The P10K Database
A Data Portal for the Protist 10,000 Genomes Project

The P10K Database
A Data Portal for the Protist 10,000 Genomes Project

Sequencing technology

Most protists are challenging to propagate in culture or enrich in large quantities for genome sequencing. Therefore, we have categorized genome sequencing into three strategies based on culturability.

PacBio long-read sequencing: Approximately 1% of protists can be successfully cultured or enriched on a large scale, allowing for the extraction of a substantial amount of high-quality DNA. For these samples, we employ PacBio long-read sequencing, which generates high-quality reference genomes with long scaffolds and excellent completeness.
Next-generation sequencing: Approximately 9% of protists can be cultured or enriched to some extent, enabling the extraction of a moderate amount of high-quality DNA. These samples undergo next-generation sequencing, which facilitates the generation of genomes with high completeness.
Single-cell sequencing: 90% of protists are unculturable or difficult to enrich in large quantities. For these samples, we utilize single-cell technologies to acquire their genomes, thereby overcoming the challenges associated with limited culturability.

Genome assembly and annotation

We have developed a specialized methodology for genome assembly, decontamination, and annotation of protists that present challenges to propagate in culture. This method is also applicable to the genome analysis of protists that can be cultured.

Genome assembly: For single-cell genomes, we employed the megahit assembly algorithm, while Trinity was used for single-cell transcriptomes. Non-parasitic species with genomes size smaller than 4Mb were not included in the following analysis.
Decontamination: It is common for genomic data obtained from protists to contain sequences from cohabiting or symbiotic organisms, including bacteria, viruses, and fungi. To address this, we developed iGPD ( as a decontamination tool. iGPD utilizes several techniques, such as homology search, telomere reads-assisted analysis, and clustering. Successful decontamination can be identified by the presence of a single peak in the GC distribution of the scaffolds.
Annotation: Gene prediction in our pipeline involves both homologous prediction and de novo prediction methods. We utilize multiple databases, such as pfam, KEGG, and NR, to annotate gene functions.

Genome quality evaluation

To evaluation the quality of the genome, we employ a combination of genome completeness and CDS (Coding DNA Sequence) completeness. CDS completeness measures the proportion of gene models with both start and stop codons. The assessment of genome quality is divided into three levels: high, medium, and low.

The calculation method is as follows:

Genome quality (%) = Genome completeness(%) × 0.5 + (Number of CDS with complete structure / Total number of CDS)(%) × 0.5.

The levels are as follows:

High: Genome quality ranging from 80% to 100%
Medium: Genome quality ranging from 50% to 80
Low: Genome quality ranging from 0% to 50%

National Data/Resource Center

National Aquatic Biological Resource Center National Genomics Data Center