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Abstract Stabilizing active PtNi alloy catalyst toward oxygen reduction reaction is essential for fuel cell. Doping of specific metals is an empirical strategy, however, the atomistic insight into how dopant boosts the stability of PtNi catalyst still remains elusive. Here, with typical examples of Mo and Au dopants, we identify the distinct roles of Mo and Au in stabilizing PtNi nanowires catalysts. Specifically, due to the stronger interaction between atomic orbital for Ni-Mo and Pt-Au, the Mo dopant mainly suppresses the outward diffusion of Ni atoms while the Au dopant contributes to the stabilization of surface Pt overlayer. Inspired by this atomistic understanding, we rationally construct the PtNiMoAu nanowires by integrating the different functions of Mo and Au into one entity. Such catalyst assembled in fuel cell cathode thus presents both remarkable activity and durability, even surpassing the United States Department of Energy technical targets for 2025.

“Tongguan Liqiao” acupuncture method established by Xuemin Shi, a master of traditional Chinese medicine in China and academician of the Chinese Academy of Engineering, derives from the famous “Xing Nao Kai Qiao” therapy (activating the brain and opening the orifices) acupuncture method. It fundamentally takes “adjusting the spirit” as the root of selecting acupoints based on syndrome differentiation. Neiguan (PC 6), Renzhong (DU 26), and Sanyinjiao (SP 6) are selected as the main acupoints to adjust the spirit and revive the brain, nourish the liver and kidney, which treats the root cause. Acupoints such as Lianquan (RN 23), Yifeng (SJ 17), Wangu (GB 12), and Fengchi (GB 20) in the neck region are selected for “unblocking orifices,” which relieves the symptoms. This acupuncture method features deep needling, which aligns with modern swallowing function anatomy. The method can improve the function of poststroke dysphagia by enhancing cerebral blood supply and metabolism and promoting neural functional remodeling.

Nanozymes with superior antioxidant properties offer new hope for treating oxidative stress-related inflammatory skin diseases. However, lacking sufficient catalytic activity or having complex material designs limit the application of current metallic nanozymes in inflammatory skin diseases. Here, we report a simple and effective twin-defect platinum nanowires (Pt NWs) enzyme with multiple mimetic enzymes and broad-spectrum ROS scavenging capability for the treatment of inflammatory skin diseases in mice (including psoriasis and rosacea). Pt NWs with simultaneous superoxide dismutase, glutathione peroxidase and catalase mimetic enzyme properties exhibit cytoprotective effects against ROS-mediated damage at extremely low doses and significantly improve treatment outcomes in psoriasis- and rosacea-like mice. Meanwhile, these ultrasmall sizes of Pt NWs allow the nanomaterials to effectively penetrate the skin and do not produce significant biotoxicity. Therefore, Pt NWs have potential applications in treating diseases related to oxidative stress or inflammation.

Akebia species, belonging to Lardizabalaceae, are widespread from subtropical to temperate environments of China, Japan, and Korea. All known Akebia species have medicinal and dietary value and have been widely cultivated as a new fruit crop in many areas of China. However, compared with other crop species, the breeding improvement and commercial cultivation of Akebia remain in their infancy. This review systematically introduces the present germplasm resources, geographical distribution, biological characteristics, interspecific and intraspecific cross compatibility, molecular biology, and breeding progress in Akebia species. Akebia plants are widely distributed in Shanxi, Henan, Sichuan, Chongqing, Hunan, Hubei, Jiangxi, Zhejiang, and Fujian provinces of China, and wild Akebia plants exhibit abundant phenotypic and genetic diversity due to their wide range of geographical distribution and high adaptability in different habitats. Interspecific artificial hybridization experiments have been conducted in our Akebia germplasm resources nursery. The results showed that there was no reproductive isolation between Akebia species, and fertile progeny could be produced. The synthesis of knowledge on these species provides insights for the rational development and utilization of these germplasm resources, and can facilitate the development of new breeding lines or varieties for commercial cultivation or production. Finally, perspectives on Akebia breeding research are discussed and conclusions are provided. This review provided breeders with new insights into Akebia domestication and breeding, and we also proposed five basic steps in the domestication of new fruit crops.

The kiwifruit, Actinidia genus, has emerged as a nutritionally rich and economically significant crop with a history rooted in China. This review paper examines the global journey of the kiwifruit, its genetic diversity, and the role of advanced breeding techniques in its cultivation and improvement. The expansion of kiwifruit cultivation from China to New Zealand, Italy, Chile and beyond, driven by the development of new cultivars and improved agricultural practices, is discussed, highlighting the fruit’s high content of vitamins C, E, and K. The genetic resources within the Actinidia genus are reviewed, with emphasis on the potential of this diversity in breeding programs. The review provides extensive coverage to the application of modern omics technologies, including genomics, transcriptomics, proteomics, and metabolomics, which have revolutionized the understanding of the biology of kiwifruit and facilitated targeted breeding efforts. It examines both conventional breeding methods and modern approaches, like marker-assisted selection, genomic selection, mutation breeding, and the potential of CRISPR-Cas9 technology for precise trait enhancement. Special attention is paid to interspecific hybridization and cisgenesis as strategies for incorporating beneficial traits and developing superior kiwifruit varieties. This comprehensive synthesis not only sheds light on the current state of kiwifruit research and breeding, but also outlines the future directions and challenges in the field, underscoring the importance of integrating traditional and omics-based approaches to meet the demands of a changing global climate and market preferences.

