Building the sugarcane genome for biotechnology and identifying evolutionary trends

Author(s):Show less -

de Setta, Nathalia ^{[1, 2]} ; Monteiro-Vitorello, Claudia Barros ^[3] ; Metcalfe, Cushla Jane ^[1] ; Queiroga Cruz, Guilherme Marcelo ^[1] ; Del Bem, Luiz Eduardo ^[4] ; Vicentini, Renato ^[4] ; Silveira Nogueira, Fabio Tebaldi ^[5] ; Campos, Roberta Alvares ^[6] ; Nunes, Sideny Lima ^[6] ; Gasperazzo Turrini, Paula Cristina ^[1] ; Vieira, Andreia Prata ^[1] ; Ochoa Cruz, Edgar Andres ^[1] ; Silveira Correa, Tatiana Caroline ^[1] ; Hotta, Carlos Takeshi ^[6] ; Varani, Alessandro de Mello ^[3] ; Vautrin, Sonia ^[7] ; da Trindade, Adilson Silva ^[8] ; Vilela, Mariane de Mendonca ^[4] ; Lembke, Carolina Gimiliani ^[6] ; Sato, Paloma Mieko ^[6] ; de Andrade, Rodrigo Fandino ^[6] ; Nishiyama, Jr., Milton Yutaka ^[6] ; Cardoso-Silva, Claudio Benicio ^[4] ; Scortecci, Katia Castanho ^[8] ; Franco Garcia, Antonio Augusto ^[3] ; Carneiro, Monalisa Sampaio ^[9] ; Kim, Changsoo ^{[10, 11, 12]} ; Paterson, Andrew H. ^{[10, 11, 12]} ; Berges, Helene ^[7] ; D'Hont, Angelique ^[13] ; de Souza, Anete Pereira ^[4] ; Souza, Glaucia Mendes ^[6] ; Vincentz, Michel ^[4] ; Kitajima, Joao Paulo ^[14] ; Van Sluys, Marie-Anne ^[1]

Affiliation:Show less -

^[1] Univ Sao Paulo, Inst Biociencias, Dept Bot, BR-05508090 Sao Paulo - Brazil

^[2] Univ Fed ABC, BR-09210170 Santo Andre - Brazil

^[3] Univ Sao Paulo, Dept Genet, Escola Super Agr Luiz de Queiroz, BR-13418900 Piracicaba, SP - Brazil

^[4] Univ Estadual Campinas, Ctr Biol Mol & Engn Genet, BR-13083875 Campinas, SP - Brazil

^[5] Univ Estadual Paulista, Inst Biociencias, Dept Genet, BR-18618000 Botucatu, SP - Brazil

^[6] Inst Quim, Dept Bioquim, BR-05508900 Sao Paulo, SP - Brazil

^[7] INRA CNRGV, F-31326 Castanet Tolosan - France

^[8] Dept Biol Celular & Genet UFRN, BR-59072970 Natal, RN - Brazil

^[9] Univ Fed Sao Carlos, Ctr Ciencias Agr, Araras, SP - Brazil

^[10] Univ Georgia, Dept Plant Biol, Athens, GA 30602 - USA

^[11] Univ Georgia, Dept Crop & Soil Sci, Athens, GA 30602 - USA

^[12] Univ Georgia, Dept Genet, Athens, GA 30602 - USA

^[13] CIRAD, UMR1096, F-34398 Montpellier 5 - France

^[14] Mendel Genom Anal, Sao Paulo - Brazil

• Document type: Journal article
• Source: BMC Genomics; v. 15, JUN 30 2014.
• Web of Science Citations: 50

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. (AU)

• FAPESP's process: 09/51632-1 - Análises estruturais, funcionais e evolutivas de helitrons em cana-de-açúcar
• Grantee: Nathalia de Setta Costa
• Support Opportunities: Scholarships in Brazil - Post-Doctoral
• FAPESP's process: 10/05591-9 - Genetic studies of the Sporosorium scitamineum, the causal agent of sugarcane smut
• Grantee: Claudia Barros Monteiro Vitorello
• Support Opportunities: Regular Research Grants
• FAPESP's process: 08/54201-9 - Identification and characterization of sugarcane promoters induced by drought
• Grantee: CAROLINA GIMILIANI LEMBKE
• Support Opportunities: Scholarships in Brazil - Doctorate (Direct)
• FAPESP's process: 09/09116-6 - Redes regulatórias da cana-de-açúcar
• Grantee: Roberta Alvares Campos
• Support Opportunities: Scholarships in Brazil - Post-Doctoral
• FAPESP's process: 11/05317-7 - Estudo estrutural gênico de BACs de cana-de-açúcar pelo método de pirosequenciamento
• Grantee: Sideny Lima Nunes
• Support Opportunities: Scholarships in Brazil - Scientific Initiation
• FAPESP's process: 08/52074-0 - Sugarcane genome sequence: plant transposable elements are active contributors to gene structure variation, regulation and function
• Grantee: Marie-Anne Van Sluys
• Support Opportunities: Program for Research on Bioenergy (BIOEN) - Thematic Grants
• FAPESP's process: 09/09217-7 - Estudos sobre a organização do genoma de cana de açúcar e expressão gênica associada a presença de elementos de transposição
• Grantee: Cushla J Metcalfe
• Support Opportunities: Scholarships in Brazil - Post-Doctoral
• FAPESP's process: 08/58031-0 - Sugarcane energetic balance: a systems approach towards understanding regulation of sucrose metabolism and sugar signaling
• Grantee: Renato Vicentini dos Santos
• Support Opportunities: Program for Research on Bioenergy (BIOEN) - Young Investigators Grants
• FAPESP's process: 08/52197-4 - Genomic-assisted breeding of sugarcane: using molecular markers for understanding the genetic architecture of quantitative traits and to implement marker assisted selection
• Grantee: Anete Pereira de Souza
• Support Opportunities: Program for Research on Bioenergy (BIOEN) - Thematic Grants
• FAPESP's process: 08/58243-8 - Retrotransposons das famílias scMaximus, scAle e scDel: desvendando as interações com o genoma da cana-de-açúcar
• Grantee: Guilherme Marcello Queiroga Cruz
• Support Opportunities: Scholarships in Brazil - Doctorate (Direct)
• FAPESP's process: 08/52146-0 - Sugarcane signaling and regulatory networks
• Grantee: Glaucia Mendes Souza
• Support Opportunities: Program for Research on Bioenergy (BIOEN) - Thematic Grants