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Open Access Highly Accessed Research article

Construction of a plant-transformation-competent BIBAC library and genome sequence analysis of polyploid Upland cotton (Gossypium hirsutum L.)

Mi-Kyung Lee1, Yang Zhang1, Meiping Zhang12, Mark Goebel1, Hee Jin Kim3, Barbara A Triplett3, David M Stelly1 and Hong-Bin Zhang1*

  • * Corresponding author: Hong-Bin Zhang hbz7049@tamu.edu

  • † Equal contributors

Author affiliations

1 Department of Soil and Crop Sciences, 2474 TAMU, Texas A&M University, College Station, TX, 77843-2474, USA

2 College of Life Science, Jilin Agricultural University, Changchun, Jilin, China

3 USDA-ARS, Southern Regional Research Center, Cotton Fiber Bioscience, 1100 Robert E. Lee Blvd, New Orleans, LA, 70124, USA

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Citation and License

BMC Genomics 2013, 14:208  doi:10.1186/1471-2164-14-208

Published: 28 March 2013

Abstract

Background

Cotton, one of the world’s leading crops, is important to the world’s textile and energy industries, and is a model species for studies of plant polyploidization, cellulose biosynthesis and cell wall biogenesis. Here, we report the construction of a plant-transformation-competent binary bacterial artificial chromosome (BIBAC) library and comparative genome sequence analysis of polyploid Upland cotton (Gossypium hirsutum L.) with one of its diploid putative progenitor species, G. raimondii Ulbr.

Results

We constructed the cotton BIBAC library in a vector competent for high-molecular-weight DNA transformation in different plant species through either Agrobacterium or particle bombardment. The library contains 76,800 clones with an average insert size of 135 kb, providing an approximate 99% probability of obtaining at least one positive clone from the library using a single-copy probe. The quality and utility of the library were verified by identifying BIBACs containing genes important for fiber development, fiber cellulose biosynthesis, seed fatty acid metabolism, cotton-nematode interaction, and bacterial blight resistance. In order to gain an insight into the Upland cotton genome and its relationship with G. raimondii, we sequenced nearly 10,000 BIBAC ends (BESs) randomly selected from the library, generating approximately one BES for every 250 kb along the Upland cotton genome. The retroelement Gypsy/DIRS1 family predominates in the Upland cotton genome, accounting for over 77% of all transposable elements. From the BESs, we identified 1,269 simple sequence repeats (SSRs), of which 1,006 were new, thus providing additional markers for cotton genome research. Surprisingly, comparative sequence analysis showed that Upland cotton is much more diverged from G. raimondii at the genomic sequence level than expected. There seems to be no significant difference between the relationships of the Upland cotton D- and A-subgenomes with the G. raimondii genome, even though G. raimondii contains a D genome (D5).

Conclusions

The library represents the first BIBAC library in cotton and related species, thus providing tools useful for integrative physical mapping, large-scale genome sequencing and large-scale functional analysis of the Upland cotton genome. Comparative sequence analysis provides insights into the Upland cotton genome, and a possible mechanism underlying the divergence and evolution of polyploid Upland cotton from its diploid putative progenitor species, G. raimondii.

Keywords:
BIBAC library; Gossypium hirsutum; Gossypium raimondii; BIBAC end sequence (BES); Genome evolution; SSR; Polyploidization and evolution