Description of Service

The yeast genome sequencing service is intended for whole-genome sequencing and assembly of genomic DNA (gDNA) from a clonal population (single species) of yeast.

When you send pre-extracted gDNA, we deliver yeast genome sequencing results within 1-2 business days of receipt of your samples. When our genomic DNA extraction option is selected, we deliver yeast genome sequencing results within 3-5 business days of receipt of your samples.

This service is performed using the latest long-read sequencing technology from Oxford Nanopore Technologies (ONT), and includes the following components:

• Constructing an amplification-free long-read sequencing library using the newest v14 library prep chemistry, including minimal fragmentation of the gDNA in a sequence independent-manner.
• Sequencing the library with a primer-free protocol using the most accurate R10.4.1 flow cells (raw data is delivered in .fastq format).
• Producing a high-quality genome assembly (How is the yeast genome assembly generated?)
• Producing a set of yeast genome annotations with Augustus (delivered in various file formats).

Data & File Types Delivered

When your results are ready, you will receive an email notification. Once you sign in to your account, you can download these results from your Dashboard. More detailed information about data & file types can be found in the Results Interpretation Guide.

• .fastq.gz = a compressed file of all the raw ONT sequencing reads
• .fasta = polished consensus sequence of the genome (may contain multiple contigs)
• .gff = gene annotations for the polished genome
• .html = A summary report compiling the assembly metrics, including completeness of the assembly based on Busco v5.7.1 and general species identification of the contigs. The metrics summarized in the report are also delivered as discrete files:
  • reads.png = histogram of all raw reads (indicating read length vs. Phred score), including coloration to distinguish reads that are retained for assembly vs. reads that are rejected
  • stats.tsv = metrics assessing the quality and size of the polished genome assembly and the raw reads that were used for assembly
  • busco-short-summary.txt = metrics assessing the completeness of the polished genome assembly
  • contigs.png = graph of the contig topology and their connections in the assembly
  • contigs.txt = metrics assessing the quantity and lengths of the contigs

The target output of this service is a high-accuracy contig or contigs for each chromosome, with a set of yeast genome annotations. However, our ability to deliver the target output is directly dependent on the quantity, quality, and purity of the gDNA or yeast cells sent to us. We do not guarantee any specific output.

Successful sequencing is defined by achieving at least one of the following deliverables:

• A high-quality genome assembly
• 600 Mb of raw .fastq ONT sequencing data (i.e. 30x genome coverage of a single 20 Mb genome)

If we are not able to achieve at least one of those deliverables, then our repeat policy applies. Even when a high-quality assembly cannot be generated, we still provide the raw data and the report, and you may also still receive some of the other file types.

We are now offering a Hybrid ONT + Illumina yeast genome sequencing service that polishes your long-read ONT assembly with Illumina short reads. We use the Polypolish v0.6.0 tool to improve the consensus quality at those tricky homopolymer runs and methylation motifs, resulting in higher per-nucleotide accuracy. This Hybrid sequencing service is available both for pre-extracted yeast gDNA and with the genomic DNA extraction option.

In addition to the ONT-only target deliverables listed above (ONT-only assembly and files), this hybrid service adds on these additional target deliverables:

• 600 Mb of raw .fastq Illumina data (2x150bp paired-end configuration)
• Polished .fasta assembly reference file generated with Polypolish v0.6.0, with the ONT .fna file and Illumina .fastq files as input

IMPORTANT NOTE: Hybrid sequencing requires 30μL of sample at a concentration of 50 ng/μL.

Preparing Your Yeast gDNA Samples

This service requires 1 µg of high quality, high purity, high molecular weight (HMW), double-stranded gDNA (NOTE: this increases to 1.5μg for Hybrid sequencing), with recommended >50% of the DNA above 15 kb in length and recommended purity of 260/280 above 1.8 and 260/230 between 2.0-2.2. Our low sequencing prices and fast turnaround times do not include gDNA quality control (QC) services, so it is your responsibility to verify that you are preparing suitable samples that meet these requirements prior to shipping them to us.

Preparing Cell Pellets for the Yeast DNA Extraction Option

*** IMPORTANT - PLEASE READ ***

This new yeast extraction service uses a rapid, high-throughput protocol that is ONLY COMPATIBLE with the following approved list of genera:

• Asbya
• Kluyveromyces
• Candida
• Lipomyces
• Debaryomyces
• Metschikowia
• Eremothecium
• Pichia/Komagataella
• Endomyces
• Saccharomyces
• Hansenula
• Saccharomycopsis
• Hanseniaspora
• Schizosaccharomyces
• Issatchenkia
• Torulopsis
• Kloekera
• Yarrowia

Please DO NOT send cells for extraction from any genus that is not listed above, nor cells of any other types of microbe (such as filamentous fungi), as they are likely to fail and will not be eligible for rerun.

If you send us pre-extracted gDNA instead, we can sequence ANY yeast genus!

Yeast cell pellets must be resuspended in Zymo 1X DNA/RNA Shield preservative. Please do not use any other type of preservation media, such as RNAlater, as they do not preserve the DNA as effectively and do not fully inactivate the host cells, which is required for safe handling in our lab. We accept cell pellets from both BSL1 and BSL2 yeast strains.

We strongly recommend growing a fresh clonal culture of your yeast in liquid broth and harvesting the cells when they are in exponential growth or early stationary phase. Please do not send cells from older cultures or cultures that are in the death phase.

NOTE: Our extraction service does not include growing your samples; we extract DNA directly from the preserved yeast cells that you send us. It is important that enough cells have been collected, otherwise the gDNA extraction will likely fail.

Due to customs regulations, the yeast extraction service is currently only available to US and UK customers.