De Novo Transcriptome Sequencing in Kiwifruit (Actinidia chinensis var. deliciosa (A Chev) Liang et Ferguson) and Development of Tissue-Specific Transcriptomic Resources

Abstract

Kiwifruit (Actinidia chinensis var. deliciosa (A Chev) Liang et Ferguson) is a sub-tropical vine species from the Actinidiaceae family native to China. This species has an allohexaploid genome (from diploid and autotetraploid parents), contained in 174 chromosomes producing a climacteric and fleshy fruit called kiwifruit. Currently, only a small body of transcriptomic and proteomic data are available for A. chinensis var. deliciosa. In this low molecular knowledge context, the main goal of this study is to construct a tissue-specific de novo transcriptome assembly, generating differential expression analysis among these specific tissues, to obtain new useful transcriptomic information for a better knowledge of vegetative, floral and fruit growth in this species. In this study, we have analyzed different whole transcriptomes from shoot, leaf, flower bud, flower and fruit at four development stages (7, 50, 120 and 160 days after flowering; DAF) in kiwifruit obtained through RNA-seq sequencing. The first version of the developed A. chinensis var. deliciosa de novo transcriptome contained 142,025 contigs (x¯ = 1044 bp, N50 = 1133 bp). Annotation was performed with BLASTX against the TAIR10 protein database, and we found an annotation proportion of 35.6% (50,508), leaving 64.4% (91,517) of the contigs without annotation. These results represent a reference transcriptome for allohexaploid kiwifruit generating a database of A. chinensis var. deliciosa genes related to leaf, flower and fruit development. These results provided highly valuable information identifying over 20,000 exclusive genes including all tissue comparisons, which were associated with the proteins involved in different biological processes and molecular functions.

Genome-Wide Analysis of Multiple Organellar RNA Editing Factor (MORF) Family in Kiwifruit (Actinidia chinensis) Reveals Its Roles in Chloroplast RNA Editing and Pathogens Stress

“…Based on merged RNA sequencing (RNA-seq) data [29] from different kiwifruit tissues (shoots, leaves, flower buds, flowers, and different developmental stages of fruits after full bloom), we used REDO tools to identify all RNA editing sites by following the protocol in our previous study [9]. The overall mapping depth is ~50X, which is adequate for the identification of RNA editing sites.…”

Identification and expression analysis of the lipid phosphate phosphatases gene family reveal their involvement in abiotic stress response in kiwifruit

“…To understand the tissue-specific expression profile of AcLPP genes, FPKM (fragments per million mapped readings per thousand base transcripts) was used to evaluate their expression levels in different organs and stages of development. The RNA-seq data (PRJNA564374) of kiwifruit were extracted from the public database for analysis (Salazar et al, 2021 ). As shown in Figure 4A , AcLPP2B and AcLPP1B were highly expressed in flowers and flower buds, suggesting that AcLPP2B and AcLPP1B might coordinate the expression of target genes involved in flower development.…”

Genomic Colinearity and Transcriptional Regulatory Networks of BES1 Gene Family in Horticultural Plants Particularly Kiwifruit and Peach

“…Large-scale expression datasets of various hormone treatments, developmental and postharvest stages, and adversity were obtained from the SRA database of the NCBI. We collected 70 samples, including the expression data of different tissues of kiwifruit as well as different development periods of fruit from growth to postharvest storage [34,35]. Data from 45 transcriptome samples of kiwifruit during postharvest storage treated with ethylene (ETH) and 1-methylcyclopropene (1-MCP, an ethylene inhibitor) were obtained from SRA (accession numbers: PRJNA638129, PRJNA445209, and PRJNA593865).…”