Characterization of 14 microsatellite loci in a tropical palm, Attalea phalerata (Arecaceae)

? Premise of the study: We developed microsatellite primers for the widely distributed tropical palm Attalea phalerata for studies on the dispersal and spatial genetic structure of palm populations. ? Methods and Results: Fourteen di-, tri-, and tetra-nucleotide microsatellite primer pairs were identified. The number of alleles in the population tested ranged between 3 and 25, with a mean of 12.1. Ten microsatellite loci exhibited no significant deviations from Hardy-Weinberg Equilibrium or presence of null alleles, and their combined probability of exclusion was 0.998. ? Conclusions: These microsatellite loci will be useful in parentage analysis and population genetics studies of Attalea phalerata.     

Seed banks on Attalea phalerata (Arecaceae) stems in the Pantanal wetland, Brazil

Background and Aims

Seeds can accumulate in the soil or elsewhere, such as on the stems of palms when these are covered by persistent sheaths. These sheaths could act as a safe site for some species. Here, we studied whether persistent sheaths of the palm Attalea phalerata (Arecaceae) are available sites for seed accumulation in the Pantanal wetland of Brazil. We also investigated whether the composition, richness and diversity of species of seeds in the persistent sheaths are determined by habitat (riparian forest and forest patches) and/or season (wet and dry).

Methods

All accumulated material was collected from ten persistent sheaths along the stems of 64 A. phalerata individuals (16 per habitat and 16 per season). The material was then individually inspected under a stereomicroscope to record seed species and number.

Key Results

Of the 640 sheaths sampled, 65 % contained seeds (n = 3468). This seed bank included 75 species belonging to 12 families, and was primarily composed of small, endozoochoric seeds, with a few abundant species (Cecropia pachystachya and Ficus pertusa). Moraceae was the richest family (four species) and Urticaceae the most abundant (1594 seeds). Stems of A. phalerata in the riparian forest had 1·8 times more seeds and 1·3 times more species than those in forest patches. In the wet season we sampled 4·1 times more seeds and 2·2 more species on palm stems than in the dry season. Richness did not differ between habitats, but was higher in the wet season. Abundance was higher in forest patches and in the wet season.

Conclusions

Attalea phalerata stems contain a rich seed bank, comparable to soil seed banks of tropical forests. As most of these seeds are not adapted to grow in flooding conditions, palm stems might be regarded as safe sites for seeds (and seedlings) to escape from the seasonal flooding of the Pantanal.     

Geonoma polyandra (Arecaceae), a new species from Ecuador

Geonoma polyandra , a new species of Arecaceae from Ecuador is described. It has staminate flowers with 10–12 stamens. Species with more than six stamens have previously not been described in the genus.     

Coccothrinax torrida (Arecaceae), a new species from southeastern Cuba

A new palm species,Coccothrinax torrida, endemic to a karst hill of semidesert southeastern Cuba, is described and illustrated. The new species is small sized, related toC. pauciramosa, and is characterized by the following features: narrow semiorbicular flat leaves that are covered on the adaxial surface by white wax; a small irregular palman; long and erect inflorescences; and small, white, smooth fruits.     

Geonoma irena (Arecaceae), a new species from western Ecuador

A new palm species, Geonoma irena from western Ecuador, is described and illustrated. It is separated from the polymorphic G. cuneata on the basis of differences in floral morphology, associated with major differences in flowering biology.     

The chloroplast DNA locus psbZ-trnfM as a potential barcode marker in Phoenix L. (Arecaceae)

The genus Phoenix (Arecaceae) comprises 14 species distributed from Cape Verde Islands to SE Asia. It includes the economically important species Phoenix dactylifera. The paucity of differential morphological and anatomical useful characters, and interspecific hybridization, make identification of Phoenix species difficult. In this context, the development of reliable DNA markers for species and hybrid identification would be of great utility. Previous studies identified a 12 bp polymorphic chloroplast minisatellite in the trnG (GCC)-trnfM (CAU) spacer, and showed its potential for species identification in Phoenix. In this work, in order to develop an efficient DNA barcode marker for Phoenix, a longer cpDNA region (700 bp) comprising the mentioned minisatellite, and located between the psbZ and trnfM (CAU) genes, was sequenced. One hundred and thirty-six individuals, representing all Phoenix species except P. andamanensis,were analysed. The minisatellite showed 2-7 repetitions of the 12 bp motif, with 1-3 out of seven haplotypes per species. Phoenix reclinata and P. canariensis had species-specific haplotypes. Additional polymorphisms were found in the flanking regions of the minisatellite, including substitutions, indels and homopolymers. All this information allowed us to identify unambiguously eight out of the 13 species, and overall 80% of the individuals sampled. Phoenix rupicola and P. theophrasti had the same haplotype, and so had P. atlantica, P. dactylifera, and P. sylvestris (the “date palm complex” sensu Pintaud et al. 2013). For these species, additional molecular markers will be required for their unambiguous identification. The psbZ-trnfM (CAU) region therefore could be considered as a good basis for the establishment of a DNA barcoding system in Phoenix, and is potentially useful for the identification of the female parent in Phoenix hybrids.     

