GCGVD

GCGVD provides integrated visualization and analysis of the grass carp (Ctenopharyngodon idellus) genome, supporting gene collinearity, genome annotation, RNA-seq alignment visualization, and whole-genome alternative splicing examination.

Key Features:

• Integration of diverse data resources: Consolidates the grass carp draft genome, genomic annotations, genetic data, and related resources into a unified dataset.
• SVG-based collinearity and linkage map visualization: Uses Scalable Vector Graphics (SVG) to display gene collinearity between grass carp and zebrafish and to render the genetic linkage map.
• JBrowse genomic visualization: Employs JBrowse to display genomic annotations and RNA-seq read alignments, including per-sample RNA-seq read density maps.
• RNA-seq alignment processing: Provides RNA-seq read alignments produced by Bowtie2 mapping to the grass carp reference genome.
• Alternative splicing analysis: Conducts preliminary whole-genome alternative splicing studies using RNA-seq data from 15 samples.
• Enhanced annotation data model: Implements a universal grass carp genome annotation data model aimed at improving retrieval speed and scalability.
• Conserved domain and additional annotations: Incorporates conserved domain annotations and supplementary genomic annotations alongside RNA-seq alignments.

Scientific Applications:

• Genomic research: Enables detailed investigation of grass carp genome structure and gene annotations.
• Comparative genomics: Facilitates comparison of gene collinearity and synteny with zebrafish to study evolutionary relationships and conserved loci.
• Molecular mechanism exploration: Supports analysis of molecular mechanisms underlying traits of interest through integrated genomic and RNA-seq data.

Methodology:

RNA-seq data from 15 samples were aligned to the grass carp reference genome using Bowtie2; genomic annotations and RNA-seq alignments are visualized with JBrowse, and gene collinearity and linkage maps are rendered in SVG format.