Gene Amplification and Diversification During Speciation of the Grasses

One of the main characteristics of flowering plants is an increase of gene content from about 9,500 to 27,000 mainly due to gene amplification and diversification. Because several genomes of the grass family have now been sequenced, one can reconstruct gene insertion and deletion events in chronological order. New chromosomes have been formed by the breakage and fusion of chromosomal fragments of their progenitors. Homoeologous chromosomal fragments can now be used to align multiple sequences from closely related species along conserved gene order. Deviation in gene order can be explained by insertions and deletions. Nucleotide substitution rates then can be used to order copying and insertion events. Furthermore, multiple alignments also indicate if a donor copy was retained or lost after gene amplification. If a donor copy is lost in the genome of a species, that one will then exhibit a faster pace of gene diversification, giving rise to new gene subfamilies, which is characteristic for different taxonomic groups. We have investigated this pattern by focusing on one of the seed storage proteins, the prolamins, with a preponderance of the amino acids proline and glutamine, which represent the major seed protein in grass species and whose function is to store nitrogen in the seed.