Genome sequence and population genomics provide insights into chromosomal evolution and phytochemical innovation of Hippophae rhamnoides

Integrated analysis reveals functional genes and regulators associated with fatty acid biosynthesis in Elaeagnus mollis Diels

Elaeagnus mollis Diels. is a newly developed oil plant in China, which harbors high fatty acid (FA) in its kernel oil. Functional genes and regulators associated with FA biosynthesis are widely characterized in oil crops, but it still remains elusive in E. mollis. In this study, the FA and carbohydrate content, functional genes and metabolites involved in FA biosynthesis, and the potential regulator were investigated. Results demonstrated that FA and carbohydrate contents fluctuated accompanied with kernel development and reached relatively stable status at mature stage, indicating lipid and carbohydrate metabolism orchestrated for FA biosynthesis. Unsaturated FA (85.80-465.86 mg/g) occupied ∼90% of total FA (97.97-507.07 mg/g), oleic acid (OA) and linoleic acid (LA) were two major components. We identified 436 and 2735 genes involved in lipid and carbohydrate metabolism, while 178 genes directly in FA biosynthesis. Weighted gene co-expression analysis elucidated the turquoise module illustrated significant association with OA and LA content, respectively. Co-expression analysis revealed EmWRI1 was a vital regulator in E. mollis FA biosynthesis, which was proved by transgenic of EmWRI1 in Arabidopsis. Furthermore, RNA-Seq and yeast one-hybrid assay revealed the direct interaction between EmWRI1 and proEmBCCP2. This study deciphers the FA biosynthetic regulatory mechanism in E. mollis and sets a solid foundation for genetic breeding of this newly developed oil crops.

Characterization of DnaJ gene family in Castanea mollissima and functional analysis of CmDnaJ27 under cold and heat stresses

BACKGROUND

The DnaJ gene family plays crucial roles in the plant abiotic stress response. Although the DnaJ gene family has been extensively characterized in various plants, its distribution in the Castanea mollissima genome is still unclear.

RESULTS

In this study, 78 CmDnaJ genes were identified and characterized in the C. mollissima genome, divided into three subfamilies based on the phylogeny analysis. The abundance of cis-acting elements related to temperature stress in the promoter regions of the CmDnaJ genes suggested a close relationship between this family and temperature stress response. Dispersed duplication was identified as the main driving force behind the expansion of the CmDnaJ family. RNA-seq data from 192 runs across nine projects were analyzed, revealing the potential roles of CmDnaJ genes in the growth, development, and environmental stress response of C. mollissima. Weighted gene co-expression network analysis showed that CmDnaJ27 and CmDnaJ34 were located in the red module and significantly correlated with temperature stimulus-response. RT-qPCR experiments and subcellular localization validated the expression levels and specific locations of CmDnaJ genes under cold and heat stresses. Overexpression of CmDnaJ27 in Nicotiana tabacum significantly reduces its tolerance to cold and heat stresses.

CONCLUSIONS

This study provides insights into the important roles of the DnaJ gene family in C. mollissima growth, development, and response to environmental stress, and provides reference to the research of CmDnaJs in cold and heat stresses response.

Sea buckthorn flavonoids: Purification, identification, and in vitro anti-inflammatory effects

As the first step of resource utilization, the extraction and separation of active ingredients play an important role in the evaluation and application of their activity. In this study, a macroporous resin purification process was optimized to obtain high-purity sea buckthorn flavonoids (SBF). The AB-8 resin exhibited optimal adsorption and desorption properties, with adsorption and desorption rates of 75.25 % and 84.78 %, respectively. Under optimal purification conditions, the purity of the flavonoid extract was enhanced from 17.17 ± 0.19 % to 63.2 ± 0.16 %. Kinetic and thermodynamic analyses demonstrated that the purification of SBF on AB-8 resin conformed to the pseudo-secondary kinetic model and the Langmuir adsorption isotherm model. The major components of the SBF were taxifolin, isoquercitrin, narcissoside, and quercetin. The SBF not only inhibited lipopolysaccharide-induced nitric oxide production but also exerted significant anti-inflammatory effects, suppressing the expression of proteins such as nitric oxide synthase, tumor necrosis factor, interleukin 6, and interleukin 1β and inhibiting apoptosis. Therefore, the purified SBF demonstrated improved anti-inflammatory activity, which can be applied in the development of drugs and functional foods.