Commonness of Amazonian palm (Arecaceae) species: Cross-scale links and potential determinants

The mechanisms that cause variation in commonness (abundances and range sizes) of species remain debated in ecology, and a repeatedly observed pattern is the positive relation between local abundances and larger scale range sizes. We used the Amazonian palm species (Arecaceae) to investigate the dependence between and potential determinants of commonness across three (local, landscape, continental) spatial scales. Commonness at the smaller scales (local abundance, landscape frequency) was estimated using data from 57 transects (5 × 500 m) in primary, non-inundated (terra firme) rainforest in a western Amazonian landscape, while commonness at the largest scale (continental range size) was estimated from digitized distribution maps. Landscape frequency was positively related to both local abundance and continental range size, which, however, were not related to each other. Landscape frequency was positively related to topographic niche breadth. Stem height correlated with continental range size and was the only species life-history trait related to any commonness measure. Distance from the study area to a species' range centre did not influence any of the commonness measures. The factors determining commonness in the Amazonian palm flora appear to be scale-dependent, with the unrelated local scale abundance and continental range size probably being controlled by different driving factors. Interestingly, commonness at the intermediate, landscape scale seems linked to both the smaller and the larger scale. Our results point towards topographic niche breadth at the smaller scales and stem height, possibly reflecting species' dispersal potential, at the continental scale as important determinants of commonness.     

Attalea crassispatha,a rare and endemic Haitian palm

The taxonomic history of the poorly known Haitian endemic palmAttalea crassispatha is given. Morphology and pollen morphology are described and illustrated. A discussion is given concerning its position within the Attaleinae. In particular, staminate flower morphology of the subtribe is discussed.     

Selfing and resource allocation in Schiedea salicaria (Caryophyllaceae), a gynodioecious species

Abstract Levels of selfing and resource allocation patterns were investigated in Schiedea salicaria (Caryophyllaceae), a gynodioecious species with high levels of inbreeding depression and nuclear control of male sterility. Selfing levels were higher in hermaphrodites than females, especially when adjusted for early acting inbreeding depression. The sexes of S. salicaria were similar in most allocation patterns including number of flowers and capsules per inflorescence, seeds per flower, and seed mass. Seeds produced by females had higher levels of germination than seeds of hermaphrodites, a likely result of high selfing levels and the expression of inbreeding depression in the progeny of hermaphrodites. Invasion of females in populations of S. salicaria is probably related to the expression of inbreeding depression at germination and in later life history stages. Comparisons with related species of Schiedea that also have nuclear control of male sterility suggest that reallocation of resources in hermaphrodites to male function occurs as females increase in frequency, but that resource reallocation is not important for the success of females when they first invade populations.     

The patterns of genetic diversity in Carpentaria acuminata (Arecaceae), and rainforest history in northern Australia

Carpentaria acuminata occurs in monsoon rainforest and is endemic to the Northern Territory, Australia. The genetic diversity of C. acuminata populations was surveyed across the geographical range of the species using isozyme analysis. Genetic diversity within C. acuminata populations ( H _E = 0.143) was typical of rainforest species and woody angiosperms generally. Genetic diversity was not correlated with rainforest patch size. However, there was significant heterogeneity among populations ( F _ST = 0.379), with infrequent effective gene flow among populations ( Nm = 0.39). Genetic diversity was negatively correlated with increasing distance between neighbouring C. acuminata populations, but geographical distance was not a good predictor of genetic similarity. C. acuminata is a favoured food of mobile frugivores such as Torres Strait pigeons and flying foxes. The decreased diversity with decreasing density of populations indicated that seed dispersal by frugivores has been important for the maintenance of diversity in this species. Populations known to have originated on relatively young, Holocene landforms were not necessarily genetically depauperate. Gene flow by pollen is apparently limited because C. acuminata populations are significantly inbred regardless of genetic diversity ( F = 0.641). The distribution and diversity of rare alleles, i.e. those occurring in few populations, is consistent with the theory of rainforest contraction during the Pleistocene.     

