LanceletDB

LanceletDB provides integrated genomic and functional datasets for Branchiostoma belcheri and Branchiostoma floridae to support comparative analyses of lancelet genomes and reconstruction of chordate ancestral states.

Key Features:

• Integrated Genome Sequences: Reference haploid genome sequences and diploid genome annotation data for Branchiostoma floridae are included for comparative genomic analyses.
• Gene Annotation Data: Detailed gene models and annotations for lancelet genes enable study of gene evolution and orthologue relationships.
• Protein Domain Analysis: Extensive protein domain type annotations and domain-combination data support investigation of ancient non-vertebrate-specific domains and novel domain combinations.
• Gene Expression Patterns: Gene expression profiles across embryogenesis stages are provided to analyze developmental regulation in lancelets.
• Alternative Polyadenylation (APA) Sites: APA sites profiled by sequencing methods are cataloged to support analysis of post-transcriptional regulation.
• Sequence Search and Genome Browser: Computational tools include a basic local alignment search tool (BLAST) and a genome browser for integrated display of sequence and annotation data.

Scientific Applications:

• Chordate ancestral-state reconstruction: Comparative analyses of lancelet genomes facilitate inference of ancestral chordate genomic features relevant to vertebrate evolution.
• Protein domain evolution: Investigation of domain loss, gain, and the emergence of novel domain combinations across orthologues and species.
• Gene function and regulation: Analysis of gene models, expression across embryogenesis, and APA sites to study gene function and post-transcriptional regulatory mechanisms.

Methodology:

LanceletDB integrates multiple genomic datasets to compare protein domain types and combinations among orthologues across species, catalogs APA sites profiled by sequencing methods, and provides computational tools including BLAST and a genome browser for sequence alignment and integrated data display.