Full-Length Transcriptome Sequencing Analysis and Characterization of Gene Isoforms Involved in Flavonoid Biosynthesis in the Seedless Kiwifruit Cultivar ‘Chengxiang’ (Actinidia arguta)

Abstract

Kiwifruit an important horticultural crop that is widely cultivated and is known as the king of fruits. Recently, a new seedless kiwifruit cultivar, ‘Chengxiang’ (Actinidia arguta), was discovered by field transplantation. It exhibited distinguishable characteristics such as parthenocarpy, and a unique flavor and appearance when compared to other cultivated type. Flavonoids are known to play an important role in fertility and parthenocarpy in plants. However, the genes responsible for flavonoid biosynthesis in seedless kiwifruit remain largely unknown. Especially, chalcone synthase (CHS), as a key enzyme catalyzing the first committed step in the flavonoid pathway, remains a mystery. In this study, we combined a full-length transcriptome survey by PacBio single-molecule real-time (SMRT) sequencing, CHS gene family analysis, and analysis of the gene expression involved in flavonoid pathways to further enhance the understanding of parthenocarpy. Based on SMRT, we obtained 80,615 high-quality full-length consensus transcripts. In total, 52,406 (90.79%) transcripts were functionally annotated, and more than 80% of the transcripts were longer than 1Kb. Among them, 39,117 (74.64%) transcripts were assigned to GO terms, the majority of which were associated with the cell (19,089, 48.80%) and metabolic process (19,859, 50.77%). Furthermore, 25,289 (48.26%) transcripts were mapped into 129 KEGG pathways. We identified the majority of putative genes as being involved in the flavonoid biosynthesis pathway, including 14 key enzyme gene families, such as CHS, chalcone isomerase (CHI), flavonol synthase (FLS), and so on. Moreover, we also identified 13 CHS genes and characterized the CHS gene family in seedless kiwifruit. We further evaluated the expression pattern of 10 flavonoid-related key enzyme genes in flowers using quantitative real-time PCR. This is the first time that the full-length transcriptome have been studied in seedless kiwifruit, and the findings enhance our understanding the molecular mechanisms of parthenocarpy.