Your browser doesn't support javascript.
Mostrar: 20 | 50 | 100
Resultados 1 - 20 de 2.770
Filtrar
1.
PLoS One ; 15(1): e0224188, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-31999713

RESUMO

The present study aimed to perform molecular identification of lepidopteran larvae from canopy fogging including gut-content analyses. A total of 130 lepidopteran larvae were selected from 37 fogging samples at the Panguana station, district Yuyapichis, province Puerto Inca, department Huánuco, Peru. Target trees were pre-identified and subsequently submitted to molecular confirmation of identity with three markers (rbcL, psbA and trnL-F). The COI gene of 119 lepidopteran larvae was successfully sequenced and found to belong to 92 species: Comparison of DNA barcodes with the reference database of adult moths resulted in 65 (55%) matches at species level, 32 (27%) at genus level, 19 (16%) at subfamily or family level, three just to order level. Three larvae could not be assigned to a family. For these larvae the fogged target tree now suggests a potential host-plant relationship. Molecular gut content analysis, based on High-Throughput-Sequencing was successfully tested for ten larvae corroborating feeding on the target plant in some cases but elucidating several other cases of potential 'alternative feeding'. We propose a larger-scale approach using this rapid and efficient method including molecular gut-content analyses for comprehensively testing the ratio of 'alternative feeders' and pitfalls caused by collateral fogging of larvae from neighboring trees.


Assuntos
Código de Barras de DNA Taxonômico/métodos , Mariposas/genética , Filogenia , Animais , DNA/genética , Sequenciamento de Nucleotídeos em Larga Escala , Insetos/classificação , Insetos/genética , Larva/genética , Mariposas/classificação , Peru , Plantas/classificação , Plantas/genética , Especificidade da Espécie , Clima Tropical
2.
J Agric Food Chem ; 68(6): 1684-1690, 2020 Feb 12.
Artigo em Inglês | MEDLINE | ID: mdl-31957431

RESUMO

The carotenoid-derived volatile ß-ionone plays an important role in the formation of green and black tea flavors due to its low odor threshold, but its formation and the gene(s) involved in its biosynthesis during the tea withering process is(are) still unknown. In this study, we found that the content of ß-ionone increased during the tea withering process catalyzed by an unknown enzyme(s). Correlation analysis of expression patterns of Camellia sinensis carotenoid cleavage dioxygenase genes (CsCCDs) and the ß-ionone content during the withering period revealed CsCCD4 as the most promising candidate. The full-length CsCCD4 gene was amplified from C. sinensis, and the biochemical function of the recombinant CsCCD4 protein was studied after coexpression in Escherichia coli strains engineered to accumulate ß-carotene. The recombinant protein was able to cleave a variety of carotenoids at the 9-10 and 9'-10' double bonds. Volatile ß-ionone was detected as the main product by gas and liquid chromatography-mass spectrometry. The accumulation of ß-ionone was consistent with the expression levels of CsCCD4 in different tissues and during the withering process. The CsCCD4 expression was induced by low temperature and mechanical damage stress but not by dehydration stress. The results demonstrate that CsCCD4 catalyzes the production of ß-ionone in the tea plant and provide insight into its formation mechanism during the withering process.


Assuntos
Camellia sinensis/enzimologia , Carotenoides/metabolismo , Dioxigenases/metabolismo , Norisoprenoides/metabolismo , Proteínas de Plantas/metabolismo , Sequência de Aminoácidos , Biocatálise , Camellia sinensis/química , Camellia sinensis/genética , Camellia sinensis/metabolismo , Dioxigenases/genética , Manipulação de Alimentos , Espectrometria de Massas , Filogenia , Folhas de Planta/química , Folhas de Planta/enzimologia , Folhas de Planta/metabolismo , Proteínas de Plantas/genética , Plantas/classificação , Plantas/enzimologia , Plantas/genética , Alinhamento de Sequência
3.
J Ethnobiol Ethnomed ; 15(1): 51, 2019 Nov 05.
Artigo em Inglês | MEDLINE | ID: mdl-31690333

