300 BACs Accomplished

The sequencing of 1000 BAC inserts (1x coverage) is part of a larger initiative to generate a sugarcane genome draft for understanding genome polyploidy variation and enable gene and transposable element characterization. BAC clones containing sugarcane inserts were selected based on probes and/or primers representing genes of interest and transposable elements. Two different approaches were used: macroarray membrane hybridization and qPCR using 3D BAC pools. Up to now, 300 BACs of the R570 cultivar have been sequenced and assembled into contigs longer than 100 Kbp in average. Expressed sugarcane genes from the SUCEST Project database were mapped to sequenced 1 contig BACs in order to assess both the amount of putative genes and transcriptionally active transposable elements that were sequenced. The annotation pipeline based on BLASTx (sorghum and rice protein databases) and UniProt revealed an average of 5 genes per 100 kbp. Sugarcane GC content in gene rich regions averages 55% (~45% for all contig sequences).  As other plant genomes, LTR retrotransposons are the most common type of repetitive sequences, followed by DNA transposons. Among the LTR retrotransposons, the Gypsy superfamily is the most frequent. Distinct transposable element produce informative tools regarding molecular markers, promoters, genome organization compared to other crops. These results provide the initial steps towards to understand sugarcane genome structure.