Tariq Pervaiz

Jasmonic acid involves in grape fruit ripening and resistant against Botrytis cinerea

Fruit ripening is a complex process that is regulated by a signal network. Whereas the regulatory mechanism of abscisic acid has been studied extensively in non-climacteric fruit, little is know about other signaling pathways involved in this process. In this study, we performed that plant hormone jasmonic acid plays an important role in grape fruit coloring and softening by increasing the transcription levels of several ripening-related genes, such as the color-related genes PAL1, DFR, CHI, F3H, GST, CHS, and UFGT; softening-related genes PG, PL, PE, Cell, EG1, and XTH1; and aroma-related genes Ecar, QR, and EGS. Lastly, the fruit anthocyanin, phenol, aroma, and cell wall materials were changed. Jasmonic acid positively regulated its biosynthesis pathway genes LOS, AOS, and 12-oxophytodienoate reductase (OPR) and signal pathway genes COI1 and JMT. RNA interference of grape jasmonic acid pathway gene VvAOS in strawberry fruit appeared fruit un-coloring phenotypes; exogenous jasmonic acid rescued this phenotypes. On the contrary, overexpression of grape jasmonic acid receptor VvCOI1 in the strawberry fruit accelerated the fruit-ripening process and induced some plant defense-related gene expression level. Furthermore, jasmonic acid treatment or strong jasmonic acid signal pathway in strawberry fruit make the fruit resistance against Botrytis cinerea.

Evaluation of Genome Sequencing Quality in Selected Plant Species Using Expressed Sequence Tags

Background With the completion of genome sequencing projects for more than 30 plant species, large volumes of genome sequences have been produced and stored in online databases. Advancements in sequencing technologies have reduced the cost and time of whole genome sequencing enabling more and more plants to be subjected to genome sequencing. Despite this, genome sequence qualities of multiple plants have not been evaluated. Methodology/Principal Finding Integrity and accuracy were calculated to evaluate the genome sequence quality of 32 plants. The integrity of a genome sequence is presented by the ratio of chromosome size and genome size (or between scaffold size and genome size), which ranged from 55.31% to nearly 100%. The accuracy of genome sequence was presented by the ratio between matched EST and selected ESTs where 52.93% ∼ 98.28% and 89.02% ∼ 98.85% of the randomly selected clean ESTs could be mapped to chromosome and scaffold sequences, respectively. According to the integrity, accuracy and other analysis of each plant species, thirteen plant species were divided into four levels. Arabidopsis thaliana, Oryza sativa and Zea mays had the highest quality, followed by Brachypodium distachyon, Populus trichocarpa, Vitis vinifera and Glycine max, Sorghum bicolor, Solanum lycopersicum and Fragaria vesca, and Lotus japonicus, Medicago truncatula and Malus × domestica in that order. Assembling the scaffold sequences into chromosome sequences should be the primary task for the remaining nineteen species. Low GC content and repeat DNA influences genome sequence assembly. Conclusion The quality of plant genome sequences was found to be lower than envisaged and thus the rapid development of genome sequencing projects as well as research on bioinformatics tools and the algorithms of genome sequence assembly should provide increased processing and correction of genome sequences that have already been published.

Transcriptomic Analysis of Grapevine (cv. Summer Black) Leaf, Using the Illumina Platform