Pejibaye palm (Bactris gasipaes,Arecaceae): Multi-use potential for the lowland humid tropics

Pejibaye (Bactris gasipaes) was domesticated and widely used in the lowland humid neotropics during pre-Colombian times. Several research programs are underway to study and improve the species for use by farmers in ecologically suitable regions. Five breeding programs are outlined, each for a use to which the pejibaye may be put: (1) palmito (heart of palm), (2) whole fruit for human consumption, (3) flour and meal production, (4) oil production, and (5) animal ration from residues or purposefully bred varieties. Yield estimates and breeding problems are discussed. It is certain that the pejibaye can again become an important crop for the humid tropics.     

Evaluation of the bromatological potential of seeds and fruits ofSabal Mexicana Mart. (Arecaceae)

This work presents bromatological analyses performed on seeds and fruits of Sabal mexicana Mart.; a comparison with data existent of other palms and some phytochemical data are presented. A discussion of the possible importance of some results obtained and the potential use of this palm is presented

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Evaluacion del potencial bromatologico de semillas y frutos de sabal mexicana, mart. (arecaceae)

Résumé  Este trabajo presenta análisis bromatolólogicos realizados en semillas y frutos de Salbal mexicana Mart. Los resultados se comparan con datos existentes para otras palmas y se presentan algunos datos fitoquimicos; ademús se discute acerca de la posible importancia de algunos de los resultados obtenidos y su uso potential

     

Microsatellites in palm (Arecaceae) sequences

Microsatellites are the most promising co-dominant markers, widely distributed throughout the genome. Identification of these repeating genomic subsets is a tedious and iterative process making computational approaches highly useful for solving this biological problem. Here 38,083 microsatellites were localized in palm sequences. A total of 2, 97,023 sequences retrieved from public domains were used for this study. The sequences were unstained using the tool Seqclean and consequently clustered using CAP3. SSRs are located in the sequences using the microsatellite search tool, MISA. Repeats were detected in 33,309 sequences and more than one SSR had appeared in 3,943 sequences. In the present study, dinucleotide repeats (49%) were found to be more abundant followed by mononucleotide (30%) and trinucleotide (19%). Also among the dinucleotides, AG/GA/TC/CT motifs (55.8%) are predominantly repeating within the palm sequences. Thus in future this study will lead to the development of specific algorithm for mining SSRs exclusively for palms.     

Palms (Arecaceae) from a Paleocene rainforest of northern Colombia

Palms are a monophyletic group with a dominantly tropical distribution; however, their fossil record in low latitudes is strikingly scarce. In this paper, we describe fossil leaves, inflorescences, and fruits of palms from the middle to late Paleocene Cerrejón Formation, outcropping in the Ranchería River Valley, northern Colombia. The fossils demonstrate the presence of at least five palm morphospecies in the basin ca. 60 Ma. We compare the morphology of the fossils with extant palms and conclude that they belong to at least three palm lineages: the pantropical Cocoseae of the subfamily Arecoideae, the monotypic genus Nypa, and either Calamoideae or Coryphoideae. The fossil fruits and inflorescences are among the oldest megafossil records of these groups and demonstrate that the divergence of the Cocoseae was more than 60 Ma, earlier than has previously been thought. These fossils are useful in tracing the range expansion or contraction of historical or current neotropical elements and also have profound implications for the understanding of the evolution of neotropical rainforests.     

