|DENVER, D - Oregon State University|
|BROWN, A - Oregon State University|
|HOWE, D - Oregon State University|
Submitted to: PLoS Pathogens
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/20/2016
Publication Date: 8/4/2016
Citation: Denver, D., Brown, A.M., Howe, D.K., Peetz, A.B., Phillips, W.S., Zasada, I.A. 2016. Genome skimming: A rapid approach to gaining diverse biological insights into multicellular pathogens. PLoS Pathogens. 12(8):e1005713. doi: 10.1371/journal.ppat.1005713.
Interpretive Summary: Plant-parasitic nematodes are microscopic roundworms that have been shown to cause significant yield loss to a range of crops. The focus of this research was to explore the genomes of six economically important plant-parasitic nematodes. The DNA from these nematodes was extracted and sequenced. An number of analyses were conducted to explore the unique features of the DNA. It was discovered that several of the plant-parasitic nematodes had bacterial endosymbionts not previously know to occur in these nematodes. This data analysis approach also identified similarities and differences in genes responsible for these nematodes to cause damage to plants. These results are significant because they provide the first draft genomes of six plant-parasitic nematodes.The data from this project will be freely shared with the other scientists to allow for further exploration into nematode genomics.
Technical Abstract: New genome sequence information can now be generated very quickly and cheaply for virtually any organism. The dive into genomics is increasingly tempting to scientists studying plant pathogens and other eukaryotic species without reference genomes. The ease of data collection, however, is tempered by complicated downstream genomic data analysis (and re-analysis) that often takes years. Hesitation might arise due to apprehensions associated with these bioinformatic bottlenecks and uncertainties. Here we overview a shallow genome sequencing and analysis strategy, ‘genome skimming’, designed to provide rapid basic insights into the structure and composition of nematode and other animal genomes. We analyzed DNA from six plant-parasitic nematode species that lack reference genomes (Anguina agrostis, Globodera ellingtonae, Pratylenchus neglectus, P. penetrans, P. thornei, and Xiphinema americanum), multiplexed together on a single Illumina MiSeq run. After data collection, basic bioinformatic procedures were performed to yield key summary information about the focal genomes and associated microbial DNA. Our analysis revealed novel insights into nematode microbiomes, including evidence for bacterial endosymbionts (Xiphinematobacter sp., Cardinium sp., Wolbachia sp.) in two species. Candidate effector genes and other loci of interest were readily identified in the genomic data by creating and querying local BLAST search databases. Characterization of genetic polymorphism in each sample sequenced revealed different levels of genetic variation. Our approach provides a low-cost and low-time investment path to characterize basic features of nematode genomes that rapidly results in new discoveries and testable biological hypotheses relevant to basic and applied questions.