RESUMO

BACKGROUND: This paper aims to record the species used for flavouring and making alcoholic drinks, mainly rakija, on the islands of the Adriatic (Croatia). METHODS: Our data comes from 295 interviews performed on 36 islands, in both the Dalmatian and Kvarner areas of the Adriatic. RESULTS: Altogether, 114 species are used-46% from wild locations only, 15% both wild and cultivated, 38% only cultivated and two species are imported. The most common local alcohol is wine, made without spices, but grape pomace distillate is often flavoured with single or mixed species. The mix is called travarica. The most commonly used species are Foeniculum vulgare Mill., Myrtus communis L., Salvia officinalis L., Ruta graveolens L., Juniperus oxycedrus L., Ceratonia siliqua L., Juglans regia L., Citrus spp., Ficus carica L., Laurus nobilis L., Rosmarinus officinalis L., Artemisia absinthium L., Rosa centifolia L., Mentha × piperita L. and M. spicata L. Unfortunately, the widespread phenomenon of distilling Arbutus unedo L. fruits and fermenting Juniperus 'wine' is now extinct. Apart from grapes, the only commonly distilled fruit now is Ficus carica. CONCLUSIONS: It is striking that nearly all the plants are either wild or cultivated locally, which, in addition to the fact that the alcohol is made locally, shows the incredible local culinary self-sufficiency of the area. The number of species used is also very impressive.


Assuntos
Bebidas Alcoólicas , Plantas/classificação , Croácia , Etnobotânica
4.
Hist Philos Life Sci ; 41(4): 46, 2019 Oct 17.
Artigo em Inglês | MEDLINE | ID: mdl-31624931

RESUMO

This paper addresses early modern botanical nomenclature, the practices of identifying and publishing synonyms in particular, as a collaborative "information science". Before Linnaean nomenclature became the lingua franca of botany, it was inevitable that, over time, the same plant was given several names by different people, which created confusion and made communication among botanists increasingly difficult. What names counted as synonyms and actually referred to the same plant had to be identified by meticulously comparing living and dried specimens of this and similar plants as well as relevant illustrations und descriptions in the botanical literature. Identifying synonyms required and generated an ever-expanding mass of data, which was used continuously to adjust and rearrange plant names. Despite the greatest care, judgements on synonyms were not definitive, which meant that published lists of synonyms for individual species of plants were in a state of flux and had to be constantly updated, corrected, and rewritten. This required long-term international collaborations, the accumulated results of which were not published once but consecutively, in augmented and corrected editions of a book. As a result of this networked approach, synonyms are networked names that reflect the epistemic interconnectedness of the botanical community. These questions will be discussed with a focus on the Dutch botanist Johannes Burman (1706-1779), who placed synonyms at the centre of his work as posthumous editor-and co-author-of the botanical manuscripts that were left behind by other botanists.


Assuntos
Botânica/história , Classificação/métodos , Plantas/classificação , Comunicação Acadêmica/história , Terminologia como Assunto , Europa (Continente) , História do Século XVIII , Países Baixos
5.
An Acad Bras Cienc ; 91(suppl 3): e20190396, 2019 Sep 12.
Artigo em Inglês | MEDLINE | ID: mdl-31531554

RESUMO

Amazonia is often cited as having the most diverse flora on the planet. However, the total number of species of higher plants in the region has been largely a matter of guesswork. Some recent publications have estimated the total number of species present, which indicate a lower overall diversity than was estimated in the past. However, analysis of the sampling density across the region, and data from various sources suggest that there may be reason why the recent figures may be considerable underestimates. I believe that much more investment in extensive collecting of quality plant specimens is needed to encounter the very large number of rare and local species that might never have been collected. Unfortunately the tendencies of investment in botany, in terms of geography and types of project, suggest that we will probably not be able to accurately assess the real diversity of the region.


