Single-cell transcriptome atlas reveals developmental trajectories in the leaves of two kiwifruit (Actinidia chinensis) genotypes
Ontology highlight
ABSTRACT:
ORGANISM(S): Actinidia chinensis
PROVIDER: GSE233296 | GEO | 2025/05/01
REPOSITORIES: GEO
Similar Datasets
Project description:BackgroundTranscriptomic studies combined with a well annotated genome have laid the foundations for new understanding of molecular processes. Tools which visualise gene expression patterns have further added to these resources. The manual annotation of the Actinidia chinensis (kiwifruit) genome has resulted in a high quality set of 33,044 genes. Here we investigate gene expression patterns in diverse tissues, visualised in an Electronic Fluorescent Pictograph (eFP) browser, to study the relationship of transcription factor (TF) expression using network analysis.ResultsSixty-one samples covering diverse tissues at different developmental time points were selected for RNA-seq analysis and an eFP browser was generated to visualise this dataset. 2839 TFs representing 57 different classes were identified and named. Network analysis of the TF expression patterns separated TFs into 14 different modules. Two modules consisting of 237 TFs were correlated with floral bud and flower development, a further two modules containing 160 TFs were associated with fruit development and maturation. A single module of 480 TFs was associated with ethylene-induced fruit ripening. Three "hub" genes correlated with flower and fruit development consisted of a HAF-like gene central to gynoecium development, an ERF and a DOF gene. Maturing and ripening hub genes included a KNOX gene that was associated with seed maturation, and a GRAS-like TF.ConclusionsThis study provides an insight into the complexity of the transcriptional control of flower and fruit development, as well as providing a new resource to the plant community. The Actinidia eFP browser is provided in an accessible format that allows researchers to download and work internally.
| S-EPMC7913447 | biostudies-literature
Project description:The kiwifruit (Actinidia chinensis) is an economically and nutritionally important fruit crop with remarkably high vitamin C content. Here we report the draft genome sequence of a heterozygous kiwifruit, assembled from ~140-fold next-generation sequencing data. The assembled genome has a total length of 616.1 Mb and contains 39,040 genes. Comparative genomic analysis reveals that the kiwifruit has undergone an ancient hexaploidization event (?) shared by core eudicots and two more recent whole-genome duplication events. Both recent duplication events occurred after the divergence of kiwifruit from tomato and potato and have contributed to the neofunctionalization of genes involved in regulating important kiwifruit characteristics, such as fruit vitamin C, flavonoid and carotenoid metabolism. As the first sequenced species in the Ericales, the kiwifruit genome sequence provides a valuable resource not only for biological discovery and crop improvement but also for evolutionary and comparative genomics analysis, particularly in the asterid lineage.
| S-EPMC4089393 | biostudies-literature
Project description:In this study, an image-analysis-based method is proposed to estimate the length and width of plant leaves, some of which have concave tips and petiole insertions. Here, kiwifruit leaves are used. Using the proposed method, orthophotographs of the leaves were obtained through image segmentation and image correction. The coordinates of the pixels along the edge of the kiwifruit leaf were then extracted. Finally, the leaf length was determined based on the sum of the number of pixels between the leaf tip and petiole insertion, and the leaf width was calculated based on the sum of the number of pixels for the widest region of the leaf. The experimental results were evaluated by analyzing the mean absolute error (MAE), root mean square error (RMSE), and accuracy. The maximum MAE and RMSE for the three examined cultivars are 0.281 and 0.366 cm, respectively. The analysis also showed that the proposed method outperforms other prevalent approaches, achieving high accuracy rates of 98.88% and 98.83% for the length and width of kiwifruit leaves, respectively. The low MAE and RMSE and high accuracy prove the capability of the proposed method with regard to calculating the length and width of such leaves. In addition, the proposed method can be extended to other plants whose leaf shape is comparable to that of a kiwifruit leaf.
| S-EPMC7337316 | biostudies-literature
Project description:Actinidia chinensis (kiwifruit) is a perennial horticultural crop species of the Actinidiaceae family with high nutritional and economic value. Two versions of the A. chinensis genomes have been previously assembled, based mainly on relatively short reads. Here, we report an improved chromosome-level reference genome of A. chinensis (v3.0), based mainly on PacBio long reads and Hi-C data. The high-quality assembled genome is 653 Mb long, with 0.76% heterozygosity. At least 43% of the genome consists of repetitive sequences, and the most abundant long terminal repeats were further identified and account for 23.38% of our novel genome. It has clear improvements in contiguity, accuracy, and gene annotation over the two previous versions and contains 40,464 annotated protein-coding genes, of which 94.41% are functionally annotated. Moreover, further analyses of genetic collinearity revealed that the kiwifruit genome has undergone two whole-genome duplications: one affecting all Ericales families near the K-T extinction event and a recent genus-specific duplication. The reference genome presented here will be highly useful for further molecular elucidation of diverse traits and for the breeding of this horticultural crop, as well as evolutionary studies with related taxa.
| S-EPMC6804796 | biostudies-literature
Project description:BackgroundWith the advent of high throughput genomic tools, it is now possible to undertake detailed molecular studies of individual species outside traditional model organisms. Combined with a good understanding of physiological processes, these tools allow researchers to explore natural diversity, giving a better understanding of biological mechanisms. Here a detailed study of fruit development from anthesis through to fruit senescence is presented for a non-model organism, kiwifruit, Actinidia chinensis ('Hort16A').ResultsConsistent with previous studies, it was found that many aspects of fruit morphology, growth and development are similar to those of the model fruit tomato, except for a striking difference in fruit ripening progression. The early stages of fruit ripening occur as the fruit is still growing, and many ripening events are not associated with autocatalytic ethylene production (historically associated with respiratory climacteric). Autocatalytic ethylene is produced late in the ripening process as the fruit begins to senesce.ConclusionBy aligning A. chinensis fruit development to a phenological scale, this study provides a reference framework for subsequent physiological and genomic studies, and will allow cross comparison across fruit species, leading to a greater understanding of the diversity of fruits found across the plant kingdom.
| S-EPMC3261216 | biostudies-literature
Project description:The response of kiwifruit vine (Actinidia chinensis 'Hort16A') canes to feeding by the armoured scale insect Hemiberlesia lataniae was tested by screening RNA extracted from bark against a cDNA library of 17,512 unigenes. Substantial transcriptional changes were noted after 7 days for approximately 30% of the ESTs. Transcripts associated with photosynthesis were down-regulated and those associated with secondary metabolism up-regulated. A large number of transcripts orthologous with defence-related genes were differentially expressed including several orthologous with resistance and pathogenesis. This is the first such analysis of changes to transcript expression in a plant challenged by feeding by insects from the family diaspididae.
2015-10-13 | GSE73922 | GEO
Project description:Kiwifruit, economically important fruit tree
| PRJNA187537 | ENA
Project description:Transcriptome of Kiwifruit (Actinidia chinensis cv. Hongyang)
| PRJNA717384 | ENA
Project description:Transcriptome of "Hongyang" Kiwifruit (Actinidia chinensis) Raw sequence reads
| PRJNA717391 | ENA
Project description:ranscriptome of Kiwifruit (Actinidia chinensis cv. Hongyang) Raw reads
| PRJNA717387 | ENA