Abstract Background The base editors can introduce point mutations accurately without causing double-stranded DNA breaks or requiring donor DNA templates. Previously, cytosine base editors (CBEs) containing different deaminases are reported for precise and accurate base editing in plants. However, the knowledge of CBEs in polyploid plants is inadequate and needs further exploration. Results In the present study, we constructed three polycistronic tRNA-gRNA expression cassettes CBEs containing A3A, A3A (Y130F), and rAPOBEC1(R33A) to compare their base editing efficiency in allotetraploid N. benthamiana (n = 4x). We used 14 target sites to compare their editing efficiency using transient transformation in tobacco plants. The sanger sequencing and deep sequencing results showed that A3A-CBE was the most efficient base editor. In addition, the results showed that A3A-CBE provided most comprehensive editing window (C1 ~ C17 could be edited) and had a better editing efficiency under the base background of TC. The target sites (T2 and T6) analysis in transformed N. benthamiana showed that only A3A-CBE can have C-to-T editing events and the editing efficiency of T2 was higher than T6. Additionally, no off-target events were found in transformed N. benthamiana. Conclusions All in all, we conclude that A3A-CBE is the most suitable vector for specific C to T conversion in N. benthamiana. Current findings will provide valuable insights into selecting an appropriate base editor for breeding polyploid plants.

Abstract Background Human-guided crop domestication has lasted for more than 10,000 years. In terms of the domestication and breeding of vegetables, cellulose content in edible tissues is one of the most important traits. Primulina eburnea is a recently developed calcium-rich vegetable with a high soluble and bioavailable calcium content in its leaves. However, the high cellulose content in the leaves hampers the taste, and no research has been reported on the genetic basis of cellulose biosynthesis in this calcium-rich vegetable. Results We identified 36 cellulose biosynthesis-involved genes belonging to eight gene families in the P. eburnea genome. The cellulose accumulated decreasingly throughout leaf development. Nineteen genes were considered core genes in cellulose biosynthesis, which were highly expressed in buds but lowly expressed in mature leaves. In the nitrogen fertilization experiment, exogenous nitrogen decreased the cellulose content in the buds. The expressing pattern of 14 genes were consistent with phenotypic variation in the nitrogen fertilization experiment, and thus they were proposed as cellulose toolbox genes. Conclusions The present study provides a strong basis for the subsequent functional research of cellulose biosynthesis-involved genes in P. eburnea, and provides a reference for breeding and/or engineering this calcium-rich vegetable with decreased leaf cellulose content to improve the taste.

The basal eudicot Epimedium (Barrenwort) exhibits innovative floral morphology in the form of petal spurs filled with nectar and petaloid sepals. The B-class MADS-box genes APETALAS3 (AP3) and PISTILLA (PI) determine sepal and petal identity while the C-class gene AGAMOUS (AG) determines carpel and stamen identity in Arabidopsis. Complex histories of gene duplication resulted in subsequent subfunctionalization or neofunctionalization of paralogs. Here, a total of four B- and two C-class genes were successfully isolated from E. sagittatum. Phylogenetic analysis showed that EsAP3-1, EsAP3-2, and EsAP3-3 are part of the AP3 clade; EsPI is part of the PI group; and EsAG and EsAG11 clustered into the AG and AG11 groups, respectively. Quantitative real-time PCR was utilized to detect the expression patterns of these genes, and all B-class genes except for EsAP3-3 were found to be universally expressed. The transcribed EsAG and EsAG11 genes were confined to reproductive organs. In addition, yeast three and two hybrid assays were used to explore the status of protein complexes. EsAP3-1 was found to have broadly interactive partners, and EsPI can form a heterodimer with EsAP3-1 and EsAP3-2. Transgenic EsAG overexpression in wild-type Arabidopsis confirmed the conserved function determining carpel development.

