Assembly, annotation and analysis of the chloroplast genome of the Algarrobo tree Neltuma pallida (subfamily: Caesalpinioideae).

BACKGROUND: Neltuma pallida is a tree that grows in arid soils in northwestern Peru. As a predominant species of the Equatorial Dry Forest ecoregion, it holds significant economic and ecological value for both people and environment. Despite this, the species is severely threatened and there is a lack of genetic and genomic research, hindering the proposal of evidence-based conservation strategies. RESULTS: In this work, we conducted the assembly, annotation, analysis and comparison of the chloroplast genome of a N. pallida specimen with those of related species. The assembled chloroplast genome has a length of 162,381 bp with a typical quadripartite structure (LSC-IRA-SSC-IRB). The calculated GC content was 35.97%. However, this is variable between regions, with a higher GC content observed in the IRs. A total of 132 genes were annotated, of which 19 were duplicates and 22 contained at least one intron in their sequence. A substantial number of repetitive sequences of different types were identified in the assembled genome, predominantly tandem repeats (> 300). In particular, 142 microsatellites (SSR) markers were identified. The phylogenetic reconstruction showed that N. pallida grouped with the other Neltuma species and with Prosopis cineraria. The analysis of sequence divergence between the chloroplast genome sequences of N. pallida, N. juliflora, P. farcta and Strombocarpa tamarugo revealed a high degree of similarity. CONCLUSIONS: The N. pallida chloroplast genome was found to be similar to those of closely related species. With a size of 162,831 bp, it had the classical chloroplast quadripartite structure and GC content of 35.97%. Most of the 132 identified genes were protein-coding genes. Additionally, over 800 repetitive sequences were identified, including 142 SSR markers. In the phylogenetic analysis, N. pallida grouped with other Neltuma spp. and P. cineraria. Furthermore, N. pallida chloroplast was highly conserved when compared with genomes of closely related species. These findings can be of great potential for further diversity studies and genetic improvement of N. pallida.

Microbacterium plantarum sp. nov. and Microbacterium thalli sp. nov., two endophytic metal-resistant bacteria isolated from Sphaeralcea angustifolia (Cav.) G. Don and Prosopis laevigata (Humb. et Bonpl. ex Willd) M.C. Johnston.

Four Gram-positive, aerobic, catalase- and oxidase-negative, rod-shaped, motile endophytic bacterial strains, designated NM3R9T, NE1TT3, NE2TL11 and NE2HP2T, were isolated from the inner tissues (leaf and stem) of Sphaeralcea angustifolia and roots of Prosopis laevigata. They were characterized using a polyphasic approach, which revealed that they represent two novel Microbacterium species. Phylogenetic analysis based on 16S rRNA gene sequencing showed that the species closest to NE2HP2T was Microbacterium arborescens DSM 20754T (99.6 %) and that closest to NM3R9T, NE2TL11 and NE2TT3 was Microbacterium oleivorans NBRC 103075T (97.4 %). The whole-genome average nucleotide identity value between strain NM3R9T and Microbacterium imperiale DSM 20530T was 90.91 %, and that between strain NE2HP2T and M. arborecens DSM 20754T was 91.03 %. Digital DNA-DNA hybridization showed values of less than 70 % with the type strains of related species. The polar lipids present in both strains included diphosphatidylglycerol, phosphatidylglycerol, glycolipids and unidentified lipids, whereas the major fatty acids included anteiso-C15 : 0, anteiso-C17 : 0, iso-C16 : 0 and C16 : 0. Whole-cell sugars included mannose, rhamnose and galactose. Strains NM3R9T and NE2HP2T showed physiological characteristics different from those present in closely related Microbacterium species. According to the taxonomic analysis, both strains belong to two novel species. The name Microbacterium plantarum sp. nov. is proposed for strain NE2HP2T (=LMG 30875T=CCBAU 101117T) and Microbacterium thalli sp. nov. for strains NM3R9T (=LMG 30873T=CCBAU 101116T), NE1TT3 (=CCBAU 101114) and NE2TL11 (=CCBAU 101115).

Rhizobacterial Isolates from Prosopis limensis Promote the Growth of Raphanus sativus L. Under Salt Stress.

