Elucidating the Mesocarp Drupe Transcriptome of Açai (Euterpe oleracea Mart.): An Amazonian Tree Palm Producer of Bioactive Compounds.

Euterpe oleracea palm, endemic to the Amazon region, is well known for açai, a fruit violet beverage with nutritional and medicinal properties. During E. oleracea fruit ripening, anthocyanin accumulation is not related to sugar production, contrarily to grape and blueberry. Ripened fruits have a high content of anthocyanins, isoprenoids, fibers, and proteins, and are poor in sugars. E. oleracea is proposed as a new genetic model for metabolism partitioning in the fruit. Approximately 255 million single-end-oriented reads were generated on an Ion Proton NGS platform combining fruit cDNA libraries at four ripening stages. The de novo transcriptome assembly was tested using six assemblers and 46 different combinations of parameters, a pre-processing and a post-processing step. The multiple k-mer approach with TransABySS as an assembler and Evidential Gene as a post-processer have shown the best results, with an N50 of 959 bp, a read coverage mean of 70x, a BUSCO complete sequence recovery of 36% and an RBMT of 61%. The fruit transcriptome dataset included 22,486 transcripts representing 18 Mbp, of which a proportion of 87% had significant homology with other plant sequences. Approximately 904 new EST-SSRs were described, and were common and transferable to Phoenix dactylifera and Elaeis guineensis, two other palm trees. The global GO classification of transcripts showed similar categories to that in P. dactylifera and E. guineensis fruit transcriptomes. For an accurate annotation and functional description of metabolism genes, a bioinformatic pipeline was developed to precisely identify orthologs, such as one-to-one orthologs between species, and to infer multigenic family evolution. The phylogenetic inference confirmed an occurrence of duplication events in the Arecaceae lineage and the presence of orphan genes in E. oleracea. Anthocyanin and tocopherol pathways were annotated entirely. Interestingly, the anthocyanin pathway showed a high number of paralogs, similar to in grape, whereas the tocopherol pathway exhibited a low and conserved gene number and the prediction of several splicing forms. The release of this exhaustively annotated molecular dataset of E. oleracea constitutes a valuable tool for further studies in metabolism partitioning and opens new great perspectives to study fruit physiology with açai as a model.

Patterns of genetic diversity and structure of a threatened palm species (Euterpe edulis Arecaceae) from the Brazilian Atlantic Forest.

The detection of distribution patterns of genetic diversity of plant and animal species has contributed to the understanding of biodiversity and evolutionary history of the Atlantic Forest. We used microsatellite markers to access the genetic diversity and structure of 26 populations and 527 adult individuals of Euterpe edulis, a native palm which is an important food resource for fauna and is intensively exploited due to economic reasons. We found high genetic diversity and inbreeding in all populations analyzed. We report highest rates of inbreeding for this species, which could reflect the anthropic impacts of selective cutting, fragmentation, and change in foraging behavior from pollinators and less availability and mobility of large dispersers. We detected by STRUCTURE, two genetic groups, Northern and Southern, which divide the Brazilian Atlantic Forest geographically. These groups have low genetic admixtures, but we found a region of lineage hybridization in the contact zone with low recent gene flow. Distribution pattern of this species corroborates results from previous studies reporting the Last Glacial Maximum (LGM) have shaped the structuring of the species through movements of forests' expansion and contraction. The STRUCTURE analysis of each group revealed the presence of genetic subgroups with low rates of recurrent gene flow. Southern subgroups have higher rates of admixtures than the Northern subgroups, revealing greater historical connectivity of forests in this region.

Plastid genome evolution in Amazonian açaí palm (Euterpe oleracea Mart.) and Atlantic forest açaí palm (Euterpe edulis Mart.).

KEY MESSAGE: The plastomes of E. edulis and E. oleracea revealed several molecular markers useful for genetic studies in natural populations and indicate specific evolutionary features determined by vicariant speciation. Arecaceae is a large and diverse family occurring in tropical and subtropical ecosystems worldwide. E. oleracea is a hyperdominant species of the Amazon forest, while E. edulis is a keystone species of the Atlantic forest. It has reported that E. edulis arose from vicariant speciation after the emergence of the belt barrier of dry environment (Cerrado and Caatinga biomes) between Amazon and Atlantic forests, isolating the E. edulis in the Atlantic forest. We sequenced the complete plastomes of E. edulis and E. oleracea and compared them concerning plastome structure, SSRs, tandem repeats, SNPs, indels, hotspots of nucleotide polymorphism, codon Ka/Ks ratios and RNA editing sites aiming to investigate evolutionary traits possibly affected by distinct environments. Our analyses revealed 303 SNPs, 91 indels, and 82 polymorphic SSRs among both species. Curiously, the narrow correlation among localization of repetitive sequences and indels strongly suggests that replication slippage is involved in plastid DNA mutations in Euterpe. Moreover, most non-synonymous substitutions represent amino acid variants in E. edulis that evolved specifically or in a convergent manner across the palm phylogeny. Amino acid variants observed in several plastid proteins in E. edulis were also identified as positive signatures across palm phylogeny. The higher incidence of specific amino acid changes in plastid genes of E. edulis in comparison with E. oleracea probably configures adaptive genetic variations determined by vicariant speciation. Our data indicate that the environment generates a selective pressure on the plastome making it more adapted to specific conditions.

