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Flowering plant genomes are amongst the largest and most complex, caused by highly proliferative repetitive elements and frequent genome duplications. The sequencing revolution has now delivered over 30 plant genomes ranging from the 82 Mbp genome of floating bladderwort to the nearly 5 Gbp genome of diploid wheat. While a high quality reference genome is now a pivotal research tool in all crop improvement efforts, many projects emphasise delivery timeframes at the expense of genome quality.
Our species of interest is sugarcane (Saccharum hybrid) which possesses a highly aneupolyploid genome 10 Gbp in size. In line with international efforts, our group has contributed a range of approaches to elucidate the sugarcane genome sequence. The first of these has been an international BAC-by-BAC sequencing effort to determine a "monoploid" genome sequence for the genotype R570, in which we have assembled Illumina paired-read data for 465 BACs into one or a few contigs each. Secondly, we have applied second-generation whole-genome shotgun sequencing up to 45x to de novo assemble the genome of R570. Our preliminary assembly represents over two thirds of the expected genome size with a contig NG50 of 1200 bp. Finally, we are now progressing a third-generation sequencing approach to supplement the results of the short-read approach and progress towards a final hybrid assembly.
Without a robust approach structural and functional annotation cannot inform meaningful biological interpretation. As our work approaches completion, it is becoming clear that ultimately a hybrid approach combining all of these outputs will be required for a high quality reference genome for sugarcane. There is no single technology or approach to solve this problem. With an "out-of-the-box" approach nowhere in sight, assembling high quality genome sequences will likely remain an important problem for some time yet.