Assuntos
Biodiversidade , Plantas/classificação , Brasil , Florestas , Geografia , Magnoliopsida/classificação , Sapotaceae/classificação , Especificidade da Espécie
6.
J Agric Food Chem ; 67(40): 11262-11276, 2019 Oct 09.
Artigo em Inglês | MEDLINE | ID: mdl-31509416

RESUMO

Tartary buckwheat (Fagopyrum tataricum) seeds are rich in flavonoids. However, the detailed flavonoid compositions and the molecular basis of flavonoid biosynthesis in tartary buckwheat seeds remain largely unclear. Here, we performed a combined metabolite profiling and transcriptome analysis to identify flavonoid compositions and characterize genes involved in flavonoid biosynthesis in the developing tartary buckwheat seeds. In total, 234 flavonoids, including 10 isoflavones, were identified. Of these, 80 flavonoids were significantly differential accumulation during seed development. Transcriptome analysis indicated that most structural genes and some potential regulatory genes of flavonoid biosynthesis were significantly differentially expressed in the course of seed development. Correlation analysis between transcriptome and metabolite profiling shown that the expression patterns of some differentially expressed structural genes and regulatory genes were more consistent with the changes in flavonoids profiles during seed development and promoted one SG7 subgroup R2R3-MYB transcription factors (FtPinG0009153900.01) was identified as the key regulatory gene of flavonoid biosynthesis. These findings provide valuable information for understanding the mechanism of flavonoid biosynthesis in tartary buckwheat seeds and the further development of tartary buckwheat health products.


Assuntos
Fagopyrum/metabolismo , Flavonoides/biossíntese , Proteínas de Plantas/genética , Sementes/crescimento & desenvolvimento , Fagopyrum/química , Fagopyrum/genética , Fagopyrum/crescimento & desenvolvimento , Perfilação da Expressão Gênica , Regulação da Expressão Gênica de Plantas , Filogenia , Proteínas de Plantas/metabolismo , Plantas/classificação , Plantas/genética , Plantas/metabolismo , Sementes/química , Sementes/genética , Sementes/metabolismo
7.
Environ Monit Assess ; 191(10): 635, 2019 Sep 15.
Artigo em Inglês | MEDLINE | ID: mdl-31522254

RESUMO

This study aimed to analyze the spatial and temporal variation of the vegetation in the northern Argentine Puna, utilizing both field sampling and remote-sensing tools. The study was performed within the Pozuelos Biosphere Reserve (Jujuy province, Argentina), which aims to generate socio-economic development compatible with biodiversity conservation. Our study was designed to analyze the dynamics of the Puna vegetation at local scale and assess and monitor the seasonal (dry and wet seasons), interannual, and spatial variation of the vegetation cover, biomass, dominant species, and vegetation indices. Ten vegetation units (with differences in composition, cover, and high and low stratum biomass) were identified at our study site. The diversity of these vegetation units correlated with geomorphology and soil type. In the dry season, the vegetation unit with greatest vegetation cover and biomass was the Festuca chrysophylla grassland, whereas in the wet season, the units with greatest cover and biomass were vegas (peatlands) and short grasslands. The Festuca chrysophylla grasslands and short grasslands were located in areas with clay soils, except peatlands, associated with valleys and coarse-texture soils. The vegetation indices used (NDVI, SAVI, and MSAVI2) were able to differentiate functional types of vegetation and showed a good statistical fit with cover values. Our results suggest that the integrated utilization of remote-sensing tools and field surveys improves the assessment of the Puna vegetation and would allow a periodic monitoring at production unit scale taking into account its spatial and temporal variation.


Assuntos
Monitoramento Ambiental/métodos , Pradaria , Plantas/classificação , Argentina , Biodiversidade , Biomassa , Parques Recreativos , Tecnologia de Sensoriamento Remoto , Estações do Ano , Solo/química
8.
Environ Monit Assess ; 191(10): 613, 2019 Sep 05.
Artigo em Inglês | MEDLINE | ID: mdl-31489508

