Abstract
BackgroundSmall peptides encoded as one- or two-exon genes in plants have recently been shown to affect multiple aspects of plant 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. This is largely due to the high sequence divergence among family members and the limited availability of experimentally verified small peptides to use as training sets for homology search and ab initio prediction. Consequently, there is an urgent need for both experimental and computational studies in order to further advance the accurate prediction of small peptides.ResultsWe present here a homology-based gene prediction program to accurately predict small peptides at the genome 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 homologues) as well as non-secreted peptides outside the plant kingdom (e.g., the alpha-amanitin toxin gene family in the mushroom, Amanita bisporigera).ConclusionsSPADA is a free software tool that accurately identifies and predicts the gene structure for short peptides with one or two exons. SPADA is able to incorporate information from profile alignments into the model prediction process and makes use of it to score different candidate models. SPADA achieves high sensitivity and specificity in predicting small plant peptides such as the cysteine-rich peptide families. A systematic application of SPADA to other classes of small peptides by research communities will greatly improve the genome annotation of different protein families in public genome databases.
Highlights
Small peptides encoded as one- or two-exon genes in plants have recently been shown to affect multiple aspects of plant development, reproduction and defense responses
Our approach focuses on finding all related paralogous genes within a target gene family and using signals from the corresponding multiple sequence alignment to aid in refining the model predictions
Performance evaluation of SPADA on plant Cysteine Rich Peptide (CRP) families SPADA performance under different search E-value thresholds Using our manually-curated high-quality Cysteine-Rich Peptide (CRP) test set from Arabidopsis and Medicago, we first evaluated the performance of SPADA under different search E-value thresholds
Summary
Small peptides encoded as one- or two-exon genes in plants have recently been shown to affect multiple aspects of plant development, reproduction and defense responses. Our approach focuses on finding all related paralogous genes within a target gene family and using signals from the corresponding multiple sequence alignment to aid in refining the model predictions We have implemented this approach in an open-source and freely available application called SPADA (Small Peptide Alignment Discovery Application). SPADA can be used directly with a user’s own protein family alignments or with a comprehensive set of protein family alignments from public sources such as Pfam [8], InterPro [9] or PROSITE [10], enabling the exhaustive discovery of essentially all members of the input families within a given genome sequence Because these public resources continue to expand and include new and novel protein families, SPADA’s ability to comprehensively identify arbitrarily large families of small peptides in genomes will steadily grow
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