De novo Transcriptome Analysis in Physiological Disorders of Mangosteen (Garcinia mangostana L.) Fruits by RNA-Seq

Mangosteen is one of the most important Indonesian tropical fruits because it has high economic value and a pleasing taste, and a rich aroma as well as anti-oxidants. However, the quality of fruit depends on the occurrence of physiological disorders, like gamboge disorder (GD) and the fruit translucent disorder (TFD). In order to identify the differential gene expression on the normal fruit and the physiological disorder-affected fruits, the transcriptome was analyzed using the Ion Proton™ system. First, we collected 4 types of the tissues: GD-affected rind (GDR), normal rind (NR), TFD-affected aril (TFDA) and normal aril (NA). The 11 libraries were sequenced and a total of 202.48 million short reads (16.52 billion bases) were produced. The bases of low Q values were trimmed and a total of 38.6 million short reads were produced. The de novo assembly was performed with the trimmed reads by Trinity. This assembling produced 236,152 contigs with an average of 484 bp in length ranging between 224 – 5557 bp. The contigs were annotated using EnsemblePlant database. The transcripts of the trimmed reads were mapped individually into the assembled-contigs by Bowtie2. We identified 5,525 transcripts to be further analyzed in the differential gene expression (DGE). After normalization and fisher’s exact test (q-value ≦0.05), DGE analysis identified the transcript difference in 147 transcripts between GDA and NR, and 932 transcripts between TFDA and NA, respectively. These results provide a starting information to further discovering and understanding the regulating genes involved in the physiological disorders of mangosteen.