Comparative genomics analysis of endangered wild Egyptian Moringa peregrina (Forssk.) Fiori plastome, with implications for the evolution of Brassicales order.

Moringa is a mono-genus belonging to the Moringaceae family, which includes 13 species. Among them, Moringa peregrina is plant species native to the Arabian Peninsula, Southern Sinai in Egypt, and the Horn of Africa, and comprehensive studies on its nutritional, industrial, and medicinal values have been performed. Herein, we sequenced and analyzed the initial complete chloroplast genome of Moringa peregrina. Concurrently, we analyzed the new chloroplast genome along with 25 chloroplast genomes related to species representing eight families in the Brassicales order. The results indicate that the plastome sequence of M. peregrina consists of 131 genes, with an average GC content of 39.23%. There is a disparity in the IR regions of the 26 species ranging from 25,804 to 31,477 bp. Plastome structural variations generated 20 hotspot regions that could be considered prospective DNA barcode locations in the Brassicales order. Tandem repeats and SSR structures are reported as significant evidence of structural variations among the 26 tested specimens. Furthermore, selective pressure analysis was performed to estimate the substitution rate within the Moringaceae family, which revealing that the ndhA and accD genes are under positive selective pressure. The phylogenetic analysis of the Brassicales order produced an accurate monophyletic annotation cluster of the Moringaceae and Capparaceae species, offering unambiguous identification without overlapping groups between M. oleifera and M. peregrina, which are genetically strongly associated. Divergence time estimation suggests that the two Moringa species recently diversified, 0.467 Ma. Our findings highlight the first complete plastome of the Egyptian wild-type of M. peregrina, which can be used for determining plastome phylogenetic relationships and systematic evolution history within studies on the Moringaceae family.

Molecular characterization of a Novel NAD+-dependent farnesol dehydrogenase SoFLDH gene involved in sesquiterpenoid synthases from Salvia officinalis.

Salvia officinalis is one of the most important medicinal and aromatic plants in terms of nutritional and medicinal value because it contains a variety of vital active ingredients. Terpenoid compounds, particularly monoterpenes (C10) and sesquiterpenes, are the most important and abundant among these active substances (C15). Terpenes play a variety of roles and have beneficial biological properties in plants. With these considerations, the current study sought to clone theNAD+-dependent farnesol dehydrogenase (SoFLDH, EC: 1.1.1.354) gene from S. officinalis. Functional analysis revealed that, SoFLDH has an open reading frame of 2,580 base pairs that encodes 860 amino acids.SoFLDH has two conserved domains and four types of highly conserved motifs: YxxxK, RXR, RR (X8) W, TGxxGhaG. However, SoFLDH was cloned from Salvia officinalis leaves and functionally overexpressed in Arabidopsis thaliana to investigate its role in sesquiterpenoid synthases. In comparison to the transgenic plants, the wild-type plants showed a slight delay in growth and flowering formation. To this end, a gas chromatography-mass spectrometry analysis revealed that SoFLDH transgenic plants were responsible for numerous forms of terpene synthesis, particularly sesquiterpene. These results provide a base for further investigation on SoFLDH gene role and elucidating the regulatory mechanisms for sesquiterpene synthesis in S. offcinalis. And our study paves the way for the future metabolic engineering of the biosynthesis of useful terpene compounds in S. offcinalis.

Patterns of genetic structure and evidence of Egyptian Citrus rootstock based on informative SSR, LTR-IRAP and LTR-REMAP molecular markers.

BACKGROUND: Releasing the draft genome of sweet orange provides useful information on genetic structure and molecular marker association with heritable breeding traits in citrus species and their structures. Last decades, microsatellite and retrotransposons are well known as a significant diverse component of the structural evolution. They represented the most potent elements for assessing sustainable utilization of the complicated classification in citrus breeding. Our study was performed to verify the structure analysis and the parentage genetic diversity among the Egyptian citrus rootstocks and the related species. RESULTS: Here, the performance of 26 SSR and 14 LTR-IRAP in addition to 20 LTR-REMAP markers have been used to conduct the discriminating power and the status of the genetic structure analysis among twenty specimens of citrus genotypes. As a result, the three markers approach exhibited a remarkable variation among the tested genotypes. Overall, the three markers have different discrimination power; the co-dominant SSR markers can differentiate within the group level only in addition to the species level of sour orange, while the dominant markers LTR-IRAP had the ability to discriminate among the group level in addition to species level and the origin of acids. Similarly, LTR-REMAP is suitable for classifying the group level and species level for mandarins as well the origin of Egyptian acids; probably due to it is integration of SSR and LTR-IRAP techniques. Structure and PCoA results of LTR-REMAP marker in strong support for the group structure of citrus species have been divided into four sets: acids, grapefruit/pummelo, mandarin/orange, and sour orange. CONCLUSION: Our findings of the genetic structure analysis support the monophyletic nature of the citrus species; are able to provide unambiguous identification and disposition of true species and related hybrids like lemon, lime, citron, sour orange, grapefruit, mandarin, sweet orange, pummelo, and fortunella; and resulted in their placement in individual or overlap groups. The outcomes of these results will offer helpful and potential information for breeding programs and conservation approaches as a key stage toward identifying the interspecific admixture and the inferred structure origins of Egyptian citrus rootstock and acid cultivars.

A systematic revision of Capparaceae and Cleomaceae in Egypt: an evaluation of the generic delimitations of Capparis and Cleome using ecological and genetic diversity.