High temperatures have a significant impact on plant growth and metabolism. In recent years, the fruit industry has faced a serious threat due to high-temperature stress on fruit plants caused by global warming. In the present study, we explored the molecular regulatory mechanisms that contribute to high-temperature tolerance in kiwifruit. A total of 36 Hsf genes were identified in the A. chinensis (Ac) genome, while 41 Hsf genes were found in the A. eriantha (Ae) genome. Phylogenetic analysis revealed the clustering of kiwifruit Hsfs into three distinct groups (groups A, B, and C). Synteny analysis indicated that the expansion of the Hsf gene family in the Ac and Ae genomes was primarily driven by whole genome duplication (WGD). Analysis of the gene expression profiles revealed a close relationship between the expression levels of Hsf genes and various plant tissues and stress treatments throughout fruit ripening. Subcellular localization analysis demonstrated that GFP-AcHsfA2a/AcHsfA7b and AcHsfA2a/AcHsfA7b -GFP were localized in the nucleus, while GFP-AcHsfA2a was also observed in the cytoplasm of Arabidopsis protoplasts. The results of real-time quantitative polymerase chain reaction (RT-qPCR) and dual-luciferase reporter assay revealed that the majority of Hsf genes, especially AcHsfA2a, were expressed under high-temperature conditions. In conclusion, our findings establish a theoretical foundation for analyzing the potential role of Hsfs in high-temperature stress tolerance in kiwifruit. This study also offers valuable information to aid plant breeders in the development of heat-stress-resistant plant materials.

Summary: T cell activation is a key event in adaptive immunity. However, the dynamics and influencing factors of T cell activation remain unclear. Here, we analyzed CD4 T cells that were stimulated with anti-CD3/CD28 under several conditions to explore the factors affecting T cell activation. We found a stimulated T subset (HSPhi T) highly expressing heat shock proteins, which was derived from stimulated naive T. We identified and characterized inert T, a stimulated T cell subset in transitional state from resting T to activated T. Interestingly, resting CXCR4low T responded to stimulation more efficiently than resting CXCR4hi T. Furthermore, stimulation of CD4 T in the presence of CD8 T resulted in more effector T and more homogeneous expressions of CD25, supporting that presence of CD8 T reduces the extreme response of T cells, which can be explained by regulation of CD4 T activation through CD8 T-initiated cytokine signaling and FAS/FASLG signaling.

Attaining high selectivity for CO2 electroreduction in acid is usually difficult due to competing hydrogen evolution. Here, the authors demonstrate efficient CO2 reduction to multicarbon products in strongly acidic medium (pH ≤ 1) on a porous Cu catalyst by combining confinement and cation effects.

Abstract Despite of superior performance of the oxide‐derived copper (OD‐Cu) in producing valuable hydrocarbons during CO2RR, its fabrication process is still ambiguous and complicated. In this work, we develop a simple microwave‐assisted method to synthesize the oxide‐derived Cu nanosheet (OD‐Cu NS) and reveal that the oxidation state of Cu species is controlled by varying the Cu precursor amount. Notably, the simultaneous formation of nano‐sized Cu domains influence the surface roughness of OD‐Cu NS. The partially oxidized Cu surface exhibits a superior faradaic efficiency (FE) of C2+ products up to 72%, along with a partial current density of 55 mA cm−2 in a neutral KHCO3 solution. More importantly, the as‐obtained OD‐Cu NS shows a synergetic effect on dissociating of CO2 molecules by the strong binding energy and promoting of C2+ compounds productivity by the enlarged electrochemical surface area. This work provides a new insight for designing efficient OD‐Cu catalysts toward CO2RR.

Abstract The current kiwifruit industry is mainly based on the cultivars derived from the species Actinidia chinensis (Ac) which may bring risks such as canker disease. Introgression of desired traits from wild relatives is an important method for improving kiwifruit cultivars. Actinidia eriantha (Ae) is a particularly important taxon used for hybridization or introgressive breeding of new kiwifruit cultivars because of its valued species-specific traits. Here, we assembled a chromosome-scale high-quality genome of a Ae sample which was directly collected from its wild populations. Our analysis revealed that 41.3% of the genome consists of repetitive elements, comparable to the percentage in Ac and Ae cultivar “White” genomes. The genomic structural variation, including the presence/absence-variation (PAV) of genes, is distinct between Ae and Ac, despite both sharing the same two kiwifruit-specific whole genome duplication (WGD) events. This suggests that a post-WGD divergence mechanism occurred during their evolution. We further investigated genes involved in ascorbic acid biosynthesis and disease-resistance of Ae, and we found introgressive genome could contribute to the complex relationship between Ae and other representative kiwifruit taxa. Collectively, the Ae genome offers valuable genetic resource to accelerate kiwifruit breeding applications.

