PmDscam

PmDscam performs sequence alignment and analysis of the hypervariable Dscam (Down syndrome cell adhesion molecule) gene in Penaeus monodon to characterize genomic structure and alternative splicing diversity.

Key Features:

• Sequence alignment and analysis: Performs sequence alignment and analysis of the Dscam gene to investigate hypervariability and isoform diversity.
• Genomic structure analysis: Integrates Illumina short-read and PacBio long-read sequencing data with hybrid assembly to reconstruct the complete Dscam genomic region spanning approximately 250 kilobases.
• Exon cataloguing: Identifies a total of 175 exons, including constitutive and alternative splice variants across the gene.
• Exon variant quantification: Detects 26, 81, and 26 alternative exon variants in the N-terminal Ig2, N-terminal Ig3, and Ig7 regions respectively, and two alternative variants in the cytoplasmic tail exons.
• Splicing combination estimation: Calculates 54,756 potential extracellular-region isoform combinations and 512 cytoplasmic-tail combinations from a single genomic locus, with alternative stop-codon selection contributing to diversity.
• Alternative splicing analysis: Identifies and catalogs exon variants and their potential combinations through cDNA and genomic analyses.

Scientific Applications:

• Pancrustacean immunity studies: Enables investigation of Dscam isoform diversity and its potential roles in immune responses in Penaeus monodon and other pancrustaceans.
• Cellular interaction and adhesion research: Supports analysis of how Dscam hypervariability may influence cellular adhesion and interaction mechanisms.
• Isoform diversity characterization: Facilitates quantification and comparative analysis of alternative splicing-derived isoform repertoires from a single genomic locus.

Methodology:

Integrates Illumina short-read and PacBio long-read sequencing, performs hybrid assembly of sequencing data, and conducts alternative splicing analysis by identifying and cataloging exon variants via cDNA and genomic analysis.