Nuclear DNA Amounts in Palms (Arecaceae)

Nuclear DNA amounts are reported for 83 species and 53 genera of palms, covering all of the six subfamilies. 4C DNA contents range between 3.89 and 55.62 pg in diploids, showing an approximate 14.3-fold variation in genome size. Polyploids have DNA contents of up to 156.40 pg/4c which demonstrates a 40.2-fold variation. Diploids with high DNA contents occur in three subfamilies of palms (Coryphoideae, Calamoideae, Arecoideae), and seem to be further restricted to particular tribes or subtribes (Thrinacinae, Borasseae, Lepidocaryeae, Caryoteae, some subtribes of Areceae). Palms from the subfamilies Nypoideae and Phytelephantoideae have the lowest DNA amounts, followed by the Phoeniceae and the Corypheae: Livistoninae from the subfamily Coryphoideae. Although DNA amounts in some genera and subtribes are usually constant, e.g., in Phoenix, Phytelephas, the Livistoninae, Dypsidinae, diploid Butiinae), considerable variation occurs at the diploid level in some large and apparently actively evolving genera such as Chamaedorea, Pinanga, Cenoma and possibly Bactris. Formaldehyde fixation is recommended for palms, as conventional ethanol-acetic acid fixation has proved to be unsuitable for DNA estimation of Feulgen-stained nuclei by microdensitometry, since it can lead to errors up to 2.5-fold in extent. Chromosome counts are reported for 72 of the species studied, of which 42 are new.     

Thrombospondin related adhesive protein (TRAP), a potential malaria vaccine candidate

We have investigated whether naturally induced immunity to Plasmodium falciparum thrombospondin related adhesive protein contributes to protection against malaria in humans. We have carried out a case control study in children living in an endemic region of West Africa to reveal associations between PfTRAP seroprevalence and the risk of cerebral malaria. Sera collected from the case and control groups were analysed by ELISA to compare their serum reactivity against PfTRAP, the circumsporozoite protein and the merozoite surface protein 1. Children with uncomplicated malaria had a significantly higher PfTRAP seroprevalence when compared to children with cerebral malaria. The risk of developing cerebral malaria appeared to depend on the reciprocal relationship between sporozoite inoculation rates and humoral immunity against PfTRAP. Our results suggest that naturally induced humoral immunity against PfTRAP contributes to the development of protection against severe malaria. Experimentally induced immunity against TRAP in different rodent models has consistently proven to elicit a high degree of protection against malaria. This together with the functional properties of TRAP and data describing CD4 and CD8 epitopes for PfTRAP indicate that this molecule could increase the protective efficiency of available sporozoite malaria vaccines.     

Marine derived biosurfactants: a vast potential future resource

Surfactants and emulsifiers are surface-active compounds (SACs) which play an important role in various industrial processes and products due to their interfacial properties. Many of the chemical surfactants in use today are produced from non-renewable petrochemical feedstocks, while biosurfactants (BS) produced by microorganisms from renewable feedstocks are considered viable alternatives to petroleum based surfactants, due to their biodegradability and eco-friendly nature. However, some well-characterised BS producers are pathogenic and therefore, not appropriate for scaled-up production. Marine-derived BS have been found to be produced by non-pathogenic organisms making them attractive possibilities for exploitation in commercial products. Additionally, BS produced from marine bacteria may show excellent activity at extreme conditions (temperature, pH and salinity). Despite being non-pathogenic, marine-derived BS have not been exploited commercially due to their low yields, insufficient structural elucidation and uncharacterised genes. Therefore, optimization of BS production conditions in marine bacteria, characterization of the compounds produced as well as the genes involved in the biosynthesis are necessary to improve cost-efficiency and realise the industrial demands of SACs.     

Caleosin-assembled oil bodies as a potential delivery nanocarrier

Encapsulation of hydrophobic agents with nanocarriers is challenging. Therefore, we have sought to use nanoscale artificial oil bodies (NOBs) as an alternative delivery carrier. To constitute NOBs, caleosin (Cal), a structural protein of plant seed oil bodies, was first fused with ZH2 (Cal-ZH2). ZH2 is a bivalent anti-HER2/neu affibody with a high affinity towards the HER2/neu receptor. After overproduction in Escherichia coli, insoluble Cal-ZH2 was isolated and used to assemble NOBs in one step. Consequently, resulting NOBs had a zeta potential around −49 mV and ranged in size from 150 to 200 nm. Upon loading with a hydrophobic fluorescence dye, NOBs were found to be selectively internalized into HER2/neu-positive tumor cells. Further analyses showed that more than 90% cells were invaded by dye-loaded NOBs and the cargo dye was released in cells with time. In addition, the in vitro assay revealed the release of the dye from NOBs in a slow and prolong manner. Overall, these results indicate the potential of Cal-based NOBs as a delivery vehicle.