IntroductionFlower color is an ideal trait for studying the molecular basis for phenotypic variations in natural populations of species. Epimedium (Berberidaceae) species exhibit a wide range of flower colors resulting from the varied accumulation of anthocyanins and other pigments in their spur-like petals and petaloid sepals.MethodsIn this work, the anthocyanidins of eight different Epimedium species with different floral pigmentation phenotypes were analyzed using HPLC. Twelve genes involved in anthocyanin biosynthesis were cloned and sequenced, and their expression was quantified.ResultsThe expression levels of the catalytic enzyme genes DFR and ANS were significantly decreased in four species showing loss of floral pigmentation. Complementation of EsF3’H and EsDFR in corresponding Arabidopsis mutants together with overexpression of EsF3’5’H in wild type Arabidopsis analysis revealed that these genes were functional at the protein level, based on the accumulation of anthocyanin pigments.DiscussionThese results strongly suggest that transcriptional regulatory changes determine the loss of anthocyanins to be convergent in the floral tissue of Epimedium species.

The differences between the “Tong Guan Li Qiao” acupuncture therapy and the conventional and current other acupuncture methods for poststroke dysphagia are as follows: first, it adheres to the basic idea of “Xing Nao Kai Qiao” acupuncture therapy in selecting and combining acupoints, centers on the brain, and combines the dysphagia symptoms of the mouth, tongue, and throat-related orifices with the root cause of “brain”; second, there are strict and standard requirements in the acupuncture operation, that is, manipulation quantification. In addition to standardized twirling, lifting, and thrusting, the techniques of deep needling on the acupoints in the neck region, blood-letting puncturing at the posterior wall of the pharynx, and the needling sensation of “like a fishbone getting stuck in the throat” are all unique.

Herein, the preparation of AuAgPt alloy yolk‐shell nanostructures with tunable elemental compositions and morphologies by conducting the mild, successive galvanic replacement reaction (GRR) between Au@Ag core‐shell nanocubes and H2PtCl6 is reported. In particular, the resulting products can be featured with well‐defined cubic frames and the distribution of all the three metals over the whole particle, which is enabled by the unique “etching and regrowth” mechanism. Due to the strong absorbance in visible region, the current products exhibit superb performances in two localized surface plasmon resonance (LSPR)‐based applications, photothermal heat conversion, and plasmon‐enhanced catalytic reduction of 4‐nitrophenol (4‐NP). In particular, the optimized photothermal heat conversion efficiency and the apparent rate constant of photocatalytic 4‐NP reduction reach 12.9% and 0.155 min−1, respectively, for the sample AuAgPt‐6 and AuAgPt‐12, respectively. Herein the present study, a feasible strategy for fabrication of plasmonic‐active multimetallic alloy nanocrystals with yolk‐shell structure and cubic frame‐like edges is offered and their promising use in photothermal heat conversion and photocatalysis is validated, which could be extended to other alloys or material combinations for rational design of nanoscale materials with plasmon‐enhanced properties.

Elaeagnus L. is found in wild or grown as ornamental plants and is increasingly regarded as underutilized berry shrubs by breeders. This genus has cosmopolitan distribution with various species widely distributed in China, Europe, the United States, and Canada. Interspecific hybrids, which have been reported several times, have attracted intense interest from plant breeders attempting to develop a fruit crop of Elaeagnus. Orthogonal projections to latent structures discriminant analysis (OPLS-DA) is a powerful statistical modeling tool that provides insights into separations between experimental groups. In this study, the molecular phylogeny of Elaeagnus species was first discussed using the ITS and matK sequences for guiding the construction of a genetic basis pool. A morphological OPLS-DA clustering model based on the genetic divergence was also constructed for the first time, which effectively realized the morphological grouping of Chinese Elaeagnus species. The results showed that a total of 10 wild species widely distributed in China have the potential to develop fruit crops. Particularly, Elaeagnus conferta has the potential to provide a founder species with a large fruit size, while Elaeagnus Gonyanthes has the potential to provide important genetic resources with long pedicel. Elaeagnus lanceolata and Elaeagnus delavayi could be used to domesticate hybrids without spines, and the other five climbing shrubs could be used to develop high-yield crown-type commercial cultivars for automated field management. The top five contributing morphological traits affecting the current clustering model were V9 (flower color), V1 (flowering), V5 (evergreen or deciduous), V3 (leaf size), and V2 (fruiting). Furthermore, the grouping analysis indicated that the V9 was the most important factor affecting morphological clustering. Thereafter, the temporally calibrated phylogeny inferred from the matK sequence was used to reconstruct the origin and evolution of the genus Elaeagnus, and the results inferred an interesting geographic distribution pattern and potential cross-species interactions of Elaeagnus species at low latitudes in China. Our study also highlighted dispersal pattern investigation and genetic background analysis to improve future practices and policies related to species introduction of genetic basis pool.

