Supporting data for "Assembly of the 373K gene space of the polyploid sugarcane genome reveals reservoirs of functional diversity in the world’s leading biomass crop"

Sugarcane cultivars are polyploid interspecific hybrids of giant genomes, typically with 10-13 sets of chromosomes from two Saccharum species. The ploidy, hybridity and size of the genome, estimated to have in excess of 10 Gb, pose a great challenge for sequencing. Here we present a gene space assembly of SP80-3280, including 373,869 putative genes and their potential regulatory regions. The alignment of single-copy genes in diploid grasses to the putative genes, indicates that we could resolve 2-6 (up to 15) putative homo(eo)logs that are 99.1% identical within their coding sequences. Dissimilarities increase in their regulatory regions and gene promoter analysis shows differences in regulatory elements within gene families and are species-specific expressed. We exemplify these differences for sucrose synthase (SuSy) and phenylalanine ammonia-lyase (PAL), two gene families central to carbon partitioning. SP80-3280 have particular regulatory elements involved in sucrose synthesis not found in the ancestor S. spontaneum. PAL regulatory elements are found in co-expressed genes related to fiber synthesis within gene networks defined during plant growth and maturation. Comparison to sorghum reveals predominantly biallelic variations in sugarcane, consistent with the formation of two ‘subgenomes’ after their divergence ca. 3.8~4.6 MYA and reveals SNVs that may underlie their differences. This assembly represents a large step towards a whole genome assembly of a commercial sugarcane cultivar. It includes a rich diversity of genes and homo(eo)logous resolution for a representative fraction of the gene space, relevant to improve biomass and food production.