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Building the sugarcane genome for biotechnology and identifying evolutionary trends.

ABSTRACT: 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.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.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.

SUBMITTER: de Setta N

PROVIDER: S-EPMC4122759 | biostudies-literature | 2014 Jun

REPOSITORIES: biostudies-literature

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Building the sugarcane genome for biotechnology and identifying evolutionary trends.

de Setta Nathalia N Monteiro-Vitorello Cláudia Barros CB Metcalfe Cushla Jane CJ Cruz Guilherme Marcelo Queiroga GM Del Bem Luiz Eduardo LE Vicentini Renato R Nogueira Fábio Tebaldi Silveira FT Campos Roberta Alvares RA Nunes Sideny Lima SL Turrini Paula Cristina Gasperazzo PC Vieira Andreia Prata AP Ochoa Cruz Edgar Andrés EA Corrêa Tatiana Caroline Silveira TC Hotta Carlos Takeshi CT de Mello Varani Alessandro A Vautrin Sonia S da Trindade Adilson Silva AS de Mendonça Vilela Mariane M Lembke Carolina Gimiliani CG Sato Paloma Mieko PM de Andrade Rodrigo Fandino RF Nishiyama Milton Yutaka MY Cardoso-Silva Claudio Benicio CB Scortecci Katia Castanho KC Garcia Antônio Augusto Franco AA Carneiro Monalisa Sampaio MS Kim Changsoo C Paterson Andrew H AH Bergès Hélène H D'Hont Angélique A de Souza Anete Pereira AP Souza Glaucia Mendes GM Vincentz Michel M Kitajima João Paulo JP Van Sluys Marie-Anne MA

BMC genomics 20140630

<h4>Background</h4>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.<h4>Results</h ...[more]

PMID: 24984568

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Project description:Sugarcane (Saccharum spp.) is highly polyploid and aneuploid. Modern cultivars are derived from hybridization between S. officinarum and S. spontaneum. This combination results in a genome exhibiting variable ploidy among different loci, a huge genome size (~10 Gb) and a high content of repetitive regions. An approach using genomic, transcriptomic, and genetic mapping can improve our knowledge of the behavior of genetics in sugarcane. The hypothetical HP600 and Centromere Protein C (CENP-C) genes from sugarcane were used to elucidate the allelic expression and genomic and genetic behaviors of this complex polyploid. The physically linked side-by-side genes HP600 and CENP-C were found in two different homeologous chromosome groups with ploidies of eight and ten. The first region (Region01) was a Sorghum bicolor ortholog region with all haplotypes of HP600 and CENP-C expressed, but HP600 exhibited an unbalanced haplotype expression. The second region (Region02) was a scrambled sugarcane sequence formed from different noncollinear genes containing partial duplications of HP600 and CENP-C (paralogs). This duplication resulted in a non-expressed HP600 pseudogene and a recombined fusion version of CENP-C and the orthologous gene Sobic.003G299500 with at least two chimeric gene haplotypes expressed. It was also determined that it occurred before Saccharum genus formation and after the separation of sorghum and sugarcane. A linkage map was constructed using markers from nonduplicated Region01 and for the duplication (Region01 and Region02). We compare the physical and linkage maps, demonstrating the possibility of mapping markers located in duplicated regions with markers in nonduplicated region. Our results contribute directly to the improvement of linkage mapping in complex polyploids and improve the integration of physical and genetic data for sugarcane breeding programs. Thus, we describe the complexity involved in sugarcane genetics and genomics and allelic dynamics, which can be useful for understanding complex polyploid genomes.

Dataset Information

Building the sugarcane genome for biotechnology and identifying evolutionary trends.

Publications

Building the sugarcane genome for biotechnology and identifying evolutionary trends.

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