Abstract
A set of Elaeis guineensis genes had been generated by combining two gene prediction pipelines: Fgenesh++ developed by Softberry and Seqping by the Malaysian Palm Oil Board. PalmXplore was developed to provide a scalable data repository and a user-friendly search engine system to efficiently store, manage and retrieve the oil palm gene sequences and annotations. Information deposited in PalmXplore includes predicted genes, their genomic coordinates, as well as the annotations derived from external databases, such as Pfam, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes. Information about genes related to important traits, such as those involved in fatty acid biosynthesis (FAB) and disease resistance, is also provided. The system offers Basic Local Alignment Search Tool homology search, where the results can be downloaded or visualized in the oil palm genome browser (MYPalmViewer). PalmXplore is regularly updated offering new features, improvements to genome annotation and new genomic sequences. The system is freely accessible at http://palmxplore.mpob.gov.my.
Highlights
Oil palm is a major source of oil that has become a common ingredient in many consumer products and industrial applications, such as biofuel, a renewable alternative to petroleum
A breakthrough achievement by Malaysian Palm Oil Board (MPOB) was the discovery of the SHELL gene that is responsible for the dura, pisifera and tenera fruit forms [5], which have a significant impact on yield
In order to assist in the use of these datasets, we have developed a searchable database and information system called PalmXplore
Summary
Oil palm is a major source of oil that has become a common ingredient in many consumer products and industrial applications, such as biofuel, a renewable alternative to petroleum. The upstream subsectors of oil palm industry in genomics-based technologies have gone through. Singh et al (2014) successfully identified the VIRESCENS gene that controls the exocarp colour of the oil palm fruit [6] Another major success was the identification of the epimutation in the MANTLED gene that causes the mantled somaclonal abnormality in oil palm that often results in bunch failure and drastic yield reduction [7]
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