Genome-wide identification, phylogeny, and expression analysis of PEBP gene family in Castanea mollissima

The phosphatidylethanolamine binding protein (PEBP) family plays an important part in growth and development of plants. Castanea mollissima is an economic plant with significant financial value and has become an important food source in the Northern Hemisphere. However, the PEBP genes in C. mollissima have not been studied yet. In this study, six PEBP genes (CmPEBP1 ∼ CmPEBP6) were identified in C. mollissima and comprehensively analyzed in terms of physicochemical properties, phylogeny, gene structures, cis-regulatory elements (CREs), transcription factor interaction, and expression profiles. The six CmPEBP genes were categorized into three subfamilies according to the phylogeny analysis, and all of them share extremely similar gene and protein structures. A total of 136 CREs were identified in the promoter regions of the CmPEBP genes, mainly related to growth and development, environmental stress, hormone response, and light response. Comparative genomic analysis indicated that the expansion of the CmPEBP genes was mainly driven by dispersed duplication, and the CmPEBP3/CmPEBP5 derived from eudicot common hexaploidization (ECH) events retained orthologous genes in all species studied. A total of 259 transcription factors (TFs) belonging to 39 families were predicted to be regulators of CmPEBP genes, and CmPEBP4 was predicted to interact with the most TFs. The RNA-seq data analysis indicated the potential roles of CmPEBP genes in the ovule, bud, and flower development of C. mollissima, as well as in the response to temperature stress, drought stress, and the gall wasp Dryocosmus kuriphilus (GWDK) infestation. Additionally, the expression of CmPEBP genes in C. mollissima seed kernel development and their response to temperature stress were confirmed by RT-qPCR assays. This study gives references and directions for future in-depth studies of PEBP genes.

The chromosome-scale genome of black wolfberry (Lycium ruthenicum) provides useful genomic resources for identifying genes related to anthocyanin biosynthesis and disease resistance

The black wolfberry (L ycium ruthenicum; 2n = 2x = 24) is an important medicinal plant with ecological and economic value. Its fruits have numerous beneficial pharmacological activities, especially those of anthocyanins, polysaccharides, and alkaloids, and have high nutritional value. However, the lack of available genomic resources for this species has hindered research on its medicinal and evolutionary mechanisms. In this study, we developed the telomere-to-telomere (T2T) nearly gapless genome of L. ruthenicum (2.26 Gb) by integrating PacBio HiFi, Nanopore Ultra-Long, and Hi-C technologies. The assembled genome comprised 12 chromosomes with 37,149 protein-coding genes functionally annotated. Approximately 80% of the repetitive sequences were identified, of which long terminal repeats (LTRs) were the most abundant, accounting for 73.01%. The abundance of LTRs might be the main reason for the larger genome of this species compared to that of other Lycium species. The species-specific genes of L. ruthenicum were related to defense mechanisms, salt tolerance, drought resistance, and oxidative stress, further demonstrating their superior adaptability to arid environments. Based on the assembled genome and fruit transcriptome data, we further constructed an anthocyanin biosynthesis pathway and identified 19 candidate structural genes and seven transcription factors that regulate anthocyanin biosynthesis in the fruit developmental stage of L. ruthenicum, most of which were highly expressed at a later stage in fruit development. Furthermore, 154 potential disease resistance-related nucleotide-binding genes have been identified in the L. ruthenicum genome. The whole-genome and proximal, dispersed, and tandem duplication genes in the L. ruthenicum genome enriched the number of genes involved in anthocyanin synthesis and resistance-related pathways. These results provide an important genetic basis for understanding genome evolution and biosynthesis of pharmacologically active components in the Lycium genus.

