Abstract
BackgroundGenetically 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.ResultsA 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.ConclusionSeveral 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.
Highlights
Anchored physical maps of large eukaryotic genomes have proven useful both for their intrinsic merit and as an adjunct to genome sequencing
There exist at least a dozen published genetic maps for various Gossypium crosses, most involving members of the superior-fiber-quality G. barbadense species crossed with high-yielding G. hirsutum
Comparative analysis between cotton, Arabidopsis, and Vitis genomes illustrates the potential for translational genomics across these species, and several regions with an unusually high degree of conserved collinearity may be interesting for further research
Summary
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. There exist at least a dozen published genetic maps for various Gossypium crosses, most involving members of the superior-fiber-quality G. barbadense species crossed with high-yielding G. hirsutum. These maps collectively include > 5,000 public DNA markers (~3,300 RFLP, 700 AFLP, >2,000 SSR, and 100 SNP). At refers to the A-subgenome of tetraploid cottons.) Gossypium genomes that include respectively, 2584 loci at 1.72 cM (~600 kb) intervals based on 2007 probes (AtDt); and 1014 loci at 1.42 cM (~600 kb) intervals detected by 809 probes (D) [4,14]. Monosomics and telosomics have been used to assign 20 of the 26 cotton linkage groups to chromosomes, and the remaining six linkage groups were assigned to chromosomes by translocation and fluorescence in situ hybridization mapping [17]
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