An efficient methodology for the purification of date palm peroxidase: Stability comparison with horseradish peroxidase (HRP)

In the present study, Peroxidase from date palm (Phoenix dactylifera) leaves was purified to homogeneity by three-step procedure including aqueous two-phase system, hydrophobic and Ion-exchange chromatography. The enzyme migrated as single band on SDS-PAGE giving molecular weight of 68?±?3?kDa. The purification factor for purified date palm peroxidase was 68 with high 41% yield. Enzymatic assays together with far-UV circular dichroism (CD), intrinsic and extrinsic fluorescence studies were carried out to monitor the structural stability of date palm and horseradish peroxidase (HRP) against various pH and temperatures. Activity measurements illustrated different pH stability for date palm and HRP. Both peroxidases are more susceptible to extreme acidic conditions as suggested by 4 & 15?nm red shift in date palm and HRP, respectively. Secondary structure analysis using far UV-CD exhibited predominance of α-helical (43.8%) structure. Also, pH induces loss in the secondary structure of date palm peroxidase. Thermal stability analysis revealed date palm peroxidase is more stable in comparison to HRP. In summary, date palm peroxidases could be promising enzymes for various applications where extreme pH and temperature is required.     

Genetic structure of the date palm (Phoenix dactylifera) in the Old World reveals a strong differentiation between eastern and western populations

Background and Aims Date palms (Phoenix dactylifera, Arecaceae) are of great economic and ecological value to the oasis agriculture of arid and semi-arid areas. However, despite the availability of a large date palm germplasm spreading from the Atlantic shores to Southern Asia, improvement of the species is being hampered by a lack of information on global genetic diversity and population structure. In order to contribute to the varietal improvement of date palms and to provide new insights on the influence of geographic origins and human activity on the genetic structure of the date palm, this study analysed the diversity of the species.Methods Genetic diversity levels and population genetic structure were investigated through the genotyping of a collection of 295 date palm accessions ranging from Mauritania to Pakistan using a set of 18 simple sequence repeat (SSR) markers and a plastid minisatellite.Key Results Using a Bayesian clustering approach, the date palm genotypes can be structured into two different gene pools: the first, termed the Eastern pool, consists of accessions from Asia and Djibouti, whilst the second, termed the Western pool, consists of accessions from Africa. These results confirm the existence of two ancient gene pools that have contributed to the current date palm diversity. The presence of admixed genotypes is also noted, which points at gene flows between eastern and western origins, mostly from east to west, following a human-mediated diffusion of the species.Conclusions This study assesses the distribution and level of genetic diversity of accessible date palm resources, provides new insights on the geographic origins and genetic history of the cultivated component of this species, and confirms the existence of at least two domestication origins. Furthermore, the strong genetic structure clearly established here is a prerequisite for any breeding programme exploiting the effective polymorphism related to each gene pool.     

Harvesting Effects and Population Ecology of the Buriti Palm (<Emphasis Type="Italic">Mauritia flexuosa</Emphasis> L. f., Arecaceae) in the Jalapão Region,Central Brazil<Superscript>1</Superscript>

Harvesting Effects and Population Ecology of Buriti Palm (Mauritia flexuosa L. f., Arecaceae) in the Jalapão Region, Central Brazil. Buriti palm is used for several purposes in Jalapão, Brazil, among which harvesting of young leaves has the greatest potential impact on palm populations. This work aimed to (i) assess buriti palm uses, (ii) identify experimentally the impacts of young-leaf harvesting on growth, survival, and leaf production of individuals, (iii) evaluate density and structure of buriti populations at different distances from a local harvester community, and (iv) quantify the fiber yield of young leaves. We conducted 21 interviews, sampled six buriti palm populations, and monitored 60 buriti individuals to evaluate the impacts of harvesting young leaves. The harvesting practices of artisans did not affect the survival, leaf production, or growth of buriti individuals. The buriti palm is abundant and has a “reverse J” population structure, indicating population regeneration. However, some signs of overexploitation were pointed out by local harvesters and observed in the field; therefore, we recommend management practices that would contribute to sustainability, such as harvesting young leaves from individuals with a large number of mature green leaves, and harvesting young leaves in sites far from the communities.     

