A draft physical map of a D-genome cotton species (Gossypium raimondii)

Abstract

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.

Conclusion: 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.

Figure 1

Comparison of band number distribution between agarose-based fingerprints and HICF. A: agarose-based fingerprints; B: HICF; C: an example of two agarose FPC contig joined in HICF. Red bands are matching bands to the highlighted (in blue) BAC. Counts of matching bands to the BAC are listed below each lane. The four BACs on the right were not assembled into the same contig.

Figure 2

Aligned physical map contigs along the consensus map. Homologous Group 1 of the integrated genetic-physical map, drawn using data from Rong et al. [14].

Figure 3

Aligned GR contigs along Arabidopsis and Vitis chromosomes. Blue and purple bars next to the chromosomes show the GR contigs. Green lines to the left of each chromosome indicate gene-density of the target genomes. The length of the bar represents the physical distance between anchoring markers on the target genomes. Putative centromeric regions on Arabidopsis chromosomes are marked out in rectangles. Centromeric regions on Vitis chromosomes cannot be determined.

Figure 4

Alignment of contig 500 to the genome sequences. A. The contig is mapped to four regions in Arabidopsis, which are paralogs produced by the α and β duplications after the cotton-Arabidopsis divergence. The contigs are only anchored to a single Vitis chromosomal location. B. dot plot generated by MCscan on Plant Genome Duplication Database, showing conserved syntenic blocks between Vitis chr.8 and Arabidopsis chromosomes. The region corresponding to GR ctg 500 is marked by red circles.