BACKGROUND: The Capparaceae family is commonly recognized as a caper, while Cleomaceae represents one of small flowering family within the order Brassicales. Earlier, Cleomaceae was included in the family Capparaceae; then, it was moved to a distinct family after DNA evidence. Variation in habits and a bewildering array of floral and fruit forms contributed to making Capparaceae a "trash-basket" family in which many unrelated plants were placed. Indeed, family Capparaceae and Cleomaceae are in clear need of more detailed systematic revision. RESULTS: Here, in the present study, the morphological characteristics and the ecological distribution as well as the genetic diversity analysis among the twelve species of both Capparaceae and Cleomaceae have been determined. The genetic analysis has been checked using 15 ISSR, 30 SRAP, and 18 ISTR to assess the systematic knots between the two families. In order to detect the molecular phylogeny, a comparative analysis of the three markers was performed based on the exposure of discriminating capacity, efficiency, and phylogenetic heatmap. Our results indicated that there is a morphological and ecological variation between the two families. Moreover, the molecular analysis confirmed that ISTR followed by SRAP markers has superior discriminating capacity for describing the genetic diversity and is able to simultaneously distinguish many polymorphic markers per reaction. Indeed, both the PCA and HCA data have drawn a successful annotation relationship in Capparaceae and Cleome species to evaluate whether the specific group sort individual or overlap groups. CONCLUSION: The outcomes of the morphological and ecological characterization along with the genetic diversity indicated an insight solution thorny interspecies in Cleome and Gynandropsis genera as a distinct family (Cleomaceae) and the other genera (Capparis, Cadaba, Boscia, and Maerua) as Capparaceae. Finally, we recommended further studies to elucidate the systematic position of Dipterygium glaucum.

ycf1-ndhF genes, the most promising plastid genomic barcode, sheds light on phylogeny at low taxonomic levels in Prunus persica.

BACKGROUND: Chloroplast genome sequencing is becoming a valuable process for developing several DNA barcodes. At present, plastid DNA barcode for systematics and evolution in flowering plant rely heavily on the use of non-coding genes. The present study was performed to verify the novelty and suitability of the two hotspot barcode plastid coding gene ycf1 and ndhF, to estimate the rate of molecular evolution in the Prunus genus at low taxonomic levels. RESULTS: Here, 25 chloroplast genomes of Prunus genus were selected for sequences annotation to search for the highly variable coding DNA barcode regions. Among them, 5 genera were of our own data, including the ornamental, cultivated, and wild haplotype, while 20 genera have been downloaded from the GenBank database. The results indicated that the two hotspot plastid gene ycf1 and ndhF were the most variable regions within the coding genes in Prunus with an average of 3268 to 3416 bp in length, which have been predicted to have the highest nucleotide diversity, with the overall transition/transversion bias (R = 1.06). The ycf1-ndhF structural domains showed a positive trend evident in structure variation among the 25 specimens tested, due to the variant overlap's gene annotation and insertion or deletion with a broad trend of the full form of IGS sequence. As a result, the principal component analysis (PCA) and the ML tree data drew an accurate monophyletic annotations cluster in Prunus species, offering unambiguous identification without overlapping groups between peach, almond, and cherry. CONCLUSION: To this end, we put forward the domain of the two-locus ycf1-ndhF genes as the most promising coding plastid DNA barcode in P. persica at low taxonomic levels. We believe that the discovering of further variable loci with high evolutionary rates is extremely useful and potential uses as a DNA barcode in P. persica for further phylogeny study and species identification.

Identification of EIL and ERF Genes Related to Fruit Ripening in Peach.

Peach (Prunus persica) is a climacteric fruit with a relatively short shelf life due to its fast ripening or softening process. Here, we report the association of gene families encoding ethylene insensitive-3 like (EIL) and ethylene response factor (ERF) with fruit ripening in peach. In total, 3 PpEILs and 12 PpERFs were highly expressed in fruit, with the majority showing a peak of expression at different stages. All three EILs could activate ethylene biosynthesis genes PpACS1 and PpACO1. One out of the 12 PpERFs, termed PpERF.E2, is a homolog of ripening-associated ERFs in tomato, with a consistently high expression throughout fruit development and an ability to activate PpACS1 and PpACO1. Additionally, four subgroup F PpERFs harboring the EAR repressive motif were able to repress the PpACO1 promoter but could also activate the PpACS1 promoter. Promoter deletion assay revealed that PpEILs and PpERFs could participate in transcriptional regulation of PpACS1 through either direct or indirect interaction with various cis-elements. Taken together, these results suggested that all three PpEILs and PpERF.E2 are candidates involved in ethylene biosynthesis, and EAR motif-containing PpERFs may function as activator or repressor of ethylene biosynthesis genes in peach. Our study provides an insight into the roles of EILs and ERFs in the fruit ripening process.

Maximum parsimony based resolution of inter-species phylogenetic relationships in Citrus L. (Rutaceae) using ITS of rDNA.

The present study aims to analyse phylogenetic relationships, using internal transcribed spacer sequence data of ribosomal DNA (rDNA), across 24 Citrus species and close relatives by the evaluation of several parameters such as nucleotide substitution (r), nucleotide diversity (π) and the estimated values of transition/transversion bias (R). The observed results indicated the presence of a wide divergence pattern of rDNA in subfamily Aurantioideae. Maximum parsimony (MP) analysis inferred divergence pattern in the Citrus genus. We observed seven strongly supported clades among the subfamily Aurantioideae. We postulate that the present investigation provides a more robust topology of Citrus and its close relatives, which can significantly prove as an additional support to resolve the phylogenetic relationships in Citrus genera. Therefore, sequences of noncoding regions should exhibit more phylogenetically informative sites than the coding regions do, which is in accordance with the present study.