Abstract
Simple sequence repeats (SSRs) are widespread units on genome sequences, and play many important roles in plants. In order to reveal the evolution of plant genomes, we investigated the evolutionary regularities of SSRs during the evolution of plant species and the plant kingdom by analysis of twelve sequenced plant genome sequences. First, in the twelve studied plant genomes, the main SSRs were those which contain repeats of 1–3 nucleotides combination. Second, in mononucleotide SSRs, the A/T percentage gradually increased along with the evolution of plants (except for P. patens). With the increase of SSRs repeat number the percentage of A/T in C. reinhardtii had no significant change, while the percentage of A/T in terrestrial plants species gradually declined. Third, in dinucleotide SSRs, the percentage of AT/TA increased along with the evolution of plant kingdom and the repeat number increased in terrestrial plants species. This trend was more obvious in dicotyledon than monocotyledon. The percentage of CG/GC showed the opposite pattern to the AT/TA. Forth, in trinucleotide SSRs, the percentages of combinations including two or three A/T were in a rising trend along with the evolution of plant kingdom; meanwhile with the increase of SSRs repeat number in plants species, different species chose different combinations as dominant SSRs. SSRs in C. reinhardtii, P. patens, Z. mays and A. thaliana showed their specific patterns related to evolutionary position or specific changes of genome sequences. The results showed that, SSRs not only had the general pattern in the evolution of plant kingdom, but also were associated with the evolution of the specific genome sequence. The study of the evolutionary regularities of SSRs provided new insights for the analysis of the plant genome evolution.
Highlights
Plant genomes are filled with low-complexity repetitive sequences
This duplication event might have triggered the angiosperm radiation during the Late Cretaceous, which is apparent in fossil record [9]
The genome sequences of A. thaliana (Col-0), B. distachyon, G. max, O. sativa (Japonica Group), S. lycopersicum, V. vinifera and D. melanogaster were downloaded from the National Center for Biotechnology Information (NCBI) genome database
Summary
Plant genomes are filled with low-complexity repetitive sequences. One of the most frequent low complexity sequences is simple sequence repeats (SSRs, defined as1~6 bp unit) [1]. Angiosperms are paleopolyploids, that is to say the genome of their common ancestor was subject to a large-scale or even genome wide duplication event during the Late Jurassic or Early Cretaceous, 100~160 million years ago [7,8]. This duplication event might have triggered the angiosperm radiation during the Late Cretaceous, which is apparent in fossil record [9]. The retention of genes after such large-scale duplication events has been shown to be biased towards certain functional classes [20,21,22]. It has been argued that such biased retention of duplicated genes were a driving force for morphological complexity, increase in biological diversity and eukaryote adaptive radiation [8, 23]
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