Antioxidant, Anticancer, and PXR-Dependent CYP3A4 Attributes of Schweinfurthia papilionacea (Burm.f.) Boiss., Tricholepis glaberrima DC. and Viola stocksii Boiss.

Present study established the biological potential of Schweinfurthia papilionacea, Tricholepis glaberrima and Viola stocksii extracts for their potential applications in drug formulations. Initially, FTIR was performed to ascertain functional groups and then plant extracts were prepared using five solvents depending on the polarity. Total phenolic contents were observed in the range of 36.36 ± 1.08 mg GAE/g to 95.55 ± 2.46 mg GAE/g while flavonoid contents were found in the range of 10.51 ± 0.25 mg QE/g to 22.17 ± 1.79 mg QE/g. Antioxidant activity was determined using TRP, CUPRAC, TAC and DPPH assays and was recorded highest in S. papilionacea followed by T. glaberrima extracts. TPC and TFC were found to be strongly correlated with TRP (r > 0.50), CUPRAC (r > 0.53) and DPPH (r = 0.31 and 0.72) assay while weakly correlated with TAC (r = 0.08 and 0.03) as determined by Pearson correlation analysis. Anticancer activity showed that S. papilionacea chloroform extracts possess highest cell viability (85.04 ± 4.24%) against HepG2 cell lines while T. glaberrima chloroform extracts exhibited highest activity (82.80 ± 2.68%) against HT144 cell lines. Afterwards, highest PXR activation was observed in T. glaberrima (3.49 ± 0.34 µg/mL fold) at 60 µg/mL and was correlated with increase in CYP3A4 activity (15.0 ± 3.00 µg/mL IC50 value). Furthermore, antimalarial activity revealed >47600 IC50 value against P. falciparum D6 and P. falciparum W2 and antimicrobial assay indicated highest activity (32 ± 2.80 mm) in S. papilionacea against C. neoformans. At the end, GC-MS analysis of n-hexane plant extracts showed 99.104% of total identified compounds in T. glaberrima and 94.31% in V. stocksii. In conclusion, present study provides insight about the different biological potentials of S. papilionacea and T. glaberrima extracts that rationalize the applications of these extracts in functional foods and herbal drugs for the management of oxidative-stress related diseases, antimicrobial infections and liver and skin cancer.

Simultaneous diversification of Polypodiales and angiosperms in the Mesozoic.

Comprising about 82% of the extant fern species diversity, Polypodiales are generally believed to have diversified in the Late Cretaceous. We estimated the divergence times of Polypodiales using both penalized likelihood and Bayesian methods, based on a dataset consisting of 208 plastomes representing all 28 families and 14 fossil constraints reflecting current interpretations of fossil record. Our plastome phylogeny recovered the same six major lineages as a recent nuclear phylogeny, but the position of Dennstaedtiineae was different. The present phylogeny showed high resolution of relationships among the families of Polypodiales, especially among those forming the Aspleniineae. The divergence time estimates supported the most recent common ancestor of Polypodiales and its closest relative dating back to the Triassic, establishment of the major lineages in the Jurassic, and a likely accelerated radiation during the late Jurassic and the Early Cretaceous. The estimated divergence patterns of Polypodiales and angiosperms converge to a scenario in which their main lineages were established simultaneously shortly before the onset of the Cretaceous Terrestrial Revolution, and further suggest a pre-Cretaceous hidden history for both lineages. The pattern of simultaneous diversifications shown here elucidate an important gap in our understanding of the Terrestrial Revolution that shaped today's ecosystems.

Isolipidic replacement of krabok oil by whole krabok seed reduces in vitro methanogenesis, but negatively affects fermentation.

