Cotton Genome
A public genome sequencing effort of cotton was initiated in 2007 by a consortium of public researchers. They agreed on a strategy to sequence the genome of cultivated, tetraploid cotton. "Tetraploid" means that cultivated cotton actually has two separate genomes within its nucleus, referred to as the A and D genomes. The sequencing consortium first agreed to sequence the D-genome relative of cultivated cotton (G. raimondii, a wild Central American cotton species) because of its small size and limited number of repetitive elements. It is nearly one-third the number of bases of tetraploid cotton (AD), and each chromosome is only present once. The A genome of G. arboreum would be sequenced next. Its genome is roughly twice the size of G. raimondii's. Part of the difference in size between the two genomes is the amplification of retrotransposons (GORGE). Once both diploid genomes are assembled, then research could begin sequencing the actual genomes of cultivated cotton varieties. This strategy is out of necessity; if one were to sequence the tetraploid genome without model diploid genomes, the euchromatic DNA sequences of the AD genomes would co-assemble and the repetitive elements of AD genomes would assembly independently into A and D sequences respectively. Then there would be no way to untangle the mess of AD sequences without comparing them to their diploid counterparts.
The public sector effort continues with the goal to create a high-quality, draft genome sequence from reads generated by all sources. The public-sector effort has generated Sanger reads of BACs, fosmids, and plasmids as well as 454 reads. These later types of reads will be instrumental in assembling an initial draft of the D genome. In 2010, two companies (Monsanto and Illumina), completed enough Illumina sequencing to cover the D genome of G. raimondii about 50x. They announced that they would donate their raw reads to the public. This public relations effort gave them some recognition for sequencing the cotton genome. Once the D genome is assembled from all of this raw material, it will undoubtedly assist in the assembly of the AD genomes of cultivated varieties of cotton, but a lot of hard work remains.
Read more about this topic: Cotton
Famous quotes containing the word cotton:
“It is remarkable with what pure satisfaction the traveler in these woods will reach his camping-ground on the eve of a tempestuous night like this, as if he had got to his inn, and, rolling himself in his blanket, stretch himself on his six-feet-by-two bed of dripping fir twigs, with a thin sheet of cotton for roof, snug as a meadow-mouse in its nest.”
—Henry David Thoreau (1817–1862)