Differential duplicate gene retention

Article By:

Freeling, Michael Department of Plant and Microbial Biology, University of California, Berkeley, California.

Last reviewed:2009

Eukaryotic organisms occasionally double their chromosomes, and this new tetraploid sometimes founds a new lineage whose descendants continue to possess some of the duplicated genes. If the tetraploidy (whole genome duplication) happened recently—within the last approximately 1 million years—then this might be recognized by an increase in chromosome number. This is a result of the fact that the centromere deletions, segmental deletions, and chromosome rearrangements that occur naturally to duplicate genomes have not had enough time to reduce the chromosome number. Recent tetraploidies are especially common among existing flowering plant species, perhaps because they often self-fertilize and have an asexual reproductive option. Ancient tetraploidies, however, are widespread, have a chromosome number similar to that of the ancestor, and are thus more difficult to detect. At the base of the vertebrate phylogenetic tree are two well-supported tetraploidies (wherein the genome of jawed vertebrates underwent two rounds of whole genome duplication that took place between the emergence of urochordates and the radiation of jawed vertebrates); occasional more recent tetraploidies have occurred in fish, amphibians, and yeasts; and multiple, ancient tetraploidies punctuate all plant lineages. These ancient tetraploidies were inferred from the pattern of gene content within genomes that have been sequenced and annotated. Figure 1 shows an example of data presented as a dot plot supporting the inference of polyploidy from within the genome of a French grape variety, the species useful in wine making. This plot compares the gene content and order of grape chromosome 14 (y axis) with that of grape chromosome 17 (x axis). Each dot indicates where one gene in chromosome 14 matches a gene of similar sequence in chromosome 17. Many such similarities are scattered around the plot, but some form lines. Each line indicates genes of similar sequence and in a similar order that exist on chromosome 14 and most of chromosome 17. Most of these two chromosomes must have been derived from a single ancestral sequence that doubled and then rearranged. Evidence of tetraploidy is observed when these lines of gene colinearity largely cover an entire genome.

The content above is only an excerpt.