In 2009 the SugarcaneGenome Sequencing Initiative (SUGESI) was formed in which it was determinedthat the sugarcane variety R570 would be selected as the reference genometo be sequenced.

There were a number of other tools available for R570including a high density genetic map and a Bacterial Artificial Chromosome(BAC) library and some genome sequence of R570 had already been generated tocontribute to the consortium. The first strategy of the consortium was to use astandard approach that was successfully used to generate some of the firstplant genomes sequenced (Arabidopsis Genome Initiative, 2000; Goff et al., 2002,Yu et al., 2002). This method chooses the whole DNA sequence and dividesit into a BAC library which consists of manageable small pieces of all thegenome of sugarcane; the R570 BAC library has over 103 000 clones eachcontaining approximately 130 kb of DNA. The sorghum genome is also used in thismethod to simplify the sugarcane sequence by selecting BAC clones that coverthe equivalent of one chromosome from each homology group in sugarcane. Thiswould represent the ‘monoploid’ sequence of sugarcane.

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Around 5000 BAC clonesare needed to cover the monoploid genome sequence of sugarcane. The generationof the monoploid sequence is now almost towards the finished sequence andrecently a project has been initiated (2015) by the International Consortium ofSugarcane Biotechnologists to sequence further BAC clones and finish themonoploid sequence within the next few years. Another complementary and moreambitious approach undertaken by the consortium was to generate a whole genomeshotgun assembly. This method has been successful for smaller genomes (Schmutz etal.

, 2010; The Potato Genome Sequencing Consortium, 2011; Varshney et al.,2012) and more recently for the D genome of wheat (Chapman et al.,2015). Initially the sugarcane genome is cleaved into different size fragmentsand sequenced on a high throughput sequencer machines which produces shortsequence reads from either end of the fragments. These fragments are randomlysequenced and the whole fragment can be assembled together if enough fragments aresequenced.