SPPG

SPPG facilitates integration and phylogenetic analysis of plant protein sequences and expressed sequence tags (ESTs) to identify gene families and study their evolutionary distribution across green algae, mosses, gymnosperms, and angiosperms.

Key Features:

• Integration of Diverse Data Types: SPPG combines publicly available EST and protein sequences from 32 plant species, including green algae, mosses, gymnosperms, and angiosperms.
• Identification of Gene Families: SPPG organized over 250,000 plant proteins into more than 12,000 gene families, with approximately 60% of these proteins absent from current sequence databases.
• Phylogenetic Profiling and Insights: SPPG performs phylogenetic profiling to reveal species- and lineage-specific gene families, orphan genes, and conserved core genes across the green plant lineage.
• Comparative Analysis Across Species: SPPG compares gene family distributions showing monocotyledonous and eudicotyledonous plants share approximately 9,500 gene families and provides evidence for at least 33,700 genes in rice (Oryza sativa) relative to Arabidopsis thaliana.
• Gene Family Size Analysis: SPPG characterizes gene family size differences, noting that families with more than 50 genes are generally larger in rice while smaller families tend to be larger in Arabidopsis.

Scientific Applications:

• Comparative genomics: Enables cross-species comparison of gene families and gene counts among 32 diverse plant species.
• Evolutionary studies: Supports analysis of lineage-specific, orphan, and conserved core genes to infer evolutionary patterns across green plants.
• Gene discovery and annotation: Facilitates identification of novel proteins absent from current databases and provides gene count estimates, for example in Oryza sativa.
• Agriculture, conservation, and biotechnology: Supplies gene family distribution data relevant to species-specific trait analysis and applied research.

Methodology:

Integration of publicly available EST and protein sequences from 32 plant species; organization of approximately 250,000 proteins into more than 12,000 gene families; phylogenetic profiling and comparative analysis of gene family distributions across species.