The STAY-GREEN (SGR) proteins play an important role in chlorophyll (Chl) degradation and are closely related to plant photosynthesis. However, the availability of inadequate studies on SGR motivated us to conduct a comprehensive study on the identification and functional dissection of SGR superfamily members in kiwifruit. Here, we identified five SGR genes for each of the kiwifruit species [Actinidia chinensis (Ac) and Actinidia eriantha (Ae)]. The phylogenetic analysis showed that the kiwifruit SGR superfamily members were divided into two subfamilies the SGR subfamily and the SGRL subfamily. The results of transcriptome data and RT-qPCR showed that the expression of the kiwifruit SGRs was closely related to light and plant developmental stages (regulated by plant growth regulators), which were further supported by the presence of light and the plant hormone-responsive cis-regulatory element in the promoter region. The subcellular localization analysis of the AcSGR2 protein confirmed its localization in the chloroplast. The Fv/Fm, SPAD value, and Chl contents were decreased in overexpressed AcSGR2, but varied in different cultivars of A. chinensis. The sequence analysis showed significant differences within AcSGR2 proteins. Our findings provide valuable insights into the characteristics and evolutionary patterns of SGR genes in kiwifruit, and shall assist kiwifruit breeders to enhance cultivar development.

Abstract Background Goji (Lycium spp., 2n = 24) is a fruit bearing woody plant popular as a superfood for extensive medicinal and nutritional advantages. Fruit size associated attributes are important for evaluating small-fruited goji berry and plant architecture. The domestication traits are regulated quantitatively in crop plants but few studies have attempted on genomic regions corresponding to fruit traits. Results In this study, we established high-resolution map using specific locus amplified fragment (SLAF) sequencing for de novo SNPs detection based on 305 F1 individuals derived from L. chinense and L. barbarum and performed quantitative trait loci (QTL) analysis of fruit size related traits in goji berry. The genetic map contained 3495 SLAF markers on 12 LGs, spanning 1649.03 cM with 0.47 cM average interval. Female and male parents and F1 individuals` sequencing depth was 111.85-fold and 168.72-fold and 35.80-fold, respectively. The phenotype data were collected for 2 successive years (2018–2019); however, two-year mean data were combined in an extra year (1819). Total 117 QTLs were detected corresponding to multiple traits, of which 78 QTLs in 2 individual years and 36 QTLs in extra year. Six Promising QTLs (qFW10–6.1, qFL10–2.1, qLL10–2.1, qLD10–2.1, qLD12–4.1, qLA10–2.1) were discovered influencing fruit weight, fruit length and leaf related attributes covering an interval ranged from 27.32–71.59 cM on LG10 with peak LOD of 10.48 and 14.6% PVE. Three QTLs targeting fruit sweetness (qFS3–1, qFS5–2) and fruit firmness (qFF10–1) were also identified. Strikingly, various traits QTLs were overlapped on LG10, in particular, qFL10–2.1 was co-located with qLL10–2.1, qLD10–2.1 and qLA10–2.1 among stable QTLs, harbored tightly linked markers, while qLL10–1 was one major QTL with 14.21 highest LOD and 19.3% variance. As LG10 harbored important traits QTLs, we might speculate that it could be hotspot region regulating fruit size and plant architectures. Conclusions This report highlights the extremely saturated linkage map using SLAF-seq and novel loci contributing fruit size-related attributes in goji berry. Our results will shed light on domestication traits and further strengthen molecular and genetic underpinnings of goji berry; moreover, these findings would better facilitate to assemble the reference genome, determining potential candidate genes and marker-assisted breeding.

The exploration and use of wild plant resources goes back to our rooted history of human civilization over about 20,000 years ago, before Ancient Mesopotamia in the Valley of the Tigris and Euphrates where barley, lentil and wheat were first domesticated [...]

Light-harvesting chlorophyll a/b-binding (LHC) protein is a superfamily that plays a vital role in photosynthesis. However, the reported knowledge of LHCs in kiwifruit is inadequate and poorly understood. In this study, we identified 42 and 45 LHC genes in Actinidia chinensis (Ac) and A. eriantha (Ae) genomes. Phylogenetic analysis showed that the kiwifruit LHCs of both species were grouped into four subfamilies (Lhc, Lil, PsbS, and FCII). Expression profiles and qRT-PCR results revealed expression levels of LHC genes closely related to the light, temperature fluctuations, color changes during fruit ripening, and kiwifruit responses to Pseudomonas syringae pv. actinidiae (Psa). Subcellular localization analysis showed that AcLhcb1.5/3.1/3.2 were localized in the chloroplast while transient overexpression of AcLhcb3.1/3.2 in tobacco leaves confirmed a significantly increased content of chlorophyll a. Our findings provide evidence of the characters and evolution patterns of kiwifruit LHCs genes in kiwifruit and verify the AcLhcb3.1/3.2 genes controlling the chlorophyll a content.

