Transcriptomics analysis of Chinese hawthorn (Crataegus pinnatifida) provides insights into the biosynthesis of polyphenolic compounds

Due to its high polyphenolic compound content, Chinese hawthorn, which belongs to the Rosaceae family, is a popular fruit consumed as food and medicine source in China. However, little genetic studies have been performed on hawthorn, partially because of the lack of genomic resources. To this end, we performed de novo transcriptomics analysis of hawthorn using the cost-effective Illumina paired-end RNA sequencing technology. Briefly explain how study was conducted and what measured then. 6.5 Gbp data were obtained and assembled into 83,817 transcripts. Approximately 98% of the transcripts had homologous in the available database, and 97% had homologous hits in the apple, pear and peach genomes. A total of 208 candidate key enzymes potentially involved in polyphenolic compound biosynthetic pathways were identified and compared to their homologous in related species. Approximately 77.12% of transcripts (64,636) were predicted to contain CDS (coding sequences). Using gene family comparative analysis, 14,800 gene families and 20,943 specific genes of hawthorn were identified. These specific genes were enriched in 3 secondary metabolite pathways (stilbenoid, diarylheptanoid and gingerol biosynthesis, phenylpropanoid biosynthesis and plavone and flavonol biosynthesis) that are related to phenolic compound biosynthesis and other basic metabolic processes. In addition, 10,472 simple sequence repeats (SSRs) were detected.