The Genome Sequence of a Sugarcane Hybrid: Exploring Genes, Alleles and Transcripts

The increase in bioenergy efficiency and the transition to a biobased economy depends on the improvement of biomass production, such as sugarcane. This implies in the integration and deepening of the knowledge on agronomic practices, biochemistry and genetics. We are conducting the genome sequencing of a sugarcane cultivar and integrating it with transcriptome data. The challenges in sequencing the sugarcane genome relies in the assembly and analysis of a highly complex genome that is polyploid and aneuploid. To sequence sugarcane genome we combined BAC-by-BAC and shotgun approaches and different sequencing platforms. The development of Illumina Moleculo synthetic long-read sequencing technology showed to be a promising technology to sequence the sugarcane genome. We sequenced 26 libraries and obtained a total of 21.8 Gb of sequencing data, which approximately corresponds to 2.18 X coverage of the 10 Gb polyploid sugarcane genome. The Celera Assembler was modified for usage with longer reads. The assembly yielded 450,609 contigs in 4.26 Gb, with contig length average of 9,452 bp (min, 1,500; max 468,011). For the identification of putative sugarcane alleles we first  selected single copy sorghum genes (6,761) and aligned them to the predicted sugarcane coding sequences. The number of copies varied between 1 and 15. With pairwise alignments between the putative alleles we could verify the distance between them. Aligning cDNA reads from a full-length enriched cDNA libraries from S. officinarum, S. spontaneum and SP803280, we detected allele expression. For the 10 most expressed GO categories, we evaluated the percentage of alleles expressed.