Akebia trifoliata is a high-value medicinal and edible fruit crop in China, and it has begun to be widely cultivated as a new fruit crop in many areas of China. Its fruits crack longitudinally when fully ripe and should be harvested before fruit cracking. Physicochemical characteristics and nutritional composition of the ripening process are prerequisites to establishing proper harvest maturity windows. In the current study, we have investigated the fruit quality characteristics of two A. trifoliata clonal lines (‘Luqing’ and ‘Luyu’) that were harvested at four time points (S1: 120 days after full bloom (DAFB), S2: 134 DAFB, S3: 148 DAFB, S4: 155 DAFB). An increase in fruit size (fruit weight, fruit length, and fruit diameter) was associated with delayed harvest maturity. The firmness of A. trifoliata fruit exhibited a decreasing trend with delaying the harvest stage. In particular, the firmness decreased sharply from S2 to S3 stage. The TSS, fructose, and glucose content in A. trifoliata fruit continuously increased from the S1 to S4 stage and accumulated sharply from S2 to S3 stage. However, the sucrose and starch content showed an increasing trend from the S1 to S2 stage but declined sharply in the S3 or S4 stage. Ascorbic acid progressively increased with the advancement of A. trifoliata maturity stages, while total phenolics and total flavonoids levels declined with fruit ripening. Considering the results of all quality parameters mentioned above, the A. trifoliata fruit harvested at the S3 maturity stage was the ideal harvest maturity for long-distance transportation and higher consumer acceptability before fruit cracking. Our research reveals the dynamic changes in physicochemical characteristics and nutritional composition during fruit ripening of A. trifoliata. Results in this study reflect the importance of maturity stages for fruit quality and provide basic information for optimal harvest management of A. trifoliata.

Abstract 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.

The role of living collections-based research and discovery has been a prominent feature throughout the history of evolution and advance of botanical science: such research is the core and soul of the botanical gardens. Currently, there are c. 162 Chinese botanical gardens, harboring c. 20,000 species in China. As an example of initiatives to utilize the garden cultivated flora to address plant diversity conservation and germplasm discovery for sustainable agriculture and the bio-industries, the Ex situ Flora of China project aims to catalog and document this mega-diversity of plants that are cultivated in the Chinese botanical gardens. The concept of Ex situ Flora of China is a complete new formulation of species, based on garden cultivated individuals and populations, to obtain better morphological descriptions, provide multi-purpose applicability and a fundamental data service that will support national bio-strategies and bio-industries. It emphasises integrative information, accurately collected from living collections across different Chinese botanical gardens, on biology, phenology, cultivation requirements and uses of plant resources, which are normally not available from traditional Floras based on herbarium specimens. The ex situ flora should provide better information coverage for taxonomy, biological and introduction and collection data and color photos of stems, leaves, flowers, fruits and seed, as well as useful information of cultivation key points and main use of each plant. In general, the Ex situ Flora of China provides more useful information than the traditional Flora Reipublicae Popularis Sinicae. The project of Ex situ Flora of China is planned to be one of the most important initiatives of the plant diversity research platform for sustainable economic and social development in China. Keywords: Botanical garden, Living collections, Ex situ conservation, Botanical sciences, Cultivated flora

Abstract An outbreak of kiwifruit bacterial canker disease caused by Pseudomonas syringae pv. actinidiae (Psa) beginning in 2008 caused disaster to the kiwifruit industry. However the mechanisms of interaction between kiwifruit and Psa are unknown. Long noncoding RNAs (lncRNAs) are known to regulate many biological processes, but comprehensive repertoires of kiwifruit lncRNAs and their effects on the interaction between kiwifruit and Psa are unknown. Here, based on in-depth transcriptomic analysis of four kiwifruit materials at three stages of infection with Psa, we identified 14,845 transcripts from 12,280 loci as putative lncRNAs. Hierarchical clustering analysis of differentially-expressed transcripts reveals that both protein-coding and lncRNA transcripts are expressed species-specifically. Comparing differentially-expressed transcripts from different species, variations in pattern-triggered immunity (PTI) were the main causes of species-specific responses to infection by Psa. Using weighted gene co-expression network analysis, we identified species-specific expressed key lncRNAs which were closely related to plant immune response and signal transduction. Our results illustrate that different kiwifruit species employ multiple different plant immunity layers to fight against Psa infection, which causes distinct responses. We also discovered that lncRNAs might affect kiwifruit responses to Psa infection, indicating that both protein-coding regions and noncoding regions can affect kiwifruit response to Psa infection.

Premise of the Study Euchresta horsfieldii (Fabaceae) is a rare and endangered medicinal plant in Indonesia with restricted distribution. Single‐copy nuclear DNA (scnDNA) markers were developed for this species to facilitate further investigation of genetic diversity and population structure. Methods and Results We performed RNA‐Seq and de novo assembly of the transcriptome. Ten primer sets were developed for E. horsfieldii, all of which also amplified in E. japonica and E. tubulosa. Conclusions These scnDNA markers will be an important resource for the study of genetic diversity and population structure of E. horsfieldii and other species in the genus Euchresta.