RESUMO

The present study investigating the variation in plant diversity in Taitemar Lake before and after ecological water transfer is critical for the restoration of the ecological environment of the lower Tarim River. A comprehensive study of the vegetation in Taitemar Lake from 2000 to 2017 was conducted, to determine differences between the overflow and the non-overflow areas, which were monitored along belt transects. There are some conclusions: (1) the ecological benefits of Taitemar Lake gradually emerged with increased water transfer: in the overflow area, the number of species per unit area, vegetation cover, and vegetation density were 6.8 species per 100 m2, 30%, and 1350 per 100 m2, respectively, while the three indices above in the non-overflow area were 1.7 species per 100 m2, 7.0%, and 27.0 per 100 m2, respectively. (2) In recent decades, the major changes in Taitemar Lake were as follows: in the early stage of water transport (2000-2006), the surface vegetation was dominated by newly germinated annual herbs (important value (IV) 0.50), followed by perennial herbs (IV 0.20), and finally shrubs (IV 0.10). After a few years, in 2008, the annual herbs almost disappeared in the overflow are and were replaced by shrubs and perennial herbs. Shrubs were the newly germinating seedlings of native species, and perennial herbs were dominated by Phragmites australis. From 2012 to 2016, under the abundant water conditions, the dominant species composition tended to be simple and the local vegetation developed in the direction of a saline meadow. (3) From 2011 to 2017, P. australis became the dominant species on the shoreline with the Simpson and Shannon indices remaining at low levels.


Assuntos
Biodiversidade , Monitoramento Ambiental , Lagos/análise , Plantas , Movimentos da Água , Recuperação e Remediação Ambiental , Desenvolvimento Vegetal , Plantas/classificação , Rios , Abastecimento de Água
9.
Ecotoxicol Environ Saf ; 183: 109493, 2019 Nov 15.
Artigo em Inglês | MEDLINE | ID: mdl-31376802

RESUMO

Vinasses obtained from the distillation of winemaking by-products (WDV) are complex effluents with variable physicochemical properties. Frequently, WDVs are used to irrigate agricultural soil, and/or discharged into aquatic bodies, which may result in serious environmental pollution, due to the presence of organic acids and recalcitrant compounds (polyphenols, tannins and metals). The present study aimed to evaluate the toxicity impact of an untreated WDV on terrestrial and aquatic organisms, at different levels of biological organization. The effluent was collected at the distillation column exit and characterized according to several physicochemical properties. The WDV potential phytotoxicity was assessed by germination inhibition assays on six agricultural crops, and its acute toxicity was assessed on Aliivibrio fisheri (microtox assay), Daphnia magna neonates (freshwater crustacean), and zebrafish Danio rerio (fish embryo toxicity test, FET). The WDV presented a low pH (3.88), high levels of electrical conductivity, ECond (6.36 dS m-1) and salinity (3.3 ppt), besides high level of potassium (2.1 g L-1) and organic compounds (TOC = 17.7 g L-1), namely polyphenols (1.7 g L-1). The diluted WDV displayed variable inhibitory effects on the plant endpoints (percentage of inhibition of germination and radicle elongation and germination index). Overall, plants' susceptibility to increasing concentrations of WDV were differential (onion ≈ garden cress ≥ tomato > lettuce > maize > green beans) and the germination index EC50 varied from 10.9 to 64.4% v/v. Also, the acute negative effects toward aquatic organisms were determined, decreasing from the more complex organism to the simpler one: zebrafish embryos (96 h-LC50 = 0.34% v/v)>D. magna (48 h-LC50 = 4.8% v/v)>A. fisheri (30min-EC50 = 7.0% v/v). In conclusion, the findings suggest that WDVs might have a high toxicological impact on both terrestrial plants and aquatic organisms, even at high dilution levels, reinforcing the need for appropriate treatments before considering its discharge or reuse.


Assuntos
Organismos Aquáticos/efeitos dos fármacos , Resíduos Industriais , Plantas/efeitos dos fármacos , Poluentes Químicos da Água/toxicidade , Vinho , Animais , Organismos Aquáticos/crescimento & desenvolvimento , Germinação/efeitos dos fármacos , Dose Letal Mediana , Compostos Orgânicos/química , Plantas/classificação , Testes de Toxicidade , Poluentes Químicos da Água/química
10.
Elife ; 82019 08 02.
Artigo em Inglês | MEDLINE | ID: mdl-31373555

RESUMO

Although geographic isolation is a leading driver of speciation, the tempo and pattern of divergence at the genomic level remain unclear. We examine genome-wide divergence of putatively single-copy orthologous genes (POGs) in 20 allopatric species/variety pairs from diverse angiosperm clades, with 16 pairs reflecting the classic eastern Asia-eastern North America floristic disjunction. In each pair, >90% of POGs are under purifying selection, and <10% are under positive selection. A set of POGs are under strong positive selection, 14 of which are shared by 10-15 pairs, and one shared by all pairs; 15 POGs are annotated to biological processes responding to various stimuli. The relative abundance of POGs under different selective forces exhibits a repeated pattern among pairs despite an ~10 million-year difference in divergence time. Species divergence times are positively correlated with abundance of POGs under moderate purifying selection, but negatively correlated with abundance of POGs under strong purifying selection.


