The P10K database: a data portal for the protist 10 000 genomes project.
Xinxin Gao1,2, Kai Chen1, Jie Xiong1,3
1Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
Nucleic Acids Research
|November 6, 2023
Summary
The Protist 10,000 Genomes Project (P10K) database now offers nearly 3,000 protist genomes and transcriptomes, significantly expanding genetic resources. This valuable data aids protist research and reveals unique genetic features in ciliates.
Area of Science:
- Microbiology
- Genomics
- Eukaryotic Biology
Background:
- Protists are diverse, ecologically vital microorganisms, but genomic data is scarce.
- Limited public genomic data hinders comprehensive protist research.
Purpose of the Study:
- To establish a comprehensive database of protist genomes and transcriptomes.
- To address the lack of accessible genetic information for protist species.
Main Methods:
- Development of a specialized pipeline for single-cell genome/transcriptome assembly, decontamination, and annotation.
- Integration of newly sequenced and publicly available protist datasets into a centralized database.
Main Results:
- The Protist 10,000 Genomes Project (P10K) database currently houses 2959 genomes and transcriptomes.
- The database covers 45% of protist orders, with 53% coverage of ciliates.
- Analysis revealed unique codon table usage in ciliates, suggesting revisions to existing taxonomic systems.
Conclusions:
- The P10K database is a crucial resource for protist genomics.
- The database aims for continued expansion with more data and analytical tools.
- Findings highlight the need for updated codon tables in protist taxonomy.
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