In silico SSRs Analysis of Mitochondrial Genome (mtDNA) of Oryza rufipogon Griff.

Abstract

Cultivated rice is one of the most important crops for human diet. The Oryza genus includes 21 wild species and 2 cultivated species. Oryza rufipogon Griff. is the wild ancestor of cultivated rice and has AA genome structure as cultivated rice species (Oryza sativa L. and Oryza glaberrima Steud. ). Microsatellites also known as simple sequence repeats (SSRs) are small tandem repeats (1-6 bp) that are interspersed throughout the genome. In this study, in silico we identified mitochondrial SSRs (mtSSR) in O. rufipogon mitochondrial genome (mtDNA) by using bioinformatics tools. We determined 594 SSRs in the mitochondrial genome with an average of 1 SSR/1.06 kb and a total of 4% mtSSRs were observed in genic regions while a total of 96% mtSSRs were observed in intergenic regions. Trinucleotide SSRs were the most abundant repeats in mitochondrial genome while mononucleotide SSRs were predominant in genic regions. The most frequent motifs were A/T (85.5%) for mononucleotide repeats, AG/CT (70.59%) for dinucleotide repeats , AAG/CTT (30.9%) for trinucleotide repeats, AAAG/CTTT (24.5%) for tetranucleotide repeats, AAATT/AATTT, AAGAT/ATCTT, AATTC/GAATT and CCCGG/CCGGG were equal (16.7%) for pentanucleotide repeats and AAAAAT/ATTTTT (100%) for hexanucleotide repeats. In conclusion, this study results provide scientific basis for phylogenetics, evolutionary genetics, genetic mapping and diversity studies based on mtSSRs for different Oryza species in future.

Keywords

• Oryza rufipogon, rice, mtDNA, SSR, in silico analysis.

Oryza rufipogon Griff. Mitokondri Genomunun (mtDNA) In silico SSR Analizi

Abstract

Kültüvarı yapılan çeltik türleri, insan beslenmesi için en önemli ürünlerden biridir. Oryza cinsi 21 yabani ve 2 kültüvar tür barındırmaktadır. Oryza rufipogon Griff. kültüvar çeltiğin yabani atasıdır ve aynen kültüvar çeltik türleri gibi (Oryza sativa L. ve Oryza glaberrima Steud. ) AA genom yapısına sahiptir. Basit dizi tekrarları (SSRs) olarak da bilinen mikrosatellitler, bütün genomda dağılmış halde bulunan küçük ve birbirini izleyen tekrarlardır (1-6 bç). Bu çalışmada, biyoenformatik araçlar kullanılarak in silico O. rufipogon mitokondriyal genomunda SSR’ları (mtSSR) tanımladık. Mitokondriyal genomda 594 SSR ortalama 1 SSR/1.06 kb olarak belirledik ve mtSSR’ların %96’sının kodlama yapmayan bölgelerde olmasına karşın mtSSR’ların %4’ü kodlama yapan bölgelerde gözlemlendi. Tek nükleotid SSR’lar kodlama bölgelerinde baskın olmasına karşın üç nükleotid SSR’lar mitokondriyal genomda en fazla bulunan tekrarlardır. Tek nükleotid tekrarları için en sık tekrar A/T (85.5%), ikili nükleotid tekrarları için AG/CT (70.59%), üçlü nükleotid tekrarları için AAG/CTT (30.9%), dörtlü nükleotid tekrarları için AAAG/CTTT (24.5%), beşli nükleotid tekrarları için eşit AAATT/AATTT, AAGAT/ATCTT, AATTC/GAATT ve CCCGG/CCGGG (16.7%), altılı nükleotid tekrarları için AAAAAT/ATTTTT (100%) bulunmuştur. Sonuç olarak, bu çalışmanın bulguları gelecekte farklı Oryza türleri için filogenetik, evrimsel genetik, genetik haritalama ve mtSSR temelli genetik çeşitlilik çalışmalarına bilimsel bir zemin sağlayacaktır.

Keywords

• Oryza rufipogon, çeltik, mtDNA, SSR, in silico analiz.

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