Assuntos
Evolução Molecular , Genes de Plantas , Variação Genética , Plantas/genética , Seleção Genética , Extremo Oriente , Especiação Genética , América do Norte , Folhas de Planta/genética , Plantas/classificação
11.
J Basic Microbiol ; 59(10): 992-1003, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31410872

RESUMO

Revegetation accelerates the recovery of degraded lands. Different microbial trophic groups underpin this acceleration from the aspects of soil structure stabilization, nutrient accumulation, and ecosystem functions. However, little is known about how revegetation influences the community and biodiversity of different soil microbial trophic groups. Here, six revegetation treatments with different plantings of plant species were established at an excavation pit in the Qinghai-Tibetan Plateau. Communities of plant, bacteria, and several key soil fungal groups were investigated after 12 years of revegetation. Plant and all microbial trophic group compositions were markedly influenced by revegetation treatments. Total fungal and pathogenic fungal compositions were not significantly predicted by any factor of plant and soil, but arbuscular mycorrhizal fungal composition could be mainly predicted by plant composition and plant P content. Bacterial composition was mainly determined by soil total N, organic carbon concentration, and moisture content; and saprotrophic fungal composition was mainly determined by soil organic carbon. Soil pH was the strongest factor to predict bacterial metabolic functions. Our findings highlight that even the differences of microbial compositions were because of different revegetation treatments, but each trophic microbial composition had different relations with plant and/or soil; especially, the bacterial community and metabolic functions and saprotrophic fungal community were more correlated with soil properties rather than plant community or characteristics per se.


Assuntos
Recuperação e Remediação Ambiental , Pradaria , Plantas/classificação , Microbiologia do Solo , Bactérias/classificação , Bactérias/isolamento & purificação , Bactérias/metabolismo , Carbono/análise , Carbono/metabolismo , Fungos/classificação , Fungos/isolamento & purificação , Fungos/metabolismo , Micorrizas/classificação , Micorrizas/isolamento & purificação , Micorrizas/metabolismo , Nitrogênio/análise , Nitrogênio/metabolismo , Fosfatos/análise , Fosfatos/metabolismo , Plantas/química , Plantas/metabolismo , Plantas/microbiologia , Solo/química , Tibet
12.
Ecol Lett ; 22(10): 1650-1657, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31364805

RESUMO

While biodiversity loss continues globally, assessments of regional and local change over time have been equivocal. Here, we assess changes in plant species richness and beta diversity over 140 years at the level of regions within a country. Using 19th-century flora censuses for 14 Danish regions as a baseline, we overcome previous criticisms concerning short time series and neglect of completely altered habitats. We find that species composition has changed dramatically and directionally across all regions. Substantial species losses were more than offset by large gains, resulting in a net increase in species richness in all regions. The occupancy of initially widespread species increased, while initially rare species lost terrain. These changes were accompanied by strong biotic homogenization; i.e. regions are more similar now than they were 140 years ago. Species declining in Denmark were found to be in similar decline all over Northern Europe.


Assuntos
Biodiversidade , Ecossistema , Plantas/classificação , Dinamarca
13.
Ecol Lett ; 22(9): 1449-1461, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31267650

RESUMO

The mechanisms underpinning forest biodiversity-ecosystem function relationships remain unresolved. Yet, in heterogeneous forests, ecosystem function of different strata could be associated with traits or evolutionary relationships differently. Here, we integrate phylogenies and traits to evaluate the effects of elevational diversity on above-ground biomass across forest strata and spatial scales. Community-weighted means of height and leaf phosphorous concentration and functional diversity in specific leaf area exhibited positive correlations with tree biomass, suggesting that both positive selection effects and complementarity occur. However, high shrub biomass is associated with greater dissimilarity in seed mass and multidimensional trait space, while species richness or phylogenetic diversity is the most important predictor for herbaceous biomass, indicating that species complementarity is especially important for understory function. The strength of diversity-biomass relationships increases at larger spatial scales. We conclude that strata- and scale- dependent assessments of community structure and function are needed to fully understand how biodiversity influences ecosystem function.


