Materials and Methods

Data Collection:

• Raw RNA-Seq data for tropical and sub-tropical fruit crops, as recognized by FAO was collected from public domains.
• Corresponding reference genomes and annotations were retrieved.

Preprocessing:

• Read quality was assessed using FastQC.
• Low-quality reads were trimmed or removed using Trimmomatic.

Mapping and Gene Expression:

• Reference genomes were indexed using HISAT2 .
• Reads were mapped to the genomes using HISAT2.
• Gene expression levels (FPKM) were estimated using StringTie.

Tissue Specificity:

• Tissue specificity scores (tau) were calculated for each gene using the 'tispec' R package.
• Genes were categorized as Highly/ Absolutely Specific (Tau score ranging from 0.8 to 1.0), Intermediate Specific (Tau score of 0.2 to 0.8), or Non/Low Specificity, Housekeeping Genes (Tau score ranging from 0 to 0.2).

Functional Annotation:

• Functional annotations (GO terms) were assigned to tissue-specific genes using Blast2GO .

Pathway Analysis:

• KEGG pathway analysis was performed on tissue-specific genes using Blast2GO.

Fruit Expression Atlas (FEAtl) Development:

• A web-accessible database (FEAtl) was created to store and display gene expression data from the study.
• FEA allows users to search for expression data based on various criteria.