In 2009 the Sugarcane
Genome Sequencing Initiative (SUGESI) was formed in which it was determined
that the sugarcane variety R570 would be selected as the reference genome
to be sequenced. There were a number of other tools available for R570
including a high density genetic map and a Bacterial Artificial Chromosome
(BAC) library and some genome sequence of R570 had already been generated to
contribute to the consortium. The first strategy of the consortium was to use a
standard approach that was successfully used to generate some of the first
plant genomes sequenced (Arabidopsis Genome Initiative, 2000; Goff et al., 2002,
Yu et al., 2002). This method chooses the whole DNA sequence and divides
it into a BAC library which consists of manageable small pieces of all the
genome of sugarcane; the R570 BAC library has over 103 000 clones each
containing approximately 130 kb of DNA. The sorghum genome is also used in this
method to simplify the sugarcane sequence by selecting BAC clones that cover
the equivalent of one chromosome from each homology group in sugarcane. This
would represent the ‘monoploid’ sequence of sugarcane. Around 5000 BAC clones
are needed to cover the monoploid genome sequence of sugarcane. The generation
of the monoploid sequence is now almost towards the finished sequence and
recently a project has been initiated (2015) by the International Consortium of
Sugarcane Biotechnologists to sequence further BAC clones and finish the
monoploid sequence within the next few years. Another complementary and more
ambitious approach undertaken by the consortium was to generate a whole genome
shotgun assembly. This method has been successful for smaller genomes (Schmutz et
al., 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 fragments
and sequenced on a high throughput sequencer machines which produces short
sequence reads from either end of the fragments. These fragments are randomly
sequenced and the whole fragment can be assembled together if enough fragments are