Proceeding to illumina sequencing, determining RNA integrity numbers for poly RNA were separated from each of the four developmental stages of cv. Summer Black leaves by using Illumina HiSeq™ 2000. The sums of 272,941,656 reads were generated from vitis vinifera leaf at four different developmental stages, with more than 27 billion nucleotides of the sequence data. At each growth stage, RNA samples were indexed through unique nucleic acid identifiers and sequenced. KEGG annotation results depicted that the highest number of transcripts in 2,963 (2Avs4A) followed by 1Avs4A (2,920), and 3Avs4A (2,294) out of 15,614 (71%) transcripts were recorded. In comparison, a total of 1,532 transcripts were annotated in GOs, including Cellular component, with the highest number in “Cell part” 251 out of 353 transcripts (71.1%), followed by intracellular organelle 163 out of 353 transcripts (46.2%), while in molecular function and metabolic process 375 out of 525 (71.4%) transcripts, multicellular organism process 40 out of 525 (7.6%) transcripts in biological process were most common in 1Avs2A. While in case of 1Avs3A, cell part 476 out of 662 transcripts (71.9%), and membrane-bounded organelle 263 out of 662 transcripts (39.7%) were recorded in Cellular component. In the grapevine transcriptome, during the initial stages of leaf development 1Avs2A showed single transcript was down-regulated and none of them were up-regulated. While in comparison of 1A to 3A showed one up-regulated (photosystem II reaction center protein C) and one down regulated (conserved gene of unknown function) transcripts, during the hormone regulating pathway namely SAUR-like auxin-responsive protein family having 2 up-regulated and 7 down-regulated transcripts, phytochrome-associated protein showed 1 up-regulated and 9 down-regulated transcripts, whereas genes associated with the Leucine-rich repeat protein kinase family protein showed 7 up-regulated and 1 down-regulated transcript, meanwhile Auxin Resistant 2 has single up-regulated transcript in second developmental stage, although 3 were down-regulated at lateral growth stages (3A and 4A). In the present study, 489 secondary metabolic pathways related genes were identified during leaf growth, which mainly includes alkaloid (40), anthocyanins (21), Diterpenoid (144), Monoterpenoid (90) and Flavonoids (93). Quantitative real-time PCR was applied to validate 10 differentially expressed transcripts patterns from flower, leaf and fruit metabolic pathways at different growth stages.

Insights into grapevine defense response against drought as revealed by biochemical, physiological and RNA-Seq analysis

Grapevine is an important and extensively grown fruit crop, which is severely hampered by drought worldwide. So, comprehending the impact of drought on grapevine genetic resources is necessary. In the present study, RNA-sequencing was executed using cDNA libraries constructed from both drought-stress and control plants. Results generated 12,451 differentially expressed genes (DEGs), out of which 8,021 genes were up-regulated, and 4,430 were down-regulated. Further physiological and biochemical investigations were also performed to validate the biological processes associated with the development of grapevine in response to drought stress. Results also revealed that decline in the rate of stomatal conductance, in turn, decrease the photosynthetic activity and CO2 assimilation in the grapevine leaves. Reactive oxygen species, including stress enzymes and their related proteins, and secondary metabolites were also activated in the present study. Likewise, various hormones also induced in response to drought stress. Overall, the present study concludes that these DEGs play both positive and negative roles in drought tolerance by regulating various biological pathways of grapevine. Nevertheless, our findings have provided valuable gene information for future studies of abiotic stress in grapevine and various other fruit crops.

Grapevine immune signaling network in response to drought stress as revealed by transcriptomic analysis

Drought is a ubiquitous abiotic factor that severely impedes growth and development of horticulture crops. The challenge postured by global climate change is the evolution of drought-tolerant cultivars that could cope with concurrent stress. Hence, in this study, biochemical, physiological and transcriptome analysis were investigated in drought-treated grapevine leaves. The results revealed that photosynthetic activity and reducing sugars were significantly diminished which were positively correlated with low stomatal conductance and CO2 exchange in drought-stressed leaves. Further, the activities of superoxide dismutase, peroxidase, and catalase were significantly actuated in the drought-responsive grapevine leaves. Similarly, the levels of abscisic acid and jasmonic acid were also significantly increased in the drought-stressed leaves. In transcriptome analysis, 12,451 differentially-expressed genes (DEGs) were annotated, out of which 8021 DEGs were up-regulated and 4430 DEGs were down-regulated in response to drought stress. In addition, the genes encoding pathogen-associated molecular pattern (PAMP) triggered immunity (PTI), including calcium signals, protein phosphatase 2C, calcineurin B-like proteins, MAPKs, and phosphorylation (FLS2 and MEKK1) cascades were up-regulated in response to drought stress. Several genes related to plant-pathogen interaction pathway (RPM1, PBS1, RPS5, RIN4, MIN7, PR1, and WRKYs) were also found up-regulated in response to drought stress. Overall the results of present study showed the dynamic interaction of DEG in grapevine physiology which provides the premise for selection of defense-related genes against drought stress for subsequent grapevine breeding programs.

