A Draft Physical Map of a D-genome Cotton Species (Gossypium raimondii)

Abstract

<p>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, <em>Gossypium hirsutum </em>and <em>G. barbadense</em>, 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 <em>Gossypium raimondii </em>for complete sequencing. A whole genome physical map of <em>G. raimondii</em>, 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 <em>Arabidopsis thaliana </em>(AT) and <em>Vitis vinifera </em>(VV) whole genome sequences. Several lines of evidence suggest that the <em>G. raimondii </em>genome is comprised of two qualitatively different components. Much of the gene rich component is aligned to the <em>Arabidopsis </em>and <em>Vitis vinifera </em>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.</p>