Microbial biotechnology employes techniques that rely based on the natural interactions that occur in ecosystems. Bacteria, including rhizobacteria, play an important role in plant growth, providing agricultural crops with an alternative that can mitigate the negative effects of abiotic stress, such as those caused by saline environments. In this study, bacterial isolates were obtained from soil and roots of Prosopis limensis Bentham from the department of Lambayeque, Peru. This region has high salinity levels, therefore, the collected samples were used to isolate plant growth-promoting rhizobacteria (PGPR), which were identified through morphological, and physical-biochemical characteristics. These salt tolerant bacteria were screened phosphate solubilization, indole acetic acid, deaminase activity and molecular characterization by 16S rDNA sequencing. Eighteen samples from saline soils of the Prosopis limensis plants in the northern coastal desert of San Jose district, Lambayeque, Peru. The bacterial isolates were screened for salt tolerance ranging from 2 to 10%, a total of 78 isolates were found. Isolates 03, 13 and 31 showed maximum salt tolerance at 10%, in vitro ACC production, phosphate solubilization and IAA production. The three isolates were identified by sequencing the amplified 16S rRNA gene and were found to be Pseudomonas sp. 03 (MW604823), Pseudomonas sp. 13 (MW604824) and Bordetella sp. 31 (MW604826). These microorganisms promoted the germination of radish plants and increased the germination rates for treatments T2, T3 and T4 by 129, 124 and 118% respectively. The beneficial effects of salt tolerant PGPR isolates isolated from saline environments can be new species, used to overcome the detrimental effects of salt stress on plants. The biochemical response and inoculation of the three isolates prove the potential of using these strains as a source of products that can be employed for the development of new compounds proving their potential as biofertilizers for saline environments.

The Genome of the Mimosoid Legume Prosopis cineraria, a Desert Tree.

The mimosoid legumes are a clade of ~40 genera in the Caesalpinioideae subfamily of the Fabaceae that grow in tropical and subtropical regions. Unlike the better studied Papilionoideae, there are few genomic resources within this legume group. The tree Prosopis cineraria is native to the Near East and Indian subcontinent, where it thrives in very hot desert environments. To develop a tool to better understand desert plant adaptation mechanisms, we sequenced the P. cineraria genome to near-chromosomal assembly, with a total sequence length of ~691 Mb. We predicted 77,579 gene models (76,554 CDS, 361 rRNAs and 664 tRNAs) from the assembled genome, among them 55,325 (~72%) protein-coding genes that were functionally annotated. This genome was found to consist of over 58% repeat sequences, primarily long terminal repeats (LTR-)-retrotransposons. We find an expansion of terpenoid metabolism genes in P. cineraria and its relative Prosopis alba, but not in other legumes. We also observed an amplification of NBS-LRR disease-resistance genes correlated with LTR-associated retrotransposition, and identified 410 retrogenes with an active burst of chimeric retrogene creation that approximately occurred at the same time of divergence of P. cineraria from a common lineage with P. alba~23 Mya. These retrogenes include many biotic defense responses and abiotic stress stimulus responses, as well as the early Nodulin 93 gene. Nodulin 93 gene amplification is consistent with an adaptive response of the species to the low nitrogen in arid desert soil. Consistent with these results, our differentially expressed genes show a tissue specific expression of isoprenoid pathways in shoots, but not in roots, as well as important genes involved in abiotic salt stress in both tissues. Overall, the genome sequence of P. cineraria enriches our understanding of the genomic mechanisms of its disease resistance and abiotic stress tolerance. Thus, it is a very important step in crop and legume improvement.

Low genetic variation of foliar traits among Prosopis chilensis (Leguminosae) provenances.

