Research article

Development of a physical map of the soybean pathogen Fusarium virguliforme based on synteny with Fusarium graminearum genomic DNA

Jeffry L Shultz¹ , Sikander Ali² , Linda Ballard³ and David A Lightfoot⁴

¹Currently, USDA-ARS, Crop Genetics and Production Research Unit, PO Box 345, Stoneville, MS, 38776, USA

²Institute of Industrial Biotechnology, GC University Lahore, Pakistan

³Mississippi Valley State University, Itta Bena, MS. Currently, USDA-ARS MSA Genomics Laboratory, P.O. Box 345, Stoneville, MS, 38776, USA

⁴Dept. of Plant, Soil and Agricultural Systems, Genomics and Biotechnology Core Facility, Center for Excellence in Soybean Research, Southern Illinois University, Carbondale IL, 62901, USA

author email corresponding author email

BMC Genomics 2007, 8:262doi:10.1186/1471-2164-8-262

Published:	3 August 2007

Abstract

Background

Reference genome sequences within the major taxa can be used to assist the development of genomic tools for related organisms. A major constraint in the use of these sequenced and annotated genomes is divergent evolution. Divergence of organisms from a common ancestor may have occurred millions of years ago, leading to apparently un-related and un-syntenic genomes when sequence alignment is attempted.

Results

A series of programs were written to prepare 36 Mbp of Fusarium graminearum sequence in 19 scaffolds as a reference genome. Exactly 4,152 Bacterial artificial chromosome (BAC) end sequences from 2,178 large-insert Fusarium virguliforme clones were tested against this sequence. A total of 94 maps of F. graminearum sequence scaffolds, annotated exonic fragments and associated F. virguliforme sequences resulted.

Conclusion

Developed here was a technique that allowed the comparison of genomes based on small, 15 bp regions of shared identity. The main power of this method lay in its ability to align diverged sequences. This work is unique in that discontinuous sequences were used for the analysis and information not readily apparent, such as match direction, are presented. The 94 maps and JAVA programs are freely available on the Web and by request.