Flower Development of Heterodichogamous Juglans mandshurica (Juglandaceae)

Genome-wide characterization and expression analysis of the CONSTANS-like gene family of Juglans mandshurica Maxim

The zinc-finger proteins encoded by the CONSTANS-like (COLs) gene family in Juglans mandshurica Maxim. play a significant role in regulating photoperiod-dependent flowering time, as well as in various processes such as growth and development. In this study, 15 members of the CONSTANS-like gene family were identified based on the genomic data of Juglans mandshurica. All of these proteins possess an N-terminal zinc-finger B-box domain and a C-terminal CCT domain. Phylogenetic analysis indicates that the JmCOLs proteins can be divided into three subgroups, with gene structures and motif compositions varying among these subgroups. Chromosomal analysis reveals that the 15 JmCOLs genes are distributed across nine chromosomes. The promoters of genes in this family contain stress-related cis-acting elements, hormone-related response elements, and other elements associated with growth and development. Notably, the most prominent elements are the light-responsive elements, suggesting that genes in this family are predominantly expressed in leaves. The expression patterns of JmCOLs genes differ among the members. Specifically, JmCOL5 and JmCOL10 are expressed exclusively in flower buds (p < 0.05). Throughout the 10 stages of flower bud development, the overall expression level of JmCOL4a peaks at approximately 50 to 100 times higher than its lowest point. The expression pattern of JmCOL5, which first reaches its maximum during the physiological differentiation stage of protogynous male flower buds before declining, suggests its potential involvement in the development of heteromorphic and dichogamous flowers.

Gene and Its Promoter Cloning, and Functional Validation of JmSOC1 Revealed Its Role in Promoting Early Flowering and the Interaction with the JmSVP Protein

Juglans mandshurica, a notable woody oil tree species, possesses both fruit and timber value. However, the complete heterodichogamous flowering mechanism in this species remains elusive. SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1) is a crucial regulator of flower bud development in Arabidopsis thaliana. In this study, we cloned the coding DNA sequence (CDS) of the JmSOC1 gene, revealing a 705 base pair (bp) sequence that encodes a protein of 234 amino acids. The JmSOC1 protein contains a highly conserved MADS-box domain, indicating its role as a transcription factor, and is predominantly localized in the nucleus. The JmSOC1 gene expressed the highest in flower buds. The peak expression level of JmSOC1 during the physiological differentiation phase occurred earlier in male flower buds of protandry (MPD) on April 10th compared to female flower buds of protandry (FPD) on April 14th; similarly, the peak expression in female flower buds of protogyny (FPG) on April 2nd preceded that in male flower buds of protogyny (MPG) on April 14th. This may be the primary reason for the earlier differentiation of the male flowers in protandry individuals and the female flowers in protogyny individuals. Overexpression of JmSOC1 in wild-type A. thaliana resulted in earlier flowering, accompanied by an upregulation of key flowering-related genes such as LEAFY (LFY), APETALA1 (AP1), and FLOWERING LOCUS T (FT). To further explore the function of JmSOC1, a 782 bp promoter sequence of JmSOC1 gene was cloned, which has been verified to have promoter activity by GUS staining. Furthermore, the interaction between the JmSOC1 gene promoter and its upstream regulatory protein JmSVP was verified using a yeast one-hybrid. These results offer valuable insights into the molecular mechanisms underpinning the promotion of early flowering in J. mandshurica and hold promise for laying a theoretical foundation for the flowering regulation network of this species.

Genome-wide identification analysis of the 4-Coumarate: CoA ligase (4CL) gene family expression profiles in Juglans regia and its wild relatives J. Mandshurica resistance and salt stress

Persian walnut (Juglans regia) and Manchurian walnut (Juglans mandshurica) belong to Juglandaceae, which are vulnerable, temperate deciduous perennial trees with high economical, ecological, and industrial values. 4-Coumarate: CoA ligase (4CL) plays an essential function in plant development, growth, and stress. Walnut production is challenged by diverse stresses, such as salinity, drought, and diseases. However, the characteristics and expression levels of 4CL gene family in Juglans species resistance and under salt stress are unknown. Here, we identified 36 Jr4CL genes and 31 Jm4CL genes, respectively. Based on phylogenetic relationship analysis, all 4CL genes were divided into three branches. WGD was the major duplication mode for 4CLs in two Juglans species. The phylogenic and collinearity analyses showed that the 4CLs were relatively conserved during evolution, but the gene structures varied widely. 4CLs promoter region contained multiply cis-acting elements related to phytohormones and stress responses. We found that Jr4CLs may be participated in the regulation of resistance to anthracnose. The expression level and some physiological of 4CLs were changed significantly after salt treatment. According to qRT-PCR results, positive regulation was found to be the main mode of regulation of 4CL genes after salt stress. Overall, J. mandshurica outperformed J. regia. Therefore, J. mandshurica can be used as a walnut rootstock to improve salt tolerance. Our results provide new understanding the potential functions of 4CL genes in stress tolerance, offer the theoretical genetic basis of walnut varieties adapted to salt stress, and provide an important reference for breeding cultivated walnuts for stress tolerance.

