Open Access Open Badges Research article

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

Lifeng Lin16, Gary J Pierce1, John E Bowers16, James C Estill16, Rosana O Compton1, Lisa K Rainville1, Changsoo Kim1, Cornelia Lemke1, Junkang Rong17, Haibao Tang18, Xiyin Wang1, Michele Braidotti3, Amy H Chen1, Kristen Chicola1, Kristi Collura3, Ethan Epps1, Wolfgang Golser3, Corrinne Grover2, Jennifer Ingles1, Santhosh Karunakaran1, Dave Kudrna3, Jaime Olive1, Nabila Tabassum4, Eareana Um1, Marina Wissotski3, Yeisoo Yu3, Andrea Zuccolo3, Mehboob ur Rahman4, Daniel G Peterson15, Rod A Wing3, Jonathan F Wendel2 and Andrew H Paterson16*

Author Affiliations

1 Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30605, USA

2 Department of Ecology, Evolution, & Organismal Biology, Iowa State University, Ames, IA 50011, USA

3 Arizona Genomics Institute, School of Plant Sciences and BIO5 Institute for Collaborative Research, University of Arizona, Tucson, AZ 85721, USA

4 National Institute for Biotechnology & Genetic Engineering (NIBGE), Faisalabad, Pakistan

5 Life Sciences & Biotechnology Institute, Mississippi State University, Mississippi State, MS 39762 USA

6 Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA

7 School of Agriculture and Food Sciences, Zhejiang Forestry University, Lin'an, Hangzhou, Zhejiang, 311300, China

8 Department of Plant and Microbiology, College of Natural Resources, University of California, Berkeley, CA, USA

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BMC Genomics 2010, 11:395  doi:10.1186/1471-2164-11-395

Published: 22 June 2010



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.


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.


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.