Comparison between two inbred soybean cyst nematode biotypes
Genomic DNA sequence comparison between two inbred soybean cyst nematode biotypes facilitated by massively parallel 454 micro-bead sequencing.
The genomic DNA sequence comes from the nematode Heterodera glycines, the common name is the soybean cyst nematode.  DNA sequence data collected from two strains of the nematode, one called TN20 and the other is called TN10.  Whole genome shotgun sequencing conducted  for both nematode strains using a GS20 454 sequencer.  10 machine runs conducted for TN20.  2 machine runs for TN10.   This data was not generated at a Center, but the sequencing was contracted by the Kris Lambert and Matthew Hudson Laboratories with 454 life sciences conducing the sequencing.
Sadia Bekal, Craig, J., Hudson, M., Niblack, T., Domier, L., Lambert, K. N.  Abstract  Heterodera glycines, the soybean cyst nematode (SCN), is a damaging agricultural pest that could be effectively managed if critical phenotypes, such as virulence and host range could be understood.  While SCN is amenable to genetic analysis, lack of DNA sequence data prevents the use of such methods to study this pathogen.  Fortunately, new methods of DNA sequencing that produced large amounts of data and permit whole genome comparative analyses have become available.  In this study, 400 million bases of genomic DNA sequence were collected from two inbred biotypes of SCN using micro-bead DNA sequencing.  Comparisons to a BAC, sequenced by Sanger sequencing, showed that the micro-bead sequences could identified low and high copy number regions within the BAC.  Potential single nucleotide polymorphisms (SNPs) between the two SCN biotypes were identified by comparing the two sets of sequences.  Selected resequencing revealed that up to 84% of the SNPs were correct.  We conclude that the quality of the micro-bead sequence data was sufficient for SNP identification and should be applicable to organisms with similar genome sizes and complexities.  The SNPs identified will be an important starting point in associating phenotypes with specific regions of the SCN genome.