Phylogeny of some Solanum species (Solanaceae) based on complete chloroplast genomes (cpDNA) and individual chloroplast genes

Chloroplast DNA sequences can be used to estimate phylogenetic relationships among plant taxa. There are many chloroplast sequences have been made available in public databases and these data have been used for phlyogenetic relationship and evolutionary processes. We used three Solanum species (Solanum bulbocastanum, Solanum tuberosum and Solanum lycopersicum) and Nicotiana tabacum as outgroup. We performed phylognetic analysis four species based on complete  chloroplast DNA (cpDNA), matK coding region and trnL-trnF noncoding region by using Maximum Likelihood (ML), Neighbor-joining (NJ) and unweighted pair group method with arithmetic mean (UPGMA) models. The all tree resulting from complete cpDNA clearly separated Solanum species with high bootstrap values and all the chloroplast segments clearly differentiated the genus Nicotiana tabacum from Solanum species. Tajima’s neutrality test revealed that the highest nucleotide diversity (0.01667) was observed in trnL-trnF non-coding region. UPGMA phylogenetic inference has been shown to be more robust to ML and NJ due to bootstrap values. Particularly, ML inference has lower phylogenetic resolution than UPGMA and NJ tree

Comparative analysis of metallothionein proteins (MTs) from different grass species

Plant metallothioneins (MTs) are small proteins, having rich cysteine residues andappear to play key roles in metal homeostasis. In current study, MTs of 9 grass species (Brachypodium distachyon, Festuca rubra, Hordeum vulgare, Oryza sativa japonica, Oryza sativa indica, Saccharum officinarum, Sorghum bicolor, Triticum aestivum, and Zea mays) were used for in silico comparative analysis. Physicochemical analyses showed that pIvalues and GRAVY index were found to be in the range of (4.44) - (7.36) and (-0.037) - (-0.376), respectively. All MTs investigated in this study exhibited hydrophilic characterand 8 of 9 MTs had acidic nature. Also, there were no sequences containing tryptophan(Trp) residues. While the highest and lowest similar sequence identities were foundbetween S. bicolor & S. officinarum (0.928), and Z. mays & H. vulgare (0.183), respectively. Phylogenetic analysis revealed that one main group observed including two subgroups.The highest bootstrap value was observed between S. bicolor and S. officinarum (92%). Interestingly, H. vulgare appears not to be within any grass species group

In silico EST-SSRs Analysis in UniGene of Quercus robur L.

Pedunculate oak (Quercus robur L.) is one of the most important tree componentsof Europe’s forest ecosystems, possessing both ecological and economical value. Development of genomic resources, such as genetic markers, is needed to support geneconservation and tree improvement activities. Experimental methods to develop SSR markers are laborious, time consuming and expensive, while in silico approaches havebecome a practicable and inexpensive alternative in genetic studies. The aim of this studywas to characterize simple sequence repeat (EST-SSR) markers and functional annotationof SSR containing sequences in Q. robur unigene sequences. 7170 unigene sequences(5147.315 kb) of Q. robur were downloaded from National Center for BiotechnologyInformation (NCBI). A total of 475 (6.62 %) unigene sequences containing 525 SSRs (microsatellites) were identified by using MISA software. The average frequency ofmicrosatellites was found, on average, one in every 9.8 kb of sequence. The analysisrevealed that tri-nucleotide repeats (42.6%) were most abundant followed by dinucleotide(36.9%), hexa-nucleotide (11.8%), penta-nucleotide (4.9%) and tetra-nucleotiderepeats (3.8%), respectively. Flanking sequences of the 525 SSRs generated 500 primers(95.2%) with forward and reverse strands by using Primer3 software. Gene based SSRmarkers can be used for studies of genetic diversity, population genetics, geneticmapping, gene tagging and more. Large numbers of unigenes containing SSRs (77.4%),annotations were available 46.75% of which were predicted, 23.91% were hypothetical,8.83% were putative and 20.51% belonged to other protein types. Only 22.5% sequencecould not assign to any specific protein class

