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Supplemental Information

Comparison of Velvet to SPAdes assemblies of 14 isolates associated with crown gall

DOI: 10.7287/peerj.preprints.1998v3/supp-1

Validation of the Phytopath-type tool

The 16S rDNA sequence from isolate originally labeled as Agrobacterium isolate 14-2641 was analyzed using the Phytopath-type tool. The isolate is labeled in red, as “query_isolate”; inset shows the clade that circumscribes the isolate.

DOI: 10.7287/peerj.preprints.1998v3/supp-2

The SPAdes assembler produces high quality assemblies

Genome sequences assembled using Velvet v. 1.2.10 (blue) and SPAdes v. 3.7.0 (orange) were compared based on scaffold N50 and number of scaffolds greater than 1kb in size.

DOI: 10.7287/peerj.preprints.1998v3/supp-3

Whole genome alignment of 13-626 assemblies to a close reference sequence indicates collinearity of genomes

The A. radiobacter K84 genome sequence (top) and assemblies of 13-626 generated using SPAdes v. 3.7.0 (middle; 47 scaffolds) and Velvet (bottom; 527 scaffolds) were aligned using Mauve. Shared locally collinear blocks (LCBs) between the reference and the two assemblies are color-coded and connected by color-coded lines. Scaffold and replicon ends are depicted as vertical red lines.

DOI: 10.7287/peerj.preprints.1998v3/supp-4

Additional Information

Competing Interests

JH Chang and NJ Grünwald are academic editors for PeerJ.

Author Contributions

Edward W Davis II performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Alexandra J Weisberg performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Javier F Tabima performed the experiments, analyzed the data, contributed reagents/materials/analysis tools.

Niklaus J. Grunwald conceived and designed the experiments, wrote the paper, reviewed drafts of the paper.

Jeff Chang conceived and designed the experiments, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

DNA Deposition

The following information was supplied regarding the deposition of DNA sequences:

BioProject number PRJNA319063

Data Deposition

The following information was supplied regarding data availability:

All scripts are available from:

http://gall-id.cgrb.oregonstate.edu/

Funding

This work was supported by the National Institute of Food and Agriculture, U.S. Department of Agriculture award 2014-51181-22384 (JHC and NJG). Partial support also was provided by the USDA Agricultural Research Service Grant 5358-22000-039-00D (NJG), USDA National Institute of Food and Agriculture Grant 2011-68004-30154 (NJG), and the USDA ARS Floriculture Nursery Research Initiative (NJG). EWD is supported by a Provost’s Distinguished Graduate Fellowship awarded by Oregon State University. This material is based upon work supported by the National Science Foundation Graduate Research Fellowship under Grant No. DGE-1314109 to EDW. The summer camps were supported by National Science Foundation awards IOS #1340112 and #1127112 to Pankaj Jaiswal. Any opinion, findings, and conclusions or recommendations expressed in this material are those of the authors(s) and do not necessarily reflect the views of the U. S. Department of Agriculture or National Science Foundation. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.


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