A chromosome-scale genome of Hippophae neurocarpa provides new insights into serotonin biosynthesis and chlorophyll-derived brown fruit coloration

Sea buckthorn (Hippophae neurocarpa), a plant with both medicinal and edible properties, exhibits high content of serotonin with a unique brown color. Here, we assemble the 1002.54 Mb genome sequence of H. neurocarpa and find that it has evolved from two sequential polyploidizations with four sub-genomes. Based on in vitro enzyme activity and transient overexpression experiments, we confirm that the expression of both HnT5H1 and HnT5H2 genes from tandem duplication contributes to high accumulation of serotonin in sea buckthorn. Furthermore, we verify that the HnGLK1 gene plays a crucial role in continuous chlorophyll accumulation, driving the brown color formation of H. neurocarpa fruit. Collectively, the high-quality genome of H. neurocarpa offers valuable insights into the mechanisms underlying serotonin biosynthesis and abnormal coloration and serves as a valuable resource for further functional genomic studies and molecular breeding efforts in sea buckthorn.

Genome-wide identification, phylogeny, evolutionary expansion, and expression analyses of ABC gene family in Castanea mollissima under temperature stress

The ATP-binding cassette (ABC) gene family comprises some of the most critical transporter proteins in plants, playing vital roles in maintaining cellular homeostasis and adapting to environmental changes. While ABC transporters have been extensively characterized in various plant species, their profile in C. mollissima remains less understood. In this study, 164 ABC genes were identified and characterized within the C. mollissima genome, and subsequently classified into eight subfamilies. Collinear analysis suggested that dispersed duplication was the primary mechanism driving the expansion of the CmABC gene family. The study also examined morphological and physiological changes in C. mollissima under temperature stress, highlighting significant decreases in photosynthetic indicators and SOD enzyme activity, while other indicators varied. Transcriptome analysis revealed distinct expression patterns of various CmABC genes under temperature stress, identifying CmABCG29c and CmABCB11e as key candidates for responding to temperature stress. This was based on their expression patterns, correlation with physiological indicators, and WGCNA analysis. The expression levels of CmABC genes measured in RT-qPCR experiments were consistent with those observed in RNA-seq analysis. This research provides a theoretical foundation for understanding the physiological and gene expression responses of C. mollissima to temperature stress.

Identification and Analysis of KAS II, FAT, SAD, and FAD Gene Families in Hippophae rhamnoides

KAS II (β-ketoacyl-acyl carrier protein (ACP) synthases II), FAT (fatty acid thioesterases), SAD (stearoyl-ACP desaturase), and FAD (fatty acid desaturases) are the vital gene families involved in fatty acid (FA) synthesis in Hippophae rhamnoides L. However, information on the number and location of these genes and which ones are key to the formation of FAs in fruit seeds and pulp was not complete. Our study aimed to solve this issue using the available genomic sequences and transcriptome data that we obtained. We compared the protein sequences of sea buckthorn with those of Arabidopsis thaliana and checked for the presence of conserved domains. As a result of structure and phylogenetic analyses, 4 KAS II, 8 FAT, 9 SAD, and 12 FAD genes were identified in the H. rhamnoides genome, which were classified into subfamilies: KAS II, FATA, FATB, FAD2, FAD3, FAD6, and FAD7/8. To analyze the expression of the identified genes, we sequenced the transcriptomes of sea buckthorn seeds and fruit pulp at four development stages, as well as leaves. The analysis revealed representatives of the FAT, SAD, and FAD families with high tissue-and stage-specific expression in seeds and pulp. These genes are likely to play a key role in the biosynthesis of sea buckthorn FAs. The obtained results may help to establish the precise biosynthesis mechanisms of FAs and will promote the breeding of new sea buckthorn varieties that have oil with a defined FA composition.

