Identification and characterization of conserved micrornas in wheat (Triticum monococcum ssp. monococcum) by high-throughput sequencing and computational analysis
Küçük Resim Yok
Tarih
2016
Yazarlar
Dergi Başlığı
Dergi ISSN
Cilt Başlığı
Yayıncı
Bolu Abant İzzet Baysal Üniversitesi
Erişim Hakkı
info:eu-repo/semantics/openAccess
Özet
Buğday; yıllık 615.8 milyon metre küp tonun üzerindeki yıllık hasatıyla, zirvedeki üç ana tahılın en önemli ikinci tarım ürünüdür. Kuraklık ve tuzluluk buğday çeşitlerinin verimini ve kalitesini en fazla etkileyen olumsuz çevresel stres faktörleridir. Bitkiler, öte yandan, bu abiyotik streslerle mücadele etmek için kendi savunma sistemlerini geliştirmişlerdir. Savunma mekanizmalarından biri microRNA'lar (miRNAlar) yoluyla gen açıklanmasının değiştirilmesidir. miRNAlar spesifik mRNAların 3'-dönüştürülmemiş bölgesine (3'-UTR) bağlanarak post transkripsiyonel seviyelerde gen ifadelerini düzenleyen ortalama 22 nükleotit uzunluğuyla kodlamayan RNAların geniş bir sınıfıdır. miRNA genetik modifikasyonlarI, bu nedenle kurak ve tuz stresine karşı olan tepkiyi anlama ve buğdayın kurak ve tuz toleransını geliştirme potansiyeline sahiptir. Son yıllarda miRNAların çeşitli bitki türleri ve buğday genomlarında tuz ve kuraklık stresine tabi tutulduğu çalışmalar rapor edilmesine krşın siyez (Triticum monococcum ssp. monococcum) buğdayında henüz herhangi bir çalışma yapılmamıştır. Bu çalışma; korunmuş miRNAları kurak ve tuz stresi altında, gelecek generasyon dizilemesi ve simulasyon analizinin bir kombinsayonu ile incelemişitr. Bu yaklaşımın kullanılmasıyla 15,139,448 ham okumadan 75,164 özgün okuma elde edilmiş ve 142 belirgin miRNA familyasından 167 olgun miRNA dizisi tanımlanmıştır. Aynı şekilde; Triticum urartu tabanı kullanılarak ikincil yapı tahminleri microRNA prekursorları elde edilmiştir. Sonuçta; ve Triticum urartu genomunun %100 homologu olan 111 prekursor dizileri Mfold bilgisayar programı ile analiz edilmiştir. Bu çalışmadan elde edilen veriler; siyez buğdayının epigenetik düzenlenmesindeki transkriptlerin rolüne ilişkin bir araştırma başlatılabilmesi için gerekli kritik bilgilerin elde edilmesi ve miRNAlarla bunların dahil oldukları biyolojik süreçlerin daha iyi anlaşılabilmesi için uygun bir zemin sağlayacaktır.
Wheat is the second most important agricultural crop amongst the top three major cereal crops, with over 615.8 million metric tons of annual production. Drought and salinity are the most adversely influential environmental stress factors that affect yield and quality of wheat cultivars. Plants, on the other hand, have developed their own defense systems to cope with these abiotic stresses. One of these defense mechanisms is the altering of gene expression by microRNAs (miRNAs). miRNAs are an extensive class of noncoding RNAs, approximately 22 nucleotide lengths, which regulate the expression of genes at posttranscriptional levels by binding to the 3'-untranslated regions (3'-UTR) of specific mRNAs. MicroRNA-based genetic modifications, therefore, have the potential to understand the drought and salinity stress response and to enhance the drought and salinity tolerance in wheat. Even though miRNAs, which were implicated under salt and drought stress have widely been reported in numerous plant species and wheat genomes in the last years, studies on einkorn wheat (Triticum monococcum spp. monococcum) have not been available yet. This study investigated conserved miRNAs under drought and salinity stresses by combining next generation sequencing and computational analysis approaches. Using these approaches, 75,164 unique reads were obtained from 15,139,448 raw reads and 167 putative mature miRNA sequences belonging to 142 distinct miRNA families were identified. For secondary structure prediction, we used available sequences from Triticum urartu as template to extract precursor microRNA sequences. 111 of precursor sequences showing 100% homology to Triticum urartu genome was analyzed by using Mfold software. Data from this study provides critical information necessary to begin an investigation into a role for these transcripts in the epigenetic regulation of einkorn wheat and provide a basis for further understanding of miRNAs and the biological processes in which they are involved in wheat species
Wheat is the second most important agricultural crop amongst the top three major cereal crops, with over 615.8 million metric tons of annual production. Drought and salinity are the most adversely influential environmental stress factors that affect yield and quality of wheat cultivars. Plants, on the other hand, have developed their own defense systems to cope with these abiotic stresses. One of these defense mechanisms is the altering of gene expression by microRNAs (miRNAs). miRNAs are an extensive class of noncoding RNAs, approximately 22 nucleotide lengths, which regulate the expression of genes at posttranscriptional levels by binding to the 3'-untranslated regions (3'-UTR) of specific mRNAs. MicroRNA-based genetic modifications, therefore, have the potential to understand the drought and salinity stress response and to enhance the drought and salinity tolerance in wheat. Even though miRNAs, which were implicated under salt and drought stress have widely been reported in numerous plant species and wheat genomes in the last years, studies on einkorn wheat (Triticum monococcum spp. monococcum) have not been available yet. This study investigated conserved miRNAs under drought and salinity stresses by combining next generation sequencing and computational analysis approaches. Using these approaches, 75,164 unique reads were obtained from 15,139,448 raw reads and 167 putative mature miRNA sequences belonging to 142 distinct miRNA families were identified. For secondary structure prediction, we used available sequences from Triticum urartu as template to extract precursor microRNA sequences. 111 of precursor sequences showing 100% homology to Triticum urartu genome was analyzed by using Mfold software. Data from this study provides critical information necessary to begin an investigation into a role for these transcripts in the epigenetic regulation of einkorn wheat and provide a basis for further understanding of miRNAs and the biological processes in which they are involved in wheat species
Açıklama
Fen Bilimleri Enstitüsü, Biyoloji Ana Bilim Dalı
Anahtar Kelimeler
Biyoloji, Biology
