Analysis and functional annotation of an expressed sequence tag collection for tropical crop sugarcane.
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.
Vettore
André L
AL
Centro de Biologia Molecular e Engenharia Genética, Instituto da Computação, Universidade Estadual de Campinas, 13083-970 Campinas-SP, Brazil.
da Silva
Felipe R
FR
Kemper
Edson L
EL
Souza
Glaucia M
GM
da Silva
Aline M
AM
Ferro
Maria Inês T
MI
Henrique-Silva
Flavio
F
Giglioti
Eder A
EA
Lemos
Manoel V F
MV
Coutinho
Luiz L
LL
Nobrega
Marina P
MP
Carrer
Helaine
H
França
Suzelei C
SC
Bacci Júnior
Mauricio
M
Goldman
Maria Helena S
MH
Gomes
Suely L
SL
Nunes
Luiz R
LR
Camargo
Luis E A
LE
Siqueira
Walter J
WJ
Van Sluys
Marie-Anne
MA
Thiemann
Otavio H
OH
Kuramae
Eiko E
EE
Santelli
Roberto V
RV
Marino
Celso L
CL
Targon
Maria L P N
ML
Ferro
Jesus A
JA
Silveira
Henrique C S
HC
Marini
Danyelle C
DC
Lemos
Eliana G M
EG
Monteiro-Vitorello
Claudia B
CB
Tambor
José H M
JH
Carraro
Dirce M
DM
Roberto
Patrícia G
PG
Martins
Vanderlei G
VG
Goldman
Gustavo H
GH
de Oliveira
Regina C
RC
Truffi
Daniela
D
Colombo
Carlos A
CA
Rossi
Magdalena
M
de Araujo
Paula G
PG
Sculaccio
Susana A
SA
Angella
Aline
A
Lima
Marleide M A
MM
de Rosa Júnior
Vicente E
VE
Siviero
Fábio
F
Coscrato
Virginia E
VE
Machado
Marcos A
MA
Grivet
Laurent
L
Di Mauro
Sonia M Z
SM
Nobrega
Francisco G
FG
Menck
Carlos F M
CF
Braga
Marilia D V
MD
Telles
Guilherme P
GP
Cara
Frank A A
FA
Pedrosa
Guilherme
G
Meidanis
João
J
Arruda
Paulo
P
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
D018076:DNA, Complementary; D018744:DNA, Plant; D010455:Peptides; D010940:Plant Proteins