The fertilization process in Lithocarpus dealbatus (Fagaceae) and its implication on the sexual reproduction evolution of Fagales

MAIN CONCLUSION

The pistillate flowers of Lithocarpus dealbatus show two pollen tube (PT) arresting sites (the style-joining and micropyle) within the pistil during the postpollination-prezygotic stage. The PT, arrested at the pre-ovule stage, enhanced PT competition allowing the most compatible PTs to enter the ovary to ensure the highest fertilization success. During the shift from animal pollination to wind pollination, plants require a series of changes in reproductive traits. The mode of pollination is striking labile in Fagaceae. Lithocarpus is insect pollinated and is closely related to wind-pollinated Quercus. Little is known about the sexual reproduction of Lithocarpus. This study aimed to reveal the sexual reproduction of Lithocarpus dealbatus and to explore the evolutionary pattern of the key sexual reproduction traits to better understand their possible role in labile pollination. We found that after pollination, L. dealbatus PTs grew slowly in the style reaching style-joining in mid-January of the second year; then PT growth was arrested at style-joining for four months. Only two to three PTs resumed growth in mid-May to reach the micropyle, where PT growth ceased for one month before one PT resumed growth and passed through the micropyle to the embryo sac. Fagaceae showed a generalized mating system. Vast pollen production, small-sized pollen grains, long stigmatic receptive time, and reduced perianth were compatible with beetle pollination syndrome, representing the plesiomorphic status in Fagaceae. A large stigmatic surface and dry pollen grains linked to wind pollination might be independently derived several times in fagaceous lineages. Beetle pollination syndrome can cope with the uncertainty of pollinators to ensure conspecific pollen capture, which represents pre-adaptation status and has a selective advantage when conditions change, favouring wind pollination. The arrest of the PT at style-joining is a unique mechanism in later derived fagaceous lineages to enhance PT competition and promote outcrossing.

Genome-Wide Identification of AP2/ERF Superfamily Genes in Juglans mandshurica and Expression Analysis under Cold Stress

Juglans mandshurica has strong freezing resistance, surviving temperatures as low as -40 °C, making it an important freeze tolerant germplasm resource of the genus Juglans. APETALA2/ethylene responsive factor (AP2/ERF) is a plant-specific superfamily of transcription factors that regulates plant development, growth, and the response to biotic and abiotic stress. In this study, phylogenetic analysis was used to identify 184 AP2/ERF genes in the J. mandshurica genome, which were classified into five subfamilies (JmAP2, JmRAV, JmSoloist, JmDREB, and JmERF). A significant amount of discordance was observed in the 184 AP2/ERF genes distribution of J. mandshurica throughout its 16 chromosomes. Duplication was found in 14 tandem and 122 segmental gene pairs, which indicated that duplications may be the main reason for JmAP2/ERF family expansion. Gene structural analysis revealed that 64 JmAP2/ERF genes contained introns. Gene evolution analysis among Juglandaceae revealed that J. mandshurica is separated by 14.23 and 15 Mya from Juglans regia and Carya cathayensis, respectively. Based on promoter analysis in J. mandshurica, many cis-acting elements were discovered that are related to light, hormones, tissues, and stress response processes. Proteins that may contribute to cold resistance were selected for further analysis and were used to construct a cold regulatory network based on GO annotation and JmAP2/ERF protein interaction network analysis. Expression profiling using qRT-PCR showed that 14 JmAP2/ERF genes were involved in cold resistance, and that seven and five genes were significantly upregulated under cold stress in female flower buds and phloem tissues, respectively. This study provides new light on the role of the JmAP2/ERF gene in cold stress response, paving the way for further functional validation of JmAP2/ERF TFs and their application in the genetic improvement of Juglans and other tree species.

Analysis of Floral Organ Development and Sex Determination in Schisandra chinensis by Scanning Electron Microscopy and RNA-Sequencing

S. chinensis is a typical monoecious plant, and the number and development of female flowers determines the yield of S. chinensis. Due to a lack of genetic information, the molecular mechanism of sex differentiation in S. chinensis remains unclear. In this study, the combination of scanning electron microscopy (SEM) and RNA sequencing (RNA-seq) was used to understand the way of sex differentiation of S. chinensis and to mine the related genes of sex determination. The result shows the development of male and female S. chinensis flowers was completed at the same time, the unisexual S. chinensis flowers did not undergo a transition stage between sexes, and sex may have been determined at an early stage in flower development. The results of the gene function analysis of the plant hormone signaling pathway and sucrose metabolism pathway suggest that auxin and JA could be the key hormones for sex differentiation in S. chinensis, and sucrose may promote pollen maturation at the later stage of male flower development. Two AGAMOUS (GAG) genes, 10 AGAMOUS-like MADS-box (AGLs) genes, and the MYB, NAC, WRKY, bHLH, and Trihelix transcription factor families may play important roles in sex determination in S. chinensis. Taken together, the present findings provide valuable genetic information on flower development and sex determination in S. chinensis.

