Building the sugarcane genome for biotechnology and identifying evolutionary trends

Autor: João Paulo Kitajima, Nathalia de Setta, Adilson Silva da Trindade, Mariane de Mendonça Vilela, Luiz Eduardo Vieira Del Bem, Marie-Anne Van Sluys, Monalisa Sampaio Carneiro, Renato Vicentini, Carolina Gimiliani Lembke, Sonia Vautrin, Guilherme M. Q. Cruz, R. Andrade, Michel Vincentz, Changsoo Kim, Fabio Tebaldi Silveira Nogueira, Edgar Andrés Ochoa Cruz, Angélique D'Hont, Andréia Prata Vieira, Cushla J. Metcalfe, Katia Castanho Scortecci, Antonio Augusto Franco Garcia, Roberta Alvares Campos, Claudia Barros Monteiro-Vitorello, Glaucia Mendes Souza, Paula Cristina Gasperazzo Turrini, Claudio Benicio Cardoso-Silva, Paloma Mieko Sato, Tatiana Caroline Silveira Corrêa, Anete Pereira de Souza, Alessandro M. Varani, Milton Y. Nishiyama, Hélène Bergès, Carlos Takeshi Hotta, Sideny Lima Nunes, Andrew H. Paterson
Přispěvatelé: Universidade de São Paulo (USP), Universidade Federal do ABC (UFABC), Universidade Estadual de Campinas (UNICAMP), Universidade Estadual Paulista (Unesp), Inst Quim, INRA CNRGV, Dept Biol Celular & Genet UFRN, Universidade Federal de São Carlos (UFSCar), Univ Georgia, CIRAD, Mendel Genom Anal, Instituto de Biociências, Departamento de Genética, Universidade Estadual Paulista Júlio de Mesquita Filho = São Paulo State University (UNESP), Univ Sao Paulo, Dept Genet, Escola Super Agr Luiz de Queiroz, BR-13418900 Piracicaba, SP, Brazil, Partenaires INRAE, Centre National de Ressources Génomiques Végétales (CNRGV), Institut National de la Recherche Agronomique (INRA), Universidade Federal do Rio Grande do Norte [Natal] (UFRN), Centro de Ciências Agrárias, Universidade Federal de Santa Catarina = Federal University of Santa Catarina [Florianópolis] (UFSC), University of Georgia [USA], Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Mendelics Genomic Analysis, FAPESP [MAVS- 2008/52074-0, CBMV- 2010/05591-9, RV- 2008/58031-0, APS 2008/52197-4, GMS 08/52146-0, 2009/51632-1, 2009/09217-7, 2008/58243-8, 2009/09116-6, 2011/05317-7, 2008/54201-9], CNPq (MV- INCT BIOETHANOL), CAPES, International Consortium for Sugarcane Biotechnology [24], Consortium for Plant Biotechnology Research [DE-FG36-02GO12026], Univ. Georgia Office of the Vice President for Research
Jazyk: angličtina
Rok vydání: 2014
Předmět:
0106 biological sciences
Chromosomes
Artificial
Bacterial
Euchromatin
Métabolisme des glucides
[SDV]Life Sciences [q-bio]
01 natural sciences
Genome
F30 - Génétique et amélioration des plantes
Intergenic region
Gene Duplication
Gene duplication
Plant Proteins
2. Zero hunger
0303 health sciences
Saccharum officinarum
Biological Evolution
Saccharum
séquence chromosomique
DNA microarray
Genome
Plant
Metabolic Networks and Pathways
Biotechnology
Research Article
Transposable element
Séquence nucléotidique
F60 - Physiologie et biochimie végétale
Molecular Sequence Data
Biology
Polyploidy
03 medical and health sciences
polyploïdie
Genetics
[SDV.BV]Life Sciences [q-bio]/Vegetal Biology
Bacterial artificial chromosome sequencing
Grasses
Gene
Sorghum
030304 developmental biology
Synteny
Gene Library
Saccharum spontaneum
Génie génétique
Base Sequence
business.industry
Sequence Analysis
RNA
génome
graminée
15. Life on land
Phosphoric Monoester Hydrolases
chromosome bactérien artificiel
Haplotypes
Carte génétique
RNA
business
010606 plant biology & botany
Zdroj: Web of Science
Repositório Institucional da UNESP
Universidade Estadual Paulista (UNESP)
instacron:UNESP
BMC Genomics
BMC Genomics, BioMed Central, 2014, 15, ⟨10.1186/1471-2164-15-540⟩
BMC Genomics (15), . (2014)
ISSN: 1471-2164
Popis: Made available in DSpace on 2015-03-18T15:55:48Z (GMT). No. of bitstreams: 0 Previous issue date: 2014-06-30Bitstream added on 2015-03-18T16:28:35Z : No. of bitstreams: 1 WOS000339583200001.pdf: 1890820 bytes, checksum: e8843ac2cf7ccc2d8f25d37aca12bda6 (MD5) Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) International Consortium for Sugarcane Biotechnology Consortium for Plant Biotechnology Research Univ. Georgia Office of the Vice President for Research 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. Univ Sao Paulo, Inst Biociencias, Dept Bot, BR-05508090 Sao Paulo, Brazil Univ Fed ABC, BR-09210170 Santo Andre, Brazil Univ Sao Paulo, Dept Genet, Escola Super Agr Luiz de Queiroz, BR-13418900 Piracicaba, SP, Brazil Univ Estadual Campinas, Ctr Biol Mol & Engn Genet, BR-13083875 Campinas, SP, Brazil Univ Estadual Paulista, Inst Biociencias, Dept Genet, BR-18618000 Botucatu, SP, Brazil Inst Quim, Dept Bioquim, BR-05508900 Sao Paulo, SP, Brazil INRA CNRGV, F-31326 Castanet Tolosan, France Dept Biol Celular & Genet UFRN, BR-59072970 Natal, RN, Brazil Univ Fed Sao Carlos, Ctr Ciencias Agr, Araras, SP, Brazil Univ Georgia, Dept Plant Biol, Athens, GA 30602 USA Univ Georgia, Dept Crop & Soil Sci, Athens, GA 30602 USA Univ Georgia, Dept Genet, Athens, GA 30602 USA CIRAD, UMR1096, F-34398 Montpellier 5, France Mendel Genom Anal, Sao Paulo, Brazil Univ Estadual Paulista, Inst Biociencias, Dept Genet, BR-18618000 Botucatu, SP, Brazil FAPESP: 08/52074-0 FAPESP: 10/05591-9 FAPESP: 08/58031-0 FAPESP: 08/52197-4 FAPESP: 08/52146-0 FAPESP: 09/51632-1 FAPESP: 09/09217-7 FAPESP: 08/58243-8 FAPESP: 09/09116-6 FAPESP: 11/05317-7 FAPESP: 08/54201-9 International Consortium for Sugarcane Biotechnology24 Consortium for Plant Biotechnology ResearchDE-FG36-02GO12026
Databáze: OpenAIRE
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