The sugarcane genome challenges: Strategies for sequencing a highly complex genome

Souza, Glaucia Mendes, Berges, Helene, Bocs, Stephanie, Casu, Rosanne, D’Hont, Angelique, Ferreira, Joao Eduardo, Henry, Robert, Ming, Ray, Potier, Bernard, Van Sluys, Marie-Anne, Vincentz, Michel and Paterson, Andrew H. (2011) The sugarcane genome challenges: Strategies for sequencing a highly complex genome. Tropical Plant Biology, 4 3-4: 145-156. doi:10.1007/s12042-011-9079-0


Author Souza, Glaucia Mendes
Berges, Helene
Bocs, Stephanie
Casu, Rosanne
D’Hont, Angelique
Ferreira, Joao Eduardo
Henry, Robert
Ming, Ray
Potier, Bernard
Van Sluys, Marie-Anne
Vincentz, Michel
Paterson, Andrew H.
Title The sugarcane genome challenges: Strategies for sequencing a highly complex genome
Journal name Tropical Plant Biology   Check publisher's open access policy
ISSN 1935-9756
1935-9764
Publication date 2011-12
Sub-type Article (original research)
DOI 10.1007/s12042-011-9079-0
Volume 4
Issue 3-4
Start page 145
End page 156
Total pages 12
Place of publication New York, United States
Publisher Springer
Collection year 2012
Language eng
Formatted abstract
Sugarcane cultivars derive from interspecific hybrids obtained by crossing Saccharum officinarum and Saccharum spontaneum and provide feedstock used worldwide for sugar and biofuel production. The importance of sugarcane as a bioenergy feedstock has increased interest in the generation of new cultivars optimised for energy production. Cultivar improvement has relied largely on traditional breeding methods, which may be limited by the complexity of inheritance in interspecific polyploid hybrids, and the time-consuming process of selection of plants with desired agronomic traits. In this sense, molecular genetics can assist in the process of developing improved cultivars by generating molecular markers that can be used in the breeding process or by introducing new genes into the sugarcane genome. For meeting each of these, and additional goals, biotechnologists would benefit from a reference genome sequence of a sugarcane cultivar. The sugarcane genome poses challenges that have not been addressed in any prior sequencing project, due to its highly polyploid and aneuploid genome structure with a complete set of homeologous genes predicted to range from 10 to 12 copies (alleles) and to include representatives from each of two different species. Although sugarcane’s monoploid genome is about 1 Gb, its highly polymorphic nature represents another significant challenge for obtaining a genuine assembled monoploid genome. With a rich resource of expressed-sequence tag (EST) data in the public domain, the present article describes tools and strategies that may aid in the generation of a reference genome sequence.
Keyword Sugarcane
Genome
Sequencing
Sorghum
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Official 2012 Collection
Queensland Alliance for Agriculture and Food Innovation
 
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Created: Wed, 08 Feb 2012, 16:20:17 EST by Professor Robert Henry on behalf of Qld Alliance for Agriculture and Food Innovation