The Manchurian Walnut Genome: Insights into Juglone and Lipid Biosynthesis

BACKGROUND

Manchurian walnut (Juglans mandshurica Maxim.) is a tree with multiple industrial uses and medicinal properties in the Juglandaceae family (walnuts and hickories). J. mandshurica produces juglone, which is a toxic allelopathic agent and has potential utilization value. Furthermore, the seed of J. mandshurica is rich in various unsaturated fatty acids and has high nutritive value.

FINDINGS

Here, we present a high-quality chromosome-scale reference genome assembly and annotation for J. mandshurica (n = 16) with a contig N50 of 21.4 Mb by combining PacBio high-fidelity reads with high-throughput chromosome conformation capture data. The assembled genome has an estimated sequence size of 548.7 Mb and consists of 657 contigs, 623 scaffolds, and 40,453 protein-coding genes. In total, 60.99% of the assembled genome consists of repetitive sequences. Sixteen super-scaffolds corresponding to the 16 chromosomes were assembled, with a scaffold N50 length of 33.7 Mb and a BUSCO complete gene percentage of 98.3%. J. mandshurica displays a close sequence relationship with Juglans cathayensis, with a divergence time of 13.8 million years ago. Combining the high-quality genome, transcriptome, and metabolomics data, we constructed a gene-to-metabolite network and identified 566 core and conserved differentially expressed genes, which may be involved in juglone biosynthesis. Five CYP450 genes were found that may contribute to juglone accumulation. NAC, bZip, NF-YA, and NF-YC are positively correlated with the juglone content. Some candidate regulators (e.g., FUS3, ABI3, LEC2, and WRI1 transcription factors) involved in the regulation of lipid biosynthesis were also identified.

CONCLUSIONS

Our genomic data provide new insights into the evolution of the walnut genome and create a new platform for accelerating molecular breeding and improving the comprehensive utilization of these economically important tree species.

Development of Quercus acutissima (Fagaceae) pollen tubes inside pistils during the sexual reproduction process

Extensive histology of pistillate flowers revealed two pollen tube arresting sites (the style-joining and micropyle) within the pistil of Quercus acutissima during the postpollination-prezygotic stage, which reflects a unique female and male gametophyte recognition/selection mechanism. Sexual reproduction is among the most delicate and essential stages in plant life cycles and involves a series of precise interactions between pistils and male gametophytes. Quercus is a woody genus that dominates Northern Hemisphere forests and is notorious for interspecific hybridization, but its sexual reproduction is poorly understood, especially its pollen tube (PT) growth dynamics within pistils. This study used microtome techniques and scanning electron microscopy to observe the postpollination-prezygotic process in the biennially fruiting oak Quercus acutissima. Many pollen grains germinated at anthesis instantly, and PTs penetrated stigmatic surfaces and elongated through the stylar transmitting tissue, then arrested at style-joining for about 12-13 months. Few PTs resumed growth along the compitum in the upper ovarian locule wall in the subsequent April, concurrent with the rapid growth of rudimentary ovules. PTs arrived in the micropyle, and upper septum during megaspore mother cell meiosis, then arrested again for 7-10 days waiting for the embryo sac maturation. Fertilization occurred one week later. Our study shows a clear female dominant crosstalk growth pattern between PT and the ovule. The intermittent PT growth might reflect a unique male gametophyte recognition/selection mechanism to avoid self-pollination and enhance PT competition while increasing interspecific hybridization.

Characterization of Phytohormones and Transcriptomic Profiling of the Female and Male Inflorescence Development in Manchurian Walnut (Juglans mandshurica Maxim.)

Flowers are imperative reproductive organs and play a key role in the propagation of offspring, along with the generation of several metabolic products in flowering plants. In Juglans mandshurica, the number and development of flowers directly affect the fruit yield and subsequently its commercial value. However, owing to the lack of genetic information, there are few studies on the reproductive biology of Juglans mandshurica, and the molecular regulatory mechanisms underlying the development of female and male inflorescence remain unclear. In this study, phytohormones and transcriptomic sequencing analyses at the three stages of female and male inflorescence growth were performed to understand the regulatory functions underlying flower development. Gibberellin is the most dominant phytohormone that regulates flower development. In total, 14,579 and 7188 differentially expressed genes were identified after analyzing the development of male and female flowers, respectively, wherein, 3241 were commonly expressed. Enrichment analysis for significantly enriched pathways suggested the roles of MAPK signaling, phytohormone signal transduction, and sugar metabolism. Genes involved in floral organ transition and flowering were obtained and analyzed; these mainly belonged to the M-type MADS-box gene family. Three flowering-related genes (SOC1/AGL20, ANT, and SVP) strongly interacted with transcription factors in the co-expression network. Two key CO genes (CO3 and CO1) were identified in the photoperiod pathway. We also identified two GA20xs genes, one SVP gene, and five AGL genes (AGL8, AGL9, AGL15, AGL19, and AGL42) that contributed to flower development. The findings are expected to provide a genetic basis for the studies on the regulatory networks and reproductive biology in inflorescence development for J. mandshurica.