The background of the current in vitro study involves the issue of methane (CH4 ) production inherent to rumen fermentation. One of the dietary strategies to reduce enteric CH4 production by ruminants involves the supplementation of medium-chain fatty acids in diets. As such, oils containing high amounts of MCFA, such as coconut, palm kernel and krabok oil, are of much interest to formulate energy efficient and environmentally friendly rations for ruminants. Krabok oil (KO) reduces methanogenesis, but the appropriate inclusion level of dietary KO is unclear. We therefore investigated the dose-response relationship between krabok oil and CH4 production. In practice, the use of whole krabok seed (WKS), instead of KO, is easier, but the efficacy of WKS to inhibit methanogenesis was hitherto unknown. Thus, we also investigated whether WKS provides an alternative tool to inhibit CH4 production. The experimental substrates contained either KO, WKS, the residue of WKS after fat extraction residue (FER) or FER + KO. Appropriate amounts of WKS or its derivatives were added to a basal substrate so as to attain either a low, medium or high content of KO, that is, 37-46, 90-94 and 146-153 g/kg dry matter respectively. The experimental substrates were formulated to keep the amounts of incubated fat-free OM, crude protein, neutral detergent fibre and acid detergent fibre constant in order to avoid biased results through potential differences in fermentability between WKS and its derivatives, and the basal substrate. The latter resembled the ingredient composition of a total mixed ration commonly used in Thai dairy cows. Fully automated gas production (GP) equipment was used to measure gas- and CH4 production. Irrespective of the type of substrate (p ≥ .115), both the absolute (ml/g fat-free OM) and relative (% of total GP) CH4 production was reduced at the highest inclusion level of WKS or its derivatives (p ≤ .019). Total GP (ml/g fat-free OM), however, was reduced after incubation of FER, FER + KO, and WKS, but not KO, at the highest inclusion level of the respective substrates (p = .019). Volatile fatty acids were likewise affected (p ≤ .001). Krabok oil can inhibit CH4 production but only when the dietary KO content is at least 9.4% (DM). Supplementation of KO in the form of WKS, however, is considered not opportune because the fat extracted residue of WKS is poorly degraded during fermentation.

RNA-seq, de novo transcriptome assembly and flavonoid gene analysis in 13 wild and cultivated berry fruit species with high content of phenolics.

BACKGROUND: Flavonoids are produced in all flowering plants in a wide range of tissues including in berry fruits. These compounds are of considerable interest for their biological activities, health benefits and potential pharmacological applications. However, transcriptomic and genomic resources for wild and cultivated berry fruit species are often limited, despite their value in underpinning the in-depth study of metabolic pathways, fruit ripening as well as in the identification of genotypes rich in bioactive compounds. RESULTS: To access the genetic diversity of wild and cultivated berry fruit species that accumulate high levels of phenolic compounds in their fleshy berry(-like) fruits, we selected 13 species from Europe, South America and Asia representing eight genera, seven families and seven orders within three clades of the kingdom Plantae. RNA from either ripe fruits (ten species) or three ripening stages (two species) as well as leaf RNA (one species) were used to construct, assemble and analyse de novo transcriptomes. The transcriptome sequences are deposited in the BacHBerryGEN database (http://jicbio.nbi.ac.uk/berries) and were used, as a proof of concept, via its BLAST portal (http://jicbio.nbi.ac.uk/berries/blast.html) to identify candidate genes involved in the biosynthesis of phenylpropanoid compounds. Genes encoding regulatory proteins of the anthocyanin biosynthetic pathway (MYB and basic helix-loop-helix (bHLH) transcription factors and WD40 repeat proteins) were isolated using the transcriptomic resources of wild blackberry (Rubus genevieri) and cultivated red raspberry (Rubus idaeus cv. Prestige) and were shown to activate anthocyanin synthesis in Nicotiana benthamiana. Expression patterns of candidate flavonoid gene transcripts were also studied across three fruit developmental stages via the BacHBerryEXP gene expression browser (http://www.bachberryexp.com) in R. genevieri and R. idaeus cv. Prestige. CONCLUSIONS: We report a transcriptome resource that includes data for a wide range of berry(-like) fruit species that has been developed for gene identification and functional analysis to assist in berry fruit improvement. These resources will enable investigations of metabolic processes in berries beyond the phenylpropanoid biosynthetic pathway analysed in this study. The RNA-seq data will be useful for studies of berry fruit development and to select wild plant species useful for plant breeding purposes.

