De novo transcriptome analysis of Taxus chinensis var. mairei to identify significant pathways associated with the fruit color of this species

The goal of this study was to find significant pathways associated with fruit color in Taxus chinensis var. mairei. Two Taxus chinensis var. mairei with fruits of different colors were sequenced using high-throughput sequencing. Then, unigene assembly, unigene annotation, and classification of Clusters of Orthologous Groups of proteins (COGs) were performed. Gene ontology (GO) classification and pathway enrichment analysis for unigenes were also conducted. Protein coding sequences (CDS) were predicted. Subsequently, differentially expressed unigenes, functional enrichment pathways of differentially expressed unigenes, single nucleotide polymorphisms (SNPs), and simple sequence repeats (SSRs) were analyzed. The data of Taxus chinensis var. mairei were assembled into 45,112 unigenes with an average size of 1232 bp and an N50 of 1882 bp. The significantly enriched biological processes (BP) were metabolic processes, and cellular processes, followed by single-organism processes, and reproductive processes. Significantly enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were metabolic pathways, pathways related to the biosynthesis of secondary metabolites, and RNA transport pathways. Transition had a higher number of SNP sites than transversion. Trinucleotide had the highest SSR motif numbers. Metabolic pathways and the biosynthesis of secondary metabolites may play significant roles in determining fruit color in Taxus chinensis var. mairei. In addition, the present dataset would provide a basis for future functional genomic research on Taxus chinensis var. mairei.