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TRANSNAP: a web database providing comprehensive information on Japanese pear transcriptome.
Shizuka Koshimizu1, Yukino Nakamura1, Chikako Nishitani2
1School of Agriculture, Meiji University, Kawasaki, 214-8571, Japan.
Scientific Reports
|December 14, 2019
Summary
Researchers sequenced Japanese pear (Pyrus pyrifolia) transcripts to create TRANSNAP, the first omics database for this fruit tree. This resource aids breeding and molecular research by providing reference sequences and gene expression data.
Area of Science:
- Plant genomics
- Fruit tree breeding
- Bioinformatics
Background:
- Japanese pear (Pyrus pyrifolia) is a significant fruit crop within the Rosaceae family.
- Advancing breeding strategies and molecular research requires comprehensive genetic information.
Purpose of the Study:
- To sequence and annotate the Japanese pear transcriptome.
- To develop a user-friendly web database for Japanese pear omics data.
- To facilitate comparative genomics among pear species.
Main Methods:
- RNA sequencing using single-molecule real-time (SMRT), 454 pyrosequencing, and Sanger sequencing.
- Transcriptome assembly and protein sequence prediction.
- Development of the TRANSNAP web database (http://plantomics.mind.meiji.ac.jp/nashi).
Main Results:
- Comprehensive reference sequences and protein predictions for Japanese pear.
- Biological functional annotations assigned to predicted proteins.
- TRANSNAP established as the first omics resource for Japanese pear, including gene expression profiles.
Conclusions:
- The TRANSNAP database provides reliable omics information for Japanese pear research and breeding.
- Comparative sequence analysis identifies conserved and species-specific proteins.
- TRANSNAP supports molecular research and comparative genomics across pear species.