Characterization of the ‘reserve cellulose’ of the endosperm of Carum carvi as a β(1–4)-mannan

The reserve polysaccharide of the endosperm of Carum carvi consists of more than 90% mannose and was characterized as a β(1–4)-mannan. Total or partial acid hydrolysis, enzymatic breakdown or acetolysis of either palm or Carum carvi mannan yielded the same mono- and oligosaccharides, indicating a similar chemical structure of the two reserve polysaccharides. However, Carum carvi contains only traces of the alkali soluble mannan A dominant in the palm endosperm polysaccharide.     

The impact of utilization of palm products on the population structure of the vegetable ivory palm (Hyphaene petersiana,arecaceae) in North-Central Namibia

Indigenous trees fulfil many subsistence and economic needs in north-central Namibia.Hyphaene petersiana provides a range of products which contribute to most aspects of people’s livelihoods. Of particular importance is its income-generating capacity through the use of palm leaves for basket production and the sale of liquor distilled from the fruits. This study investigates the population structure ofHyphaene petersiana in two areas of different human and livestock densities. Data were recorded for height class distribution, basal diameter of mature, stemmed individuals and sex ratios. These parameters of population structure indicate a reduction in the recruitment of mature palms and an increase in single-stemmed, vegetatively reproduced palm suckers of the smallest size class (0.5 m). This trend is more pronounced in the site with greater human and livestock population densities. It appears to be related to high recorded levels of browsing by livestock of juvenile, unstemmed palms, despite the unpalatability of palm leaves. This acts to prevent recruitment into larger size classes and increase the compensatory growth of palm suckers, the latter being enhanced due to reduced competition through the prior removal by grazing animals of grasses and other herbaceous species. Accompanying this heavy pressure on juvenile palms are destructive uses of mature, stemmed palms, including their felling for construction purposes and tapping for palm wine. With regional human population increase, exacerbated by a recent trend to privatise land and raise pressure on remaining communal resources, it is possible that these destructive uses of mature palms will increase to unsustainable levels. Concern is thus expressed in this study regarding the long-term viability ofHyphaene petersiana populatiops in this area.     

Patterns of pollen dispersal in a small population of the Canarian endemic palm (Phoenix canariensis)

The genetic diversity of small populations is greatly influenced by local dispersal patterns and genetic connectivity among populations, with pollen dispersal being the major component of gene flow in many plants species. Patterns of pollen dispersal, mating system parameters and spatial genetic structure were investigated in a small isolated population of the emblematic palm Phoenix canariensis in Gran Canaria island (Canary Islands). All adult palms present in the study population (n=182), as well as 616 seeds collected from 22 female palms, were mapped and genotyped at 8 microsatellite loci. Mating system analysis revealed an average of 5.8 effective pollen donors (N_ep) per female. There was strong variation in correlated paternity rates across maternal progenies (ranging from null to 0.9) that could not be explained by the location and density of local males around focal females. Paternity analysis revealed a mean effective pollen dispersal distance of ∼71 m, with ∼70% of effective pollen originating from a distance of <75 m, and 90% from <200 m. A spatially explicit mating model indicated a leptokurtic pollen dispersal kernel, significant pollen immigration (12%) from external palm groves and a directional pollen dispersal pattern that seems consistent with local altitudinal air movement. No evidence of inbreeding or genetic diversity erosion was found, but spatial genetic structure was detected in the small palm population. Overall, the results suggest substantial pollen dispersal over the studied population, genetic connectivity among different palm groves and some resilience to neutral genetic erosion and subsequently to fragmentation.     