Brachypodium Genomics

Brachypodium distachyon (L.) Beauv. is a temperate wild grass species; its morphological and genomic characteristics make it a model system when compared to many other grass species. It has a small genome, short growth cycle, self-fertility, many diploid accessions, and simple growth requirements. In addition, it is phylogenetically close to economically important crops, like wheat and barley, and several potential biofuel grasses. It exhibits agricultural traits similar to those of these target crops. For cereal genomes, it is a better model than Arabidopsis thaliana and Oryza sativa (rice), the former used as a model for all flowering plants and the latter hitherto used as model for genomes of all temperate grass species including major cereals like barley and wheat. Increasing interest in this species has resulted in the development of a series of genomics resources, including nuclear sequences and BAC/EST libraries, together with the collection and characterization of other genetic resources. It is expected that the use of this model will allow rapid advances in generation of genomics information for the improvement of all temperate crops, particularly the cereals

Investigation and Computational Analysis of the Sulfotransferase (SOT) Gene Family in Potato (Solanum tuberosum): Insights into Sulfur Adjustment for Proper Development and Stimuli Responses

Various kinds of primary metabolisms in plants are modulated through sulfate metabolism, and sulfotransferases (SOTs), which are engaged in sulfur metabolism, catalyze sulfonation reactions. In this study, a genome-wide approach was utilized for the recognition and characterization of SOT family genes in the significant nutritional crop potato (Solanum tuberosum L.). Twenty-nine putative StSOT genes were identified in the potato genome and were mapped onto the nine S. tuberosum chromosomes. The protein motifs structure revealed two highly conserved 5′-phosphosulfate-binding (5′ PSB) regions and a 3′-phosphate-binding (3′ PB) motif that are essential for sulfotransferase activities. The protein–protein interaction networks also revealed an interesting interaction between SOTs and other proteins, such as PRTase, APS-kinase, protein phosphatase, and APRs, involved in sulfur compound biosynthesis and the regulation of flavonoid and brassinosteroid metabolic processes. This suggests the importance of sulfotransferases for proper potato growth and development and stress responses. Notably, homology modeling of StSOT proteins and docking analysis of their ligand-binding sites revealed the presence of proline, glycine, serine, and lysine in their active sites. An expression essay of StSOT genes via potato RNA-Seq data suggested engagement of these gene family members in plants’ growth and extension and responses to various hormones and biotic or abiotic stimuli. Our predictions may be informative for the functional characterization of the SOT genes in potato and other nutritional crops

Investigation and Computational Analysis of the Sulfotransferase (SOT) Gene Family in Potato (Solanum tuberosum): Insights into Sulfur Adjustment for Proper Development and Stimuli Responses

Various kinds of primary metabolisms in plants are modulated through sulfate metabolism, and sulfotransferases (SOTs), which are engaged in sulfur metabolism, catalyze sulfonation reactions. In this study, a genome-wide approach was utilized for the recognition and characterization of SOT family genes in the significant nutritional crop potato (Solanum tuberosum L.). Twenty-nine putative StSOT genes were identified in the potato genome and were mapped onto the nine S. tuberosum chromosomes. The protein motifs structure revealed two highly conserved 5′-phosphosulfate-binding (5′ PSB) regions and a 3′-phosphate-binding (3′ PB) motif that are essential for sulfotransferase activities. The protein–protein interaction networks also revealed an interesting interaction between SOTs and other proteins, such as PRTase, APS-kinase, protein phosphatase, and APRs, involved in sulfur compound biosynthesis and the regulation of flavonoid and brassinosteroid metabolic processes. This suggests the importance of sulfotransferases for proper potato growth and development and stress responses. Notably, homology modeling of StSOT proteins and docking analysis of their ligand-binding sites revealed the presence of proline, glycine, serine, and lysine in their active sites. An expression essay of StSOT genes via potato RNA-Seq data suggested engagement of these gene family members in plants’ growth and extension and responses to various hormones and biotic or abiotic stimuli. Our predictions may be informative for the functional characterization of the SOT genes in potato and other nutritional crops

