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Optimization and Comparative Analysis of Plant Organellar DNA Enrichment Methods Suitable for Next-generation Sequencing
Published on: July 28, 2017
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Evolution Analysis of Simple Sequence Repeats in Plant Genome
Zhen Qin1, Yanping Wang2, Qingmei Wang1
1Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China.
Plos One
|December 3, 2015
Summary
Simple sequence repeats (SSRs) show distinct evolutionary patterns across plant genomes. Analyzing SSRs in twelve plant genomes reveals trends in nucleotide composition and repeat numbers, offering insights into plant genome evolution.
Area of Science:
- Genomics
- Evolutionary Biology
- Bioinformatics
Background:
- Simple sequence repeats (SSRs) are repetitive DNA sequences found throughout plant genomes.
- SSRs play crucial roles in various biological processes within plants.
- Understanding SSR evolution is key to deciphering plant genome evolution.
Purpose of the Study:
- To investigate the evolutionary regularities of SSRs across diverse plant species and the plant kingdom.
- To analyze SSR patterns in twelve sequenced plant genomes to identify evolutionary trends.
- To provide new insights into plant genome evolution through SSR analysis.
Main Methods:
- Comparative analysis of SSRs in twelve sequenced plant genomes.
- Examination of SSR types, including mononucleotide, dinucleotide, and trinucleotide repeats.
- Analysis of SSR nucleotide composition (A/T, CG/GC) and repeat number variations.
- Correlation of SSR patterns with plant evolutionary positions and genome sequence changes.
Main Results:
- Mononucleotide SSRs showed an increasing A/T percentage with plant evolution (except P. patens).
- Dinucleotide SSRs exhibited an increasing AT/TA percentage along with plant kingdom evolution, more pronounced in dicots.
- Trinucleotide SSRs showed a rising trend in combinations with two or three A/T nucleotides during plant evolution.
Conclusions:
- SSRs exhibit general evolutionary patterns across the plant kingdom.
- Specific SSR patterns are associated with the evolution of individual plant genome sequences.
- The study of SSR evolutionary regularities enhances the analysis of plant genome evolution.
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