Yeast Whole Genome Sequencing - Haploid strain with a plasmid

We purchased a commercial yeast strain containing a GFP plasmid from The-Odin.com. The online description says it is a "sample of Saccharomyces cerevisiae French Saison Yeast Strain with the extra chromosomal DNA that contains a form of the Green Fluorescent Protein"

The strain was streaked out on YPD agar media and grown at 30°C. Then the colony was inoculated into 5 mL YPD liquid media and grown for about 20 hours until saturation. The culture was separated into two conditions based on the amount of biomass. Low_yeastGFP used only 1 mL of culture while High_yeastGFP had 4 mL of culture. Each condition was pelleted and then the genomic DNA was extracted using the commercial Zymo Research Quick-DNA Fungal/Bacterial Miniprep Kit. The genomic DNA was barcoded and sequenced using Oxford Nanopore's Rapid Barcoding Kit according to manufacturer's recommendations. 

Results:

All the results can be freely accessible by going to https://seqresults.angstrominno.com/orders/AI-1309 (just need to provide your email to receive a simple login code). The main result page gives you the option to download the data as a zip file. If you want the very large file containing the raw nanopore reads (4.4 Gigabytes) select the "Include Raw Reads" box.

When clicking the details for sample 1, you will see some summary statistics regarding the sequencing output such as Total Sequencing bases, longest read, number of contigs, and average coverage. 

We provide a fast prediction of what the strain is by using Sourmash. A more comprehensive analysis can be done by running a BLAST search using the full genomic FASTA data.

Looking further down the page, you can see the read length histogram. From this plot, it is looks like there might be multiple plasmids around 6 kbp.

Using our "PlasmidHunter" tool, we are able to extract these plasmid sequences and provide fully annotated maps. The plasmid data can be found in the zip file. The first peak around 6,060 bp is the GFP containing plasmid (annotated as obeCFP by pLannotate).

The second plasmid appears to the native 2µ plasmid. The third plasmid peak at ~12,856 bp is the dimer of this 6,428 bp plasmid. 

Yeast is known to be able to handle multiple 2µ plasmids and using our yeast WGS you can discover the full genomic sequence (and plasmids) for your strains.