The Conservation of VIT1-Dependent Iron Distribution in Seeds

One third of people suffer from anemia, with iron (Fe) deficiency being the most common reason. The human diet includes seeds of staple crops, which contain Fe that is poorly bioavailable. One reason for low bioavailability is that these seeds store Fe in cellular compartments that also contain antinutrients, such as phytate. Thus, several studies have focused on decreasing phytate concentrations. In theory, as an alternative approach, Fe reserves might be directed to cellular compartments that are free of phytate, such as plastids. However, it is not known if seed plastid can represent a major Fe storage compartment in nature. To discover distinct types of Fe storage in nature, we investigated metal localizations in the seeds of more than twenty species using histochemical or X-ray based techniques. Results showed that in Rosids, the largest clade of eudicots, Fe reserves were primarily confined to the embryo of the seeds. Furthermore, inside the embryos, Fe accumulated specifically in the endodermal cell layer, a well-known feature that is mediated by VACUOLAR IRON TRANSPORTER1 (VIT1) in model plant Arabidopsis thaliana. In rice, Fe enrichment is lost around the provasculature in the mutants of VIT1 orthologs. Finally, in Carica papaya, Fe accumulated in numerous organelles resembling plastids; however, these organelles accumulated reserve proteins but not ferritin, failing to prove to be plastids. By investigating Fe distribution in distinct plant lineages, this study failed to discover distinct Fe storage patterns that can be useful for biofortification. However, it revealed Fe enrichment is widely conserved in the endodermal cell layer in a VIT1-dependent manner in the plant kingdom

Effects of exogenous nitric oxide on cadmium toxicity in black poplar (Populus nigra): physiological approaches

Cadmium (Cd) is a highly toxic metallic contaminant that negatively affects plant metabolism and causes reductions in productivity. Nitric oxide (NO) is a signaling molecule that regulates various physiological processes and is involved in response to biotic/abiotic stresses. This work investigated the effects of exogenous sodium nitroprusside (SNP), a nitric oxide (NO) donor, application on Cd toxicity in black poplar (Populus nigra). Black poplars were exposed to individual/combined CdCl2 and SNP treatments for 21 days by complete randomized design with three replications. Cd concentrations increased in leaves, bark, and roots at Cd treatments, whereas Cd + SNP applications had alleviative effects on Cd exposures, except for leaves. Photosynthetic pigments (chlorophyll a, b, a + b and carotenoids) reduced with Cd treatments in leaves, while they increased in Cd + SNP applications. Similarly, plant biomass was reduced with Cd treatments, but Cd + SNP application prevented these reductions. SNP also alleviated malondialdehyde (MDA) and hydrogen peroxide (H2O2) accumulation in leaves under Cd treatments. Catalase (CAT, EC 1.11.1.6) and ascorbate peroxidase (APX, EC 1.11.1.11) activities were also affected by Cd and Cd + SNP applications. Cd exposure also decreased Zn2+, Fe2+ and Mn2+ levels in leaves, bark and roots, while it increased Cu2+ level in leaves and roots. This study concludes that Cd toxicity caused a reduction of plant growth and mineral nutrition parameters. However, SNP indicates great potentials for improving the growth under Cd toxicity in P. nigra

Diploid brachypodium distachyon of Turkey: molecular and morphological analysis

Brachypodium distachyon is a model species for the grass family, Poaceae, which includes major cereal crops such as wheat and barley. The aim of this study were to assess morphological and phylogenetic relationships among diploid accessions of Brachypodium representing diverse geographic regions of Turkey based on Sequence related Amplified Polymorphism (SRAP) analyses. The similarity matrix indicated close relation among species used in the section using SRAP primer combinations, produced 156 fragment bands, of which 120 were polymorphic. Genetic distance ranged from 0.03 to 0.62. Plant genotypes were grouped into two major clusters based on SRAP analysis. There was a high level of diversity among the native diploid Brachypodium genotypes. These genotypes can be used for a better understanding of grass genomics