The chromosome-level Elaeagnus mollis genome and transcriptomes provide insights into genome evolution, glycerolipid and vitamin E biosynthesis in seeds

Elaeagnus mollis, which has seeds with high lipid and vitamin E contents, is a valuable woody oil plant with potential for utilization. Currently, the biosynthesis and regulation mechanism of glycerolipids and vitamin E are still unknown in E. mollis. Here, we present the chromosome-level reference genome of E. mollis (scaffold N50: ~40.66Mbp, genome size: ~591.48Mbp) by integrating short-read, long-read, and Hi-C sequencing platforms. A total of 36,796 protein-coding sequences, mainly located on 14 proto-chromosomes, were predicted. Additionally, two whole genome duplication (WGD) events were suggested to have occurred ~54.07 and ~35.06 million years ago (MYA), with Elaeagnaceae plants probably experiencing both WGD events. Furthermore, the long terminal retrotransposons in E. mollis were active ~0.23MYA, and one of them was inferred to insert into coding sequence of the negative regulatory lipid synthesis gene, EMF2. Through transcriptomic and metabonomic analysis, key genes contributing to the high lipid and vitamin E levels of E. mollis seeds were identified, while miRNA regulation was also considered. This comprehensive work on the E. mollis genome not only provides a solid theoretical foundation and experimental basis for the efficient utilization of seed lipids and vitamin E, but also contributes to the exploration of new genetic resources.

Therapeutic effect of targeted antioxidant natural products

The exploration of targeted therapy has proven to be a highly promising avenue in the realm of drug development research. The human body generates a substantial amount of free radicals during metabolic processes, and if not promptly eliminated, these free radicals can lead to oxidative stress, disrupting homeostasis and potentially contributing to chronic diseases and cancers. Before the development of contemporary medicine with synthetic pharmaceuticals and antioxidants, there was a long-standing practice of employing raw, natural ingredients to cure a variety of illnesses. This practice persisted even after the active antioxidant molecules were known. The ability of natural antioxidants to neutralise excess free radicals in the human body and so prevent and cure a wide range of illnesses. The term "natural antioxidant" refers to compounds derived from plants or other living organisms that have the ability to control the production of free radicals, scavenge them, stop free radical-mediated chain reactions, and prevent lipid peroxidation. These compounds have a strong potential to inhibit oxidative stress. Phytochemicals (antioxidants) derived from plants, such as polyphenols, carotenoids, vitamins, and others, are central to the discussion of natural antioxidants. Not only may these chemicals increase endogenous antioxidant defenses, affect communication cascades, and control gene expression, but they have also shown strong free radical scavenging properties. This study comprehensively summarizes the primary classes of natural antioxidants found in different plant and animal source that contribute to the prevention and treatment of diseases. Additionally, it outlines the research progress and outlines future development prospects. These discoveries not only establish a theoretical groundwork for pharmacological development but also present inventive ideas for addressing challenges in medical treatment.

Chromosome-level genome assembly of Hippophae tibetana provides insights into high-altitude adaptation and flavonoid biosynthesis

BACKGROUND

As an endemic shrub of the Qinghai-Tibetan Plateau (QTP), the distribution of Hippophae tibetana Schlecht. ranges between 2800 and 5200 m above sea level. As the most basal branch of the Hippophae genus, H. tibetana has an extensive evolutionary history. The H. tibetana is a valuable tree for studying the ecological evolution of species under extreme conditions.

