OrysPSSP: a comparative Platform for Small Secreted Proteins from rice and other plants

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The Rice Annotation Project: Nipponbare genome sequencing by the International Rice Genome Sequencing Project.

Rice Expression Profile Database: Repository of gene expression data in rice.

Flowering Plant Gene Picker: Annotation pipeline for flowering plant genomes.

Phytozome v8.0: Comparative genomic amongst green plants.

Arabidopsis Unannotated Secreted Peptide Database: Predictions of putative unannotated secreted peptides from Arabidopsis thaliana.
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(e.g. p450)
Introduction

    Oryza sativa (ssp. japonica), as one of the most important food crops, was among the first to be sequenced, greatly facilitating genetic and physiological research in agriculture and plant biology. However, annotation of genes in the short-length range was proved inadequate to many plant genomes in general, especially for small secreted peptides found to be involved in diverse physiological processes, i.e. stress response, flowering, hormone signaling, etc. Studies showed that the numbers of small secreted proteins were underestimated. As both an economic crop and a model plant, it is a top priority for us to address this issue in rice (Oryza sativa ssp. japonica).
    We made an effort to provide plant biologists a comprehensive comparative platform: OrysPSSP. It provides the data of small secreted proteins, 25-250 aa, on a genome-scale, integrated with a variety of search tools, validation functions and comparative resources. The current official release (v0530) contains a wholly set of 101,048 candidates. About two-thirds of them, 67,559, are located in un-annotated genome regions, while the rest, 33,489, are included in known genes. For each candidate, users are provided with chromosomal location, peptide sequence and domain(s), organelle location, gene annotation and neighboring genes. Validated with different data sets, 33,350 proteins were supported by tiling Array data, 9,431 by RNAseq data, and 18,353 by mass spectrum results. When comparing across the phylogeny of 25 green plants, we found the number of conserved SSPs between rice and other plants, in general, was inversely proportional to their evolutionary distance.
    On top of the curated data for small secreted proteins from rice, we developed a number of tools to help rice scientists and plant biologists in obtaining (sub)datasets that are relevant and valuable to their fields of studies. Users can view the distribution of small secreted proteins on rice chromosomes, and browse the data by chromosome. Alternatively, they can search for small secreted protein genes and retrieve data by applying one or more filter parameters, i.e. gene keyword, domain name, chromosome location, annotation status, etc. A "BLAST" tool is also provided to seek small secreted proteins mapped to users' query sequences. Query sequence can be chose from three different types, genomic sequence (DNA), mRNA sequence (mRNA), or protein sequence (Protein). In our testing releases, the most important function users found, is the validation tool supported by our database. Currently we offered three separate datatypes, tilingArray, transcriptomics and proteomics, (all from public available data sources) to validate and filter small secreted protein candidates. A comparative genomics tool for a comprehensive analysis of the conservation of SSPs in 26 green plants was build. We integrated the genome information from 25 plant species besides Oryza sativa ssp. japonica. Comparison across the phylogeny would yield insight into the occurrence and evolution of SSPs in green plants.

OrysPSSP web interface includes
seven modules:
  • Home: general introduction to this database such as basic goal and construction flow.
  • Browse: show distribution of predicted secreted proteins at whole genome level and browse them by chromosome accession.
  • Search & Validate: search protein of interest via protein ID, keywords, description of domains, etc.
  • Compare Genomes: apply comparative genomics approach to search for small secreted proteins conserved in Oryza sativa japonica, Oryza sativa indica, and other plants.
  • BLAST Search: blast to the core gene sets of OrysPSSP, protein and coding sequence are supported.
  • Statistics: basic statistics of predicted peptides and their verification information.
  • Help: frequently asked questions about OrysPSSP, including construction pipeline, introduction of protein entry display page, etc.
  • Contact Us: for any comments, questions, and suggestions from web users.
PDF and Citation
Pan, B., Sheng, J., Sun, W., Zhao, Y., Hao, P. and Li, X. OrysPSSP: a comparative Platform for Small Secreted Proteins from rice and other plants. Nucleic acids research. Jan;41 (2013) (Database issue):D1192-1198
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CopyRight © Team of Bioinformatic Core, Institute of Plant Physiology and Ecology, SIBS, CAS. 2012