Comparison of plant genomes by analysis of gene sequences SSR and SNP

Plant genomes have often been compared by analysis of the sequences of specific loci. High throughput genomic analysis now allows large numbers of individual loci to be considered. Comparison of the genomes of individuals within species is often based on the analysis of simple sequences repeat (SSR) loci or single nucleotide polymorphism (SNP) loci. Molecular analysis has resulted in significant recent advances in the understanding of relations between different groups of higher plants and relationships within flowering plants. For example the older division of flowering plants into monocotyledons and dicotyledons is now being replaced by a more complex understanding. Recent chloroplast genome analysis indicates frequent transfer of chloroplast genes between species. SSR sequences within genes (EST) are often conserved between closely related plant species unlike SSR sequences in other parts of the genome. Rare examples of widely conserved SSRs have been found. Analysis of the distribution of SNP within genes allows targeting of SNP discovery to regions (eg. introns, 3'UTR, 5'UTR, promoters) with suitable levels of polymorphism. High throughput SNP analysis offers an important new tool for comparison of plant genomes.