Emre Ilhan

Genome of wild olive and the evolution of oil biosynthesis

Significance We 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 approximately 28 and 59 Mya. 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 the US Food and Drug Administration. Here 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 pseudochromosomes obtained through a newly constructed genetic map. The oleaster genome contains signatures of two Oleaceae lineage-specific paleopolyploidy events, dated at ∼28 and ∼59 Mya. 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 with sesame, a closely related oil crop. Duplicated oleaster FAD2 genes are regulated by an 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.

Transcriptome analysis of wheat inoculated with Fusarium graminearum

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.

Molecular and ecological investigations on the wild populations of Glycyrrhiza L. taxa distributed in the East Mediterranean Area of Turkey

This paper covers studies on the molecular and ecological aspects of G. glabra var. glandulifera, G. flavescens ssp. flavescens and G. echinata collected from Hatay (Turkey); with the aim to better understand their genetic variation and ecological requirements for possible conservation programs. The material including total genomic DNA was extracted by the CTAB, and for PCR reaction, a total of 14 SSR primers developed for Medicago truncatula were used. PCR amplifications were performed in a Multigen® Thermal Cycler. Soil samples were analysed for their texture, pH, total soluble salts, calcium carbonate, total N content, total phosphorus and organic matter content. In order to see the association between genetic, ecological and geographical data, a similarity matrix was generated. Genetic similarity distances between genotypes were correlated with those of Eucledian distances obtained from ecological and geographical data. Analysis of molecular variance (AMOVA) was performed using GenAlEx 6.5 software to determine variation among and within genetic variations. The genetic analysis showed that the highest expected heterozygosity values were obtained from G. glabra while the lowest were obtained from G. echinata. In general heterozygosity values were low, especially for G. echinata. Therefore, variation appears to be lower within each species than among three species. The physical and chemical analysis of soil and plant samples indicates that mineral accumulation in plants is substantially affected by the soil characteristics. There is a need for identification of better strategies for the improvement of varieties, especially for small farmers managing marginal soils. More studies should be conducted in order to safeguard these taxa, especially G. glabra var. glandulifera which is collected intensively due to its economic value, the same is true for endemic taxon G. flavescens ssp. flavescens.

miR482 ve Bitkilerdeki İzoformları

Bitkilerdeki miR482 aile uyeleri genelde 22 nukleotid uzunlugunda diger mikroRNA (miRNA) ailelerinden daha degisken ve sira disi dizilere sahiptir. Calismalar miR482’nin hastalik direnciyle iliskili nukleotit-baglayici losince zengin tekrarli (Nucleotide binding-site leucine-rich repeat, NB-LRR) genlerle ilgili oldugunu gostermektedir. Bitki genomlarinda kodlanmis cesitli NB-LRR’ler bircok patojen tanimayi saglayan bir cesit bagisiklik sistemidir. NB-LRR proteinleri normal patojenlere karsi efektor-tetikleme bagisiklikligi ile iliskilidir. Bitkide temelden gelen bagisiklik reseptorleri tanilayici reseptor yapilari (Pattern recoginition receptor, PRR) ve direnc (Resistance, R) proteinleridir. R genlerinin cogu NB-LRR etki ile hucrede bagisiklik proteinlerini kodlarlar. miR482, miR1448, slmiR2118 ve ath-miR472 hastalik direnci ile iliskili miRNA’lardir. Yapilan bazi calismalarda ise miR482’nin miR1448 homologu oldugu bildirilmis ve filogenetik analizler miR482’nin tandem duplikasyon urunu miR1448 olabilecegini gostermektedir. Evrimsel surecte bu miRNA’lar ayni transkripti hedeflemislerdir. miR482 izoformlarinin baskilanmasi bitkiyi patojene karsi hassaslastirirken miR482’nin soyada nodulasyon olusumunda ve mikorizalarin calisma prensibinde etkili olabilecegi dusunulmektedir. Giderek artan kanitlar miRNA482’nin patojen saldirisinda hastalik direnci tepkilerinde kritik roller oynadigini gostermektedir.