Role of microRNAs and their target genes in salinity response in plants

Salinity is one of the most common environmental stresses that affects plant growth and development. Plants employ complex mechanisms of gene regulation to respond salinity stress. MicroRNAs (miRNAs) are small noncoding RNAs with important regulatory roles in plant growth and development. Furthermore, they are also considered as critical cell elements orchestrating plants response to stress conditions. Many approaches, such as molecular cloning and high-throughput sequencing using computational tools have been adapted to profile miRNA expression patterns during abiotic stresses. In fact, the identification of these master regulators could pave the way towards better understanding of the molecular regulation of stress adaptation in plants. Many target genes of miRNAs are transcription factors which further regulate a set of downstream genes to have effects on physiological responses. This review summarizes recent molecular studies on the regulatory roles of plant miRNAs and their target genes in plant metabolism under salt stress conditions.

Naturally Occurring Anthocyanin, Structure, Functions and BiosyntheticPathway in Fruit Plants

Anthocyanins are naturally occurring compounds, member of the flavonoid groups of photochemical, involved in defense against the damaging effects of UV irradiation in plants and protect from many oxidants. The anthocyanins, group of pigments are relatively small and diverse flavonoid family in nature, and responsible for the attractive colors, red and purple to blue in many plants. Presence of pigments in flowers and fruits seems to provide attraction for pollination and aiding seed distribution, it also provides antiviral and antimicrobial activities, however their occurrence in the vacuoles remains ambiguous. During the last decades, anthocyanin gene expression and many structural genes encoding enzymes has been extensively studied in fruits, flowers and leaves in many plants. In addition, the genetic regulating mechanism, their biosynthesis and other factors involved are well described. The biosynthesis pathway of anthocyanin is a complex with diverse branches responsible to produce variety of metabolites. In general Anthocyanins, production through the flavonoid path, are a class of vital phenolic compounds. Over six thousand diverse anthocyanins have been reported from various species. So far, the potential health benefits of anthocyanins have been reported in the contexts of their antioxidant properties. Anthocyanins are also extensively studied for their several positive effects on body. Based on these facts, the present review briefly summarizes recent advances, highlighting the importance of biosynthetic pathway of anthocyanins, thus will serve to encourage advance investigation in this field.

High Throughput Sequencing Advances and Future Challenges

High throughput sequencing (HTS) technologies were developed into indispensable for genomic investigation and recent hottest topic for research in the field of genomics, which can generate over 100 times more data in comparison with the most complicated capillary sequencers. Recent advances and developments in HTS using next generation sequencing techniques have become essential in the studies of digital gene expression profiling, in epigenomics, genomics, and transcriptomics. These methodologies are dexterous of sequencing multiple DNA molecules in corresponding; facilitate hundreds of millions of DNA molecules to be sequenced within a short period of time. Though, the expenses and time period have been significantly reduced; the inaccurate profiles and boundaries of the new policy differ considerably from those of earlier reported sequencing techniques. The technical developments and decreasing cost of NGS (Next Generation Sequencing) technology have made RNA sequencing (RNA-seq) as a worldwide popular technique for gene expression projects. Various approaches have been done for the standardization of RNA sequencing data, which have been materialized in the reports, contradictory, both in the type of bias modification and in the statistical approach. On the other hand, as data persistently build up, there has been no apparent consensus on the proper normalization techniques to be used or the impact of chosen methods on the downstream analysis. In the present article, we mentioned the key features of HT-NGS like, Key HTS platforms and different sequencing applications, ethical limitation and future prospective.