PLANET-SNP pipeline: PLants based ANnotation and Establishment of True SNP pipeline.

Acute prediction of SNPs (Single Nucleotide Polymorphisms) from high throughput sequencing data is a challenging problem, having potential to explore possible variation within plants species. For the extraction of profitable information from bulk of data, machine learning (ML) could lead to development of accurate model based on the learning of prior information. We performed state of art, in-depth learning on six different plant species. Comparative evaluation of five different algorithms showed that Random Forest substantially outperformed in selection of potential SNPs, with markedly improved prediction accuracy via 10-fold cross validation technique and integrated in system known as PLANET-SNP. We present the accurate method to extract the potential SNPs with user specific customizable parameters. It will facilitate the identification of efficient and functional SNPs in most easy and intuitive way. PLANET-SNP pipeline is very flexible in terms of data input and output formats. PLANET-SNP Pipeline is available at http://www.ncgd.nbri.res.in/PLANET-SNP-Pipeline.aspx.

Evolutionary and Comparative Expression Analyses of TCP Transcription Factor Gene Family in Land Plants.

The plant-specific Teosinte-branched 1/Cycloidea/Proliferating (TCP) transcription factor genes are involved in plants' development, hormonal pathways, and stress response but their evolutionary history is uncertain. The genome-wide analysis performed here for 47 plant species revealed 535 TCP candidates in terrestrial plants and none in aquatic plants, and that TCP family genes originated early in the history of land plants. Phylogenetic analysis divided the candidate genes into Classes I and II, and Class II was further divided into CYCLOIDEA (CYC) and CINCINNATA (CIN) clades; CYC is more recent and originated from CIN in angiosperms. Protein architecture, intron pattern, and sequence characteristics were conserved in each class or clade supporting this classification. The two classes significantly expanded through whole-genome duplication during evolution. Expression analysis revealed the conserved expression of TCP genes from lower to higher plants. The expression patterns of Class I and CIN genes in different stages of the same tissue revealed their function in plant development and their opposite effects in the same biological process. Interaction network analysis showed that TCP proteins tend to form protein complexes, and their interaction networks were conserved during evolution. These results contribute to further functional studies on TCP family genes.

Inhibition of Fusarium culmorum, Penicillium chrysogenum and Rhizoctonia solani by n-hexane extracts of three plant species as a wood-treated oil fungicide.

AIMS: Wood as a packing tool is used for packaging and transportation of fruits and vegetables for a time period varying from hours to days. During transportation, fruits and vegetables can be affected by moulds with significant postharvest problems. The present study describes the possibility of using wood-treated oil fungicide of n-hexane extracts from Eucalyptus camaldulensis (aerial parts), Vitex agenus-castus (leaves) and Matricaria chamomilla (flowers) against the infestation of Fusarium culmorum, Rhizoctonia solani and Penicillium chrysogenum. METHODS AND RESULTS: Air-dried wood samples of Melia azedarach were prepared with the dimensions of 0·5 × 1 × 2 cm and treated with the oily extracts at the concentrations of 0, 1, 2 and 3%. Oils extracted with n-hexane from E. camaldulensis and V. agenus-castus showed promising antifungal activities against the isolated and molecularly identified three fungi F. culmorum, R. solani and P. chrysogenum, while M. chamomilla observed the lowest activity against the studied fungi. GC/MS analysis of oils reported that the major components in E. camaldulensis were ß-fenchol (25·51%), Cyclobuta[1,2:3,4]dicyclooctene-1,7(2H,6bH)-dione,dodecahydro,(6αß,6ßα,12αα,12ßß)- (17·05), 1,8-cineole (eucalyptol) (12·01%) and sabinene (9·45%); in V. agenus-castus were eucalyptol (22·17%), (E)-ß-caryophyllene (18·39%), and ß-sitosterol (12·44%); while in M. chamomilla were bisabolol oxide A (27·87%), (Z)-ß-farnesene (16·11%), D-limonene (14·18%) and chamazulene (11·27%). CONCLUSIONS: The results suggest using n-hexane oily extracts from E. camaldulensis and V. agenus-castus as a biofungicide for wood protection. SIGNIFICANCE AND IMPACT OF THE STUDY: This study highlights the importance of using bio-friendly fungicide agents to protect wood against most common moulds occurring during handling of food packaging.

