PLANiTS

PLANiTS provides curated ITS reference datasets for plant DNA metabarcoding, enabling taxonomic assignment and standardization of plant community analyses.

Key Features:

• Comprehensive Coverage: Includes separate datasets for ITS1 (PLANiTS1, 100,224 sequences), ITS2 (PLANiTS2, 96,771 sequences), and full ITS (PLANiTS, 97,550 sequences).
• Curated Sequences: Sequences were retrieved from the National Center for Biotechnology Information (NCBI) and subjected to an identity check to eliminate misidentified records.
• Redundancy Reduction: Sequences were clustered at 99% identity using the 'better clustering for QIIME' (bc4q) script with representative sequences selected based on cluster composition across taxonomic levels.
• Integration with Bioinformatics Pipelines: Datasets are pre-formatted for use with QIIME for direct incorporation into metabarcoding workflows.
• Standardization for Metabarcoding: Provides a reliable reference dataset intended to establish a standardized approach for plant DNA metabarcoding studies.
• Clustering Tool: The bc4q script is provided as a clustering tool applicable to sequence clustering tasks in research contexts.

Scientific Applications:

• Taxonomic assignment in plant DNA metabarcoding: Supports identification of plant taxa from environmental ITS sequences.
• Ecological and evolutionary studies: Enables analyses of plant community composition and related evolutionary investigations.
• Biodiversity assessment and conservation: Facilitates biodiversity surveys and provides reference data useful for conservation efforts.
• Standardization and comparability: Improves accuracy and comparability of metabarcoding results across studies by providing a standardized reference.

Methodology:

Sequences were retrieved from NCBI, subjected to an identity check to remove misidentified records, clustered at 99% identity using the bc4q ('better clustering for QIIME') script with representatives chosen based on cluster composition across taxonomic levels, and exported in formats pre-formatted for QIIME.