The effects of utilization by people and livestock on Hyphaene petersiana (Arecaceae) basketry resources in the palm savanna of North-Central Namibia

Basketry production is an important informal sector activity in the palm savanna of north-central Namibia, particularly for women. This study assesses the comparative impact of utilization by basket makers and browsing livestock in areas of different human and livestock population pressures on the source of weaving fibre, leaves from juvenile individuals of the vegetable ivory palm,Hyphaene petersiana. Mature individuals of this species are an important source of edible fruit. Destructive uses of mature individuals such as tapping for palm wine and the cutting of stems for construction purposes are also practised, even though they are forbidden by customary law. Unlike other centres of basket production in southern Africa, the level of leaf utilization for basketry is low and there is potential for greater use of this resource. Despite the unpalatability of this species, a cause for concern, however, is the intensity of browsing by domestic livestock on young palms, which may affect the future structure and viability of the palm population in north-central Namibia. This predicted degradation of a multiple-use species such asH. petersiana represents the gradual erosion of an important buffer against rural poverty, loss of income and reduction in food security.     

Molecular Clocks and Archeogenomics of a Late Period Egyptian Date Palm Leaf Reveal Introgression from Wild Relatives and Add Timestamps on the Domestication

The date palm, Phoenix dactylifera, has been a cornerstone of Middle Eastern and North African agriculture for millennia. It was first domesticated in the Persian Gulf, and its evolution appears to have been influenced by gene flow from two wild relatives, P. theophrasti, currently restricted to Crete and Turkey, and P. sylvestris, widespread from Bangladesh to the West Himalayas. Genomes of ancient date palm seeds show that gene flow from P. theophrasti to P. dactylifera may have occurred by ∼2,200 years ago, but traces of P. sylvestris could not be detected. We here integrate archeogenomics of a ∼2,100-year-old P. dactylifera leaf from Saqqara (Egypt), molecular-clock dating, and coalescence approaches with population genomic tests, to probe the hybridization between the date palm and its two closest relatives and provide minimum and maximum timestamps for its reticulated evolution. The Saqqara date palm shares a close genetic affinity with North African date palm populations, and we find clear genomic admixture from both P. theophrasti, and P. sylvestris, indicating that both had contributed to the date palm genome by 2,100 years ago. Molecular-clocks placed the divergence of P. theophrasti from P. dactylifera/P. sylvestris and that of P. dactylifera from P. sylvestris in the Upper Miocene, but strongly supported, conflicting topologies point to older gene flow between P. theophrasti and P. dactylifera, and P. sylvestris and P. dactylifera. Our work highlights the ancient hybrid origin of the date palms, and prompts the investigation of the functional significance of genetic material introgressed from both close relatives, which in turn could prove useful for modern date palm breeding.     

Effects of oil palm plantations on habitat structure and fish assemblages in Amazon streams

The aim of this research is to assess the effects of oil palm plantations on stream habitat and their fish assemblage diversity. We hypothesize that streams which drain through oil palm plantations tend to be less heterogeneous, limiting the occurrence of many species, than streams that drain through forest fragments, which support higher fish diversity. A total of 17 streams were sampled; eight in forest fragments and nine in oil palm plantations. Environmental and biological variables were sampled along 150 m stretch in each stream. Of the 242 environmental variables measured, ten were considered important to assess the condition of structural habitat, and out of these variables, four were considered relevant in the distinction between streams in oil palm plantations and forest fragments. A total of 7245 fishes were collected, belonging to 63 species. Unlike our original hypothesis, the species richness did not differ between forest fragment and oil palm plantations streams, showing that it is not a good divert measure in streams disturbance assessment. However, fish assemblages differed in species composition, and 56 species were recorded in oil palm plantation streams, while 44 species were recorded in forest fragments streams. Some species were identified as indicators of either altered (Aequidens tetramerus and Apistogramma agassizii) or undisturbed areas (Helogenes marmoratus). Overall, oil palm plantations were proven to change stream habitat structure and fish species distribution, corroborating other studies that have evidenced changes in patterns of biological community structure due to impacts by different land uses.     

Phylogenetic utility of the nuclear genes AGAMOUS 1 and PHYTOCHROME B in palms (Arecaceae): an example within Bactridinae

Background and Aims

Molecular phylogenetic studies of palms (Arecaceae) have not yet provided a fully resolved phylogeny of the family. There is a need to increase the current set of markers to resolve difficult groups such as the Neotropical subtribe Bactridinae (Arecoideae: Cocoseae). We propose the use of two single-copy nuclear genes as valuable tools for palm phylogenetics.

