Abstract

Doc number: 540

Abstract

Background: Sugarcane is the source of sugar in all tropical and subtropical countries and is becoming increasingly important for bio-based fuels. However, its large (10 Gb), polyploid, complex genome has hindered genome based breeding efforts. Here we release the largest and most diverse set of sugarcane genome sequences to date, as part of an on-going initiative to provide a sugarcane genomic information resource, with the ultimate goal of producing a gold standard genome.

Results: Three hundred and seventeen chiefly euchromatic BACs were sequenced. A reference set of one thousand four hundred manually-annotated protein-coding genes was generated. A small RNA collection and a RNA-seq library were used to explore expression patterns and the sRNA landscape. In the sucrose and starch metabolism pathway, 16 non-redundant enzyme-encoding genes were identified. One of the sucrose pathway genes, sucrose-6-phosphate phosphohydrolase, is duplicated in sugarcane and sorghum, but not in rice and maize. A diversity analysis of the s6pp duplication region revealed haplotype-structured sequence composition. Examination of hom(e)ologous loci indicate both sequence structural and sRNA landscape variation. A synteny analysis shows that the sugarcane genome has expanded relative to the sorghum genome, largely due to the presence of transposable elements and uncharacterized intergenic and intronic sequences.

Conclusion: This release of sugarcane genomic sequences will advance our understanding of sugarcane genetics and contribute to the development of molecular tools for breeding purposes and gene discovery.

Details

Title
Building the sugarcane genome for biotechnology and identifying evolutionary trends
Author
de Setta, Nathalia; Monteiro-Vitorello, Cláudia Barros; Metcalfe, Cushla Jane; Cruz, Guilherme Marcelo Queiroga; Del Bem, Luiz Eduardo; Vicentini, Renato; Nogueira, Fábio Tebaldi Silveira; Campos, Roberta Alvares; Nunes, Sideny Lima; Turrini, Paula Cristina Gasperazzo; Vieira, Andreia Prata; Ochoa Cruz, Edgar Andrés; Corrêa, Tatiana Caroline Silveira; Hotta, Carlos Takeshi; de Mello Varani, Alessandro; Vautrin, Sonia; da Trindade, Adilson Silva; de Mendonça Vilela, Mariane; Lembke, Carolina Gimiliani; Sato, Paloma Mieko; de Andrade, Rodrigo Fandino; Nishiyama, Milton Yutaka, Jr; Cardoso-Silva, Claudio Benicio; Scortecci, Katia Castanho; Garcia, Antônio Augusto Franco; Carneiro, Monalisa Sampaio; Kim, Changsoo; Paterson, Andrew H; Bergès, Hélène; D'Hont, Angélique; de Souza, Anete Pereira; Souza, Glaucia Mendes; Vincentz, Michel; Kitajima, João Paulo; Van Sluys, Marie-Anne
Publication year
2014
Publication date
2014
Publisher
BioMed Central
e-ISSN
14712164
Source type
Scholarly Journal
Language of publication
English
ProQuest document ID
1550536145
Copyright
© 2014 de Setta et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.