Prosopis chilensis (Molina) Stuntz (Leguminosae) is a valuable native species in Argentina that has been proposed to be used in reforestation, afforestation and restoration programmes. Natural provenances show important differentiation in height, shape, spine size, fruits and foliar traits throughout their distribution in the semiarid Monte ecoregion. The goal of this work was to characterize the genetic basis of the leaf variation in P. chilensis aiming to contribute to the improvement management program. We analyzed morphological variation and estimate narrow sense heritability for ten quantitative traits from a provenance-progeny trial founded from open pollinated families. We assessed the variance components by a generalized linear mixed model. Differences among provenances were quantified through univariate QST statistics and multivariate discriminant analysis of principal components. Finally, univariate and multivariate neutrality test were conducted to unveil the evolutionary forces that shape the variation. Univariate and multivariate analysis showed low genetic variation in foliar traits among provenances grown in the common garden. Consistently, the QST estimates for each trait were low. Both, the univariate (QST-FST comparison) and the multivariate neutrality test suggest that the leaf variation among provenances may be shaped by genetic drift rather than selective forces. Heritability estimates were significant only for leaflet apex and leaflet apex/leaflet area. Since genetic variation for most foliar traits among provenances estimated under controlled environmental conditions were very low or absent, the variation described in the wild would be explained merely by plastic response to varying environments. These results are discussed in terms of adaptive strategies and the use of different provenances as seed sources within the framework of the improvement program. It is expected that P. chilensis seeds or seedlings from trees selected under economical criteria will be able to develop in different areas thanks to the phenotypic plasticity of leaf traits.

Unraveling the Chloroplast Genomes of Two Prosopis Species to Identify Its Genomic Information, Comparative Analyses and Phylogenetic Relationship.

Genus Prosopis (family Fabaceae) are shrubby trees, native to arid and semi-arid regions of Asia, Africa, and America and known for nitrogen fixation. Here, we have sequenced the complete chloroplast (cp) genomes of two Prosopis species (P. juliflora and P. cineraria) and compared them with previously sequenced P. glandulosa, Adenanthera microsperma, and Parkia javanica belonging to the same family. The complete genome sequences of Prosopis species and related species ranged from 159,389 bp (A. microsperma) to 163,677 bp (P. cineraria). The overall GC contents of the genomes were almost the similar (35.9-36.6%). The P. juliflora and P. cineraria genomes encoded 132 and 131 genes, respectively, whereas both the species comprised of 85 protein-coding genes higher than other compared species. About 140, 134, and 129 repeats were identified in P. juliflora, P. cineraria and P. glandulosa cp genomes, respectively. Similarly, the maximum number of simple sequence repeats were determined in P. juliflora (88), P. cineraria (84), and P. glandulosa (78). Moreover, complete cp genome comparison determined a high degree of sequence similarity among P. juliflora, P. cineraria, and P. glandulosa, however some divergence in the intergenic spacers of A. microsperma and Parkia javanica were observed. The phylogenetic analysis showed that P. juliflora is closer to P. cineraria than P. glandulosa.

The detection of a non-anemophilous plant species using airborne eDNA.

Genetic analysis of airborne plant material has historically focused (generally implicitly rather than as a stated goal) on pollen from anemophilous (wind-pollinated) species, such as in multiple studies examining the relationship of allergens to human health. Inspired by the recent influx of literature applying environmental DNA (eDNA) approaches to targeted-species and whole-ecosystem study, we conducted a proof-of-concept experiment to determine whether airborne samples reliably detect genetic material from non-anemophilous species that may not be releasing large plumes of pollen. We collected airborne eDNA using Big Spring Number Eight dust traps and quantified the amount of eDNA present for a flowering wind-pollinated genus (Bouteloua) and insect-pollinated honey mesquite (Prosopis glandulosa) that was not flowering at the time of the study. We were able to detect airborne eDNA from both species. Since honey mesquite is insect-pollinated and was not flowering during the time of this study, our results confirm that airborne eDNA consists of and can detect species through more than just pollen. Additionally, we were able to detect temporal patterns reflecting Bouteloua reproductive ecology and suggest that airborne honey mesquite eDNA responded to weather conditions during our study. These findings suggest a need for more study of the ecology of airborne eDNA to uncover its potential for single-species and whole-community research and management in terrestrial ecosystems.

Exploring genetic variability in Prosopis cineraria using two gene targeted CAAT box-derived polymorphism (CBDP) and start codon targeted (SCoT) polymorphism markers.