Methods

New primers were developed for the amplification of the AGAMOUS 1 (AG1) and PHYTOCHROME B (PHYB) genes. For the AGAMOUS gene, the paralogue 1 of Elaeis guineensis (EgAG1) was targeted. The region amplified contained coding sequences between the MIKC K and C MADS-box domains. For the PHYB gene, exon 1 (partial sequence) was first amplified in palm species using published degenerate primers for Poaceae, and then specific palm primers were designed. The two gene portions were sequenced in 22 species of palms representing all genera of Bactridinae, with emphasis on Astrocaryum and Hexopetion, the status of the latter genus still being debated.

Key Results

The new primers designed allow consistent amplification and high-quality sequencing within the palm family. The two loci studied produced more variability than chloroplast loci and equally or less variability than PRK, RPBII and ITS nuclear markers. The phylogenetic structure obtained with AG1 and PHYB genes provides new insights into intergeneric relationships within the Bactridinae and the intrageneric structure of Astrocaryum. The Hexopetion clade was recovered as monophyletic with both markers and was weakly supported as sister to Astrocaryum sensu stricto in the combined analysis. The rare Astrocaryum minus formed a species complex with Astrocaryum gynacanthum. Moreover, both AG1 and PHYB contain a microsatellite that could have further uses in species delimitation and population genetics.

Conclusions

AG1 and PHYB provide additional phylogenetic information within the palm family, and should prove useful in combination with other genes to improve the resolution of palm phylogenies.     

Characterization of the chloroplast genome sequence of oil palm (Elaeis guineensis Jacq.)

Oil palm (Elaeis guineensis Jacq.) is an economically important crop, which is grown for oil production. To better understand the molecular basis of oil palm chloroplasts, we characterized the complete chloroplast (cp) genome sequence obtained from 454 pyrosequencing. The oil palm cp genome is 156,973 bp in length consisting of a large single-copy region of?85,192 bp flanked on each side by inverted repeats of 27,071 bp with a small single-copy region of 17,639 bp joining the?repeats. The genome contains 112 unique genes: 79 protein-coding genes, 4 ribosomal RNA genes and 29 tRNA genes. By aligning the cp?genome sequence with oil palm cDNA sequences, we observed 18 non-silent and 10 silent RNA editing events among 19 cp protein-coding genes. Creation of an initiation codon by RNA editing in rpl2 has been reported in several monocots and was also found in the oil palm cp genome. Fifty common chloroplast protein-coding genes from 33 plant taxa were used to construct ML and MP?phylogenetic trees. Their topologies are similar and strongly support for the position of E. guineensis as the sister of closely related species Phoenix dactylifera in Arecaceae (palm families) of monocot subtrees.     

Diversity and occupancy of small carnivores within oil palm plantations in central Sumatra,Indonesia

In Southeast Asia, the conversion of native forests to oil palm plantations threatens tropical biodiversity, but very little is known about the impacts of oil palm cultivation on small carnivore species. To determine the diversity and occupancy of small carnivores within oil palm plantations and to investigate possible factors that might affect their presence within oil palm, we used camera-traps within two oil palm plantations in central Sumatra, analysed the data using occupancy modelling and tested whether two covariates (distance to the edge of the oil palm habitat and distance from extensive areas of lowland forest) affected the model parameters for each small carnivore species. From 3164 camera-trap days, we detected only three small carnivores: leopard cat (Prionailurus bengalensis), common palm civet (Paradoxurus hermaphroditus) and Malay civet (Viverra tangalunga), which indicates that there was a low diversity of small carnivores within the oil palm plantations. Both the leopard cat and common palm civet were found deep within the oil palm, whereas the Malay civet was only detected near the edge in one of the plantations. The leopard cat and common palm civet had very high occupancy values, whereas the Malay civet had low values for both occupancy and detection probability. Neither covariate affected occupancy of the leopard cat and common palm civet, but distance from the edge of the oil palm habitat did influence their detection probabilities. Malay civet occupancy decreased with distance from the oil palm edge, and detection probability was affected by distance from extensive areas of lowland forest. Forests and rest/den site availability are suggested to be important features for small carnivores with oil palm-dominated landscapes.     