Possible clues for camptothecin biosynthesis from the metabolites in camptothecin-producing plants.

The plant derived camptothecin (CPT) is a pentacyclic pyrroloquinoline alkaloid with unique antitumor activity. Successive discoveries of new CPT-producing plants occurred in recent years due to market demands. The scattered distribution among angiosperms drew researchers' attention. The aim of this review is to appraise the literature available to date for CPT distribution and the phytochemistry of these CPT-producing plants. Metabolite comparative analyses between the plants were also conducted for tracking of possible clues for CPT biosynthesis. Forty-three plant species in total were reported to possess CPT-producing capability, and one hundred twenty-five alkaloids classified into three major categories are summarized herein. Metabolite comparative analysis between these plants suggests the probability that the formation of the central intermediate for CPT biosynthesis has multiple origins. A more complete biogenetic reasoning for CPT and its structural homolog was delineated based on this fragmentary phytochemical evidence from a chemical point of view. Furthermore, an in-house compound database was constructed for further metabolomic analysis.

Antimycobacterial and antimalarial activities of endophytic fungi associated with the ancient and narrowly endemic neotropical plant Vellozia gigantea from Brazil

BACKGROUND Endophytic fungi, present mainly in the Ascomycota and Basidiomycota phyla, are associated with different plants and represent important producers of bioactive natural products. Brazil has a rich biodiversity of plant species, including those reported as being endemic. Among the endemic Brazilian plant species, Vellozia gigantea (Velloziaceae) is threatened by extinction and is a promising target to recover endophytic fungi. OBJECTIVE The present study focused on bioprospecting of bioactive compounds of the endophytic fungi associated with V. gigantea, an endemic, ancient, and endangered plant species that occurs only in the rupestrian grasslands of Brazil. METHODS The capability of 285 fungal isolates to produce antimicrobial and antimalarial activities was examined. Fungi were grown at solid-state fermentation to recover their crude extracts in dichloromethane. Bioactive extracts were analysed by chromatographic fractionation and NMR and displayed compounds with antimicrobial, antimycobacterial, and antimalarial activities. FINDINGS Five fungi produced antimicrobial and antimalarial compounds. Extracts of Diaporthe miriciae showed antifungal, antibacterial, and antimalarial activities; Trichoderma effusum displayed selective antibacterial activity against methicillin-resistant Staphylococcus aureus and Mycobacterium intracellulare; and three Penicillium species showed antibacterial activity. D. miriciae extract contained highly functionalised secondary metabolites, yielding the compound epoxycytochalasin H with high antimalarial activity against the chloroquine-resistant strain of Plasmodium falciparum, with an IC50 approximately 3.5-fold lower than that with chloroquine. MAIN CONCLUSION Our results indicate that V. gigantea may represent a microhabitat repository hotspot of potential fungi producers of bioactive compounds and suggest that endophytic fungal communities might be an important biological component contributing to the fitness of the plants living in the rupestrian grassland.

Constraining the timing of whole genome duplication in plant evolutionary history.

