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. 2019 Dec 12;9(1):18922.
doi: 10.1038/s41598-019-55287-4.

TRANSNAP: a web database providing comprehensive information on Japanese pear transcriptome

Shizuka Koshimizu  1 , Yukino Nakamura  1 , Chikako Nishitani  2 , Masaaki Kobayashi  1 , Hajime Ohyanagi  1   3 , Toshiya Yamamoto  4 , Kentaro Yano  5
Affiliations

TRANSNAP: a web database providing comprehensive information on Japanese pear transcriptome

Shizuka Koshimizu et al. Sci Rep. .

Abstract

Japanese pear (Pyrus pyrifolia) is a major fruit tree in the family Rosaceae and is bred for fruit production. To promote the development of breeding strategies and molecular research for Japanese pear, we sequenced the transcripts of Japanese pear variety 'Hosui'. To exhaustively collect information of total gene expression, RNA samples from various organs and stages of Japanese pear were sequenced by three technologies, single-molecule real-time (SMRT) sequencing, 454 pyrosequencing, and Sanger sequencing. Using all those reads, we determined comprehensive reference sequences of Japanese pear. Then, their protein sequences were predicted, and biological functional annotations were assigned. Finally, we developed a web database, TRANSNAP (http://plantomics.mind.meiji.ac.jp/nashi), which is the first web resource of Japanese pear omics information. This database provides highly reliable information via a user-friendly web interface: the reference sequences, gene functional annotations, and gene expression profiles from microarray experiments. In addition, based on sequence comparisons among Japanese, Chinese and European pears, similar protein sequences among the pears and species-specific proteins in Japanese pear can be quickly and efficiently identified. TRANSNAP will aid molecular research and breeding in Japanese pear, and its information is available for comparative analysis among other pear species and families.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Figure 1
Figure 1
Schematic representation and screen shots of the Japanese pear transcriptome database TRANSNAP. (a) Screen shots of the top page. (b) Gene search result page. The information of each transcript is shown in a web page. It contains (c) example data of the KEGG pathway obtained by the KEGG API (please see Materials and Methods), (d) InterPro, (e) similar sequences in Pyrus, (f) expression profiles, and (g) cDNA and protein sequences.
Figure 2
Figure 2
Workflow for the construction of reference sequences of the Pyrus pyrifolia transcriptome. (a) PacBio reads were analyzed using the pipeline Iso-Seq. (b) Pre-processed Sanger and 454 reads were hybrid-assembled with Newbler. (c) HQ full-length cDNAs and contigs were integrated. Redundant sequences and short sequences (< 200 bp) except for ncRNAs were filtered, and reference sequences were generated.
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