Evaluation of monocot and eudicot divergence using the sugarcane transcriptome.
Over 40,000 sugarcane (Saccharum officinarum) consensus sequences assembled from 237,954 expressed sequence tags were compared with the protein and DNA sequences from other angiosperms, including the genomes of Arabidopsis and rice (Oryza sativa). Approximately two-thirds of the sugarcane transcriptome have similar sequences in Arabidopsis. These sequences may represent a core set of proteins or protein domains that are conserved among monocots and eudicots and probably encode for essential angiosperm functions. The remaining sequences represent putative monocot-specific genetic material, one-half of which were found only in sugarcane. These monocot-specific cDNAs represent either novelties or, in many cases, fast-evolving sequences that diverged substantially from their eudicot homologs. The wide comparative genome analysis presented here provides information on the evolutionary changes that underlie the divergence of monocots and eudicots. Our comparative analysis also led to the identification of several not yet annotated putative genes and possible gene loss events in Arabidopsis.
Vincentz
Michel
M
Centro de Biologia Molecular e Engenharia Genética, Universidade de Campinas, Caixa Postal 6010, 13083-970, Campinas SP, Brazil.
Cara
Frank A A
FA
Okura
Vagner K
VK
da Silva
Felipe R
FR
Pedrosa
Guilherme L
GL
Hemerly
Adriana S
AS
Capella
Adriana N
AN
Marins
Mozart
M
Ferreira
Paulo C
PC
França
Suzelei C
SC
Grivet
Laurent
L
Vettore
Andre L
AL
Kemper
Edson L
EL
Burnquist
Willian L
WL
Targon
Maria L P
ML
Siqueira
Walter J
WJ
Kuramae
Eiko E
EE
Marino
Celso L
CL
Camargo
Luis E A
LE
Carrer
Helaine
H
Coutinho
Luis L
LL
Furlan
Luiz R
LR
Lemos
Manoel V F
MV
Nunes
Luiz R
LR
Gomes
Suely L
SL
Santelli
Roberto V
RV
Goldman
Maria H
MH
Bacci
Maurício
M
Giglioti
Eder A
EA
Thiemann
Otávio H
OH
Silva
Flávio H
FH
Van Sluys
Marie-Anne
MA
Nobrega
Francisco G
FG
Arruda
Paulo
P
Menck
Carlos F M
CF
D017360:Arabidopsis / Q000145:classification / Q000235:genetics; D032461:Chromosomes, Plant / Q000235:genetics; D016384:Consensus Sequence; D019143:Evolution, Molecular; D020224:Expressed Sequence Tags; D018745:Genome, Plant; D019684:Magnoliopsida / Q000145:classification* / Q000235:genetics*; D012275:Oryza / Q000145:classification / Q000235:genetics; D031786:Saccharum / Q000145:classification* / Q000235:genetics*; D014158:Transcription, Genetic