Analysis of cotton EPSPS gene in Gossypium raimondii genomic sequence

Functional Genomics

poster

Xu, Peng; Zhang, Xiang-Gui; Guo, Qi; Gong, Yuan-Yong; Ni, Wan-Chao; Shu, Hong-Mei; Guo, Shu-Qiao; Shen, Xin-Lian

Gong, Yuan-Yong

Ni, Wan-Chao

5-enolpyruvoylshikimate-3-phosphate synthase(EPSPS), a key enzyme exists in the shikimate pathway of aromatic amino acid biosynthesis in nearly all plants, bacteria, and fungi, is also the target enzyme of the herbicide glyphosate (N-(phosphonomethyl)glycine). Cloning of EPSPS gene could provide candidate gene for creating glyphosate-resistant genetically modified crops. One EPSPS gene has been cloned from upland cotton(Gossypium hirsutum) and its complete CDS has been submitted to NCBI(Accession number: EU797516). The completed genome sequencing work of a diploid cotton Gossypium raimondii makes it possible to analysis cotton EPSPS gene in genomic level. A highly homologous gene of this cotton EPSPS was identified based on a blast assay using the EPSPS complete CDS in the genome database of Gossypium raimondii of JGI(http://www.phytozome.org). In order to facilitate the distinction of this two genes, the EPSPS gene was named EPSPS1 and its homologous gene was named EPSPS2. EPSPS1 is located at eighth chromosome with locus name Gorai.008G113600, while EPSPS2 is located at first chromosome with locus name Gorai.001G174400. These two genes in genome are in opposite directions. The length of coding region sequence of EPSPS1 and EPSPS2 are 3080 bp and 3341 bp respectively, but the CDS length of these two genes is same as 1566 bp. Both of them have the same number of exons, and the same length of corresponding exons. This shows that the introns disparity caused the main difference between these two genes. The similarity index of coding region sequence, CDS and translated amino acid sequence of these two genes are 44.2%, 86.2% and 89.2% respectively. The 74 N-terminal amino acid residues of these two amino acid sequences is chloroplast transit peptide, both of which doesn’t have homology. This research provides a theoretical basis for cloning a homologous gene of cotton EPSPS.