RESULTS

Here, we generated a high-quality chromosome-level genome of H. tibetana. The total size of the assembly genome is 917 Mb. The phylogenomic analysis of 1064 single-copy genes showed a divergence between 3.4 and 12.8 Mya for H. tibetana. Multiple gene families associated with DNA repair and disease resistance were significantly expanded in H. tibetana. We also identified many genes related to DNA repair with signs of positive selection. These results showed expansion and positive selection likely play important roles in H. tibetana's adaptation to comprehensive extreme environments in the QTP. A comprehensive genomic and transcriptomic analysis identified 49 genes involved in the flavonoid biosynthesis pathway in H. tibetana. We generated transgenic sea buckthorn hairy root producing high levels of flavonoid.

CONCLUSIONS

Taken together, this H. tibetana high-quality genome provides insights into the plant adaptation mechanisms of plant under extreme environments and lay foundation for the functional genomic research and molecular breeding of H. tibetana.

High Frankia abundance and low diversity of microbial community are associated with nodulation specificity and stability of sea buckthorn root nodule

Introduction

Actinorhizal symbioses are gaining attention due to the importance of symbiotic nitrogen fixation in sustainable agriculture. Sea buckthorn (Hippophae L.) is an important actinorhizal plant, yet research on the microbial community and nitrogen cycling in its nodules is limited. In addition, the influence of environmental differences on the microbial community of sea buckthorn nodules and whether there is a single nitrogen-fixing actinomycete species in the nodules are still unknown.

Methods

We investigated the diversity, community composition, network associations and nitrogen cycling pathways of the microbial communities in the root nodule (RN), nodule surface soil (NS), and bulk soil (BS) of Mongolian sea buckthorn distributed under three distinct ecological conditions in northern China using 16S rRNA gene and metagenomic sequencing. Combined with the data of environmental factors, the effects of environmental differences on different sample types were analyzed.

Results

The results showed that plants exerted a clear selective filtering effect on microbiota, resulting in a significant reduction in microbial community diversity and network complexity from BS to NS to RN. Proteobacteria was the most abundant phylum in the microbiomes of BS and NS. While RN was primarily dominated by Actinobacteria, with Frankia sp. EAN1pec serving as the most dominant species. Correlation analysis indicated that the host determined the microbial community composition in RN, independent of the ecological and geographical environmental changes of the sea buckthorn plantations. Nitrogen cycle pathway analyses showed that RN microbial community primarily functions in nitrogen fixation, and Frankia sp. EAN1pec was a major contributor to nitrogen fixation genes in RN.

Discussion

This study provides valuable insights into the effects of eco-geographical environment on the microbial communities of sea buckthorn RN. These findings further prove that the nodulation specificity and stability of sea buckthorn root and Frankia sp. EAN1pec may be the result of their long-term co-evolution.

Genome-wide identification, evolution, and expression analysis of the NAC gene family in chestnut (Castanea mollissima)

The NAC gene family is one of the most important transcription factor families specific to plants, responsible for regulating many biological processes, including development, stress response, and signal transduction. However, it has not yet been characterized in chestnut, an important nut tree species. Here, we identified 115 CmNAC genes in the chestnut genome, which were divided into 16 subgroups based on the phylogenetic analysis. Numerous cis-acting elements related to auxin, gibberellin, and abscisic acid were identified in the promoter region of CmNACs, suggesting that they play an important role in the growth and development of chestnut. The results of the collinear analysis indicated that dispersed duplication and whole-genome-duplication were the main drivers of CmNAC gene expansion. RNA-seq data of developmental stages of chestnut nut, bud, and ovule revealed the expression patterns of CmNAC genes. Additionally, qRT-PCR experiments were used to verify the expression levels of some CmNAC genes. The comprehensive analysis of the above results revealed that some CmNAC members may be related to chestnut bud and nut development, as well as ovule fertility. The systematic analysis of this study will help to increase understanding of the potential functions of the CmNAC genes in chestnut growth and development.