Two gene targeted molecular marker systems, CAAT box-derived polymorphism (CBDP) and start codon targeted (SCoT) polymorphism, were used to assess the genetic diversity and relatedness in Prosopis cineraria, a tree of abiotic stress tolerance, agroforestry and ethano-botanical importance. A total of ten wild populations consisting 49 individuals collected from different locations of Indian Thar Desert were examined for the genetic analysis of P. cineraria. Ten CBDP and seven SCoT primers, total 17 primers, generated 204 bands with an average of 12 bands per primer, of which 159 (76.8%) were polymorphic. The average PIC values for both CBDP and SCoT marker were 0.543 and 0.547, respectively. The cumulative data of these two markers were used to analyze different genetic diversity indices and compute pair-wise distances. The population genetic diversity analysis based on cumulative data of CBDP and SCoT markers revealed the high levels of genetic differentiation (GST = 0.341; GST > 0.15 as high), low value of gene flow (Nm = 0.966; Nm > 1 as high) and high fixation index (FST = 0. 415). The highest genetic diversity was observed among NGBAR populations followed by CHR populations, while SIK populations showed lowest genetic diversity. AMOVA revealed the percent molecular variation was higher within the populations (77%) compared to that of among populations (23%). The clustering pattern based on UPGMA and PCoA plot clearly demonstrated the genetic relationship among the genotypes collected from the different regions of Indian Thar Desert.

Fourteen simple-sequence repeats newly developed for population genetic studies in Prosopis africana (Fabaceae-Mimosoideae).

BACKGROUND: There is very limited genetic knowledge in Prosopis africana, an important sub-Saharan multi-purpose tree species. Availability of highly polymorphic genetic markers would be helpful for future genetic work. FINDINGS: Leaf samples from 15 trees were used to develop simple sequence repeat (SSR) markers. Size-selected fragments from genomic DNA were enriched for repeats and the library was analyzed on an Illumina MiSeq platform. Fourteen SSRs were selected and applied in two Burkinabe populations (40 adult trees each). The number of alleles varied from 4 to 20, evenness (effective number of alleles/observed number of alleles) averaged to 0.54 and unbiased heterozygosity ranged from 0.305 to 0.925 over all loci and populations. Null alleles were not detected. CONCLUSIONS: Due to the high level of polymorphism and lack of null alleles the developed SSRs can be effectively employed in population genetic studies.

The pre-Columbian introduction and dispersal of Algarrobo (Prosopis, Section Algarobia) in the Atacama Desert of northern Chile.

Archaeological and palaeoecological studies throughout the Americas have documented widespread landscape and environmental transformation during the pre-Columbian era. The highly dynamic Formative (or Neolithic) period in northern Chile (ca. 3700-1550 yr BP) brought about the local establishment of agriculture, introduction of new crops (maize, quinoa, manioc, beans, etc.) along with a major population increase, new emergent villages and technological innovations. Even trees such as the Algarrobos (Prosopis section Algarobia) may have been part of this transformation. Here, we provide evidence that these species were not native to the Atacama Desert of Chile (18-27°S), appearing only in the late Holocene and most likely due to human actions. We assembled a database composed of 41 taxon specific AMS radiocarbon dates from archaeobotanical and palaeoecological records (rodent middens, leaf litter deposits), as well an extensive bibliographical review comprising archaeobotanical, paleoecological, phylogenetic and taxonomic data to evaluate the chronology of introduction and dispersal of these trees. Although Algarrobos could have appeared as early as 4200 yr BP in northernmost Chile, they only became common throughout the Atacama over a thousand years later, during and after the Formative period. Cultural and natural factors likely contributed to its spread and consolidation as a major silvicultural resource.

Expression of metallothionein type 2 and 3 genes in Prosopis glandulosa leaves treated with copper.

For a better understanding of the strategies that are used by Prosopis glandulosa in heavy metal tolerance, the present study evaluated the gene expression of three metallothioneins (MTs; PgMt2-1, PgMt2, and PgMt3) in plants exposed to sub-lethal concentrations of copper. The PgMt2-1, PgMt2, and PgMt3 sequences were homologous to the MT type 2 (isoform 1), Mt2, and Mt3 sequences of other plant species found in GenBank. A reverse transcriptase-polymerase chain reaction showed that treatment with 100 mM Cu2+ induced a significant increase in PgMt2 and PgMt3 expression during the first 4 h of exposure compared to that of PgMt2-1. However, after 8 h of exposure, the expression levels of PgMt2 and PgMt3 were significantly lower than those of PgMt2-1. PgMt transcript levels only increased significantly during the first hour after exposure to copper, suggesting that PgMts could play a key role in the plant's detoxification mechanism. However, additional studies are required to confirm MTs as a mechanism of heavy metal tolerance and accumulation in this species.

