Recent Polyploidization Events in Three Saccharum Founding Species. Saccharum

To understand the genome structure and organization of the Saccharum genome, RNA-Seq 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 Molokai5829 (2n = 80, x = 10), yielding a total of 1.9 billion reads. 11,157 and 8,998 single nucleotide polymorphisms (SNPs) markers were generated for LA Purple and Mol 5829, respectively, resulting in two high density linkage maps consisting of 83 linkage groups (LGs) for S. officinarum and 105 LGs for S. robstum. The vast majority of markers in each LG of S. officinarum and S. robustum aligned to single sorghum chromosome, indicating that these two Saccharum species share a similar chromosome structure with sorghum. Interchromosomal rearrangements were detected in 40 (48.7%) and 37 (35.2%) LGs sorghum-S. officinarum and sorghum-S. robustum, respectively. Of the combined 77 Interchromosomal rearrangements in these two species, 72 (36 pairs, 93.5%) were conserved and shared by S. officinarum and S. robustum, indicating that they occurred in the ancestral genome before the speciation event separating these two species. More than 2000 gene pairs from S. spontaneum, S. officinarum, and S. robustum were analyzed to estimate their divergence time. The speciation event separating S. officinarum and S. robustum occured about 385 thousand years ago, and the second round of whole genome duplication (WGD) event via autopolyploidization occured after the speciation event because of shared interchromosomal rearrangements. The common ancestor of S. officinarum and S. robustum diverged from S. spontaneum about 769 thousand years ago, and the reduction of basic chromosome number from 10 to 8 in S. Spontaneum occured after the speciation event and before the second round of WGD.