The Systematics, Reproductive Biology, Biochemistry, and Breeding of Sea Buckthorn-A Review

Both the fruit flesh and seeds of sea buckthorn have multiple uses for medicinal and culinary purposes, including the valuable market for supplementary health foods. Bioactive compounds, such as essential amino acids, vitamins B, C, and E, carotenoids, polyphenols, ursolic acid, unsaturated fatty acids, and other active substances, are now being analyzed in detail for their medicinal properties. Domestication with commercial orchards and processing plants is undertaken in many countries, but there is a large need for improved plant material with high yield, tolerance to environmental stress, diseases, and pests, suitability for efficient harvesting methods, and high contents of compounds that have medicinal and/or culinary values. Applied breeding is based mainly on directed crosses between different subspecies of Hippophae rhamnoides. DNA markers have been applied to analyses of systematics and population genetics as well as for the discrimination of cultivars, but very few DNA markers have as yet been developed for use in selection and breeding. Several key genes in important metabolic pathways have, however, been identified, and four genomes have recently been sequenced.

Sea Buckthorn Pretreatment, Drying, and Processing of High-Quality Products: Current Status and Trends

Sea buckthorn is a kind of berry rich in nutritional and industrial value. Due to its thin skin, juicy pulp, and short shelf life, it is usually preserved via freezing methods or directly processed into sea buckthorn puree after harvest. It can also be dried and processed into products such as dried sea buckthorn fruit, freeze-dried sea buckthorn powder, and sea buckthorn oil. This review, therefore, provides an overview of the existing state of drying and high-quality processing of sea buckthorn. The effects of different pretreatment and drying techniques on the drying characteristics and quality of sea buckthorn and the existing problems of superior-quality processing of sea buckthorn products are summarised. The development trend of sea buckthorn drying methods and the ways to achieve high-quality processing of sea buckthorn products are indicated. These ways are mainly related to the following: (1) The application of combined pretreatment and drying techniques to find a balance between economy, ecology, and efficiency; (2) Introducing new online measurement and control technology into drying equipment; (3) Optimising the existing process to form a complete sea buckthorn industrial chain and develop the sea buckthorn deep-processing industry.

Complete chloroplast genome assembly and phylogenetic analysis of blackcurrant (Ribes nigrum), red and white currant (Ribes rubrum), and gooseberry (Ribes uva-crispa) provide new insights into the phylogeny of Grossulariaceae

Background

Blackcurrant (Ribes nigrum), red currant (R. rubrum), white currant (R. rubrum), and gooseberry (R. uva-crispa) belong to Grossulariaceae and are popular small-berry crops worldwide. The lack of genomic data has severely limited their systematic classification and molecular breeding.

Methods

The complete chloroplast (cp) genomes of these four taxa were assembled for the first time using MGI-DNBSEQ reads, and their genome structures, repeat elements and protein-coding genes were annotated. By genomic comparison of the present four and previous released five Ribes cp genomes, the genomic variations were identified. By phylogenetic analysis based on maximum-likelihood and Bayesian methods, the phylogeny of Grossulariaceae and the infrageneric relationships of the Ribes were revealed.

Results

The four cp genomes have lengths ranging from 157,450 to 157,802 bp and 131 shared genes. A total of 3,322 SNPs and 485 Indels were identified from the nine released Ribes cp genomes. Red currant and white currant have 100% identical cp genomes partially supporting the hypothesis that white currant (R. rubrum) is a fruit color variant of red currant (R. rubrum). The most polymorphic genic and intergenic region is ycf1 and trnT-psbD, respectively. The phylogenetic analysis demonstrated the monophyly of Grossulariaceae in Saxifragales and the paraphyletic relationship between Saxifragaceae and Grossulariaceae. Notably, the Grossularia subgenus is well nested within the Ribes subgenus and shows a paraphyletic relationship with the co-ancestor of Calobotrya and Coreosma sections, which challenges the dichotomous subclassification of the Ribes genus based on morphology (subgenus Ribes and subgenus Grossularia). These data, results, and insights lay a foundation for the phylogenetic research and breeding of Ribes species.

