Detecting Small Plant Peptides Using Spada (Small Peptide Alignment Discovery Application)

Small peptides encoded as one- or two-exon genes in plants have recently been shown to affect multiple aspects of development, reproduction and defense responses. However, popular similarity search tools and gene prediction techniques generally fail to identify most members belonging to this class of genes. We present here a homology-based gene prediction program to accurately predict small peptides at the gene level. Given a high-quality profile alignment, SPADA identifies and annotates nearly all family members in tested genomes with better performance than all general-purpose gene prediction programs surveyed.  We find numerous mis-annotations in the current Arabidopsis thaliana and Medicago truncatula genome databases using SPADA, most of which have RNA-seq expression support.  We also show that SPADA works well on other classes of small secreted peptides in plants (e.g., self-incompatibility protein homologs) as well as non-secreted peptides outside the plant kingdom (e.g., the alpha-amanitin toxin gene family in the mushroom, Amanita bisporigera). 

SPADA is freely available at https://github.com/orionzhou/SPADA/wiki.