Comparative analysis of microsatellites in chloroplast genomes of lower and higher plants

Abstract

Microsatellites, or simple sequence repeats (SSRs), contain repetitive DNA sequence where tandem repeats of one to six base pairs are present number of times. Chloroplast genome sequences have been shown to possess extensive variations in the length, number and distribution of SSRs. However, a comparative analysis of chloroplast microsatellites is not available. Considering their potential importance in generating genomic diversity, we have systematically analysed the abundance and distribution of simple and compound microsatellites in 164 sequenced chloroplast genomes from wide range of plants. The key findings of these studies are (1) a large number of mononucleotide repeats as compared to SSR(2-6)(di-, tri-, tetra-, penta-, hexanucleotide repeats) are present in all chloroplast genomes investigated, (2) lower plants such as algae show wide variation in relative abundance, density and distribution of microsatellite repeats as compared to flowering plants, (3) longer SSRs are excluded from coding regions of most chloroplast genomes, (4) GC content has a weak influence on number, relative abundance and relative density of mononucleotide as well as SSR(2-6). However, GC content strongly showed negative correlation with relative density (R (2) = 0.5, P < 0.05) and relative abundance (R (2) = 0.6, P < 0.05) of cSSRs. In summary, our comparative studies of chloroplast genomes illustrate the variable distribution of microsatellites and revealed that chloroplast genome of smaller plants possesses relatively more genomic diversity compared to higher plants.

The complete chloroplast genome sequence of an endemic monotypic genusHagenia(Rosaceae): structural comparative analysis, gene content and microsatellite detection

“…The 49 repeats constituted 22 palindrome (inverted) repeats, 19 direct (forward) repeats, seven reverse repeats and one complementary repeat (Table 4). The majority of the identified repeats were located in the non-coding regions of the genome which is in line with observations made in other chloroplast genomes of angiosperms (Provan, Powell & Hollingsworth, 2001; George et al, 2015). This trend of cpSSR distribution, has been observed in other chloroplast genomes species in Rosaceae suggesting that they may be suitable for conducting population genetic diversity, phylogenetic and evolutionary studies in species under this family.…”

The complete chloroplast genome sequence of Morus cathayana and Morus multicaulis, and comparative analysis within genus Morus L

“…Among these, there are 59 mono-, 7 di-, 3 tri-, 11 tetra-, and 3 penta-nucleotide repeats, respectively, in the M. cathayana cp genome; the corresponding numbers of these repeats in M. multicaulis are 63, 6, 2, 9, and 2. Mono-nucleotide repeats accounted for 71.1% and 76.8% of total SSRs in M. cathayana and M. multicaulis , respectively, similar to the levels found for M. mongolica and M. indica cp genomes, and the study on lower and higher plants (George et al, 2015). Six SSRs, including one di-nucleotide of (TC) 6 , one tri-nucleotide of (TTC) 4 , two tetra-nucleotides of (AAAG) 3 and (TTCT) 3 , and two penta-nucleotides of (AAGGA) 3 and (TTTCT) 3 in M. multicaulis or (ATTTC) 3 in M. cathayana , contain at least one C or G nucleotide, and the SSRs have a high AT content (97.5%).…”

Structural and Comparative Analysis of the Complete Chloroplast Genome of a Mangrove Plant: Scyphiphora hydrophyllacea Gaertn. f. and Related Rubiaceae Species

“…All SSRs were classified into five types of microsatellites: Mononucleotide, dinucleotide, trinucleotide, tetranucleotide, and pentanucleotide (Figure 2A,B). Consistent with previous reports, most of the SSRs are mononucleotide repeats [26]. In agreement with previous research, the number of mononucleotide repeats is more than the sum of other types ( Figure 2B), and all mononucleotide repeats consist of A or T bases, which is analogous to other land plants [15].…”