Isolation by distance and stochastic migration in a fragmented population of Prosopis alba.

PREMISE OF THE STUDY: Gene flow through dispersal of seeds and pollen is a fundamental determinant of spatial genetic structure (SGS) in natural populations of trees at different spatial scales. Within continuous populations, restrictions to gene flow should be manifested in a process of local genetic differentiation, known as isolation by distance. The present work examines the SGS of a Prosopis alba population in a patchy region where urban, forest, and agricultural areas coexist. The analysis discussed here expands our knowledge about the processes affecting the distribution of the genetic variability in populations of disturbed landscapes. METHODS: Three sites with different landscape and demographic characteristics were analyzed. Seven highly variable microsatellite markers were used to survey the relevance of both isolation by distance and stochastic migration in the SGS of the population. KEY RESULTS: The analyses showed that (1) the genetic similarity declined with increasing geographic distance, (2) the population may be conceived as a single genetically continuous unit showing spatial differentiation as consequence of isolation by distance, rather than a structured population following the island model, and (3) there is evidence supporting a past immigration event into one of the study sites, which promoted a local pattern of genetic structure. CONCLUSIONS: These results indicate that in spite of the population fragmentation produced by land-use changes, P. alba maintains the genetic cohesion and a continuous genetic structure in the analyzed area.

A novel heavy metal ATPase peptide from Prosopis juliflora is involved in metal uptake in yeast and tobacco.

Heavy metal pollution of agricultural soils is one of the most severe ecological problems in the world. Prosopis juliflora, a phreatophytic tree species, grows well in heavy metal laden industrial sites and is known to accumulate heavy metals. Heavy Metal ATPases (HMAs) are ATP driven heavy metal pumps that translocate heavy metals across biological membranes thus helping the plant in heavy metal tolerance and phytoremediation. In the present study we have isolated and characterized a novel 28.9 kDa heavy metal ATPase peptide (PjHMT) from P. juliflora which shows high similarity to the C-terminal region of P1B ATPase HMA1. It also shows the absence of the invariant signature sequence DKTGT, and the metal binding CPX motif but the presence of conserved regions like MVGEGINDAPAL (ATP binding consensus sequence), HEGGTLLVCLNS (metal binding domain) and MLTGD, GEGIND and HEGG motifs which play important roles in metal transport or ATP binding. PjHMT, was found to be upregulated under cadmium and zinc stress. Heterologous expression of PjHMT in yeast showed a higher accumulation and tolerance of heavy metals in yeast. Further, transgenic tobacco plants constitutively expressing PjHMT also showed increased accumulation and tolerance to cadmium. Thus, this study suggests that the transport peptide from P. juliflora may have an important role in Cd uptake and thus in phytoremediation.

Molecular Cloning and Expression of Pro J 1: A New Allergen of Prosopis Juliflora Pollen.

Pollen from mesquite (Prosopis juliflora) is one of the important causes of immediate hypersensitivity reactions in the arid and semi-arid regions of the world. The aim of present study is to produce and purify the recombinant form of allergenic Ole e 1-like protein from the pollen of this allergenic tree. Immunological and cross-inhibition assays were performed for the evaluation of IgE-binding capacity of purified recombinant protein. For molecular cloning, the coding sequence of the mesquite Ole e 1-like protein was inserted into pTZ57R/T vector and expressed in Escherichia coli using the vector pET-21b(+). After purification of the recombinant protein, its immunoreactivity was analysed by in vitro assays using sera from twenty one patients with an allergy to mesquite pollen. The purified recombinant allergen was a member of Ole e 1-like protein family and consisted of 150 amino acid residues, with a predicted molecular mass of 16.5 kDa and a calculated isoelectric point (pI) of 4.75. Twelve patients (57.14%) had significant specific IgE levels for this recombinant allergen. Immunodetection and inhibition assays indicated that the purified recombinant allergen might be the same as that in the crude extract. Herein, we introduce an important new allergen from P. juliflora pollen (Pro j 1), which is a member of the Ole e 1-like protein family and exhibits significant identity and similarity to other allergenic members of this family.