Despite substantial advances in genotyping techniques and massively accumulated data over the past half century, a uniform measurement of neutral genetic diversity derived by different molecular markers across a wide taxonomical range has not yet been formulated. We collected genetic diversity data on seed plants derived by AFLP, allozyme, ISSR, RAPD, SSR and nucleotide sequences, converted expected heterozygosity (He) to nucleotide diversity (π), and reassessed the relationship between plant genetic diversity and life history traits or extinction risk. We successfully established a uniform π criterion and developed a comprehensive plant genetic diversity database. The mean population-level and species-level π values across seed plants were 0.00374 (966 taxa, 155 families, 47 orders) and 0.00569 (728 taxa, 130 families, 46 orders), respectively. Significant differences were recovered for breeding system (p < 0.001) at the population level and geographic range (p = 0.023) at the species level. Selfing taxa had significantly lower π values than outcrossing and mixed-mating taxa, whereas narrowly distributed taxa had significantly lower π values than widely distributed taxa. Despite significant differences between the two extreme threat categories (critically endangered and least concern), the genetic diversity reduction on the way to extinction was difficult to detect in early stages.

Diversity in structure and organization is one of the main features of angiosperm mitochondrial genomes (mitogenomes). The ultra-long reads of Oxford Nanopore Technology (ONT) provide an opportunity to obtain a complete mitogenome and investigate the structural variation in unprecedented detail. In this study, we compared mitogenome assembly methods using Illumina and/or ONT sequencing data and obtained the complete mitogenome (208 kb) of Chrysanthemum nankingense based on the hybrid assembly method. The mitogenome encoded 19 transfer RNA genes, three ribosomal RNA genes, and 34 protein-coding genes with 21 group II introns disrupting eight intron-contained genes. A total of seven medium repeats were related to homologous recombination at different frequencies as supported by the long ONT reads. Subsequently, we investigated the variations in gene content and constitution of 28 near-complete mitogenomes from Asteraceae. A total of six protein-coding genes were missing in all Asteraceae mitogenomes, while four other genes were not detected in some lineages. The core fragments (~88 kb) of the Asteraceae mitogenomes had a higher GC content (~46.7%) than the variable and specific fragments. The phylogenetic topology based on the core fragments of the Asteraceae mitogenomes was highly consistent with the topologies obtained from the corresponding plastid datasets. Our results highlighted the advantages of the complete assembly of the C. nankingense mitogenome and the investigation of its structural variation based on ONT sequencing data. Moreover, the method based on local collinear blocks of the mitogenomes could achieve the alignment of highly rearrangeable and variable plant mitogenomes as well as construct a robust phylogenetic topology.

The Crabs Claw (CRC) YABBY gene is required for regulating carpel development in angiosperms and has played an important role in nectary evolution during core eudicot speciation. The function or expression of CRC-like genes has been explored in two basal eudicots, Eschscholzia californica and Aquilegia formosa. To further investigate the function of CRC orthologous genes related to evolution of carpel and nectary development in basal eudicots, a CRC ortholog, EsCRC, was isolated and characterized from Epimedium sagittatum (Sieb. and Zucc.) Maxim. A phylogenetic analysis of EsCRC and previously identified CRC-like genes placed EsCRC within the basal eudicot lineage. Gene expression results suggest that EsCRC is involved in the development of sepals and carpels, but not nectaries. Phenotypic complementation of the Arabidopsis mutant crc-1 was achieved by constitutive expression of EsCRC. In addition, over-expression of EsCRC in Arabidopsis and tobacco gave rise to abaxially curled leaves. Transgenic results together with the gene expression analysis suggest that EsCRC may maintain a conserved function in carpel development and also play a novel role related to sepal formation. Absence of EsCRC and ElCRC expression in nectaries further indicates that nectary development in non-core eudicots is unrelated to expression of CRC-like genes.

Nothotsuga longibracteata, a relic and endangered conifer species endemic to subtropical China, was studied for examining the spatial-temporal population genetic variation and structure to understand the historical biogeographical processes underlying the present geographical distribution. Ten populations were sampled over the entire natural range of the species for spatial analysis, while three key populations with large population sizes and varied age structure were selected for temporal analyses using both nuclear microsatellites (nSSR) and chloroplast microsatellites (cpSSR). A recent bottleneck was detected in the natural populations of N. longibracteata. The spatial genetic analysis showed significant population genetic differentiation across its total geographical range. Notwithstanding, the temporal genetic analysis revealed that the level of genetic diversity between different age class subpopulations remained constant over time. Eleven refugia of the Last Glacial Maximum were identified, which deserve particular attention for conservation management.

