SignificanceWe sequenced the genome and transcriptomes of the wild olive (oleaster). More than 50,000 genes were predicted, and evidence was found for two relatively recent whole-genome duplication events, dated at about 28 and 59 million years ago. Whole genome sequencing, as well as gene expression studies, provide further insights into the evolution of oil biosynthesis, and will aid future studies aimed at further increasing the production of olive oil, which is a key ingredient of the healthy Mediterranean diet and has been granted a qualified health claim by FDA. 5 AbstractHere, we present the genome sequence and annotation of the wild olive tree (Olea europaea var. sylvestris), called oleaster, which is considered an ancestor of cultivated olive trees. More than 50,000 protein-coding genes were predicted, a majority of which could be anchored to 23 pseudo-chromosomes obtained through a newly constructed genetic map. The oleaster genome contains signatures of two Oleaceae-lineage specific paleopolyploidy events, dated at approximately 28 and 59 million years ago. These events contributed to the expansion and neofunctionalization of genes and gene families that play important roles in oil biosynthesis.The functional divergence of oil biosynthesis pathway genes, such as FAD2, SACPD, EAR and ACPTE, following duplication, has been responsible for the differential accumulation of oleic and linoleic acids produced in olive compared to sesame, a closely related oil crop. Duplicated oleaster FAD2 genes are regulated by a short-interfering RNA (siRNA) derived from a transposable element-rich region, leading to suppressed levels of FAD2 gene expression.Additionally, neofunctionalization of members of the SACPD gene family has led to increased expression of SACPD2, 3, 5 and 7, consequently resulting in an increased desaturation of steric acid. Taken together, decreased FAD2 expression and increased SACPD expression likely explain the accumulation of exceptionally high levels of oleic acid in olive. The oleaster genome thus provides important insights into the evolution of oil biosynthesis and will be a valuable resource for oil crop genomics. 6 /bodyAs a symbol of peace, fertility, health and longevity, the olive tree (Olea europaea L.) is a socio-economically important oil crop that is widely grown in the Mediterranean Basin.Belonging to the Oleaceae family (order Lamiales), it can biosynthesize essential unsaturated fatty acids and other important secondary metabolites, such as vitamins and phenolic compounds (1). The olive tree is a diploid (2n = 46) allogamous crop that can be vegetatively propagated and live for thousands of years (2). Paleobotanical evidence suggests that olive oil was already produced in the Bronze Age (3). It has been thought that cultivated varieties were derived from the wild olive tree, called oleaster (O. europaea var. sylvestris), in Asia Minor, which then spread to Greece (4). Nevertheless, the exact domestication history of the olive tree is unknown (5). Due to their longevity, oleaster...

MicroRNAs (miRNAs) are small non-coding class of RNAs. They were identified in many plants with their diverse regulatory roles in several cellular and metabolic processes. A number of miRNAs were involved in biotic and abiotic stress responses. Here, fungal stress responsive wheat miRNAs were analyzed by using miRNA-microarray strategy. Two different fungi (Fusarium culmorum and Bipolaris sorokiniana) were inoculated on resistant and sensitive wheat cultivars. A total of 87 differentially regulated miRNAs were detected in the 8 × 15 K array including all of the available plant miRNAs. Using bioinformatics tools, the target transcripts of responsive miRNAs were predicted, and related biological processes and mechanisms were assessed. A number of the miRNAs such as miR2592s, miR869.1, miR169b were highly differentially regulated showing more than 200-fold change upon fungal-inoculation. Some of the miRNAs were identified as fungal-inoculation responsive for the first time. The analyses showed that some of the differentially regulated miRNAs targeted resistance-related genes such as LRR, glucuronosyl transferase, peroxidase and Pto kinase. The comparison of the two miRNA-microarray analyses indicated that fungal-responsive wheat miRNAs were differentially regulated in pathogen- and cultivar-specific manners.