Assuntos
Biodiversidade , Biomassa , Florestas , Plantas/classificação , China , Código de Barras de DNA Taxonômico , Filogenia
14.
An Acad Bras Cienc ; 91(supp 2): e20180750, 2019 Jul 22.
Artigo em Inglês | MEDLINE | ID: mdl-31340218

RESUMO

The morphology and structure of megaspores assigned to Lagenoisporites magnus from the Toregua Formation, Retama Group, mid-upper Tournaisian of Bolivia were studied. The analysis was performed with light, fluorescence and scanning electron microscopy. Megaspores were laterally compressed and presented a spherical body with a proximal gula, of the hologula type. Gula had verrucae ornamentation and the spore body presented complex processes consisting of a bulbous base and an internally partitioned projection with sharp apex. In addition to this main ornamentation, perforations were present throughout the spore surface. Megaspores showed well marked curvaturae perfectae due to the abrupt transition existing between the gula ornamentation and the spore body processes. These megaspores were assigned to heterosporous arborescent lycopsids of the Lepidocarpaceae family, as in section view, exospore structure presented a three-dimensional network of fused elements. Likewise, due to a similarity found between sporoderm and Isoetes L. structure, it is evident that megaspores structure has remained intact inside the heterosporous lycopsids. Therefore; the L. magnus structure not only would confirm its affinity with the Lycophyta fossils but also with the living ones.


Assuntos
Plantas/ultraestrutura , Esporos/ultraestrutura , Bolívia , Fósseis , Microscopia Eletrônica de Varredura , Plantas/classificação
15.
PLoS Biol ; 17(7): e3000373, 2019 07.
Artigo em Inglês | MEDLINE | ID: mdl-31329577

RESUMO

Autophagy-related protein 8 (ATG8) is a highly conserved ubiquitin-like protein that modulates autophagy pathways by binding autophagic membranes and a number of proteins, including cargo receptors and core autophagy components. Throughout plant evolution, ATG8 has expanded from a single protein in algae to multiple isoforms in higher plants. However, the degree to which ATG8 isoforms have functionally specialized to bind distinct proteins remains unclear. Here, we describe a comprehensive protein-protein interaction resource, obtained using in planta immunoprecipitation (IP) followed by mass spectrometry (MS), to define the potato ATG8 interactome. We discovered that ATG8 isoforms bind distinct sets of plant proteins with varying degrees of overlap. This prompted us to define the biochemical basis of ATG8 specialization by comparing two potato ATG8 isoforms using both in vivo protein interaction assays and in vitro quantitative binding affinity analyses. These experiments revealed that the N-terminal ß-strand-and, in particular, a single amino acid polymorphism-underpins binding specificity to the substrate PexRD54 by shaping the hydrophobic pocket that accommodates this protein's ATG8-interacting motif (AIM). Additional proteomics experiments indicated that the N-terminal ß-strand shapes the broader ATG8 interactor profiles, defining interaction specificity with about 80 plant proteins. Our findings are consistent with the view that ATG8 isoforms comprise a layer of specificity in the regulation of selective autophagy pathways in plants.


Assuntos
Família da Proteína 8 Relacionada à Autofagia/metabolismo , Autofagia , Proteínas de Plantas/metabolismo , Plantas/metabolismo , Família da Proteína 8 Relacionada à Autofagia/química , Família da Proteína 8 Relacionada à Autofagia/genética , Imunoprecipitação/métodos , Espectrometria de Massas/métodos , Filogenia , Proteínas de Plantas/química , Proteínas de Plantas/genética , Plantas/classificação , Plantas/genética , Plantas Geneticamente Modificadas , Ligação Proteica , Conformação Proteica em Folha beta , Isoformas de Proteínas/química , Isoformas de Proteínas/genética , Isoformas de Proteínas/metabolismo , Proteômica/métodos , Solanum tuberosum/genética , Solanum tuberosum/metabolismo , Tabaco/genética , Tabaco/metabolismo
16.
Genome ; 62(9): 585-595, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31271726

