The Sugarcane Genome Sequencing Initiative (SUGESI): Strategies for Sequencing a Highly Complex Genome

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Sugarcane cultivars derive from recent interspecific hybrids 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. A sugarcane R570 BAC library whose construction was funded by ICSB is available for sequencing. The genome coverage of this library is believed to be around 1,3x suggesting that recovery of all alleles would not be always efficient. In any case, BAC screening can be undertaken using a fast and efficient 3D-pool approach which has been developed at CNRGV followed by PCR amplification of genes of interest.

The Sugarcane Genome Sequencing Initiative – A particularly attractive initial strategy that lies at the intersection of the common interests of virtually all of the sugarcane research community is to capture much of the gene-rich recombinationally-active euchromatin. The Sugarcane Genome Sequencing Initiative (SUGESI) was envisaged to join efforts to produce a reference sequence of a sugarcane cultivar ( Saccharum hybrid) and ancestor genotypes ( Saccharum officinarum and  Saccharum spontaneum) using a combination of approaches but mainly focused on BAC sequencing. The SUGESI Consortium aggregates researchers from Australia, Brazil, France, South Africa and United States. The SUGESI Initiative intends to make sequences public as soon as minimum assemblies permit.

Publications related to the project :

List of participant:

Dr Marie-Anne Van Sluys, Professor of Botany GaTE Lab (Genomics and Transposable elements)
 Departamento de Botânica-IBUSP
 rua do Matao, 277 05508-900;
 São Paulo, SP, BRASIL
 tel:55-11-30917759
 fax:55-11-30917724
 email: mavsluys@usp.br

Dr Glaucia Souza
 Associate Professor
 BIOEN Program Coordinator Instituto de Química
 Universidade de São Paulo
 Tel: 55-11-3091-8511
 Cel: 55-11-9177-4319
  http://sucest-fun.org
  http://bioenfapesp.org

Dr Angélique D'Hont
 CIRAD, UMR 1098 DAP Equipe "Structure et évolution des génomes" TAA96/03,
 Avenue Agropolis
 34398 Montpellier cedex 5, FRANCE
 tel (33) (0)4 67 61 59 27
 fax (33) (0)4 67 61 56 05
  http://umr-dap.cirad.fr/index.php/umr_dap/equipes/ structure_et_evolution_des_genome_seg
  http://tropgenedb.cirad.fr

Dr Andrew Paterson
 Plant Genome Mapping Laboratory Center for Applied Genetic Technologies
 111 Riverbend Road, Athens, GA 30606
 Voice: (706) 583-0166
 Fax: (706) 583-0160

Dr Ray Ming
 University of Illinois at Urbana-Champaign
 1201 W. Gregory Drive 148 ERML, MC-051
 (217) 333-1221

Dr Robert Henry
 Southern Cross University
 Centre for Plant Conservation Genetics Bioenergy Research Institute,
 Lismore, NSW Australia

Dr Helene BERGES
 Centre National de Ressources Genomiques Vegetales
 INRA - CNRGV
 Chemin de Borde Rouge BP 52627
 31326 Castanet Tolosan FRANCE

Dr Rosanne Casu
 Queensland Bioscience Precinct -
 St Lucia 306 Carmody Road
 St Lucia QLD 4067 Australia

Dr Bernard Potier
 South African Sugarcane Research Institute
 Private Bag X02 Mount Edgecombe
 4300 South Africa