title: Analysis and functional annotation of an expressed sequence tag collection for tropical crop sugarcane.
abstract: To contribute to our understanding of the genome complexity of sugarcane, we undertook a large-scale expressed sequence tag (EST) program. More than 260,000 cDNA clones were partially sequenced from 26 standard cDNA libraries generated from different sugarcane tissues. After the processing of the sequences, 237,954 high-quality ESTs were identified. These ESTs were assembled into 43,141 putative transcripts. Of the assembled sequences, 35.6% presented no matches with existing sequences in public databases. A global analysis of the whole SUCEST data set indicated that 14,409 assembled sequences (33% of the total) contained at least one cDNA clone with a full-length insert. Annotation of the 43,141 assembled sequences associated almost 50% of the putative identified sugarcane genes with protein metabolism, cellular communication/signal transduction, bioenergetics, and stress responses. Inspection of the translated assembled sequences for conserved protein domains revealed 40,821 amino acid sequences with 1415 Pfam domains. Reassembling the consensus sequences of the 43,141 transcripts revealed a 22% redundancy in the first assembling. This indicated that possibly 33,620 unique genes had been identified and indicated that >90% of the sugarcane expressed genes were tagged.
authors: Centro de Biologia Molecular e Engenharia Genética, Instituto da Computação, Universidade Estadual de Campinas, 13083-970 Campinas-SP, Brazil.
authors: André L
authors: AL
authors: Vettore
authors: Felipe R
authors: FR
authors: da Silva
authors: Edson L
authors: EL
authors: Kemper
authors: Glaucia M
authors: GM
authors: Souza
authors: Aline M
authors: AM
authors: da Silva
authors: Maria Inês T
authors: MI
authors: Ferro
authors: Flavio
authors: F
authors: Henrique-Silva
authors: Eder A
authors: EA
authors: Giglioti
authors: Manoel V F
authors: MV
authors: Lemos
authors: Luiz L
authors: LL
authors: Coutinho
authors: Marina P
authors: MP
authors: Nobrega
authors: Helaine
authors: H
authors: Carrer
authors: Suzelei C
authors: SC
authors: França
authors: Mauricio
authors: M
authors: Bacci Júnior
authors: Maria Helena S
authors: MH
authors: Goldman
authors: Suely L
authors: SL
authors: Gomes
authors: Luiz R
authors: LR
authors: Nunes
authors: Luis E A
authors: LE
authors: Camargo
authors: Walter J
authors: WJ
authors: Siqueira
authors: Marie-Anne
authors: MA
authors: Van Sluys
authors: Otavio H
authors: OH
authors: Thiemann
authors: Eiko E
authors: EE
authors: Kuramae
authors: Roberto V
authors: RV
authors: Santelli
authors: Celso L
authors: CL
authors: Marino
authors: Maria L P N
authors: ML
authors: Targon
authors: Jesus A
authors: JA
authors: Ferro
authors: Henrique C S
authors: HC
authors: Silveira
authors: Danyelle C
authors: DC
authors: Marini
authors: Eliana G M
authors: EG
authors: Lemos
authors: Claudia B
authors: CB
authors: Monteiro-Vitorello
authors: José H M
authors: JH
authors: Tambor
authors: Dirce M
authors: DM
authors: Carraro
authors: Patrícia G
authors: PG
authors: Roberto
authors: Vanderlei G
authors: VG
authors: Martins
authors: Gustavo H
authors: GH
authors: Goldman
authors: Regina C
authors: RC
authors: de Oliveira
authors: Daniela
authors: D
authors: Truffi
authors: Carlos A
authors: CA
authors: Colombo
authors: Magdalena
authors: M
authors: Rossi
authors: Paula G
authors: PG
authors: de Araujo
authors: Susana A
authors: SA
authors: Sculaccio
authors: Aline
authors: A
authors: Angella
authors: Marleide M A
authors: MM
authors: Lima
authors: Vicente E
authors: VE
authors: de Rosa Júnior
authors: Fábio
authors: F
authors: Siviero
authors: Virginia E
authors: VE
authors: Coscrato
authors: Marcos A
authors: MA
authors: Machado
authors: Laurent
authors: L
authors: Grivet
authors: Sonia M Z
authors: SM
authors: Di Mauro
authors: Francisco G
authors: FG
authors: Nobrega
authors: Carlos F M
authors: CF
authors: Menck
authors: Marilia D V
authors: MD
authors: Braga
authors: Guilherme P
authors: GP
authors: Telles
authors: Frank A A
authors: FA
authors: Cara
authors: Guilherme
authors: G
authors: Pedrosa
authors: João
authors: J
authors: Meidanis
authors: Paulo
authors: P
authors: Arruda
mesh_terms: D019295:Computational Biology / Q000379:methods* / Q000706:statistics & numerical data; D018076:DNA, Complementary / Q000032:analysis* / Q000145:classification / Q000502:physiology*; D018744:DNA, Plant / Q000032:analysis* / Q000145:classification / Q000502:physiology*; D020224:Expressed Sequence Tags; D018506:Gene Expression Regulation, Plant; D015723:Gene Library; D008969:Molecular Sequence Data; D009928:Organ Specificity / Q000235:genetics; D010455:Peptides / Q000145:classification / Q000235:genetics / Q000502:physiology; D010940:Plant Proteins / Q000145:classification / Q000235:genetics / Q000502:physiology; D011110:Polymorphism, Genetic / Q000235:genetics; D017434:Protein Structure, Tertiary / Q000235:genetics; D031786:Saccharum / Q000235:genetics* / Q000254:growth & development / Q000502:physiology*; D017422:Sequence Analysis, DNA / Q000379:methods; D015398:Signal Transduction / Q000235:genetics
chemical_list: D018076:DNA, Complementary; D018744:DNA, Plant; D010455:Peptides; D010940:Plant Proteins