An eFP reference gene expression atlas for mangosteen

Abstract

Mangosteen is the queen of fruits with many health benefits and high pharmaceutical potential but remains an underutilized crop. There are several reports of mangosteen organelle genomes and transcriptomes from various tissues but a reference genome or transcriptome is still lacking. In this study, we aimed to generate a publicly accessible reference transcriptome of Garcinia mangostana variety Manggis (local fruit in Southeast Asia) to facilitate research in mangosteen functional genomics. De novo assembly was performed using Trinity with all the Illumina sequence datasets and generated 369,861 transcripts with an N50 of 1,433 bp. SuperTranscripts and TGICL transcript clustering approaches were taken to reduce redundant transcripts, in which the latter generated a more comprehensive reference transcriptome with a higher N50 value, Benchmarking Universal Single-Copy Orthologs (BUSCO) score, and read mapping rates. A total of 118,165 (43.7 %) unigenes were functionally annotated. To visualize gene expression across different mangosteen tissues, developmental stages, and experiments based on the reference transcriptome, we constructed a mangosteen electronic Fluorescent Pictograph (eFP) browser. This allows users to easily visualize the expression of genes in absolute, relative, and compare modes. In addition, researchers can perform online BLAST search against the in-house BAR SequenceServer for homologous sequences that match mangosteen transcripts to explore corresponding expression patterns via direct links to the eFP browser. This reference transcriptome and eFP browser (accessible at https://bar.utoronto.ca/efp_mangosteen/cgi-bin/efpWeb.cgi) provide a useful online tool for future research and improvement of mangosteen.