Genomic sequencing in sugarcane; first insight into the physical organization of the genome and microsynteny with other grasses

The genome of several cereals, although variable in size and complexity, is known to share an important level of synteny. Sugarcane, which is a heterogenous and heterologous polyploid resulting from introgression between two species Saccharum officinarum and S, spontaneum, poses many challenges in genetic analysis. Sorghum, with its small diploid genome, is sugarcane closest cultivated relative. Comparative genetic maps show an extensive colinearity between both species. The extent of this colinearity was investigated at the sequence level in order to evaluate the potential of sorghum as a model for genome studies in sugarcane. For that purpose, we took advantage of a DNA sequence of 78kb around the Adh1 gene that already exists for sorghum (PNAS, 96:7409-7414, 1999), a BAC library created from a sugarcane cultivar (TAG, 99:419-424, 1999), and a sugarcane EST database (GMB, 24(1-4), 2001). A S. officinarum BAC clone of 97kb and a S. spontaneum one of 126kb were selected for sequencing, based on their high overlap with the orthologous sorghum target region. A detailed sequence comparison was performed between the three BAC clones. Sorghum and sugarcane display a high level of gene colinearity to the exception of two adjacent sorghum genes that are absent in the orthologous sugarcane region. An important sequence identity was observed in both genic and intergenic regions of the two species. Several LTR and non-LTR retroelements were identified in sugarcane only, responsible for the major difference between sugarcane and sorghum genomic DNA. The two Saccharum BAC sequences differ in the type, location and number of retroelements: LTR retroelements were found in both S. officinarum and S. spontaneum in different genic and inter-genic regions, whereas non-LTR retroelements were observed only in S. officinarum inter-genic regions. The number and location of miniature inverted-repeat transposable elements (MITEs) also vary between the two sugarcane species. (Texte intégral)