Responses of tropical fruit bats to monoculture and polyculture farming in oil palm smallholdings

The oil palm industry is one of the main economic drivers in Southeast Asia. The industry has caused tropical deforestation on a massive scale in producing countries, and this forest conversion to oil palm agriculture has decimated the habitat of numerous native species. Monoculture and polyculture practices are two distinctive oil palm production systems. We hypothesize that polyculture farming hosts a greater diversity of species than monoculture farming. Habitat complexity in smallholdings is influenced by multiple farming practices (i.e. polyculture and monoculture). However, little is known about the effects of such farming practices in smallholdings on mammalian biodiversity, and particularly frugivorous bats. Our study aimed to find the best farming practice to reconcile oil palm production with biodiversity conservation. Mist-nets were used to trap frugivorous bats at 120 smallholdings in Peninsular Malaysia. We compared species richness and the abundance of frugivorous bats between monoculture and polyculture smallholdings. We investigated their relationships with vegetation structure characteristics. Our results revealed that species richness and abundance of frugivorous bats were significantly greater in polyculture smallholdings than monoculture smallholdings. We also found that 28.21% of the variation in species richness was explained by in situ habitat characteristics, including the number of dead standing oil palms and immature oil palms, non-grass cover, height of non-grass cover, and farming practices. The in situ habitat quality was closely associated with oil palm farming management. Commercial growers should implement polyculture rather than monoculture farming because polyculture farming has positive effects on the abundance and species richness of bats in oil palm production landscapes.     

Use of re-esterified palm oils,differing in their acylglycerol structure,in weaning-piglet diets

Re-esterified oils are new fat sources obtained from chemical esterification of acid oils with glycerol (both economically interesting by-products from oil refining and biodiesel industries, respectively). The different fatty acid (FA) positional distribution and acylglycerol composition of re-esterified oils may enhance the apparent absorption of saturated fatty acids (SFA) and, thus, their overall nutritive value. The aim of the present study was to investigate the potential use of re-esterified palm oils, in comparison with their corresponding acid and native oils, and also with an unsaturated fat source in weaning-piglet diets. The parameters assessed were: FA apparent absorption, acylglycerol and free fatty acid (FFA) composition of feces, and growth performance. One-hundred and twenty weaning piglets (average weight of 8.50±1.778 kg) were blocked by initial BW (six blocks) and randomly assigned to five dietary treatments, resulting in four piglets per pen and six replicates per treatment. Dietary treatments were a basal diet supplemented with 10% (as-fed basis) of native soybean oil (SN), native palm oil (PN), acid palm oil (PA), re-esterified palm oil low in mono- (MAG) and diacylglycerols (DAG) (PEL), or re-esterified palm oil high in MAG and DAG (PEH). Results from the digestibility balance showed that SN reached the greatest total FA apparent absorption, and statistically different from PN, PA and PEL (P<0.05). There were no statistical differences among palm-oil sources (P>0.05), but PEH achieved the greatest total FA apparent absorption. Animals fed PEL, despite the fact that PEL oil contained more sn-2 SFA, did not show an improved absorption of SFA (P>0.05). Animals fed PA and PN showed similar apparent absorption coefficients (P>0.05), despite the high FFA content of PA oil. The acylglycerol and FFA composition of feces was mainly composed of FFA. There were no significant differences in growth performance (P>0.05). Results of the present study suggest that, despite the different acylglycerol structure of re-esterified oils, there were no significant differences in digestibility or performance with respect to their corresponding PN and PA oils in weaning-piglet diets.     

Composition and properties of wood and cellulose of tropical plants

A component, chemical and morphological composition of wood of the Howea fosteriana palm and the Cereus peruvians cactus and the wood stem of the Dracaena sanderiana was studied. The supramolecular structure and the physicochemical properties of cellulose samples which were extracted from the wood species were examined by wide-angle X-ray scattering, Fourier transform infrared spectroscopy, high-resolution ¹³CP/MAS nuclear magnetic resonance in a solid state, and scanning electron microscopy.     

