PGD: Pineapple Genomics Database

Huimin Xu, Qingyi Yu, Yan Shi, Xiuting Hua, Haibao Tang, Long Yang, Ray R Ming, Jisen Zhang

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Article number66
JournalHorticulture Research
Volume5
Issue number1
DOIs
StatePublished - Dec 1 2018

Fingerprint

Ananas
Prostaglandins D
pineapples
Genomics
Databases
Genes
genomics
Ananas comosus
Photosynthesis
Data integration
Electronic mail
Bromeliaceae
Metabolism
Gene expression
Websites
e-mail
Crassulacean acid metabolism
genetic markers
Molecular Sequence Annotation
Gene Expression

ASJC Scopus subject areas

  • Biotechnology
  • Biochemistry
  • Genetics
  • Plant Science
  • Horticulture

Cite this

Xu, H., Yu, Q., Shi, Y., Hua, X., Tang, H., Yang, L., ... Zhang, J. (2018). PGD: Pineapple Genomics Database. Horticulture Research, 5(1), [66]. https://doi.org/10.1038/s41438-018-0078-2

PGD : Pineapple Genomics Database. / Xu, Huimin; Yu, Qingyi; Shi, Yan; Hua, Xiuting; Tang, Haibao; Yang, Long; Ming, Ray R; Zhang, Jisen.

In: Horticulture Research, Vol. 5, No. 1, 66, 01.12.2018.

Research output: Contribution to journalArticle

Xu, H, Yu, Q, Shi, Y, Hua, X, Tang, H, Yang, L, Ming, RR & Zhang, J 2018, 'PGD: Pineapple Genomics Database', Horticulture Research, vol. 5, no. 1, 66. https://doi.org/10.1038/s41438-018-0078-2
Xu H, Yu Q, Shi Y, Hua X, Tang H, Yang L et al. PGD: Pineapple Genomics Database. Horticulture Research. 2018 Dec 1;5(1). 66. https://doi.org/10.1038/s41438-018-0078-2
Xu, Huimin ; Yu, Qingyi ; Shi, Yan ; Hua, Xiuting ; Tang, Haibao ; Yang, Long ; Ming, Ray R ; Zhang, Jisen. / PGD : Pineapple Genomics Database. In: Horticulture Research. 2018 ; Vol. 5, No. 1.
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