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Article|17 Sep 2018|OPEN
PGD: Pineapple Genomics Database
Huimin Xu1,2, Qingyi Yu3, Yan Shi1, Xiuting Hua1, Haibao Tang1, Long Yang4, Ray Ming1,5, & Jisen Zhang1,
1Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
2College of Resource and Environment, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
3Department of Plant Pathology and Microbiology, Texas A&M AgriLife Research, Texas A&M University System, Dallas, TX 75252, USA
4Agricultural Big-Data Research Center and College of Plant Protection, Shandong Agricultural University, 271018 Taian, China
5Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA

Horticulture Research 5,
Article number: 66 (2018)
doi: 10.1038/hortres.2018.66
Views: 616

Received: 02 May 2018
Revised: 17 Jun 2018
Accepted: 06 Aug 2018
Published online: 17 Sep 2018

Abstract

Pineapple occupies an important phylogenetic position as its reference genome is a model for studying the evolution the Bromeliaceae family and the crassulacean acid metabolism (CAM) photosynthesis. Here, we developed a pineapple genomics database (PGD, http://pineapple.angiosperms.org/pineapple/html/index.html) as a central online platform for storing and integrating genomic, transcriptomic, function annotation and genetic marker data for pineapple (Ananas comosus (L.) Merr.). The PGD currently hosts significant search tools and available datasets for researchers to study comparative genomics, gene expression, gene co-expression molecular marker, and gene annotation of A. comosus (L). PGD also performed a series of additional pages for a genomic browser that visualizes genomic data interactively, bulk data download, a detailed user manual, and data integration information. PGD was developed with the capacity to integrate future data resources, and will be used as a long-term and open access database to facilitate the study of the biology, distribution, and the evolution of pineapple and the relative plant species. An email-based helpdesk is also available to offer support with the website and requests of specific datasets from the research community.