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. 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. 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.

In order to study the physicochemical and nutritional characteristics of kiwifruit varieties, 14 kiwifruits from different species with different flesh colors were selected for research. The pectin content was significantly higher in green-fleshed kiwifruits than those in red-fleshed and yellow-fleshed kiwifruits. Red-fleshed kiwifruits had the highest total flavonoid content, and green-fleshed kiwifruits in A. eriantha had the highest chlorophyll a content, chlorophyll b content and total carotenoid content. The energy and carbohydrate contents of yellow-fleshed kiwifruits were significantly lower than those of red-fleshed kiwifruit. Moreover, the protein contents in A. chinensis and A. chinensis var. deliciosa were higher than those in other species. The content of vitamin C in A. eriantha was far higher than in other kiwifruits. Red-fleshed kiwifruits had a significantly higher vitamin E and vitamin B1 content than green-fleshed kiwifruits. In addition, 1-pentanol, trans-2-hexen-1-ol, n-hexane and styrene presented only in red-fleshed kiwifruits. Therefore, these could be used as a characteristic fragrance for red-fleshed kiwifruits. Moreover, the varieties were ranked comprehensively by principal component analysis (PCA), among which the top four highest-ranking kiwifruits among the 14 varieties were ‘Huate’, ‘MHYX’, ‘Jinkui’ and ‘Xuxiang’, respectively. This study provides a reference for consumers and markets on quality improvement and processing.

Angiosperm sex chromosomes, where present, are generally recently evolved. The key step in initiating the development of sex chromosomes from autosomes is the establishment of a sex-determining locus within a region of non-recombination. To better understand early sex chromosome evolution, it is important to determine the process by which recombination is suppressed around the sex determining genes. We have used the dioecious angiosperm kiwifruit Actinidia chinensis var. chinensis, which has an active-Y sex chromosome system, to study recombination rates around the sex locus, to better understand key events in the development of sex chromosomes. We have confirmed the sex-determining region (SDR) in A. chinensis var. chinensis, using a combination of high density genetic mapping and fluorescent in situ hybridisation (FISH) of Bacterial Artificial Chromosomes (BACs) linked to the sex markers onto pachytene chromosomes. The SDR is a subtelomeric non-recombining region adjacent to the nucleolar organiser region (NOR). A region of restricted recombination of around 6 Mbp in size in both male and female maps spans the SDR and covers around a third of chromosome 25. As recombination is suppressed over a similar region between X chromosomes and between and X and Y chromosomes, we propose that recombination is suppressed in this region because of the proximity of the NOR and the centromere, with both the NOR and centromere suppressing recombination, and this predates suppressed recombination due to differences between X and Y chromosomes. Such regions of suppressed recombination in the genome provide an opportunity for the evolution of sex chromosomes, if a sex-determining locus develops there or translocates into this region.

Kiwifruit (Actinidia chinensis) roots instead of fruits are widely used as Chinese medicine, but the functional metabolites remain unclear. In this study, we conducted comparative metabolome analysis between root and fruit in kiwifruit. A total of 410 metabolites were identified in the fruit and root tissues, and of them, 135 metabolites were annotated according to the Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway. Moreover, 54 differentially expressed metabolites (DEMs) were shared in root and fruit, with 17 DEMs involved in the flavonoid pathway. Of the 17 DEMs, three flavonols (kaempferol-3-rhamnoside, L-Epicatechin and trifolin) and one dihydrochalcone (phloretin) showed the highest differences in the content level, suggesting that flavonols and dihydrochalcones may act as functional components in kiwifruit root. Transcriptome analysis revealed that genes related to flavonols and dihydrochalcones were highly expressed in root. Moreover, two AP2 transcription factors (TFs), AcRAP2-4 and AcAP2-4, were highly expressed in root, while one bHLH TF AcbHLH62 showed extremely low expression in root. The expression profiles of these TFs were similar to those of the genes related to flavonols and dihydrochalcones, suggesting they are key candidate genes controlling the flavonoid accumulation in kiwifruit. Our results provided an insight into the functional metabolites and their regulatory mechanism in kiwifruit root.

As a dioecious fruit tree, Kiwifruit requires pollination for female plants to bear fruit. This study used 2,4-Dichlorophenoxyacetic acid (2,4-D), a plant growth regulator, to induce fruit set, improve quality and increase kiwifruit yield in Actinidia chinensis var. 'Donghong' without pollination. Exogenous application of 2,4-dichlorophenoxyacetic acid (2,4-D) effectively triggered parthenocarpic fruit development in 'Donghong' kiwifruit (Actinidia chinensis var. 'Donghong'), while significantly improving fruit quality. The fruit set rate of parthenocarpic fruits reached 16.95% with 2,4-D treatment at 140 days after flowering; female flowers treated with 2,4-D showed differences in pollen structure compared to those treated with water. Also, no viability was detected in female flower pollen treated with 2,4-D. At the maturity stage, the fruits from the 2,4-D treatment were slightly smaller than those from the control group. The 2,4-D treatment group showed significant differences from the control group in skin hardness, flesh firmness and core hardness. There was no significant difference in the soluble solids content between the fruits treated with 2,4-D and those from the control group at maturity. However, the dry matter content of the 2,4-D treated fruits was lower than that of the pollinated fruits. The soluble sugar content of mature fruits from 2,4-D treatment reached 18.59 g/kg, and organic acid content was 18.10 g/kg, resulting in a significantly higher sugar-acid ratio than the control group. The seeds from 2,4-D treated fruits failed to germinate normally. This technology can facilitate the induction of fruit sets in actual production, which has significant practical value and potential in kiwifruit processing. From these results, important data were obtained regarding the establishment and production of kiwifruit orchards without including pollinator varieties, which take up a significant amount of space in the orchard establishment and cause a decrease in the yield obtained from the total area.

Kiwifruit, as a functionally dioecious fruit crop, necessitates pollination for female plants to achieve fruit set. In this study, exogenous application of the plant growth regulator 2,4-D successfully induced parthenocarpy, resulting in significantly higher fruit set rates compared to natural pollination while producing seedless fruits containing only empty seed coats. Through transcriptome analysis of the flower and young fruit, 10 key candidate genes were identified. We demonstrated that AcNAC056 and AcMADS1 transcriptionally activate AcGA2ox1 expression by binding to its promoter region, thereby elucidating the molecular mechanism underlying 2,4-D-induced seedless fruit formation. Cross-species validation in Arabidopsis revealed conserved expression patterns of AcGA2ox1, AcNAC056 and AcMADS1 following 2,4-D treatment, suggesting conservation of this regulatory mechanism. The study demonstrated that the application of 2,4-D-induced parthenocarpy technology in kiwifruit not only effectively addresses the fruit drop problem caused by insufficient pollination, but also enhances fruit yield. It provided effective technical support for kiwifruit cultivation, demonstrating broad application prospects and significant value in kiwifruit industry. The study contributed valuable insights into the molecular mechanism regulating parthenocarpy in kiwifruit.