Morphoagronomic and molecular characterization of Euterpe oleraceaaccessions from eastern Brazilian Amazon

Açaí (Euterpe oleraceaMart.) -a common tropical palm has high social, economic, and environmental importance in the Amazon region. In the light of increasing exploration to obtain the fruit and heart of this palms, comprehensive studies are warranted for conservation and genetic improvement. Here, we characterized açaí accessions using phenological, morphological, and agronomic descriptors and random amplified polymorphic DNA (RAPD)molecular markers for joint selection of accessions with greater productivity. Hundred accessions were analyzed using 18 morphoagronomic descriptors and 13 RAPD markers. The spathe and inflorescence emission phases during flowering and fruiting showed seasonality. Based on the coefficient of variation and mean squared error, the accessions exhibited high variability in the tested morphoagronomic descriptors and were distributed into seven groups. Fruit, seed, and pulp weights were important descriptors for the distinction of accessions and identification of those with greater productivity. The accessions presented >85% similarity, and 85 accessions, distributed in nine subgroups, could not be differentiated using RAPD markers. There was no correlation between grouping based on morphometric descriptors and RAPD markers. Panicle weight was 3.9-9.0 kg in 15 accessions and 100-fruit pulp weight was 35-50 g in six accessions. Therefore, accessions with high productivity could be selected.

Phytochemical profile of genotypes of Euterpe edulis Martius - Juçara palm fruits.

Juçara fruit (Euterpe edulis) has received attention due to its similarities to Euterpe oleracea (Açaí). The aim of this study was to evaluate the cytotoxicity, bioactive compounds, antioxidant capacities and chemopreventive activities of the fruit pulps of six populations of E. edulis (J1-J6) and one population of E. espiritosantense from different ecological regions. ESI(-)-FT-ICR-MS was used to evaluate the pulp composition. The varieties J1 and J4 presented higher polyphenol contents, while J2 and J5 showed higher anthocyanin contents. ESI-FT-ICR MS identified cyanidin-3-rutinoside (J1, J2, J3, J4, J5, J7), protocatechuic acid, methylhydroxybenzoate hexoside and rutin (J1 to J7) and malvidin-glicoside (J2 to J5). The J2, J3, J4, J5 and J6 samples inhibited inducible nitric oxide synthase (iNOS). The chemoprevention biomarker quinone reductase was significantly induced by J6. Pulp from plants J3, J4, J6 and J7 significantly reduced the inflammatory cytokine TNF-α, and J6 was selected as having the most potential for cultivation and consumption.

Chemical composition and antioxidant capacity of açaí (Euterpe oleracea) genotypes and commercial pulps.

BACKGROUND: Açaí has been reported to contain many bioactive compounds, including phenolic compounds such as anthocyanins. This study aimed to determine the chemical composition and antioxidant potential of pulps of three different açaí genotypes from the Active Germplasm Bank of Embrapa Eastern Amazon and three commercial açaí pulps from Belém, state of Pará, Brazil. RESULTS: Anthocyanin 3-rutinoside was the major anthocyanin present in freeze-dried açaí pulp samples. The commercial sample C showed the greatest amounts of cyanidin 3-glucoside and cyanidin 3-rutinoside (18 942 and 34 397 µg g-1 respectively). The content of phenolic compounds varied significantly among the commercial and genotype samples, and vanillic acid was found in the highest concentration in the samples studied. All açaí samples showed high DPPH, ORAC and TEAC values, confirming the exceptionally high radical-scavenging capacity of açaí pulp previously reported by other researchers. CONCLUSION: The commercial samples showed higher antioxidant capacity and higher levels of anthocyanins and non-anthocyanic compounds than those of the genotype samples. Among the genotypes studied, L4P16 stood out for its higher contents of fibre and bioactive compounds and higher antioxidant capacity, indicating that this genotype has great potential for use in plant breeding programs that should be further explored. © 2016 Society of Chemical Industry.

Defaunation leads to microevolutionary changes in a tropical palm.

Many large species have declined worldwide due to habitat fragmentation and poaching. The defaunation of large frugivores and the consequent reductions of seed dispersal services may have immediate effects on plant demography. Yet, the lasting effects of frugivore defaunation on microevolutionary processes of the plants they disperse remain understudied. We tested if the loss of large seed dispersers can lead to microevolutionary changes of a tropical palm. We show that frugivore defaunation is the main driver of changes in allelic frequency among populations. Turnover of alleles accounted for 100% of dissimilarity in allelic frequencies of individuals between defaunated and non-defaunated forests; and individuals from defaunated sites are 1.5 times more similar genetically than those found in pristine sites. Given that sizeable fractions of the palm fruit crops remain undispersed in defaunated sites due to lack of large-bodied frugivores, this distinct pattern of gene pool composition of early recruits may reveal strong dispersal limitation for specific genotypes, or collapses of gene flow between fragmented areas, or both. Because most of tropical tree species rely on seed dispersal by vertebrates, our results show that defaunation has a lasting effect on microevolutionary processes, with potential consequences for persistence under scenarios of environmental change.

