Project description:Ascorbic acid (AsA), chlorophyll and carotenoid contents and their associated gene expression patterns were analysed in Actinidia chinensis 'Hongyang' outer pericarp. The results showed chlorophyll degradation during fruit development and softening, exposed the yellow carotenoid pigments. LHCB1 and CLS1 gene expressions were decreased, while PPH2 and PPH3 gene expressions were increased, indicating that downregulation of chlorophyll biosynthesis and upregulation of its degradation, caused chlorophyll degradation. A decrease in the expression of the late carotenoid biosynthesis and maintenance genes (LCYB1, LCYE1, CYP1, CYP2, ZEP1, VDE1, VDE2, and NCED2) and degradation gene (CCD1), showed biosynthesis and degradation of carotenoid could be regulatory factors involved in fruit development. Most genes expression data of L-galactose and recycling pathway were agreement with the AsA concentrations in the fruit, suggesting these are the predominant pathways of AsA biosynthesis. GMP1, GME1 and GGP1 were identified as the key genes controlling AsA biosynthesis in 'Hongyang' outer pericarp.
Project description:Red-fleshed kiwifruit (Actinidia chinensis Planch. 'Hongyang') is a promising commercial cultivar due to its nutritious value and unique flesh color, derived from vitamin C and anthocyanins. In this study, we obtained transcriptome data of 'Hongyang' from seven developmental stages using Illumina sequencing. We mapped 39-54 million reads to the recently sequenced kiwifruit genome and other databases to define gene structure, to analyze alternative splicing, and to quantify gene transcript abundance at different developmental stages. The transcript profiles throughout red kiwifruit development were constructed and analyzed, with a focus on the biosynthesis and metabolism of compounds such as phytohormones, sugars, starch and L-ascorbic acid, which are indispensable for the development and formation of quality fruit. Candidate genes for these pathways were identified through MapMan and phylogenetic analysis. The transcript levels of genes involved in sucrose and starch metabolism were consistent with the change in soluble sugar and starch content throughout kiwifruit development. The metabolism of L-ascorbic acid was very active, primarily through the L-galactose pathway. The genes responsible for the accumulation of anthocyanin in red kiwifruit were identified, and their expression levels were investigated during kiwifruit development. This survey of gene expression during kiwifruit development paves the way for further investigation of the development of this uniquely colored and nutritious fruit and reveals which factors are needed for high quality fruit formation. This transcriptome data and its analysis will be useful for improving kiwifruit genome annotation, for basic fruit molecular biology research, and for kiwifruit breeding and improvement.
Project description:In the present study, we employed the high-throughput sequencing technology to profile miRNAs in the inner and outer pericarp of Actinidia chinensis cv. Hongyang. After sequencing and cleaning, the numbers of clean reads generated from these four libraries were 18,203,332, 9,356,430, 11,006,231 and 11,314,375, respectively. Approximately 93.62%, 93.67%, 92.75% and 93.28% clean reads were respectively mapped to the kiwifruit genome with perfect matches. Subsequently, differentially expressed genes were compared between the inner and outer pericarps. Significant differences in both up- and down-regulated genes were identified in inner and outer percarps by comparing expression levels. The results showed that there were significantly 450 up-regulated and 416 down-regulated DEGs in inner pericarp as compared to the outer pericarp. Overall design: Inner and outer pericarp in two parallel samples of Actinidia chinensis cv. Hongyang
Project description:BACKGROUND:Most published genome sequences are drafts, and most are dominated by computational gene prediction. Draft genomes typically incorporate considerable sequence data that are not assigned to chromosomes, and predicted genes without quality confidence measures. The current Actinidia chinensis (kiwifruit) 'Hongyang' draft genome has 164 Mb of sequences unassigned to pseudo-chromosomes, and omissions have been identified in the gene models. RESULTS:A second genome of an A. chinensis (genotype Red5) was fully sequenced. This new sequence resulted in a 554.0 Mb assembly with all but 6 Mb assigned to pseudo-chromosomes. Pseudo-chromosomal comparisons showed a considerable number of translocation events have occurred following a whole genome duplication (WGD) event some consistent with centromeric Robertsonian-like translocations. RNA sequencing data from 12 tissues and ab initio analysis