Recent Polyploidization and Genome Evolution In Saccharum

Sugarcane (Saccharum spp.) has become increasingly important as a first generation biofuel crop. The complexity of the autopolyploid Saccharum genomes hindered the progress of genome research and application. To understand the genome structure and organization of Saccharum genomes, RNAseq was used to sequence the transcriptomes of 59 individuals in a segregating F1 population derived from S. officinarum LA Purple (2n = 80, x = 10) and S. robustum Mol5829 (2n = 80, x = 10), yielding a total of 1.9 billion reads. A total of 11,157 and 8,998 single nucleotide polymorphisms (SNPs) markers were generated for LA Purple and Mol 5829, respectively, resulting two high density linkage maps consisting of 96 linkage groups (LGs) for LA Purple and 110 LGs for Mol 5829. Synteny between sugarcane and sorghum was assessed by comparing sugarcane homologous groups (HGs) with sorghum chromosomes. Intrachromosomal rearrangements were detected in all LGs of LA Purple and Mol 5829, whereas interchromosomal rearrangements were detected in four pairs of Saccharum and sorghum chromosomes. Vast majority of Saccharum genes are collinear between Saccharum and sorghum genomes. RNAseq data from S. spontaneum were also analyzed for estimating the divergence time of the three Saccharum species. The speciation event separating S. officinarum and S. robustum occured about 377 thousand years ago, whereas their common ancestor diverged from S. spontaneum about 770 thousand years ago. This work provides a large collection of transcriptomes, two saturated genome maps, and detailed genome organization in two Saccharum species.