LEA Genlerinin Dişbudak (Fraxinus excelsior) Genomunda Tanımlanması ve Karakterizasyonu

Çalışmanın amacı: LEA proteinleri, bitkilerin abiyotik stres koşullarına tepki vermesinde önemli rol oynamaktadır. Dişbudak zeytingiller ailesinden genom dizisi tamamlanmış bir ağaç türüdür. Dişbudak genomunda LEA genlerine dair açıklamalar bulunsa da kapsamlı bir analiz yoktur. Bu sebeple, bu çalışmada biyoinformatik araçlar kullanılarak LEA genlerinin dişbudak genomunda detaylı analizinin yapılması amaçlanmıştır. Materyal ve yöntem: Ash ve LEA protein dizileri sırasıyla Ash Tree Genome ve LEAP veri tabanından elde edilmiştir. Homolog dişbudak LEA peptitleri, CLC Genomic Workbench 11 kullanılarak bulunmuştur. Dişbudak LEA proteinlerinin özellikleri, Expasy PROTPARAM ile belirlenmiştir. MEGA7 filogenetik ağaç oluşturmak için kullanılmıştır. Dişbudak LEA proteinlerinin fonksiyonel analizi, Blast2GO ile gerçekleştirilmiştir. Dişbudak LEA proteinlerinin transkriptlerini hedef alan miRNA'lar psRNATarget ile tespit edilmiştir. Dişbudak LEA proteinlerinin üç boyutlu yapıları, PHYRE2 kullanılarak tahmin edilmiştir. Sonuçlar: Dişbudak genomunda 118 tane LEA geni (FexLEA) tanımlanmıştır. FexLEA’lar filogenetik analize göre 5 dala ayrılmıştır. Fex-LEA üyelerinin başlıca moleküler fonksiyonu bağlanma aktivitesidir. miR838'in FexLEA transkriptlerini hedef alan en yaygın miRNA olduğu görülmüştür. Önemli vurgular: Bu çalışma, dişbudak LEA proteinlerinin fonksiyonel analizleri için temel sağlayacaktır.

Anahtar Kelimeler:

Dişbudak, LEA, Genom Analizi

Identification and Characterization of LEA Genes in Ash Tree (Fraxinus excelsior) Genome

Aim of study: LEA proteins have a critical role in the abiotic stress response of plants. Ash belongs to the olive family and its genome sequence is complete. The LEA genes has not been extensively analyzed, although there are annotations in the ash genome. Therefore, it was aimed to perform genome-wide analysis of LEA genes in ash genome using bioinformatic tools in this study. Materials and methods: Ash and LEA protein sequences were obtained from the Ash Tree Genome and LEAP database respectively. Homologous LEA peptides in ash were found using CLC Genomic Workbench 11. Properties of ash LEA proteins were determined with Expasy PROTPARAM. MEGA7 was used to construct the phylogenetic tree. Functional analysis of ash LEA proteins was carried out via Blast2GO. miRNAs targeting transcripts of ash LEA proteins were detected with psRNATarget. The three-dimensional structures of ash LEA proteins were predicted using PHYRE2. Main result: 118 LEA genes (FexLEA) were identified in ash genome. FexLEA were divided into 5 distinct clusters according to phylogenetic analysis. The major molecular function of FexLEA was found as the binding activity. miR838 was the most common miRNA targeting FexLEA transcripts. Highlights: This study will provide the basis for further functional analysis of LEA proteins in ash.

Keywords:

Ash, LEA, Genome Analysis,

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