Unlocking secrets of nature's chemists: Potential of CRISPR/Cas-based tools in plant metabolic engineering for customized nutraceutical and medicinal profiles

Plant species have evolved diverse metabolic pathways to effectively respond to internal and external signals throughout their life cycle, allowing adaptation to their sessile and phototropic nature. These pathways selectively activate specific metabolic processes, producing plant secondary metabolites (PSMs) governed by genetic and environmental factors. Humans have utilized PSM-enriched plant sources for millennia in medicine and nutraceuticals. Recent technological advances have significantly contributed to discovering metabolic pathways and related genes involved in the biosynthesis of specific PSM in different food crops and medicinal plants. Consequently, there is a growing demand for plant materials rich in nutrients and bioactive compounds, marketed as "superfoods". To meet the industrial demand for superfoods and therapeutic PSMs, modern methods such as system biology, omics, synthetic biology, and genome editing (GE) play a crucial role in identifying the molecular players, limiting steps, and regulatory circuitry involved in PSM production. Among these methods, clustered regularly interspaced short palindromic repeats-CRISPR associated protein (CRISPR/Cas) is the most widely used system for plant GE due to its simple design, flexibility, precision, and multiplexing capabilities. Utilizing the CRISPR-based toolbox for metabolic engineering (ME) offers an ideal solution for developing plants with tailored preventive (nutraceuticals) and curative (therapeutic) metabolic profiles in an ecofriendly way. This review discusses recent advances in understanding the multifactorial regulation of metabolic pathways, the application of CRISPR-based tools for plant ME, and the potential research areas for enhancing plant metabolic profiles.

Genome-wide identification, evolution and expression profiles analysis of bHLH gene family in Castanea mollissima

The basic helix-loop-helix (bHLH) transcription factors (TFs) gene family is an important gene family in plants, and participates in regulation of plant apical meristem growth, metabolic regulation and stress resistance. However, its characteristics and potential functions have not been studied in chestnut (Castanea mollissima), an important nut with high ecological and economic value. In the present study, 94 CmbHLHs were identified in chestnut genome, of which 88 were unevenly distributed on chromosomes, and other six were located on five unanchored scaffolds. Almost all CmbHLH proteins were predicted in the nucleus, and subcellular localization demonstrated the correctness of the above predictions. Based on the phylogenetic analysis, all of the CmbHLH genes were divided into 19 subgroups with distinct features. Abundant cis-acting regulatory elements related to endosperm expression, meristem expression, and responses to gibberellin (GA) and auxin were identified in the upstream sequences of CmbHLH genes. This indicates that these genes may have potential functions in the morphogenesis of chestnut. Comparative genome analysis showed that dispersed duplication was the main driving force for the expansion of the CmbHLH gene family inferred to have evolved through purifying selection. Transcriptome analysis and qRT-PCR experiments showed that the expression patterns of CmbHLHs were different in different chestnut tissues, and revealed some members may have potential functions in chestnut buds, nuts, fertile/abortive ovules development. The results from this study will be helpful to understand the characteristics and potential functions of the bHLH gene family in chestnut.

The Study on Sea Buckthorn (Genus Hippophae L.) Fruit Reveals Cell Division and Cell Expansion to Promote Morphogenesis

