Plant Growth Regulation

, Volume 70, Issue 2, pp 199–206 | Cite as

Apple gene function and gene family database: an integrated bioinformatics database for apple research

  • Shizhong Zhang
  • Guang Hui Chen
  • Yukun Liu
  • Hao Chen
  • Guodong Yang
  • Xiaowei Yuan
  • Zesheng Jiang
  • Huairui ShuEmail author
Brief Communication


The apple (Malus domestica) is one of the most economically important fruit crops in the world, due its importance to human nutrition and health. To analyze the function and evolution of different apple genes, we developed apple gene function and gene family database (AppleGFDB) for collecting, storing, arranging, and integrating functional genomics information of the apple. The AppleGFDB provides several layers of information about the apple genes, including nucleotide and protein sequences, chromosomal locations, gene structures, and any publications related to these annotations. To further analyze the functional genomics data of apple genes, the AppleGFDB was designed to enable users to easily retrieve information through a suite of interfaces, including gene ontology, protein domain and InterPro. In addition, the database provides tools for analyzing the expression profiles and microRNAs of the apple. Moreover, all of the analyzed and collected data can be downloaded from the database. The database can also be accessed using a convenient web server that supports a full-text search, a BLAST sequence search, and database browsing. Furthermore, to facilitate cooperation among apple researchers, AppleGFDB is presented in a user-interactive platform, which provides users with the opportunity to modify apple gene annotations and submit publication information for related genes. AppleGFDB is available at or


Malus domestica genome AppleGFDB Database 



Abscisic acid


1-aminocyclopropane-1-carboxylic acid


Apple gene function and gene family database


Basic local alignment search tool


Conserved domain database


European Bioinformatics Institute


Expressed sequence tags


Genome database for rosaceae


Gene expression omnibus


Gene ontology


Hidden Markov model


Istituto agrario di san michele all’adige


National center for biotechnology information


Protein data bank


Plant transcription factor database


Simple modular architecture research tool


The arabidopsis information resource



This work was funded by the National Research Center for Apple Engineering and Technology of China and the “Five-second” National Science and Technology Support Program (2011BAD11B01).


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Copyright information

© Springer Science+Business Media Dordrecht 2013

Authors and Affiliations

  • Shizhong Zhang
    • 1
  • Guang Hui Chen
    • 2
  • Yukun Liu
    • 3
  • Hao Chen
    • 2
  • Guodong Yang
    • 2
  • Xiaowei Yuan
    • 2
  • Zesheng Jiang
    • 1
  • Huairui Shu
    • 1
    Email author
  1. 1.National Research Center for Apple Engineering and Technology, College of Horticulture Science and TechnologyShandong Agricultural UniversityTai’anChina
  2. 2.State Key Laboratory of Crop Biology, College of Life ScienceShandong Agricultural UniversityTai’anChina
  3. 3.Key Laboratory for Forest Resource Conservation and Utilization in the Southwest Mountains of China, Ministry of EducationSouthwest Forestry UniversityKunmingChina

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