RESUMO

Plant DNA barcoding serves as an effective approach to building community phylogenies and increasing our understanding of the factors that determine plant community assemblages. The aims of the study were to (i) barcode macrophytes with high estuarine fidelity and (ii) to determine the phylogenetic diversity (PD) of selected South African estuaries for conservation prioritisation. Three DNA barcoding gene regions (rbcLa, matK, and trnH-psbA) were assessed, and community phylogenies were constructed for 270 estuaries. Generally, the matK barcode had the greatest discrimination success rate of 67.4% (parsimony informative sites = 418). Closely related species formed clades that also represent estuarine habitat types. Estuaries with high phylogenetic diversity along the southeast coast were associated with a combination of mangrove and salt marsh habitats. Species richness was strongly and significantly correlated with PD (r = 0.93; p < 0.000). Based on mean pairwise distance (MPD), more temperate estuaries (56) showed significant phylogenetic clustering compared to subtropical estuaries (24) (p < 0.05). Similarly, based on mean nearest taxon distance (MNTD), significant phylogenetic clustering was highest in temperate estuaries (50) compared to subtropical estuaries (12) (p < 0.05). This suggests that the coexistence of plant species in estuaries is structured by both biotic and abiotic interactions.


Assuntos
Biodiversidade , Estuários , Plantas/classificação , Organismos Aquáticos/classificação , Código de Barras de DNA Taxonômico , DNA de Plantas , Filogenia , Plantas/genética , África do Sul
17.
Redox Biol ; 26: 101247, 2019 09.
Artigo em Inglês | MEDLINE | ID: mdl-31228650

RESUMO

We present a new database, specifically devoted to ROS homeostasis regulated proteins. This database replaced our previous database, the PeroxiBase, which was focused only on various peroxidase families. The addition of 20 new protein families related with ROS homeostasis justifies the new name for this more complex and comprehensive database as RedoxiBase. Besides enlarging the focus of the database, new analysis tools and functionalities have been developed and integrated through the web interface, with which the users can now directly access to orthologous sequences and see the chromosomal localization of sequences when available. OrthoMCL tool, completed with a post-treatment process, provides precise predictions of orthologous gene groups for the sequences present in this database. In order to explore and analyse orthogroups results, taxonomic visualization of organisms containing sequence of a specific orthogroup as well as chromosomal distribution of the orthogroup with one or two organisms have been included.


Assuntos
Bases de Dados de Proteínas , Oxirredutases/genética , Plantas/genética , Espécies Reativas de Oxigênio/metabolismo , Software , Mapeamento Cromossômico/métodos , Cromossomos , Homeostase/genética , Família Multigênica , Oxirredutases/classificação , Oxirredutases/metabolismo , Filogenia , Plantas/classificação , Plantas/metabolismo
18.
PLoS One ; 14(6): e0217084, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31216285

RESUMO

Taxonomic identification of biological materials can be achieved through DNA barcoding, where an unknown "barcode" sequence is compared to a reference database. In many disciplines, obtaining accurate taxonomic identifications can be imperative (e.g., evolutionary biology, food regulatory compliance, forensics). The Barcode of Life DataSystems (BOLD) and GenBank are the main public repositories of DNA barcode sequences. In this study, an assessment of the accuracy and reliability of sequences in these databases was performed. To achieve this, 1) curated reference materials for plants, macro-fungi and insects were obtained from national collections, 2) relevant barcode sequences (rbcL, matK, trnH-psbA, ITS and COI) from these reference samples were generated and used for searching against both databases, and 3) optimal search parameters were determined that ensure the best match to the known species in either database. While GenBank outperformed BOLD for species-level identification of insect taxa (53% and 35%, respectively), both databases performed comparably for plants and macro-fungi (~81% and ~57%, respectively). Results illustrated that using a multi-locus barcode approach increased identification success. This study outlines the utility of the BLAST search tool in GenBank and the BOLD identification engine for taxonomic identifications and identifies some precautions needed when using public sequence repositories in applied scientific disciplines.


