Candidate gene database and transcript map for peach, a model species for fruit trees.
Peach (Prunus persica) is a model species for the Rosaceae, which includes a number of economically important fruit tree species. To develop an extensive Prunus expressed sequence tag (EST) database for identifying and cloning the genes important to fruit and tree development, we generated 9,984 high-quality ESTs from a peach cDNA library of developing fruit mesocarp. After assembly and annotation, a putative peach unigene set consisting of 3,842 ESTs was defined. Gene ontology (GO) classification was assigned based on the annotation of the single "best hit" match against the Swiss-Prot database. No significant homology could be found in the GenBank nr databases for 24.3% of the sequences. Using core markers from the general Prunus genetic map, we anchored bacterial artificial chromosome (BAC) clones on the genetic map, thereby providing a framework for the construction of a physical and transcript map. A transcript map was developed by hybridizing 1,236 ESTs from the putative peach unigene set and an additional 68 peach cDNA clones against the peach BAC library. Hybridizing ESTs to genetically anchored BACs immediately localized 11.2% of the ESTs on the genetic map. ESTs showed a clustering of expressed genes in defined regions of the linkage groups. [The data were built into a regularly updated Genome Database for Rosaceae (GDR), available at (http://www.genome.clemson.edu/gdr/).].
Horn
Renate
R
Department of Genetics, Biochemistry and Life Science Studies, Clemson University, Clemson, SC 29634, USA.
Lecouls
Anne-Claire
AC
Callahan
Ann
A
Dandekar
Abhaya
A
Garay
Lilibeth
L
McCord
Per
P
Howad
Werner
W
Chan
Helen
H
Verde
Ignazio
I
Main
Doreen
D
Jung
Sook
S
Georgi
Laura
L
Forrest
Sam
S
Mook
Jennifer
J
Zhebentyayeva
Tatyana
T
Yu
Yeisoo
Y
Kim
Hye Ran
HR
Jesudurai
Christopher
C
Sosinski
Bryon
B
Arús
Pere
P
Baird
Vance
V
Parfitt
Dan
D
Reighard
Gregory
G
Scorza
Ralph
R
Tomkins
Jeffrey
J
Wing
Rod
R
Abbott
Albert Glenn
AG
D001947:Breeding / Q000379:methods; D002874:Chromosome Mapping; D022202:Chromosomes, Artificial, Bacterial; D030541:Databases, Genetic; D020224:Expressed Sequence Tags; D015723:Gene Library; D018745:Genome, Plant; D010957:Plasmids / Q000235:genetics; D027861:Prunus / Q000235:genetics*; D017422:Sequence Analysis, DNA