Dataset from RNAseq analysis of bud differentiation in Ficus carica

Abstract

The presented data regards the transcriptome profiling and differential analysis with RNA-Seq approach with the following goals: de novo transcriptome assembly and genome annotation of Ficus carica and the differential expression analysis of parthenocarpic and non-partenocarpic varieties in order to identify candidate genes for the production of seedless fig. Two fig varieties Dottato and Petrelli and the caprifig were grown at the fig repository at the 'P. Martucci' experimental station in Valenzano (Bari) of University of Bari 'Aldo Moro'. The data included: RNA-seq data obtained from fruits of parthenocarpic and non-parthenocarpic varieties, gene expression in the different genetic materials; genes up and down regulated. The data in this article support information presented in the research article "I. Marcotuli, A. Mazzeo, P. Colasuonno, R. Terzano, D. Nigro, C. Porfido, A. Tarantino, R. Aiese Cigliano, W. Sanseverino, A. Gadaleta, G. Ferrara, Fruit Development in Ficus carica L.: Morphological and Genetic Approaches to Fig Buds for an Evolution From Monoecy Toward Dioecy. Front. Plant Sci.(2020) 11:1208. doi: 10.3389/fpls.2020.01208.

Keywords: Brebas; Fruit production; Genetics; Main crop; RNAseq.

Fig. 1

Summary of the quality of the sequenced bases in fico and fiorone of the three genotyoes before (left) and after (right) trimming. The x-axis reports the position along the reads, the y-axis reports the quality as Phred-Like score. The yellow boxes represent the interquartile range of the quality values at each position, the red bar the median, the black line the average quality value. The whiskers of the boxes represent the 10th and the 90th percentile. The scores in the green part of the chart are considered good.

Fig. 2

Summary of the rules applied for the gene section in the fig data set using the NCBI and Maker genes against the TrEMBL Plantae and UniProt Plantae database.

Fig. 3

Graphic representation of the HTSFilter analysis result in fico and fiorone of Dottato, Petrelli and profig. The algorithm calculated a Global Jaccard index of similarity between the samples in function of different minimum TMM normalized read counts (s). The graphic shows that for s = 7.016 the replicates have the highest similarity; thus, this value was used as a threshold. All the loci with TMM normalized read counts < s in the samples were removed. This graph is in the file filter.pdf in the folder called 2-DE.

Fig. 4

Principal Component Analysis (PCA) conducted on the normalized gene expression in the values of the Dottato, Petrelli and profig samples. X- and Y-axes show the PC1 and PC2, respectively, with the amount of variance explained by each component reported in parenthesis. Each point in the plot represented a sample, dots of the same colors were replicates of a same experimental group.

Fig. 5

Total number of annotated genes in the reference genome of Dottato (Total), the number of genes that passed the low expression filter (Kept), the total number of differentially expressed up-regulated genes (UP) the total number of differentially expressed down-regulated genes (Down) and across the comparison.

Fig. 6

MA plot (On the left) and Volcano plot (on the right) on the genes identified in the fig dataset. Black dots represent the genes that are not significantly differentially expressed, while red and green dots are the genes that are significantly UP- and DOWN-regulated, respectively.