Whole genome duplication (WGD) has occurred in many lineages within the tree of life and is invariably invoked as causal to evolutionary innovation, increased diversity, and extinction resistance. Testing such hypotheses is problematic, not least since the timing of WGD events has proven hard to constrain. Here we show that WGD events can be dated through molecular clock analysis of concatenated gene families, calibrated using fossil evidence for the ages of species divergences that bracket WGD events. We apply this approach to dating the two major genome duplication events shared by all seed plants (ζ) and flowering plants (ɛ), estimating the seed plant WGD event at 399-381 Ma, and the angiosperm WGD event at 319-297 Ma. These events thus took place early in the stem of both lineages, precluding hypotheses of WGD conferring extinction resistance, driving dramatic increases in innovation and diversity, but corroborating and qualifying the more permissive hypothesis of a 'lag-time' in realizing the effects of WGD in plant evolution.

Widespread paleopolyploidy, gene tree conflict, and recalcitrant relationships among the carnivorous Caryophyllales.

PREMISE OF STUDY: The carnivorous members of the large, hyperdiverse Caryophyllales (e.g., Venus flytrap, sundews, and Nepenthes pitcher plants) represent perhaps the oldest and most diverse lineage of carnivorous plants. However, despite numerous studies seeking to elucidate their evolutionary relationships, the early-diverging relationships remain unresolved. METHODS: To explore the utility of phylogenomic data sets for resolving relationships among the carnivorous Caryophyllales, we sequenced 10 transcriptomes, including all the carnivorous genera except those in the rare West African liana family Dioncophyllaceae. We used a variety of methods to infer the species tree, examine gene tree conflict, and infer paleopolyploidy events. KEY RESULTS: Phylogenomic analyses supported the monophyly of the carnivorous Caryophyllales, with a crown age of 68-83 million years. In contrast to previous analyses, we recovered the remaining noncore Caryophyllales as nonmonophyletic, although the node supporting this relationship contained a significant amount of gene tree discordance. We present evidence that the clade contains at least seven independent paleopolyploidy events, previously unresolved nodes from the literature have high levels of gene tree conflict, and taxon sampling influences topology even in a phylogenomic data set, regardless of the use of coalescent or supermatrix methods. CONCLUSIONS: Our data demonstrate the importance of carefully considering gene tree conflict and taxon sampling in phylogenomic analyses. Moreover, they provide a remarkable example of the propensity for paleopolyploidy in angiosperms, with at least seven such events in a clade of less than 2500 species.

Polyploid species rely on vegetative reproduction more than diploids: a re-examination of the old hypothesis.

Background and Aims: Polyploidy is arguably the single most important genetic mechanism in plant speciation and diversification. It has been repeatedly suggested that polyploids show higher vegetative reproduction than diploids (to by-pass low fertility after the polyploidization), but there are no rigorous tests of it. Methods: Data were analysed by phylogenetic regressions of clonal growth parameters, and vegetative reproduction in culture on the ploidy status of a large set of species (approx. 900) from the Central European Angiosperm flora. Further, correlated evolution of ploidy and clonal traits was examined to determine whether or not polyploidy precedes vegetative reproduction. Key Results: The analyses showed that polyploidy is strongly associated with vegetative reproduction, whereas diploids rely more on seed reproduction. The rate of polyploid speciation is strongly enhanced by the existence of vegetative reproduction (namely extensive lateral spread), whereas the converse is not true. Conclusions: These findings confirm the old hypothesis that polyploids can rely on vegetative reproduction which thus may save many incipient polyploids from extinction. A closer analysis also shows that the sequence of events begins with development of vegetative reproduction, which is then followed by polyploidy. Vegetative reproduction is thus likely to play an important role in polyploid speciation.

Ancestral Gene Flow and Parallel Organellar Genome Capture Result in Extreme Phylogenomic Discord in a Lineage of Angiosperms.

