Towards sequencing the polyploid genome of sugarcane
BIOEN researchers participate in the Sugarcane Genome Sequencing Initiative
Sugarcane cultivars derive from a recent interspecific hybrid obtained by crossing Saccharum officinarum and Saccharum spontaneum and represent relevant feedstock used worldwide for biofuel production. The challenge in a sugarcane sequencing project is the size (10 Gb) and complexity of its genome structure that is highly polyploid and aneuploid with a complete set of homo(eo)logous genes predicted to range from 8 to 10 copies (alleles). Although sugarcane's monoploid genome is about 1 Gb, its highly polymorphic nature represent another significant challenge for obtaining a genuine assembled monoploid genome.
The Saccharum complex is diverse in genome content and organization. Collectively, these species present tremendous allelic diversity which in addition to the closely related species, Sorghum, Miscanthus and Erianthus represents a significant reservoir of genetic variability that could be exploited.
The goal of the Sugarcane Genome Sequencing Initiative is to identify strategies for sugarcane genome sequencing in the light of new technologies, focusing on whole genome shotgun (WGS) and/or BAC insert sequencing (BAC) approaches. We recognized the needs of an integrated bioinformatic platform and issues regarding sugarcane gene and protein nomenclature are being considered.
BAC end sequencing
R570 BAC selection and sequencing
Whole genome shot-gun sequencing (SP80-3280, Q165, LA Purple and SES 208)
High density genetic mapping