Over 100 scientists from 16 institutions worked together for five years to complete the massive and complex sugarcane genome. The crop's massive genome was difficult to sequence because in the evolutionary history of sugarcane, its genome was duplicated twice, resulting in four slightly different versions of each pair of chromosomes all crammed into the same nucleus together.
These events not only quadrupled the size of the genome, they also made highly similar sequences from the genome wide duplication much more difficult to assemble into distinct chromosomes. For this challenge, the research team used high-throughput chromatin conformation capture (Hi-C). When analyzed using ALLHIC, a customized algorithm developed by the team, the resulting data provided a rough map of which sections of sequence most likely belonged to which chromosome. By combining long sequence reads and the Hi-C physical map, the researchers found which gene sequences belonged to each of the four variations on the original, pre-duplications genome—a much higher level of detail than they expected to attain.
Understanding these changes helped the researchers resolve the mystery why Saccharum spontaneum (wild sugarcane) is such a superior source of disease resistance and stress tolerance genes. The high quality genome sequence also identified the possible origins of modern sugarcane's incredible sweetness: accumulated mutations that produced multiple copies of genes for sugar-transporting proteins.
(Source: Crop Biotech Update, International Service for Acquisition of Agri-Biotech Applications. www.isaaa.org)