While hybridization has recently received a resurgence of attention from systematists and evolutionary biologists, there remains a dearth of case studies on ancient, diversified hybrid lineages-clades of organisms that originated through reticulation. Studies on these groups are valuable in that they would speak to the long-term phylogenetic success of lineages following gene flow between species. We present a phylogenomic view of Heuchera, long known for frequent hybridization, incorporating all three independent genomes: targeted nuclear (~400,000 bp), plastid (~160,000 bp), and mitochondrial (~470,000 bp) data. We analyze these data using multiple concatenation and coalescence strategies. The nuclear phylogeny is consistent with previous work and with morphology, confidently suggesting a monophyletic Heuchera. By contrast, analyses of both organellar genomes recover a grossly polyphyletic Heuchera,consisting of three primary clades with relationships extensively rearranged within these as well. A minority of nuclear loci also exhibit phylogenetic discord; yet these topologies remarkably never resemble the pattern of organellar loci and largely present low levels of discord inter alia. Two independent estimates of the coalescent branch length of the ancestor of Heuchera using nuclear data suggest rare or nonexistent incomplete lineage sorting with related clades, inconsistent with the observed gross polyphyly of organellar genomes (confirmed by simulation of gene trees under the coalescent). These observations, in combination with previous work, strongly suggest hybridization as the cause of this phylogenetic discord. [Ancient hybridization; chloroplast capture; incongruence; phylogenomics; reticulation.].

Adaptive evolution of seed oil content in angiosperms: accounting for the global patterns of seed oils.

BACKGROUND: Studies of the biogeographic distribution of seed oil content in plants are fundamental to understanding the mechanisms of adaptive evolution in plants as seed oil is the primary energy source needed for germination and establishment of plants. However, seed oil content as an adaptive trait in plants is poorly understood. Here, we examine the adaptive nature of seed oil content in 168 angiosperm families occurring in different biomes across the world. We also explore the role of multiple seed traits like seed oil content and composition in plant adaptation in a phylogenetic and nonphylogenetic context. RESULT: It was observed that the seed oil content in tropical plants (28.4 %) was significantly higher than the temperate plants (24.6 %). A significant relationship between oil content and latitude was observed in three families Papaveraceae, Sapindaceae and Sapotaceae indicating that selective forces correlated with latitude influence seed oil content. Evaluation of the response of seed oil content and composition to latitude and the correlation between seed oil content and composition showed that multiple seed traits, seed oil content and composition contribute towards plant adaptation. Investigation of the presence or absence of phylogenetic signals across 168 angiosperm families in 62 clades revealed that members of seven clades evolved to have high or low seed oil content independently as they did not share a common evolutionary path. CONCLUSION: The study provides us an insight into the biogeographical distribution and the adaptive role of seed oil content in plants. The study indicates that multiple seed traits like seed oil content and the fatty acid composition of the seed oils determine the fitness of the plants and validate the adaptive hypothesis that seed oil quantity and quality are crucial to plant adaptation.

Morphometry and retention time as forcing functions to establishment and maintenance of aquatic macrophytes in a tropical reservoir / Morfometria e tempo de residência como fatores determinantes no estabelecimento e manutenção de macrófitas aquáticas em um reservatório tropical

