POSTERS: Proteomics / metabolomics / genomics
Assessing the bias in gene content from resequenced Phytophthora infestans strains where reads do not map to the reference genome
Shankar Shakya - Oregon State University. Niklaus Grunwald- USDA ARS, Brian Knaus- Department of Botany and Plant Pathology, Oregon State University
Next generation sequencing reads that fail to map against a reference genome are often neglected in the study and no further analysis is done. There is growing evidence that the reads which fail to map to a reference genome might provide insight into the biological functions. Thus, we hypothesized that unmapped reads represented the uniqueness of the strain and could be assembled to predict strain specific genes. We first mapped the short reads from 22 Phytophthora infestans isolates to the P. infestans reference strain T30-4 using bowtie2 and filtered the unmapped reads. The number of reads that did not map to the reference strain ranged from 3-58%. We then performed de novoassembly with the velvet assembler using those unmapped reads for each isolate and predicted the gene content using AUGUSTUS. Assembly size ranged from 1.43 - 16 Mbp and the gene content ranged from 394-3938. Orthofinder was used to identify orthologous gene clusters along with strain specific genes. We were able to identify 62 clusters with genes present from all 22P. infestans isolates anda total of 1554 singletons. These newly identified genes had orthologs in other Phytophthora species which suggests the unmapped reads are not just contaminations and can be used to improve the reference genome.