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.
Highlights
Pineapple (Ananas comosus (L.)) is an important tropical fruit displaying crassulacean acid metabolism (CAM) with high water-use efficiency
Pineapple originated when the Bromeliaceae family separated from Poaceae early in the history of Poales offering an evolutionary reference for comparative genomics analysis of cereal genomes
We provided four methods to search for pineapple genes: Comparative genomics analysis To clarify the evolutionary relationship and wholegenome duplication (WGD) events between pineapple and eight representative plant species, including Oryza sativa, Vitis vinifera, Spirodela polyrhiza, Asparagus aofficinalis, Elaeis guineensis, Phoenix dactylifera, S. bicolor, and Musa acuminata, we performed whole-genome
Summary
Pineapple (Ananas comosus (L.)) is an important tropical fruit displaying crassulacean acid metabolism (CAM) with high water-use efficiency. Pineapple originated when the Bromeliaceae family separated from Poaceae early in the history of Poales offering an evolutionary reference for comparative genomics analysis of cereal genomes. In comparison with Poaceae such as rice (Oryza sativa), maize (Zea mays), sorghum (Sorghum bicolor)[1,2], the genome sequence of pineapple were released much later, when the challenges of its highly heterozygous genome were recently solved and a reference genome assembled by Ming et al.[3] The genome assembly of pineapple was published, the samples used to assemble genome were from variety F153. Because of the pivotal phylogenetic position of pineapple at the base of the Poales[3], making its much smaller genome convenient for evolutionary studies. Many sequenced plant genomes have a genomics database for researchers to manage the biological information, such as TAIR (http:// www.arabidopsis.org) for arabidopsis, MaizeGDB (http:// www.maizeGDB.org) for maize, and RGAP Many sequenced plant genomes have a genomics database for researchers to manage the biological information, such as TAIR (http:// www.arabidopsis.org) for arabidopsis, MaizeGDB (http:// www.maizeGDB.org) for maize, and RGAP (http://rice. plantbiology.msu.edu) for rice, but the current absence of such a database for pineapple, limits the ability of researchers in obtaining genomic data for pineapple
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