CpnClassiPhyR

CpnClassiPhyR performs RFLP and phylogenetic analysis of the chaperonin-60 (cpn60) gene to classify phytoplasma strains and complement 16S ribosomal RNA-based taxonomy.

Key Features:

• RFLP Analysis of cpn60 Gene: Performs restriction fragment length polymorphism (RFLP) analysis on the chaperonin-60 (cpn60) gene using the cpn60 universal target (UT) and treating cpn60 as a single-copy protein-encoding gene.
• Automated Phylogenetic Analysis: Integrates automated phylogenetic analysis of cpn60 sequences to improve the accuracy of phytoplasma strain classification.

Scientific Applications:

• Phytoplasma Strain Differentiation: Enables refined differentiation of phytoplasma strains complementary to 16S rRNA-based systems.
• Epidemiology and Disease Management: Supports epidemiological investigations of phytoplasma diseases and informs targeted disease management strategies.
• Phytopathology and Plant Biology Research: Facilitates taxonomic and functional studies in phytopathology and plant biology with implications for mitigating crop yield losses.

Methodology:

Performs RFLP analysis of cpn60 universal target (UT) sequences with seven endonucleases and automated phylogenetic analysis to assign phytoplasmas to groups and subgroups.