Pro j 2 is mesquite profilin: molecular characteristics and specific IgE binding activity.

BACKGROUND: Pollens from mesquite (Prosopis juliflora) are potent allergen responsible in causing immediate hypersensitivity reactions in susceptible people in tropical countries. OBJECTIVE: This study aimed to clone, express and purify the mesquite pollen profilin (Pro j 2) as well as evaluating its nucleotide sequence homology in order to predict allergenic cross-reactivity with profilins of common allergenic plants. METHODS: Immunoblotting assay and specific ELISA were applied to determine the immunoreactivity of sera from 35 patients who were allergic to mesquite pollen. The mesquite profilin-coding sequence was cloned into PTZ57R/T vector and amplified. The cDNA of mesquite pollen profilin was then expressed in Escherichia coli using pET-21b (+) vector and puri?ed by one-step Ni2+ a?nity chromatography. IgE binding capacity of the recombinant mesquite profiling (rPro j 2) was analyzed by specific ELISA, immunoblotting, and inhibition assays. RESULTS: cDNA nucleotide sequencing revealed an open reading frame of 399bp encoding for 133 amino acids which belongs to the profilin family. Seventeen patients (17/35, 48.57%) had significant specific IgE level for rPro j 2. Immunodetection and inhibition assays indicated that puri?ed rPro j 2 might be similar as that in the crude extract. CONCLUSION: Pro j 2, as a new allergen from mesquite pollen, was produced in E. coli with an IgE-reactivity similar to that of its natural counterpart. The amino acid sequences homology analysis of mesquite profilin and several profilin molecules from other plants showed high degree of cross-reactivity among plant-derived profilins from unrelated families.

Characterization of microsatellite markers developed from Prosopis rubriflora and Prosopis ruscifolia (Leguminosae - Mimosoideae), legume species that are used as models for genetic diversity studies in Chaquenian areas under anthropization in South America.

BACKGROUND: Prosopis rubriflora and Prosopis ruscifolia are important species in the Chaquenian regions of Brazil. Because of the restriction and frequency of their physiognomy, they are excellent models for conservation genetics studies. The use of microsatellite markers (Simple Sequence Repeats, SSRs) has become increasingly important in recent years and has proven to be a powerful tool for both ecological and molecular studies. FINDINGS: In this study, we present the development and characterization of 10 new markers for P. rubriflora and 13 new markers for P. ruscifolia. The genotyping was performed using 40 P. rubriflora samples and 48 P. ruscifolia samples from the Chaquenian remnants in Brazil. The polymorphism information content (PIC) of the P. rubriflora markers ranged from 0.073 to 0.791, and no null alleles or deviation from Hardy-Weinberg equilibrium (HW) were detected. The PIC values for the P. ruscifolia markers ranged from 0.289 to 0.883, but a departure from HW and null alleles were detected for certain loci; however, this departure may have resulted from anthropic activities, such as the presence of livestock, which is very common in the remnant areas. CONCLUSIONS: In this study, we describe novel SSR polymorphic markers that may be helpful in future genetic studies of P. rubriflora and P. ruscifolia.

De novo assembly and characterization of leaf transcriptome for the development of functional molecular markers of the extremophile multipurpose tree species Prosopis alba.

BACKGROUND: Prosopis alba (Fabaceae) is an important native tree adapted to arid and semiarid regions of north-western Argentina which is of great value as multipurpose species. Despite its importance, the genomic resources currently available for the entire Prosopis genus are still limited. Here we describe the development of a leaf transcriptome and the identification of new molecular markers that could support functional genetic studies in natural and domesticated populations of this genus. RESULTS: Next generation DNA pyrosequencing technology applied to P. alba transcripts produced a total of 1,103,231 raw reads with an average length of 421 bp. De novo assembling generated a set of 15,814 isotigs and 71,101 non-assembled sequences (singletons) with an average of 991 bp and 288 bp respectively. A total of 39,000 unique singletons were identified after clustering natural and artificial duplicates from pyrosequencing reads.Regarding the non-redundant sequences or unigenes, 22,095 out of 54,814 were successfully annotated with Gene Ontology terms. Moreover, simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs) were searched, resulting in 5,992 and 6,236 markers, respectively, throughout the genome. For the validation of the the predicted SSR markers, a subset of 87 SSRs selected through functional annotation evidence was successfully amplified from six DNA samples of seedlings. From this analysis, 11 of these 87 SSRs were identified as polymorphic. Additionally, another set of 123 nuclear polymorphic SSRs were determined in silico, of which 50% have the probability of being effectively polymorphic. CONCLUSIONS: This study generated a successful global analysis of the P. alba leaf transcriptome after bioinformatic and wet laboratory validations of RNA-Seq data.The limited set of molecular markers currently available will be significantly increased with the thousands of new markers that were identified in this study. This information will strongly contribute to genomics resources for P. alba functional analysis and genetics. Finally, it will also potentially contribute to the development of population-based genome studies in the genera.

