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The Sugarcane Genome Challenge: Strategies for Sequencing a Highly Complex Genome

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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.

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Acknowledgements

The authors would like to thank Dr. Carol Hotton, Curator for plants of the GenBank taxonomy database, National Center for Biotechnology Information, USA for her valuable assistance in sugarcane nomenclature harmonization. The work of GMS, JEF, MAVS and MV is funded by Fundação de Amparo à Pesquisa do Estado de São Paulo. The work of AHP has been funded by the International Consortium for Sugarcane Biotechnology.

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Communicated by Paul Moore

Helene Berges, Stephanie Bocs, Rosanne Casu, Angelique D’Hont, João Eduardo Ferreira, Robert Henry, Ray Ming, Bernard Potier, Marie-Anne Van Sluys and Michel Vincentz contributed equally to the work and have been listed in alphabetical order by last name.

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Souza, G.M., Berges, H., Bocs, S. et al. The Sugarcane Genome Challenge: Strategies for Sequencing a Highly Complex Genome. Tropical Plant Biol. 4, 145–156 (2011). https://doi.org/10.1007/s12042-011-9079-0

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