Comprehensive Transcriptome Profiling Reveals Long Noncoding RNA Expression and Alternative Splicing Regulation during Fruit Development and Ripening in Kiwifruit (Actinidia chinensis)

Abstract

Genomic and transcriptomic data on kiwifruit (Actinidia chinensis) in public databases are very limited despite its nutritional and economic value. Previously, we have constructed and sequenced nine fruit RNA-Seq libraries of A. chinensis “Hongyang” at immature, mature, and postharvest ripening stages of fruit development, and generated over 66.2 million paired-end and 24.4 million single-end reads. From this dataset, here we have identified 7051 long noncoding RNAs (lncRNAs), 29,327 alternative splicing (AS) events and 2980 novel protein-coding genes that were not annotated in the draft genome of “Hongyang.” AS events were demonstrated in genes involved in the synthesis of nutritional metabolites in fruit, such as ascorbic acids, carotenoids, anthocyanins, and chlorophylls, and also in genes in the ethylene signaling pathway, which plays an indispensable role in fruit ripening. Additionally, transcriptome profiles and the contents of sugars, organic and main amino acids were compared between immature, mature, and postharvest ripening stages in kiwifruits. A total of 5931 differentially expressed genes were identified, including those associated with the metabolism of sugar, organic acid, and main amino acids. The data generated in this study provide a foundation for further studies of fruit development and ripening in kiwifruit, and identify candidate genes and regulatory elements that could serve as targets for improving important agronomic traits through marker assisted breeding and biotechnology.

Long noncoding RNAs and miRNAs regulating terpene and tartaric acid biosynthesis in rose‐scented geranium

“…A significant number of transcripts (26 784) were identified as lncRNAs in rose‐scented geranium. The number of lncRNAs detected in this study was comparable with the previous studies on T. aestivum (44 698 lncRNAs) , maize (20 163 lncRNAs) , Populus trichocarpa (2542 lncRNAs) , Arabidopsis (6480 lncRNAs) , rice (2224 lncRNAs) , sea buckthorn (3428 lncRNAs) , Actinidia chinensis (7051 lncRNAs) , tomato (3558 lncRNAs) , Cajanus cajan (3919 lncRNAs) , and Vitis vinifera (3210 lncRNAs) etc. However, out of the total lncRNAs detected in rose‐scented geranium, only 1.8% could be annotated against the different public lncRNA databases, as high‐confidence lncRNAs.…”

A MYB/bHLH complex regulates tissue‐specific anthocyanin biosynthesis in the inner pericarp of red‐centered kiwifruit Actinidia chinensis cv. Hongyang

“…Previous analyses indicated the Acc03242 / Ach03g045741 from the genome of kiwifruit ‘Hongyang’ (Huang et al ., ; Yue et al ., ; Pilkington et al ., ) encodes a WD40 protein that is highly homologous to Arabidopsis TTG1, a well‐characterized WD40 protein involved in anthocyanin metabolism (Walker et al ., ). This WD40 homolog from kiwifruit was previously shown to be expressed constitutively throughout fruit development (Tang et al ., ). Here we additionally demonstrated that there was no significant difference in expression levels of Acc03242 / Ach03g045741 between inner and outer pericarp using qRT‐PCR analysis (Figure S19).…”

Systematic identification of long noncoding RNAs expressed during light‐induced anthocyanin accumulation in apple fruit

“…A rapidly increasing number of lncRNAs have been identified in plants and associated with various biological processes, including fruit ripening (Tang et al ., ; Li et al ., ), reproduction (Zhang et al ., ,b; Huang et al ., ), disease resistance (Zhang et al ., ), stress responses (Qin et al ., ), photomorphogenesis (Wang et al ., ) and phosphate homeostasis (Franco‐Zorrilla et al ., ).…”