Yeast Genome Sequencing


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Sample Type Category Size Concentration Minimum Volume Price Per Sample (USD)
Yeast Genome < 15 Mb 50 ng/μl 20 μl 150
< 15 Mb See Instructions Below 165
< 15 Mb 50 ng/μl 30 μl 255
< 15 Mb See Instructions Below 270

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
  • 450 Mb of raw .fastq ONT sequencing data (i.e. 30x genome coverage of a single 15 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:

  • 450 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.

There are numerous approaches to yeast culture, thus we do not provide specific recommendations. Please refer to published literature for protocols.

Any extraction method that yields high quality, high purity, high molecular weight (HMW), double-stranded gDNA that is free of nicks, gaps, breaks, and contaminants is suitable for this sequencing service.

Our in-house preferred methods for extraction are the Zymo® Quick-DNA Miniprep Plus Kit with a Zymolyase pre-treatment. We have also had success with the Zymo® YeaStar Genomic DNA Kit.

How to handle gDNA samples:

  • Avoid vortexing and fast or unnecessary pipetting; pipet with wide-bore tips only
  • Elute in elution buffer, not water
  • Do not expose to high temperatures (>37°C) for >1 hour, pH extremes ( <6 or>9), intercalating fluorescent dyes, or UV radiation
  • Avoid freeze-thaw cycles; store gDNA at 4°C for 1-2 months
  • If using a speed-vac, avoid over-drying of gDNA; do not use heat in the speed-vac

  • Quantity: We require 1 µg of gDNA, at a concentration of 50 ng/µL in 20 µL of elution buffer (NOTE: this increases to 1.5μg in 30μL for Hybrid sequencing). Quantification should be performed with Qubit or an equivalent fluorometric method (such as a plate reader). We strongly discourage using Nanodrop for gDNA quantification.

    • HMW gDNA often requires extra homogenization effort (longer incubation time, increased incubation temperature, very extensive gentle mixing, etc.) to obtain accurate quantification. If separate DNA quantifications from the top and bottom of the sample are within 15% of each other, this is usually a good indication of adequate homogeneity.

    • If you have less than 1 µg of gDNA, we strongly recommend that you perform additional extractions to increase yield, but you may submit less than 1 µg at your own risk. Please email us to let us know about this before shipping your order, then prepare your gDNA at the same required concentration (50 ng/µL) but in a lower volume according to your total DNA yield.

  • Quality: We recommend gDNA samples with >50% of the total DNA mass contained within fragments above 15 kb in size. If the sample does not meet this metric, we strongly recommend repeating STEP 2.
    Size characterization may be performed with Femto Pulse, Fragment Analyzer, Bioanalyzer, or a slab gel with a HMW ladder (ideally with pulsed-field electrophoresis).

  • Purity: We recommend gDNA samples with 260/280 above 1.8 and 260/230 between 2.0-2.2. Purity assay may be performed with Nanodrop or other spectrophotometric methods. If the sample is contaminated and does not meet this metric, either re-extract the sample OR clean up the sample to remove the contaminants using a Qiagen cleanup kit or AMPure XP beads.

    • Must not contain RNA; we strongly recommend RNase treatment during extraction
    • Must not contain denaturants (guanidinium salts, phenol, etc.) or detergents (SDS, Triton-X100, etc.)
    • Must not contain residual contaminants from the organism/tissue (heme, humic acid, polyphenols, etc.)
    • Must not contain insoluble material or be colored or cloudy

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

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.

1. Pellet 50-100 mg of yeast cells from a fresh culture. It is critical that you send a pellet of the correct weight, and that your cells are from a fresh culture (not an overgrown culture). Depending on your yeast species, 50-100mg of wet cells may require 1.5-2 mL of a saturated fresh culture (8-10 A600 units per mL of culture), and may be equivalent to approx. 5 x 107 total yeast cells.

  • Pellet the cells by centrifugation at 500 g for 2 minutes.

2. Remove all growth medium (supernatant). Note, PBS wash is not necessary.

  • The weight of the cell pellet alone should be 50-100mg.

3. Resuspend the pellet in 0.5 mL of Zymo 1X DNA/RNA Shield in a 2 mL screw cap tube.

Please place an order, either for Yeast with extraction or Hybrid with extraction.

Please label each 2 mL screw cap tube with the first 2 digits of your order code and sample number. For example, the label "AB_1" would indicate order code ABCDEF, sample 1.

To prevent damage and leakage of the tubes during shipment, please place the screw cap tubes in a rigid container such as a falcon tube or tube box before shipping. If using a box, please load the samples row by row in numerical order, as this greatly reduces the handling time when receiving your samples.

Please send preserved cell pellets at room temperature. Dry ice and cold packs are not necessary.

Interpreting Your Results

Please refer to our Results Interpretation Guide for details.