Plants are frequently exposed to microorganisms like fungi, bacteria, and viruses that cause biotic stresses. Fusarium head blight (FHB) is an economically risky wheat disease, which occurs upon Fusarium graminearum (Fg) infection. Moderately susceptible (cv. “Mizrak 98”) and susceptible (cv. “Gun 91”) winter type bread wheat cultivars were subjected to transcriptional profiling after exposure to Fg infection. To examine the early response to the pathogen in wheat, we measured gene expression alterations in mock and pathogen inoculated root crown of moderately susceptible (MS) and susceptible cultivars at 12 hours after inoculation (hai) using 12X135K microarray chip. The transcriptome analyses revealed that out of 39,179 transcripts, 3668 genes in microarray were significantly regulated at least in one time comparison. The majority of differentially regulated transcripts were associated with disease response and the gene expression mechanism. When the cultivars were compared, a number of transcripts and expression alterations varied within the cultivars. Especially membrane related transcripts were detected as differentially expressed. Moreover, diverse transcription factors showed significant fold change values among the cultivars. This study presented new insights to understand the early response of selected cultivars to the Fg at 12 hai. Through the KEGG analysis, we observed that the most altered transcripts were associated with starch and sucrose metabolism and gluconeogenesis pathways.

Hexaploid bread wheat (Triticum aestivum) is one of the major crops grown and consumed all over the world. Elevated soil salinity causes reduction in crop yield and quality; therefore, several strategies were developed to improve salt-tolerant cultivars. MicroRNAs (miRNAs), small and non-coding RNAs, regulate gene expression at post-transcriptional level and play important roles in stress tolerance. Here, we used a broad-range miRNA-microarray analysis to investigate the root-miRNA profiles of two cultivars, Bezostaja (sensitive) and Seri-82 (tolerant). A total of 44 differentially regulated miRNAs were identified in the 8 × 15K array containing 11 862 plant miRNAs available in the database. Sixteen novel salt-responsive miRNAs were determined in wheat for the first time. The expression of three miRNAs (hvu-miR5049a, ppt-miR1074 and osa-miR444b.2) was up-regulated more than 260-fold in cv. Bezostaja upon salt stress. The target-gene analyses showed that several salt-stress-responsive miRNAs regulate mainly transcription factors such as bHLH135-like, AP2/ERBP, MADS-box and transporters. Gene ontology searches for 565 putative salt-stress-responsive miRNA target-genes revealed 623 processes in 10 different main topics such as metabolic process and response to stimuli. The genome-wide root miRNome study indicates salt-stress-responsive wheat miRNAs and the possible mechanisms behind the tolerance.

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The present study is aimed to identify and characterize HSP70 (PvHSP70) genes in two different common bean cultivars under salt stress. For this purpose various in silico methods such as RNAseq data and qRT-PCR analysis were used. A total of 24 candidate PvHSP70 gene were identified. Except for chromosome 4 and 7, these candidate PvHSP70 genes were distributed on the remaining chromosomes. While the lowest number of PvHSP70 genes was determined on chromosomes 1, 3, 5, 7, 9, 10 and 11 (one HSP70 gene), the highest number of PvHSP70s was on chromosomes 6 and 8 (seven HSP70 genes each). Three genes; PvHSP70-5, -9, and -10 were found to have no-introns. In addition, four tandemly and six segmentally duplicated gene couples were detected. A total of 13 PvHSP70 genes were targeted by miRNAs of 44 plant species and the most targeted genes were PvHSP70-5 and -23. The expression profile of PvHSP70 genes based on publicly available RNA-seq data was identified and salt treated leaf tissue was found to have more gene expression levels compared to the root. qRT-PCR analysis showed that the transcript concentrations of upregulated PvHSP70 genes in leaves of Zulbiye (sensitive) were mostly higher than those of Yakutiye (resistant). The present study revealed that PvHSP70 genes might play an important role in salt stress response for common bean cultivars and variability between cultivars also suggests that these genes could be used as functional markers for salt tolerance in common bean.