Gene regulation mechanism in drought-responsive grapevine leaves as revealed by transcriptomic analysis

The transcriptome of drought-stressed grapevine leaves was analyzed using RNA-sequencing (RNA-seq) technology and compared. In this experiment, 12,451 differentially expressed genes (DEGs) were recorded in response to drought by RNA-seq, which includes 7,983 up-regulated and 4,468 down-regulated transcripts, proposing that drought stress has induced/repressed many genes. Biological and physiological analysis revealed that drought has influenced the chlorophyll metabolism and photosynthetic activity in grapevine leaves. Besides, various defensive mechanism-related pathways including, reactive oxygen species (ROS), hormonal signal transduction, proline metabolism, biosynthesis of secondary metabolites, heat-shock proteins, and pathogenesis-related protein were also elucidated to understand drought-resistance related gene induction. Therefore, the transcriptional activity of ROS along with antioxidant enzymes, stress-related proteins, proline and secondary metabolites were strongly induced and played the tolerance-related role in response to drought stress. Moreover, an increased level of abscisic acid (ABA) and brassinosteroids (BRs) at physiological and transcriptomic level proved the fact that both hormones have a key defensive role against drought stress in grapevine leaves. In general, these findings will provide the drought tolerance-related gene information, which could be further used for developing drought-resistant grapevine varieties.Grapevine is economically important and widely cultivated fruit crop, which is seriously hampered by drought worldwide. It is necessary to understand the impact of glitches incurred by the drought on grapevine genetic resources. Therefore, in the present study RNA-sequencing analysis was performed using cDNA libraries constructed from both drought-stress and control plants. Results yielded, a total of 12,451 differentially expressed genes (DEGs) out of which 8,022 genes were up-regulated and 4,430 were down-regulated. Further physiological and biochemical analyses were carried out to validate the various biological processes involved in the development of grapevine in response to drought stress. Results also showed that decrease in rate of stomatal conductance in-turn decrease the photosynthetic activity and CO2 assimilation rate in the grapevine leaves and most ROS detoxification systems, including stress enzymes, stress related proteins and secondary metabolites were strongly induced. Moreover, various hormones were known to be induced in the present study in response to drought. Overall the present study concludes that these DEGs play both positive and negative role in drought tolerance by regulating different biological pathways of grapevine. However our findings have provided valuable gene information for future studies of abiotic stress in grapevine and other fruit crops.

Characterization of VvPAL-like promoter from grapevine using transgenic tobacco plants.

A 2000-bp 5′-flanking region of VvPAL-like was isolated from ‘Summer Black’ grapevine by PCR amplification, named pVvPAL-like. To gain a better understanding of the expression and regulatory mechanism of VvPAL-like, a chimeric expression unit consisting of the β-glucuronidase (GUS) reporter gene under the control of a 2000-bp fragment of the VvPAL-like promoter was transformed into tobacco via Agrobacterium tumefaciens. Histochemical staining showed that the full-length promoter directs efficient expression of the reporter gene in cotyledons and hypocotyls, stigma, style, anthers, pollen, ovary, trichomes, and vascular bundles of transgenic plants. A series of 5′ progressive deletions of the promoter revealed the presence of a negative regulatory region (−424 to −292) in the VvPAL-like promoter. Exposure of the transgenic tobacco plants to various abiotic stresses demonstrated that the full-length construct could be induced by light, copper (Cu), abscisic acid (ABA), indole-3-acetic (IAA), methyl jasmonate (MeJA) (N-1-naphthylphthalamic acid), ethylene, and drought. Furthermore, the ethylene-responsive region was found to be located in the −1461/−930 fragment, while the element(s) for the MeJA-responsive expression may be present in the −424/−292 region in the VvPAL-like promoter. These findings will help us to better understand the molecular mechanisms by which VvPAL-like participates in biosynthesis of flavonoids and stress responses.