Abstract Macrophytes may constitute an important resource for several chemical, physical and biological processes within aquatic ecosystems. This study considers that in tropical reservoirs with low retention time and with low values of shoreline development (DL), the expansion and persistence of aquatic macrophytes are mainly reported to local conditions (e.g., hydrodynamic and wind exposure) rather than trophic status and depth of the euphotic zone. In this context, this study aimed at describing and comparing the incidence of aquatic macrophytes in a throughflowing, non-dendritic tropical reservoir. During February 2006 to November 2007, eight limnological surveys were performed quarterly within the Ourinhos Reservoir, and in the mouth areas of its tributaries. At the six sampling stations 30 variables were measured. The number of sites with plants varied between 21 and 38 and at the end of the 1st year the total richness was found. The sampling survey outcome the recognition of 18 species of aquatic macrophytes; Cyperaceae (2 genera and 1 species), Pontederiaceae (3 species) and Onarograceae (3 genera) were the families with higher diversity. Seven species (Typha domingensis Pers., Myriophyllum aquaticum (Vell.) Verdec, Salvinia auriculata Aubl., Eichhornia azurea (Sw.) Kunth, Eleocharis sp1, Eichhornia crassipes (Mart.) Solms, Oxycaryum cubense (Poepp. & Kunth) Lye) always were present and were more frequent in the sites. The occurrence of emergent species predominated (45.9%), followed by submersed rooted (24.5%), free floating (19.5%), floating rooted (9.7%) and free submersed (0.3%). Although limnological variables and the distribution of macrophytes have discriminated the same sampling points, the stepwise multiple linear regressions did not pointed out strong correspondences (or coherence) among the most constant and distributed macrophyte species and the selected limnological variables, as well the trophic statuses. Seeing the low relationship among limnological variables and macrophytes distribution, in the case of Ourinhos Reservoir, the results pointed out that the water turbulence, low DL and wind exposure are the main driving forces that determine its aquatic plant distribution, life forms and species composition.

Resumo As macrófitas podem constituir um recurso importante para vários processos físicos, químicos e biológicos dos ecossistemas aquáticos. Esse estudo considera que nos reservatórios tropicais com baixo tempo de retenção e com baixos valores do grau de desenvolvimento das margens (DL), a expansão e manutenção das macrófitas aquáticas são referidas principalmente às condições locais (e.g., hidrodinâmica e exposição ao vento), ao invés do estado trófico e da profundidade de zona eufótica. Nesse contexto, o presente estudo teve como objetivo descrever e comparar a incidência de macrófitas aquáticas em um reservatório tropical de fluxo rápido e não dendrítico. De fevereiro de 2006 a novembro de 2007, oito avaliações limnológicas foram realizadas trimestralmente no reservatório Ourinhos e nas regiões de desembocadura de seus afluentes. Nas seis estações de amostragem 30 variáveis foram determinadas. O número de locais com plantas variou entre 21 e 38 e no final do primeiro ano o número total de espécies foi encontrado. Foram relacionadas 18 espécies de macrófitas aquáticas; Cyperaceae (2 gêneros e espécies), Pontederiaceae (3 espécies) e Onarograceae (3 gêneros) foram as famílias com mais diversidade. Sete espécies (Typha domingensis Pers., Myriophyllum aquaticum (Vell.) Verdec, Salvinia auriculata Aubl., Eichhornia azurea (Sw.) Kunth, Eleocharis sp1, Eichhornia crassipes (Mart.) Solms, Oxycaryum cubense (Poepp. & Kunth) Lye) sempre estiveram presentes e foram as mais frequentes. As ocorrências de espécies emergentes predominaram (45,9%), seguidas das submersas enraizadas (24,5%), flutuantes livres (19,5%), flutuantes enraizadas (9,7%) e submersas livres (0,3%). Embora as variáveis limnológicas e as distribuições de macrófitas tenham discriminado os mesmo pontos de coleta, regressões lineares múltiplas stepwise não apontaram correspondências fortes (ou coerentes) entre as espécies de macrófitas mais constantes e distribuídas e as variáveis limnológicas, assim como os estados tróficos. No reservatório Ourinhos, a baixa relação entre as variáveis limnológicas e a distribuição das macrófitas aponta que a turbulência da água, o baixo valor de DL e a exposição ao vento sejam as principais forças que determinam a distribuição das plantas aquáticas, as suas formas de vida e a composição das espécies.

Comparative and evolutionary analysis of α-amylase gene across monocots and dicots.

