In Silico Analysis of SSRs in Mitochondrial Genomes of Plants

Abstract

Simple sequence repeats (SSRs) or microsatellites constitute a countable portion of genomes. However, the significance of SSRs in organelle genomes has not been completely understood. The availability of organelle genome sequences allows us to understand the organization of SSRs in their genic and intergenic regions. In the current study we surveyed the patterns of SSRs in mitochondrial genomes of different taxa of plants. A total of 16 mitochondrial genomes, from algae to angiosperms, have been considered to analyze the pattern of simple sequence repeats present in them. Based on study, the mononucleotide repeats of A/T were found to be more prevalent in mitochondrial genomes over other repeat types. The dinucleotides repeats, TA/AT, were the second most numerous, whereas tri-, tetra-, and pentanucleotide repeats were in less number and present in intronic or intergenic portions only. Mononucleotide repeats prevailed in protein-coding exonic portions of all organisms. These results indicates that microsatellite pattern in mitochondrial genomes is different from nuclear genomes and also focuses on organization and diversity at SSR locuses in mitochondrial genomes. This is the novel report of microsatellite polymorphism in plant mitochondrion on whole genome level.

Mitochondrial SSRs and their utility in distinguishing wild species, CMS lines and maintainer lines in pigeonpea (Cajanus cajan L.)

“…While comparing organellar genomes of major cereals including rice, wheat, maize and sorghum, mononucleotides were the most frequent repeats in an earlier study by Rajendrakumar et al (2008), the commonest mononucleotide repeat being poly ''A'' and poly ''T''. These mononucleotide repeats were also relatively more abundant in mitochondrial genomes of algae and angiosperms (Kuntal and Sharma 2011). The frequency of SSRs in pigeonpea mitochondrial genome observed during the present study was relatively low, when compared with that in mitochondrial genomes of cereals (Rajendrakumar et al 2007(Rajendrakumar et al , 2008.…”

Microsatellite analysis in organelle genomes of Chlorophyta

“…The number of SSRs detected in intergenic regions of chloroplast and mitochondrial genomes is higher than SSRs in genic regions, which represented a similar pattern with SSR distribution in organelle genomes of Streptophytes [12, 13]. The differences in frequency of microsatellites in genic and intergenic regions suggest that the polymorphism associated with coding regions is lower than non-coding region.…”

“…In common algal species existing in both chloroplast and mitochondrial datasets, there was no relationship between the frequencies of simple and compound SSRs. Frequencies of SSRs were less in the Chlorophyta organelle genomes in comparison with organelle genomes of members of Streptophyta [12, 13]. …”

“…The differences in frequency of microsatellites in genic and intergenic regions suggest that the polymorphism associated with coding regions is lower than non-coding region. The density of microsatellites in mitochondrial genomes of Streptophyta ranged from 1 SSR/2.06 to SSR/75.27 kb [13] whereas in Chlorophyta this density ranged from 1 SSR/1.25 to 1 SSR/56.76 kb Table 2 (see supplementary material) Polymorphisms associated with a specific locus are due to the variation in length of the microsatellite, which in turn depends on the number of repetitions of the basic motif [14]. The lower substitution rate of chloroplast DNA compared to the nuclear genome has been documented [ 15] and the mutational processes at simple repeat loci in the chloroplast genome also occur less frequently than those in the nuclear genome [11].…”

“…Another rare pattern, AC/GT 6 , was also detected in mitochondrial genome of Ostreococcus tauri . The major di-nucleotide repeat pattern observed in Chlorophyta organellar genomes had shown the similarity with organelle and nuclear genomes of higher taxa [12, 13, 16]; but in nuclear genome of Chlamydomonas it is AC/GT [16]. …”