Herbal Epimedium species have been widely in Traditional Chinese Medicine for sexual enhancement, immunity improvement, anticancer and anti-aging treatment, with flavonoids and polysaccharides being the major active components. However, exhaustive depletion of wild sources warrants germplasm evaluation and quality resource exploration. A preliminarily analysis had previously indicated that a specific local geographic accession of Epimedium sagittatum found in Luotian (LT) county of Hubei Province (China) had a much higher content of total flavonoids and polysaccharides. In this study, we further investigated the medicinal component variation in the LT type under different light intensities and in different regions by the common-garden experiment. The results indicated a light intensity range of 40–160 μmol/m2/s was the most suitable for the synthesis and accumulation of total flavonoids, while polysaccharide accumulation was negatively correlated with the light intensity. Icariin was the component displaying the highest content among flavonoids, and the content of major flavonoid bioactive components was relatively stable in the third year after cultivation. There was significant correlation between the major flavonol glycoside constituents and the geographic location, and Central China followed by Northern China were the highly suitable regions for cultivation of LT type E. sagittatum. The results revealed that there was a functional balance between flavonoids and polysaccharides at different developmental stages, and the best harvesting stage should consider the primary contents of interest. This study provides important information on the exploration of quality resources, further breeding approaches and cultivation practices of E. sagittatum, and thus the important insights to enhance our understanding of quality control of traditional medicinal plants.

Actinidia chinensis is an important economic plant belonging to the basal lineage of the asterids. Availability of a complete Actinidia chloroplast genome sequence is crucial to understanding phylogenetic relationships among major lineages of angiosperms and facilitates kiwifruit genetic improvement. We report here the complete nucleotide sequences of the chloroplast genomes for Actinidia chinensis and A. chinensis var deliciosa obtained through de novo assembly of Illumina paired-end reads produced by total DNA sequencing. The total genome size ranges from 155,446 to 157,557 bp, with an inverted repeat (IR) of 24,013 to 24,391 bp, a large single copy region (LSC) of 87,984 to 88,337 bp and a small single copy region (SSC) of 20,332 to 20,336 bp. The genome encodes 113 different genes, including 79 unique protein-coding genes, 30 tRNA genes and 4 ribosomal RNA genes, with 16 duplicated in the inverted repeats, and a tRNA gene (trnfM-CAU) duplicated once in the LSC region. Comparisons of IR boundaries among four asterid species showed that IR/LSC borders were extended into the 5' portion of the psbA gene and IR contraction occurred in Actinidia. The clap gene has been lost from the chloroplast genome in Actinidia, and may have been transferred to the nucleus during chloroplast evolution. Twenty-seven polymorphic simple sequence repeat (SSR) loci were identified in the Actinidia chloroplast genome. Maximum parsimony analyses of a 72-gene, 16 taxa angiosperm dataset strongly support the placement of Actinidiaceae in Ericales within the basal asterids.

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.

Polyploidy and hybridization are thought to have significant impacts on both the evolution and diversification of the genus Actinidia, but the structure and patterns of morphology and molecular diversity relating to ploidy variation of wild Actinidia plants remain much less understood. Here, we examine the distribution of morphological variation and ploidy levels along geographic and environmental variables of a large mixed-ploidy population of the A. chinensis species complex. We then characterize the extent of both genetic and epigenetic diversity and differentiation exhibited between individuals of different ploidy levels. Our results showed that while there are three ploidy levels in this population, hexaploids were constituted the majority (70.3%). Individuals with different ploidy levels were microgeographically structured in relation to elevation and extent of niche disturbance. The morphological characters examined revealed clear difference between diploids and hexaploids, however tetraploids exhibited intermediate forms. Both genetic and epigenetic diversity were high but the differentiation among cytotypes was weak, suggesting extensive gene flow and/or shared ancestral variation occurred in this population even across ploidy levels. Epigenetic variation was clearly correlated with changes in altitudes, a trend of continuous genetic variation and gradual increase of epigenomic heterogeneities of individuals was also observed. Our results show that complex interactions between the locally microgeographical environment, ploidy and gene flow impact A. chinensis genetic and epigenetic variation. We posit that an increase in ploidy does not broaden the species habitat range, but rather permits A. chinensis adaptation to specific niches.

Limestone Karst areas possess high levels of biodiversity and endemism. Primulina is a typical component of Karst endemic floras. The high species richness and wide distribution in various Karst microenvironments make the genus an idea model for studying speciation and local adaptation. In this study, we obtained 10 full-length sequences of the phytochrome PHYE from available transcriptome resources of Primulina and amplified partial sequences of PHYE from the genomic DNA of 74 Primulina species. Then, we used maximum-likelihood approaches to explore molecular evolution of PHYE in this Karst cave plant. The results showed that PHYE was dominated by purifying selection in both data sets, and two sites were identified as potentially under positive selection. Furthermore, the ω ratio varies greatly among different functional domains of PHYE and among different species lineages. These results suggest that potential positive selection in PHYE might have played an important role in the adaption of Primulina to heterogeneous light environments in Karst regions, and different species lineages might have been subjected to different selective pressures.