Analysis of mangosteen fruit ripening through the assembly of organelle genomes, reference transcriptome, and co-expression network

Abstract

The xanthones in the mangosteen pericarp have pharmaceutical properties. Its content increased during fruit ripening. Fruit ripening is a complex process that requires the coordination of nuclear and organellar genes at the molecular level. Understanding the mangosteen fruit ripening mechanism helps to increase xanthone production and extend its shelf life. As such, this study aims to assemble mangosteen organelle (chloroplast and mitochondrial) genomes and transcriptomes using NCBI datasets via bioinformatic analysis. The complete plastome of mesta variety (156,580 bp) was obtained through a hybrid assembly of PacBio and Illumina sequencing reads. It was used as a reference in manggis plastome (156,582 bp) reference-guided assembly. Each plastome comprises 83 protein-coding, 37 tRNA, and 8 rRNA genes. Mesta variety has a complete mitogenome of 371,235 bp and comprises 29 protein-coding, 3 rRNA, and 21 tRNA genes. De novo assembly using Trinity followed by TGICL clustering generated a total of 270,208 unigenes. Next, gene co-expression network analysis (WGCNA) identified three modules, darkturquoise, pink, and plum2, correlated with fruit ripening. Darkturquoise module was enriched with phenolic biosynthesis genes. Further analysis of darkturquoise and pink modules identified co expressed genes that are involved in phenolic compound biosynthesis as well as cell wall and carbohydrate metabolisms. Plum2 module was enriched with xanthone related genes. There were 81, 44, and 12 hub genes identified from the darkturquoise, pink, and plum2 modules, respectively. Among them, some were reported in fruit ripening such as PAL and BPS in xanthone biosynthesis, PAL, F3GGT1, and YAB5 in phenolic biosynthesis, as well as rhiE and BGAL in cell wall metabolism. Some hub genes were unannotated or unreported in fruit ripening such as GCP1, MLO6, CYL2, GLX1, and PAP15. There were five organelle genes (psbA, psbC, matK, cox2, and nad3) identified in the pink module. Further verification through functional analysis is needed to validate the roles of these hub genes and organelle genes in fruit ripening. Lastly, the development of a publicly accessible mangosteen eFP browser enables users to visualize the expression of genes in absolute, relative, and compare modes. It serves as a useful reference portal for further studies and future crop improvement of mangosteen.