α-amylase is an important enzyme involved in starch degradation to provide energy to the germinating seedling. The present study was conducted to reveal structural and functional evolution of this gene among higher plants. Discounting polyploidy, most plant species showed only a single copy of the gene making multiple isoforms in different tissues and developmental stages. Genomic length of the gene ranged from 1472 bp in wheat to 2369 bp in soybean, and the size variation was mainly due to differences in the number and size of introns. In spite of this variation, the intron phase distribution and insertion sites were mostly conserved. The predicted protein size ranged from 414 amino acid (aa) in soybean to 449aa in Brachypodium. Overall, the protein sequence similarity among orthologs ranged from 56.4 to 97.4 %. Key motifs and domains along with their relative distances were conserved among plants although several species, genera, and class specific motifs were identified. The glycosyl hydrolase superfamily domain length varied from 342aa in soybean to 384aa in maize and sorghum while length of the C-terminal ß-sheet domain was highly conserved with 61aa in all monocots and Arabidopsis but was 59aa in soybean and Medicago. Compared to rice, 3D structure of the proteins showed 89.8 to 91.3 % similarity among the monocots and 72.7 to 75.8 % among the dicots. Sequence and relative location of the five key aa required for the ligand binding were highly conserved in all species except rice.

Nonadaptive radiation: Pervasive diet specialization by drift in scale insects?

At least half of metazoan species are herbivorous insects. Why are they so diverse? Most herbivorous insects feed on few plant species, and adaptive host specialization is often invoked to explain their diversification. Nevertheless, it is possible that the narrow host ranges of many herbivorous insects are nonadaptive. Here, we test predictions of this hypothesis with comparative phylogenetic analyses of scale insects, a group for which there appear to be few host-use trade-offs that would select against polyphagy, and for which passive wind-dispersal should make host specificity costly. We infer a strong positive relationship between host range and diversification rate, and a marked asymmetry in cladogenetic changes in diet breadth. These results are consonant with a system of pervasive nonadaptive host specialization in which small, drift- and extinction-prone populations are frequently isolated from persistent and polyphagous source populations. They also contrast with the negative relationship between diet breadth and taxonomic diversification that has been estimated in butterflies, a disparity that likely stems from differences in the average costs and benefits of host specificity and generalism in scale insects versus butterflies. Our results indicate the potential for nonadaptive processes to be important to diet-breadth evolution and taxonomic diversification across herbivorous insects.

Ancient WGD events as drivers of key innovations in angiosperms.

Polyploidy, or whole-genome duplication (WGD), is a ubiquitous feature of plant genomes, contributing to variation in both genome size and gene content. Although polyploidy has occurred in all major clades of land plants, it is most frequent in angiosperms. Following a WGD in the common ancestor of all extant angiosperms, a complex pattern of both ancient and recent polyploidy is evident across angiosperm phylogeny. In several cases, ancient WGDs are associated with increased rates of species diversification. For example, a WGD in the common ancestor of Asteraceae, the largest family of angiosperms with ∼25000 species, is statistically linked to a shift in species diversification; several other old WGDs are followed by increased diversification after a 'lag' of up to three nodes. WGD may thus lead to a genomic combination that generates evolutionary novelty and may serve as a catalyst for diversification. In this paper, we explore possible links between WGD, the origin of novelty, and key innovations and propose a research path forward.

Has the connection between polyploidy and diversification actually been tested?

Many major clades of angiosperms have several whole genome duplications (polyploidization events) in their distant past, suggesting that polyploidy drives or at least permits diversification. However, data on recently diverged groups are more equivocal, finding little evidence of elevated diversification following polyploidy. The discrepancy may be attributable at least in part to methodology. Many studies use indirect methods, such as chromosome numbers, genome size, and Ks plots, to test polyploidy, although these approaches can be misleading, and often lack sufficient resolution. A direct test of diversification following polyploidy requires a sequence-based approach that traces the history of nuclear genomes rather than species. These methods identify the point of coalescence of ancestral genomes, but may be misleading about the time and thus the extent of diversification. Limitations of existing methods mean that the connection between polyploidy and diversification has not been rigorously tested and remains unknown.