The Chloroplast Genome Sequence of Date Palm (Phoenix dactylifera L. cv. ‘Aseel’)

Date palm (Phoenix dactylifera L.) is an economically important and widely cultivated palm of the family Arecaceae. We sequenced the complete date palm chloroplast genome (cpDNA) from Pakistani cv. ??Aseel??, using a combination of Sanger-based and next-generation sequencing technologies. Being very similar to a sequence from a Saudi Arabian date palm cultivar ??Khalas?? published recently, the size of the genome was 158,458?bp with a pair of inverted repeat (IR) regions of 27,276?bp that were separated by a large single-copy (LSC) region of 86,195?bp and a small single-copy (SSC) region of 17,711?bp. Genome annotation demonstrated a total of 138 genes, of which 89 were protein coding, 39 were tRNA, and eight were rRNA genes. Comparison of cpDNA sequences of cultivars ??Aseel?? and ??Khalas?? showed following intervarietal variations in the LSC region; (a) two SNPs in intergenic spacers and one SNP in the rpoc1 gene, (b) polymorphism in two mono-nucleotide simple sequence repeats (SSR), and (c) a 4-bp indel in the accD-psaI intergenic spacer. The SSC region has a polymorphic site in the mono-nucleotide SSR located at position 120,710. We also compared cv. ??Aseel?? cpDNA sequence with partial P. dactylifera cpDNA sequence entries deposited in Genbank and identified a number of potentially useful polymorphisms in this species. Analysis of date palm cpDNA sequences revealed a close relationship with Typha latifolia. Occurrence of small numbers of forward and inverted repeats in date palm cpDNA indicated conserved genome arrangement.     

Efficient Transformation of Oil Palm Protoplasts by PEG-Mediated Transfection and DNA Microinjection

Background

Genetic engineering remains a major challenge in oil palm (Elaeis guineensis) because particle bombardment and Agrobacterium-mediated transformation are laborious and/or inefficient in this species, often producing chimeric plants and escapes. Protoplasts are beneficial as a starting material for genetic engineering because they are totipotent, and chimeras are avoided by regenerating transgenic plants from single cells. Novel approaches for the transformation of oil palm protoplasts could therefore offer a new and efficient strategy for the development of transgenic oil palm plants.

Methodology/Principal Findings

We recently achieved the regeneration of healthy and fertile oil palms from protoplasts. Therefore, we focused on the development of a reliable PEG-mediated transformation protocol for oil palm protoplasts by establishing and validating optimal heat shock conditions, concentrations of DNA, PEG and magnesium chloride, and the transfection procedure. We also investigated the transformation of oil palm protoplasts by DNA microinjection and successfully regenerated transgenic microcalli expressing green fluorescent protein as a visible marker to determine the efficiency of transformation.

Conclusions/Significance

We have established the first successful protocols for the transformation of oil palm protoplasts by PEG-mediated transfection and DNA microinjection. These novel protocols allow the rapid and efficient generation of non-chimeric transgenic callus and represent a significant milestone in the use of protoplasts as a starting material for the development of genetically-engineered oil palm plants.     

Complete Sequence and Comparative Analysis of the Chloroplast Genome of Coconut Palm (Cocos nucifera)

Coconut, a member of the palm family (Arecaceae), is one of the most economically important trees used by mankind. Despite its diverse morphology, coconut is recognized taxonomically as only a single species (Cocos nucifera L.). There are two major coconut varieties, tall and dwarf, the latter of which displays traits resulting from selection by humans. We report here the complete chloroplast (cp) genome of a dwarf coconut plant, and describe the gene content and organization, inverted repeat fluctuations, repeated sequence structure, and occurrence of RNA editing. Phylogenetic relationships of monocots were inferred based on 47 chloroplast protein-coding genes. Potential nodes for events of gene duplication and pseudogenization related to inverted repeat fluctuation were mapped onto the tree using parsimony criteria. We compare our findings with those from other palm species for which complete cp genome sequences are available.