Plastid Genome Annotator

Plastid Genome Annotator annotates plastome sequences in batch using annotated reference plastomes to identify genes, introns, and structural features for comparative and phylogenetic analyses of plant plastomes generated by high-throughput sequencing.

Key Features:

• Rapid and Accurate Annotation: Performs batch annotation of multiple plastomes using a reverse query-subject BLAST search to identify gene and intron boundaries precisely.
• Flexibility in Reference Choice: Accepts various well-annotated reference plastomes as queries against unannotated targets, exemplified by annotating Rosa roxburghii using Amborella trichopoda as reference.
• Output Formats and Logging: Produces annotations in GenBank format and generates log files documenting annotation results.
• Reduced Post-Annotation Verification: Comparative analyses indicate high annotation accuracy and explicit handling of intron loss events, reducing the need for extensive manual verification.

Scientific Applications:

• Phylogenetic analysis: Provides annotated plastomes for phylogenetic inference across plant lineages.
• Comparative genomics: Enables large-scale comparative analyses of plastome structure and gene content.
• Plastome evolution studies: Supports investigation of intron dynamics, intron loss events, and genetic diversity in plastomes.

Methodology:

Uses a reverse query-subject BLAST search approach in which annotated reference plastomes serve as queries against unannotated target plastomes to determine gene and intron boundaries and account for intron loss events.