The Complex Sugarcane Genome is Decoded
Credit: Thamizhpparithi Maari [CC BY-SA 3.0 (https://creativecommons.org/licenses/by-sa/3.0)], from Wikimedia Commons
Sugarcane, the last unsequenced major cultivated plant, has had its genome decoded. The delay was because of sugarcane's huge genomic complexity: the genome comprises between 10 and 12 copies of each chromosome, when the human genome has just two. An international team coordinated by CIRAD achieved this milestone, as reported in Nature Communications on 6 July. It will now be possible to "modernize" the methods used to breed sugarcane varieties. This will be a real boon to the sugar and biomass industry.
CIRAD and its partners* had to use cunning to establish the first sugarcane reference sequence. The plant's genome is so complex that conventional sequencing techniques had proved useless. This meant that sugarcane was the last major cultivated plant to have its genome sequenced.
A novel sequencing method
The team took up the gauntlet using a nifty approach based on a discovery made at CIRAD some 20 years previously: the genome structures of sugarcane and sorghum are very similar. The term used for this is "colinearity", which means that there is a degree of parallelism, with numerous genes occurring in the same order. Olivier Garsmeur, a CIRAD researcher and lead author of the study, was thus able to use the sorghum genome as a template to assemble and select the sugarcane chromosome fragments to sequence. "Thanks to this novel method, the reference sequence obtained for a cultivar from Réunion, R570, is very good quality", says Angélique D’Hont, a CIRAD geneticist who coordinated the study.
A key stage in investigating the genome
That reference sequence is a vital step towards fully sequencing the sugarcane genome and analysing the variations between the various sugarcane varieties more effectively. Angélique D'Hont had the same experience with the banana genome in 2012. As she says, "having a reference sequence for a species radically changes all the genomic and more broadly genetic approaches for that species".
A new era for sugarcane breeding
As with all other cultivated plants before it, sugarcane breeding will now be able to enter the age of molecular biology. Until now, for want of a reference sequence, sugarcane cultivar breeding programmes were restricted to hybridization, followed by conventional, very cumbersome field assessments. Molecular screening techniques can now be developed to supplement field trials. This is a major breakthrough, since almost 80% of the world's sugar comes from sugarcane. Moreover, the plant has also recently become a frontrunner in the race to produce biomass. This new genetic knowledge will serve to create new varieties for a wider range of uses.
This article has been republished from materials provided by CIRAD. Note: material may have been edited for length and content. For further information, please contact the cited source.
Reference: Garsmeur, O., Droc, G., Antonise, R., Grimwood, J., Potier, B., Aitken, K., … D’Hont, A. (2018). A mosaic monoploid reference sequence for the highly complex genome of sugarcane. Nature Communications, 9(1), 2638. https://doi.org/10.1038/s41467-018-05051-5
* Joint Genome Institute, Keygene, Queensland Alliance for Agriculture and Food Innovation, Commonwealth Scientific and Industrial Research Organisation, South African Sugarcane Research Institute, Universidade de São Paulo, funded by the International Consortium for Sugarcane Biotechnology and the Joint BioEnergy Institute.
Computer scientists at Carnegie Mellon University say neural networks and supervised machine learning techniques can efficiently characterize cells that have been studied using single cell RNA-sequencing (scRNA-seq). This finding could help researchers identify new cell subtypes and differentiate between healthy and diseased cells.