The risks of introduction of the Amazonian palm Euterpe oleracea in the Atlantic rainforest.

The introduction of a species may alter ecological processes of native populations, such as pollination and dispersal patterns, leading to changes in population structure. When the introduced and the native species are congeners, interference in pollination can also lead to hybridization. We aimed to understand the ecological aspects of Euterpe oleracea introduction in the Atlantic forest and the possible consequences for the conservation of the native congener Euterpe edulis. We analysed the population structure of palm populations, including hybrids, and observed the interaction with frugivorous birds of both palm species after E. oleracea introduction. We observed that E. edulis had significantly lower density and a smaller number of seedlings when occurring with E. oleracea. Native and introduced Euterpe species shared nine frugivorous bird species. E. oleracea and hybrids had dispersed outside the original planting area. Consequently, the risks of introduction of E. oleracea may mostly be related to the disruption of interactions between E. edulis and frugivorous birds and the spontaneous production of hybrids. Finally, the cultivation of E. oleracea and hybrids in Atlantic rainforest could affect the conservation of the already endangered E. edulis.

The risks of introduction of the Amazonian palm Euterpe oleracea in the Atlantic rainforest / Os riscos da introdução da palmeira amazônica Euterpe oleracea na Floresta Atlântica

Abstract The introduction of a species may alter ecological processes of native populations, such as pollination and dispersal patterns, leading to changes in population structure. When the introduced and the native species are congeners, interference in pollination can also lead to hybridization. We aimed to understand the ecological aspects of Euterpe oleracea introduction in the Atlantic forest and the possible consequences for the conservation of the native congener Euterpe edulis. We analysed the population structure of palm populations, including hybrids, and observed the interaction with frugivorous birds of both palm species after E. oleracea introduction. We observed that E. edulis had significantly lower density and a smaller number of seedlings when occurring with E. oleracea. Native and introduced Euterpe species shared nine frugivorous bird species. E. oleracea and hybrids had dispersed outside the original planting area. Consequently, the risks of introduction of E. oleracea may mostly be related to the disruption of interactions between E. edulis and frugivorous birds and the spontaneous production of hybrids. Finally, the cultivation of E. oleracea and hybrids in Atlantic rainforest could affect the conservation of the already endangered E. edulis.

Resumo A introdução de uma espécie pode alterar processos ecológicos de populações nativas, tais como padrões de polinização e dispersão, levando a mudanças na estrutura populacional. Quando espécies introduzidas e nativas são congêneres, a interferência na polinização pode levar também à hibridização. Nossos objetivos foram entender os aspectos ecológicos da introdução de Euterpe oleracea na Floresta Atlântica e as possíveis consequências sobre a conservação da congênere nativa Euterpe edulis. Para isso, analisamos a estrutura populacional, incluindo híbridos, e observamos a interação de aves frugívoras com ambas as espécies de palmeira após a introdução de E. oleracea. Observamos que E. edulis apresentou densidade total e número de plântulas menores quando coocorrente com E. oleracea. As palmeiras congenéricas compartilharam nove espécies de aves frugívoras. E. oleracea e híbridos foram dispersos além da área original de plantio. Consequentemente, os riscos da introdução de E. oleracea podem estar principalmente relacionados com o possível deslocamento de interações entre E. edulis e aves frugívoras e com a produção de híbridos. Desta forma, o cultivo de E. oleracea e híbridos podem afetar a conservação da já ameaçada E. edulis.

Contemporary and historic factors influence differently genetic differentiation and diversity in a tropical palm.

Population genetics theory predicts loss in genetic variability because of drift and inbreeding in isolated plant populations; however, it has been argued that long-distance pollination and seed dispersal may be able to maintain gene flow, even in highly fragmented landscapes. We tested how historical effective population size, historical migration and contemporary landscape structure, such as forest cover, patch isolation and matrix resistance, affect genetic variability and differentiation of seedlings in a tropical palm (Euterpe edulis) in a human-modified rainforest. We sampled 16 sites within five landscapes in the Brazilian Atlantic forest and assessed genetic variability and differentiation using eight microsatellite loci. Using a model selection approach, none of the covariates explained the variation observed in inbreeding coefficients among populations. The variation in genetic diversity among sites was best explained by historical effective population size. Allelic richness was best explained by historical effective population size and matrix resistance, whereas genetic differentiation was explained by matrix resistance. Coalescence analysis revealed high historical migration between sites within landscapes and constant historical population sizes, showing that the genetic differentiation is most likely due to recent changes caused by habitat loss and fragmentation. Overall, recent landscape changes have a greater influence on among-population genetic variation than historical gene flow process. As immediate restoration actions in landscapes with low forest amount, the development of more permeable matrices to allow the movement of pollinators and seed dispersers may be an effective strategy to maintain microevolutionary processes.