-expression networks of 11 plant species. We exemplify how the tools included in PlaNet can be used to predict gene function, transfer knowledge, and discover conserved and multiplied gene modules.


Assuntos
Biologia Computacional/métodos , Regulação da Expressão Gênica de Plantas , Redes Reguladoras de Genes , Plantas/genética , Software , Perfilação da Expressão Gênica , Ontologia Genética , Anotação de Sequência Molecular , Transcriptoma , Navegador
16.
Curr Opin Plant Biol ; 30: 143-50, 2016 04.
Artigo em Inglês | MEDLINE | ID: mdl-26990519

RESUMO

Driven by recent technological improvements, genes can be now studied in a larger biological context. Genes and their protein products rarely operate as a single entity and large-scale mapping by protein-protein interactions can unveil the molecular complexes that form in the cell to carry out various functions. Expression analysis under multiple conditions, supplemented with protein-DNA binding data can highlight when genes are active and how they are regulated. Representing these data in networks and finding strongly connected sub-graphs has proven to be a powerful tool to predict the function of unknown genes. As such networks are gradually becoming available for various plant species, it becomes possible to study how networks evolve. This review summarizes currently available network data and related tools for plants. Furthermore we aim to provide an outlook of future analyses that can be done in plants based on work done in other fields.


Assuntos
Plantas/genética , Plantas/metabolismo , Evolução Biológica , Bases de Dados Factuais , Redes Reguladoras de Genes , Modelos Biológicos
18.
Mol Plant ; 8(7): 998-1010, 2015 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-25620770

RESUMO

Growth-regulating factors (GRFs) are plant-specific transcription factors that were originally identified for their roles in stem and leaf development, but recent studies highlight them to be similarly important for other central developmental processes including flower and seed formation, root development, and the coordination of growth processes under adverse environmental conditions. The expression of several GRFs is controlled by microRNA miR396, and the GRF-miRNA396 regulatory module appears to be central to several of these processes. In addition, transcription factors upstream of GRFs and miR396 have been discovered, and gradually downstream target genes of GRFs are being unraveled. Here, we review the current knowledge of the biological functions performed by GRFs and survey available molecular data to illustrate how they exert their roles at the cellular level.


Assuntos
Proteínas de Plantas/metabolismo , Plantas/metabolismo , Fatores de Transcrição/metabolismo , Flores/crescimento & desenvolvimento , Desenvolvimento Vegetal , Proteínas de Plantas/química , Plantas/genética , Fatores de Transcrição/química
19.
Nat Genet ; 47(1): 65-72, 2015 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-25420146

RESUMO

Orchidaceae, renowned for its spectacular flowers and other reproductive and ecological adaptations, is one of the most diverse plant families. Here we present the genome sequence of the tropical epiphytic orchid Phalaenopsis equestris, a frequently used parent species for orchid breeding. P. equestris is the first plant with crassulacean acid metabolism (CAM) for which the genome has been sequenced. Our assembled genome contains 29,431 predicted protein-coding genes. We find that contigs likely to be underassembled, owing to heterozygosity, are enriched for genes that might be involved in self-incompatibility pathways. We find evidence for an orchid-specific paleopolyploidy event that preceded the radiation of most orchid clades, and our results suggest that gene duplication might have contributed to the evolution of CAM photosynthesis in P. equestris. Finally, we find expanded and diversified families of MADS-box C/D-class, B-class AP3 and AGL6-class genes, which might contribute to the highly specialized morphology of orchid flowers.


Assuntos
Genoma de Planta , Orchidaceae/genética , Evolução Molecular , Perfilação da Expressão Gênica , Regulação da Expressão Gênica no Desenvolvimento , Regulação da Expressão Gênica de Plantas , Genes de Plantas , Íntrons/genética , Proteínas de Domínio MADS , Taxa de Mutação , Orchidaceae/classificação , Orchidaceae/metabolismo , Fotossíntese/genética , Filogenia , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , RNA Mensageiro/biossíntese , RNA Mensageiro/genética , RNA de Plantas/biossíntese , RNA de Plantas/genética , Alinhamento de Sequência , Especificidade da Espécie
20.
Nucleic Acids Res ; 43(Database issue): D974-81, 2015 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-25324309

RESUMO

Comparative sequence analysis has significantly altered our view on the complexity of genome organization and gene functions in different kingdoms. PLAZA 3.0 is designed to make comparative genomics data for plants available through a user-friendly web interface. Structural and functional annotation, gene families, protein domains, phylogenetic trees and detailed information about genome organization can easily be queried and visualized. Compared with the first version released in 2009, which featured nine organisms, the number of integrated genomes is more than four times higher, and now covers 37 plant species. The new species provide a wider phylogenetic range as well as a more in-depth sampling of specific clades, and genomes of additional crop species are present. The functional annotation has been expanded and now comprises data from Gene Ontology, MapMan, UniProtKB/Swiss-Prot, PlnTFDB and PlantTFDB. Furthermore, we improved the algorithms to transfer functional annotation from well-characterized plant genomes to other species. The additional data and new features make PLAZA 3.0 (http://bioinformatics.psb.ugent.be/plaza/) a versatile and comprehensible resource for users wanting to explore genome information to study different aspects of plant biology, both in model and non-model organisms.


Assuntos
Bases de Dados Genéticas , Genoma de Planta , Genômica , Evolução Molecular , Internet , Anotação de Sequência Molecular , Filogenia , Plantas/classificação , Plantas/genética
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