Fast protocol for extraction of DNA from Prosopis spp leaves (plant adapted to arid environment) without liquid nitrogen.

The extraction of high-quality genomic DNA from Prosopis spp for polymerase chain reaction (PCR) amplification is complicated, owing to the presence of a high percentage of secondary metabolites that bind to or co-precipitate with nucleic acids. In the present study, we report a modified sodium dodecyl sulfate/phenol protocol that eliminates the use of liquid nitrogen in the maceration process, ß-mercaptoethanol in the buffer extraction, and the ethanol precipitation step. The A260/A280 absorbance ratios of the isolated DNA were approximately 2.0 to 1.9, suggesting that the DNA fraction was pure and can be used for further PCR analysis. The DNA isolated by this protocol is of sufficient quality for molecular applications; this technique could be applied to other organisms that have similar substances that hinder DNA extraction. Finally, this proposal represents an alternative fast, cheap, and effective method for the isolation of genomic DNA from fresh leaves of Prosopis spp, even in low-technology laboratories.

RAPD and microsatellite transferability studies in selected species of Prosopis (section Algarobia) with emphasis on Prosopis juliflora and P. pallida.

The genus Prosopis (Leguminosae, Mimosoideae), comprises 44 species widely distributed in arid and semi-arid zones. Prosopis pallida (Humb. and Bonpl. ex Willd.) Kunth and P. juliflora (Sw.) DC. are the two species that are truly tropical apart from P. africana, which is native to tropical Africa (Pasiecznik et al. 2004), and they have been introduced widely beyond their native ranges. However, taxonomic confusion within the genus has hampered exploitation and better management of the species. The present study focusses primarily on evaluating the genetic relationship between Prosopis species from the section Algarobia, containing most species of economic importance, though P. tamarugo from section Strombocarpa is also included for comparison. In total, 12 Prosopis species and a putative P. pallida x P. chilensis hybrid were assessed for their genetic relationships based on RAPD markers and microsatellite transferability. The results show that P. pallida and P. juliflora are not closely related despite some morphological similarity. Evidence also agrees with previous studies which suggest that the grouping of series in section Algarobia is artificial.

Isolation and characterization of endophytic plant growth-promoting (PGPB) or stress homeostasis-regulating (PSHB) bacteria associated to the halophyte Prosopis strombulifera.

This study was designed to isolate and characterize endophytic bacteria from halophyte Prosopis strombulifera grown under extreme salinity and to evaluate in vitro the bacterial mechanisms related to plant growth promotion or stress homeostasis regulation. Isolates obtained from P. strombulifera were compared genotypically by BOX-polymerase chain reaction, grouped according to similarity, and identified by amplification and partial sequences of 16S DNAr. Isolates were grown until exponential growth phase to evaluate the atmospheric nitrogen fixation, phosphate solubilization, siderophores, and phytohormones, such as indole-3-acetic acid, zeatin, gibberellic acid and abscisic acid production, as well as antifungal, protease, and 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity. A total of 29 endophytic strains were grouped into seven according to similarity. All bacteria were able to grow and to produce some phytohormone in chemically defined medium with or without addition of a nitrogen source. Only one was able to produce siderophores, and none of them solubilized phosphate. ACC deaminase activity was positive for six strains. Antifungal and protease activity were confirmed for two of them. In this work, we discuss the possible implications of these bacterial mechanisms on the plant growth promotion or homeostasis regulation in natural conditions.