Due to its unique flavor and high antioxidant content, the sea buckthorn (genus Hippophae L.) fruit is increasingly favored by consumers. Developing from the perianth tube, the sea buckthorn fruit varies greatly among species in both size and shape. However, the cellular regulation mechanism of sea buckthorn fruit morphogenesis remains unclear. This study presents the growth and development patterns, morphological changes, and cytological observations of the fruits of three Hippophae species (H. rhamnoides ssp. sinensis, H. neurocarpa, and H. goniocarpa). The fruits were monitored every 10-30 days after anthesis (DAA) for six periods in their natural population on the eastern margin of the Qinghai-Tibet Plateau in China. The results showed that the fruits of H. rhamnoides ssp. sinensis and H. goniocarpa grew in a sigmoid mode, while H. neurocarpa grew in an exponential mode under the complex regulation of cell division and cell expansion. In addition, cellular observations showed that the mesocarp cells of H. rhamnoides ssp. sinensis and H. goniocarpa were larger in the area with prolonged cell expansion activity, while H. neurocarpa had a higher cell division rate. Elongation and proliferation of the mesocarp cells were found to be essential factors affecting the formation of fruit morphology. Finally, we established a preliminary cellular scenario for fruit morphogenesis in the three species of sea buckthorn. Fruit development could be divided into a cell division phase and a cell expansion phase with an overlap between 10 and 30 DAA. In particular, the two phases in H. neurocarpa showed an additional overlap between 40 and 80 DAA. The description of the sea buckthorn fruit's transformation and its temporal order may provide a theoretical basis to explore the growth mechanism of fruits and regulate their size through certain cultivation techniques.

Genome-wide identification, evolution and transcriptome analysis of GRAS gene family in Chinese chestnut (Castanea mollissima)

GRAS transcription factors play an important role in regulating various biological processes in plant growth and development. However, their characterization and potential function are still vague in Chinese chestnut (Castanea mollissima), an important nut with rich nutrition and high economic value. In this study, 48 CmGRAS genes were identified in Chinese chestnut genome and phylogenetic analysis divided CmGRAS genes into nine subfamilies, and each of them has distinct conserved structure domain and features. Genomic organization revealed that CmGRAS tend to have a representative GRAS domain and fewer introns. Tandem duplication had the greatest contribution for the CmGRAS expansion based on the comparative genome analysis, and CmGRAS genes experienced strong purifying selection pressure based on the Ka/Ks. Gene expression analysis revealed some CmGRAS members with potential functions in bud development and ovule fertility. CmGRAS genes with more homologous relationships with reference species had more cis-acting elements and higher expression levels. Notably, the lack of DELLA domain in members of the DELLA subfamily may cause de functionalization, and the differences between the three-dimensional structures of them were exhibited. This comprehensive study provides theoretical and practical basis for future research on the evolution and function of GRAS gene family.

How to survive in the world's third poplar: Insights from the genome of the highest altitude woody plant, Hippophae tibetana (Elaeagnaceae)

Hippophae tibetana (Tibetan sea-buckthorn) is one of the highest distributed woody plants in the world (3,000-5,200 meters a.s.l.). It is characterized by adaptation to extreme environment and important economic values. Here, we combined PacBio Hifi platform and Hi-C technology to assemble a 1,452.75 Mb genome encoding 33,367 genes with a Contig N50 of 74.31 Mb, and inferred its sexual chromosome. Two Hippophae-specific whole-genome duplication events (18.7-21.2 million years ago, Ma; 28.6-32.4 Ma) and long terminal repeats retroelements (LTR-RTs) amplifications were detected. Comparing with related species at lower altitude, Ziziphus jujuba (<1, 700 meters a.s.l.), H. tibetana had some significantly rapid evolving genes involved in adaptation to high altitude habitats. However, comparing with Hippophae rhamnoides (<3, 700 meters a.s.l.), no rapid evolving genes were found except microtubule and microtubule-based process genes, H. tibetana has a larger genome, with extra 2, 503 genes (7.5%) and extra 680.46 Mb transposable elements (TEs) (46.84%). These results suggest that the changes in the copy number and regulatory pattern of genes play a more important role for H. tibetana adapting to more extreme and variable environments at higher altitude by more TEs and more genes increasing genome variability and expression plasticity. This suggestion was supported by two findings: nitrogen-fixing genes of H. tibetana having more copies, and intact TEs being significantly closer genes than fragmentary TEs. This study provided new insights into the evolution of alpine plants.