MarFERReT: A Reference Library for Marine Eukaryote Functional Genes

MarFERReT is a version-controlled reference library of protein sequences for marine microbial eukaryotes, designed for taxonomic annotation of metatranscriptomic data. The library contains sequences from 800 validated marine eukaryotic genomes and transcriptomes, covering 453 species- and strain-level taxa. It includes associated NCBI and PR2 taxonomy identifiers and Pfam functional annotations to support analysis of actively transcribed genes in environmental samples.

Use Cases

• Taxonomic annotation of marine eukaryotic metatranscriptomes based on curated reference protein sequences.
• Functional gene analysis using the associated Pfam annotations linked to the reference sequences.
• Quality assessment and filtering of environmental sequence data against a validated reference set of 800 genomes/transcriptomes.
• Tracking taxonomic coverage and updating annotation pipelines via the version-controlled framework.

Strengths

• Contains nearly 28 million protein sequences from 800 validated marine eukaryotic entries, providing substantial scale.
• Includes validated taxonomy identifiers (NCBI, PR2) and functional annotations (Pfam), enhancing utility for analysis.
• Features a version-controlled framework with containerized build scripts, supporting reproducibility and updates.

Limitations

• Sources conflict on the total number of sequences (28 million vs. over 30 million) and taxonomic coverage (453 vs. 503 species).
• Metadata completeness is low; specific column names, row counts, and the exact date of the last update are not provided.
• The library is focused on marine microbial eukaryotes, limiting its direct applicability to other environments or prokaryotic studies.

Provenance

Source

University of Washington (Armbrust Lab), with sequences gathered from multiple public sources.

Collection Method

Candidate genomes and transcriptomes were assessed for sequence quality and cross-contamination, with 800 validated entries selected from 902 candidates.

Geography

Marine environments globally.