3.6 Repetitive sequences in the mt genome of O.sin...
Repetitive genes are considered as putative elements for recombination or regulation(Ghikas et al.，2006).A local self BLASTn of the O.sinensis mt genome against itself revealed 710 repetitive sequences(e-value＜10—7)with a total length of 77583bp，accounting for 49.25%of the whole mt genome(Fig.1).As shown in the mt genome of Phlebia radiate(Salavirta et al.，2014)，the abundant repeat sequences were almost exclusively localized into intronic and intergenic region in O.sinensis，in particular between positions 110 kb to 30 kb(clockwise，Fig.1).Reputer identified a total of 3490bp(2.22%)repeats in the O.sinensis mt genome，including 30 forward repeats(61～128bp，in total 2446bp)，13 palindromic repeats(61～90bp，in total 968bp)，and 1 reverse repeat(76bp)(Table 5).Tandem Repeats Finder found 44 tandem repeats(2～123bp in copy size)，with an average length of 63bp，and accounting for 1.76%(2772bp)of the mt genome(Table 5).
Table 5 Repetitive sequences in the mt genome of.sinensis(https://www.daowen.com)
Simple sequence repeats(SSRs，also known as microsatellites)comprise tandemly repeated genetic loci of 1 to 6bp(Tautz and Renz，1984).SSRs were found in PCGs(nad5，cox1)，rRNA(rnl)，and noncoding regions(intronic and intergenic regions)，with being more abundant in non-coding regions than in exons，as previously found in nuclear genome(Karaoglu et al.，2005).It assumed that SSRs might play an active role in genome evolution by creating and maintaining genetic variation(Tautz et al.，1986)，and serve a functional role in gene expression regulation by influencing transcriptional activity or protein-protein interactions(Gerber et al.，1994；Kashi et al.，1997).Among these SSRs，most(36/43)were consisted of mono-nucleotide repeats，while the di-，tetra-，penta-，and poly-nucleotide repeats were found with much lower frequency.The reason may be that longer repeats have higher mutation rates and less stability(Wierdl et al.，1997).In agreement with the previous studies in fungi(Karaoglu et al.，2005)，a majority of sequences rich in A/T were observed.All mono-nucleotide repeats were consisted of A/T repeats and the di-nucleotide repeats were AT/TA，with G/C only found in the less identified tetra-，penta-，and poly-nucleotide repeats.