SCNBase

SCNBase provides a genomics and transcriptomics data portal for research on the soybean cyst nematode (Heterodera glycines), supporting comparative, functional, and population-level analyses.

Key Features:

• JBrowse tracks: Hosts 43 JBrowse tracks representing genomic annotations and alignments.
• Category pages: Organizes data into 21 category pages covering multiple analysis types.
• Gene predictions: Includes genome-wide gene prediction datasets for Heterodera glycines.
• Transcriptome studies: Incorporates transcriptomic datasets and analyses including read alignments.
• Read alignments: Provides aligned sequencing reads underlying transcriptome and variant analyses.
• Effectorome characterization: Identifies over 3,324 putative effector genes.
• Genomic repeat dynamics: Contains analyses of repeat content and dynamics across the genome.
• Orthology and synteny: Presents orthology assignments and synteny comparisons with related nematode species.
• Population SNPs: Reports Single Nucleotide Polymorphisms (SNPs) derived from 15 SCN populations.
• Novel splice sites: Documents identification of novel splice sites from transcriptomic data.
• Functional annotation via comparative genomics: Annotates genes by comparison to nine related plant-parasitic nematodes, covering approximately 85% of genes.
• Downloadable datasets and genomic tools: Provides datasets and integrated genomic resources for downstream analyses.

Scientific Applications:

• Heterodera glycines genomics: Supports genome annotation, repeat analysis, and gene model refinement for SCN.
• Effector discovery and characterization: Enables identification and study of putative effectors implicated in parasitism.
• Comparative genomics: Facilitates orthology and synteny analyses with related plant-parasitic nematodes.
• Population genomics: Allows analysis of SNP variation across 15 SCN populations for population structure and diversity studies.
• Transcriptomics and splicing: Enables investigation of transcriptome profiles and discovery of novel splice sites.

Methodology:

Gene prediction, transcriptome analysis with read alignments, SNP identification from 15 SCN populations, detection of novel splice sites, repeat dynamics analysis, orthology and synteny comparisons, and functional annotation by comparison to nine related plant-parasitic nematodes (covering ~85% of genes), yielding identification of >3,324 putative effector genes.