informed a genome-wide manual annotation, using the WebApollo tool. In total, 33,044 gene loci represented by 33,123 isoforms were identified, named and tagged for quality of evidential support. Of these 3114 (9.4%) were identical to a protein within 'Hongyang' The Kiwifruit Information Resource (KIR v2). Some proportion of the differences will be varietal polymorphisms. However, as most computationally predicted Red5 models required manual re-annotation this proportion is expected to be small. The quality of the new gene models was tested by fully sequencing 550 cloned 'Hort16A' cDNAs and comparing with the predicted protein models for Red5 and both the original 'Hongyang' assembly and the revised annotation from KIR v2. Only 48.9% and 63.5% of the cDNAs had a match with 90% identity or better to the original and revised 'Hongyang' annotation, respectively, compared with 90.9% to the Red5 models. CONCLUSIONS:Our study highlights the need to take a cautious approach to draft genomes and computationally predicted genes. Our use of the manual annotation tool WebApollo facilitated manual checking and correction of gene models enabling improvement of computational prediction. This utility was especially relevant for certain types of gene families such as the EXPANSIN like genes. Finally, this high quality gene set will supply the kiwifruit and general plant community with a new tool for genomics and other comparative analysis.
Project description: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.
Project description:Ripe rot caused by Botryosphaeria dothidea causes extensive production losses in kiwifruit (Actinidia chinensis Planch.). Our previous study showed that kiwifruit variety "Jinyan" is resistant to B. dothidea while "Hongyang" is susceptible. For a comparative analysis of the response of these varieties to B. dothidea infection, we performed a transcriptome analysis by RNA sequencing. A total of 305.24 Gb of clean bases were generated from 36 libraries of which 175.76 Gb was from the resistant variety and 129.48 Gb from the susceptible variety. From the libraries generated, we identified 44,656 genes including 39,041 reference genes, 5,615 novel transcripts, and 13,898 differentially expressed genes (DEGs). Among these, 2,373 potentially defense-related genes linked to calcium signaling, mitogen-activated protein kinase (MAPK), cell wall modification, phytoalexin synthesis, transcription factors, pattern-recognition receptors, and pathogenesis-related proteins may regulate kiwifruit resistance to B. dothidea. DEGs involved in calcium signaling, MAPK, and cell wall modification in the resistant variety were induced at an earlier stage and at higher levels compared with the susceptible variety. Thirty DEGs involved in plant defense response were strongly induced in the resistant variety at all three time points. This study allowed the first comprehensive understanding of kiwifruit transcriptome in response to B. dothidea and may help identify key genes required for ripe rot resistance in kiwifruit.
Project description:Actinidia chinensis is a commercially important fruit, and tetraploid breeding of A. chinensis is of great significance for economic benefit. In order to obtain elite tetraploid cultivars, tetraploid plants were induced by colchicine treatment with leaves of diploid A. chinensis ‘SWFU03’. The results showed that the best treatment was dipping leaves 30 h in 60 mg l?1 colchicine solutions, with induction rate reaching 26%. Four methods, including external morphology comparison, stomatal guard cell observation, chromosome number observation and flow cytometry analysis were used to identify the tetraploid of A. chinensis. Using the induction system and flow cytometry analysis methods, 187 tetraploid plants were identified. Three randomly selected tetraploid plants and their starting diploid plants were further subjected to transcriptome analysis, real-time quantitative polymerase chain reaction (RT-qPCR) and methylation-sensitive amplification polymorphism (MSAP) analysis. The transcriptome analysis results showed that there were a total of 2230 differentially expressed genes (DEG) between the diploid and tetraploid plants, of which 660 were downregulated and 1570 upregulated. The DEGs were mainly the genes involved in growth and development, stress resistance and antibacterial ability in plants. RT-qPCR results showed that the gene expression levels of the growth and stress resistance of tetraploid plants were higher than those of diploid ones at the transcriptome level. MSAP analysis of DNA methylation results showed that tetraploid plants had lower methylation ratio than diploid ones. The present results were valuable to further explore the epigenetics of diploid and tetraploid kiwifruit plants.