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

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 informatio...

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Autores principales: Koshimizu, Shizuka, Nakamura, Yukino, Nishitani, Chikako, Kobayashi, Masaaki, Ohyanagi, Hajime, Yamamoto, Toshiya, Yano, Kentaro
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6908688/
https://www.ncbi.nlm.nih.gov/pubmed/31831861
http://dx.doi.org/10.1038/s41598-019-55287-4
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author Koshimizu, Shizuka
Nakamura, Yukino
Nishitani, Chikako
Kobayashi, Masaaki
Ohyanagi, Hajime
Yamamoto, Toshiya
Yano, Kentaro
author_facet Koshimizu, Shizuka
Nakamura, Yukino
Nishitani, Chikako
Kobayashi, Masaaki
Ohyanagi, Hajime
Yamamoto, Toshiya
Yano, Kentaro
author_sort Koshimizu, Shizuka
collection PubMed
description 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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spelling pubmed-69086882019-12-16 TRANSNAP: a web database providing comprehensive information on Japanese pear transcriptome Koshimizu, Shizuka Nakamura, Yukino Nishitani, Chikako Kobayashi, Masaaki Ohyanagi, Hajime Yamamoto, Toshiya Yano, Kentaro Sci Rep Article 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. Nature Publishing Group UK 2019-12-12 /pmc/articles/PMC6908688/ /pubmed/31831861 http://dx.doi.org/10.1038/s41598-019-55287-4 Text en © The Author(s) 2019 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Koshimizu, Shizuka
Nakamura, Yukino
Nishitani, Chikako
Kobayashi, Masaaki
Ohyanagi, Hajime
Yamamoto, Toshiya
Yano, Kentaro
TRANSNAP: a web database providing comprehensive information on Japanese pear transcriptome
title TRANSNAP: a web database providing comprehensive information on Japanese pear transcriptome
title_full TRANSNAP: a web database providing comprehensive information on Japanese pear transcriptome
title_fullStr TRANSNAP: a web database providing comprehensive information on Japanese pear transcriptome
title_full_unstemmed TRANSNAP: a web database providing comprehensive information on Japanese pear transcriptome
title_short TRANSNAP: a web database providing comprehensive information on Japanese pear transcriptome
title_sort transnap: a web database providing comprehensive information on japanese pear transcriptome
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6908688/
https://www.ncbi.nlm.nih.gov/pubmed/31831861
http://dx.doi.org/10.1038/s41598-019-55287-4
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