BAC Sequencing Revealing Complex Genomic Organization in Sugarcane and Synteny with Sorghum Genome in a QTL Region

Sugarcane is feedstock used for biofuel and sugar production worldwide. Modern cultivars are hybrid originated from Saccharum officinarum and S. spontaneum, which has a large and highly complex genome (polyploid and aneuploid). The traditional BAC-by-BAC approach for genome sequencing produces high quality assembly and allows complexity reduction. The aim of this work is studying the synteny and collinearity between sugarcane and sorghum, exploring a genomic region in sugarcane that corresponds to region associated with sugar production in sorghum. Sugarcane genes from leaf transcriptome similar to the genes present in QTL region were used to select sugarcane genomic fragments through qPCR. Based on multiple selection approach, where at least two genes are positive for each clone, a total of 68 BAC from SP80-3280 variety (2.4x total genome coverage) were selected. The BACs were sequenced using PacBio platform with ~250x coverage. The assembly was performed using Celera assembler, after error correction and quality filter by Quiver. A total of 183 contigs were obtained and only the sequences that contain genes related to QTL region were considered for further analysis. It was observed a high synteny between sugarcane and sorghum for this region and structural variation caused mainly by transposon insertions.