Assuntos
Código de Barras de DNA Taxonômico/métodos , Bases de Dados de Ácidos Nucleicos , Animais , Fungos/classificação , Fungos/genética , Insetos/classificação , Insetos/genética , Plantas/classificação , Plantas/genética , Reprodutibilidade dos Testes
19.
Mol Ecol Resour ; 19(5): 1265-1277, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31232514

RESUMO

Most work on plant community ecology has been performed above ground, neglecting the processes that occur in the soil. DNA metabarcoding, in which multiple species are computationally identified in bulk samples, can help to overcome the logistical limitations involved in sampling plant communities belowground. However, a major limitation of this methodology is the quantification of species' abundances based on the percentage of sequences assigned to each taxon. Using root tissues of five dominant species in a semi-arid Mediterranean shrubland (Bupleurum fruticescens, Helianthemum cinereum, Linum suffruticosum, Stipa pennata and Thymus vulgaris), we built pairwise mixtures of relative abundance (20%, 50% and 80% biomass), and implemented two methods (linear model fits and correction indices) to improve estimates of root biomass. We validated both methods with multispecies mixtures that simulate field-collected samples. For all species, we found a positive and highly significant relationship between the percentage of sequences and biomass in the mixtures (R2  = .44-.66), but the equations for each species (slope and intercept) differed among them, and two species were consistently over- and under-estimated. The correction indices greatly improved the estimates of biomass percentage for all five species in the multispecies mixtures, and reduced the overall error from 17% to 6%. Our results show that, through the use of post-sequencing quantification methods on mock communities, DNA metabarcoding can be effectively used to determine not only species' presence but also their relative abundance in field samples of root mixtures. Importantly, knowledge of these aspects will allow us to study key, yet poorly understood, belowground processes.


Assuntos
Biota , Código de Barras de DNA Taxonômico/métodos , Metagenômica/métodos , Plantas/classificação , Plantas/genética , DNA de Plantas/genética , Raízes de Plantas/classificação , Raízes de Plantas/genética
20.
Phytochem Anal ; 30(5): 512-523, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31222865

RESUMO

INTRODUCTION: Mediterranean plants are characterised by a high content of bioactive secondary metabolites that play important roles in plant-plant interactions as plant growth regulators and could be useful for the development of new eco-friendly herbicides. OBJECTIVE: An NMR-based metabolomics approach was reported to seek selective phytotoxic plant extracts and putative plant-derived active molecules. METHODS: Plant extracts derived from five Mediterranean donor species (Pistacia lentiscus, Bellis sylvestris, Phleum subulatum, Petrohrhagia saxifraga and Melilotus neapolitana) were used to treat the hydroponic cultures of three receiving plants (Triticum durum, Triticum ovatum and Avena fatua). Morphological analyses of the treated receiving plants were carried out. NMR-based metabolomics was applied both to characterise the donor plant extracts and to study the effects of the treatments on the receiving plants. RESULTS: This study allowed the identification of Melilotus neapolitana and Bellis sylvestris as phytotoxic plant and good candidates for further studies. Specifically, the NMR-based metabolomics investigation showed that these species affect a specific set of metabolites (such as sugars, amino and organic acids) and therefore metabolic pathways [i.e. tricarboxylic acid (TCA) cycle, amino acid metabolism, etc.] that are crucial for the plant growth and development. Moreover, it was possible to identify the metabolite(s) probably responsible for the phytotoxicity of the active extracts. CONCLUSION: The NMR-based metabolomics approach employed in this study led to the identification of two phytotoxic plant extracts and their putative active principles. These new insights will be of paramount importance in the future to find plant derived molecules endowed with phytotoxic activities.


Assuntos
Bioensaio/métodos , Metabolômica/métodos , Extratos Vegetais/química , Plantas/química , Herbicidas/química , Herbicidas/farmacologia , Região do Mediterrâneo , Extratos Vegetais/farmacologia , Extratos Vegetais/toxicidade , Reguladores de Crescimento de Planta/química , Reguladores de Crescimento de Planta/farmacologia , Plantas/classificação , Plantas/metabolismo , Plantas Tóxicas/química , Plantas Tóxicas/metabolismo
SELEÇÃO DE REFERÊNCIAS
DETALHE DA PESQUISA