A draft physical map of a D-genome cotton species (Gossypium raimondii).
BACKGROUND
Genetically anchored physical maps of large eukaryotic genomes have proven useful both for their intrinsic merit and as an adjunct to genome sequencing. Cultivated tetraploid cottons, Gossypium hirsutum and G. barbadense, share a common ancestor formed by a merger of the A and D genomes about 1-2 million years ago. Toward the long-term goal of characterizing the spectrum of diversity among cotton genomes, the worldwide cotton community has prioritized the D genome progenitor Gossypium raimondii for complete sequencing.


RESULTS
A whole genome physical map of G. raimondii, the putative D genome ancestral species of tetraploid cottons was assembled, integrating genetically-anchored overgo hybridization probes, agarose based fingerprints and 'high information content fingerprinting' (HICF). A total of 13,662 BAC-end sequences and 2,828 DNA probes were used in genetically anchoring 1585 contigs to a cotton consensus genetic map, and 370 and 438 contigs, respectively to Arabidopsis thaliana (AT) and Vitis vinifera (VV) whole genome sequences.


CONCLUSIONS
Several lines of evidence suggest that the G. raimondii genome is comprised of two qualitatively different components. Much of the gene rich component is aligned to the Arabidopsis and Vitis vinifera genomes and shows promise for utilizing translational genomic approaches in understanding this important genome and its resident genes. The integrated genetic-physical map is of value both in assembling and validating a planned reference sequence.
Lin
Lifeng
L
Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30605, USA.
Pierce
Gary J
GJ
Bowers
John E
JE
Estill
James C
JC
Compton
Rosana O
RO
Rainville
Lisa K
LK
Kim
Changsoo
C
Lemke
Cornelia
C
Rong
Junkang
J
Tang
Haibao
H
Wang
Xiyin
X
Braidotti
Michele
M
Chen
Amy H
AH
Chicola
Kristen
K
Collura
Kristi
K
Epps
Ethan
E
Golser
Wolfgang
W
Grover
Corrinne
C
Ingles
Jennifer
J
Karunakaran
Santhosh
S
Kudrna
Dave
D
Olive
Jaime
J
Tabassum
Nabila
N
Um
Eareana
E
Wissotski
Marina
M
Yu
Yeisoo
Y
Zuccolo
Andrea
A
ur Rahman
Mehboob
M
Peterson
Daniel G
DG
Wing
Rod A
RA
Wendel
Jonathan F
JF
Paterson
Andrew H
AH
D017360:Arabidopsis / Q000235:genetics; D002736:Chloroplasts / Q000235:genetics; D022202:Chromosomes, Artificial, Bacterial / Q000235:genetics; D016384:Consensus Sequence; D020451:Contig Mapping; D016172:DNA Fingerprinting; D019143:Evolution, Molecular; D020440:Gene Duplication; D017343:Genes, Plant / Q000235:genetics; D056426:Genetic Loci / Q000235:genetics; D005819:Genetic Markers / Q000235:genetics; D018745:Genome, Plant / Q000235:genetics*; D003368:Gossypium / Q000166:cytology / Q000235:genetics*; D009693:Nucleic Acid Hybridization; D020161:Physical Chromosome Mapping / Q000379:methods*; D014176:Protein Biosynthesis; D012091:Repetitive Sequences, Nucleic Acid; D027843:Vitis / Q000235:genetics
D005819:Genetic Markers