Transcriptome sequencing and analysis during seed growth and development in Euryale ferox Salisb

Molecular identification of phenylalanine ammonia lyase-encoding genes EfPALs and EfPAL2-interacting transcription factors in Euryale ferox

Flavonoids are one of the most important secondary metabolites in plants, and phenylalanine ammonia-lyase (PAL) is the first rate-limiting enzyme for their biosynthesis. However, detailed information on the regulation of PAL in plants is still little. In this study, PAL in E. ferox was identified and functionally analyzed, and its upstream regulatory network was investigated. Through genome-wide identification, we obtained 12 putative PAL genes from E. ferox. Phylogenetic tree and synteny analysis revealed that PAL in E. ferox was expanded and mostly preserved. Subsequently, enzyme activity assays demonstrated that EfPAL1 and EfPAL2 both catalyzed the production of cinnamic acid from phenylalanine only, with EfPAL2 exhibiting a superior enzyme activity. Overexpression of EfPAL1 and EfPAL2 in Arabidopsis thaliana, respectively, both enhanced the biosynthesis of flavonoids. Furthermore, two transcription factors, EfZAT11 and EfHY5, were identified by yeast one-hybrid library assays as binding to the promoter of EfPAL2, and further luciferase (LUC) activity analysis indicated that EfZAT11 promoted the expression of EfPAL2, while EfHY5 repressed the expression of EfPAL2. These results suggested that EfZAT11 and EfHY5 positively and negatively regulate flavonoid biosynthesis, respectively. Subcellular localization revealed that EfZAT11 and EfHY5 were localized in the nucleus. Our findings clarified the key EfPAL1 and EfPAL2 of flavonoid biosynthesis in E. ferox and established the upstream regulatory network of EfPAL2, which would provide novel information for the study of flavonoid biosynthesis mechanism.

The Effect and Mechanism of Corilagin from Euryale Ferox Salisb Shell on LPS-Induced Inflammation in Raw264.7 Cells

(1) Background: Euryale ferox Salisb is a large aquatic plant of the water lily family and an edible economic crop with medicinal value. The annual output of Euryale ferox Salisb shell in China is higher than 1000 tons, often as waste or used as fuel, resulting in waste of resources and environmental pollution. We isolated and identified the corilagin monomer from Euryale ferox Salisb shell and discovered its potential anti-inflammatory effects. This study aimed to investigate the anti-inflammatory effect of corilagin isolated from Euryale ferox Salisb shell. (2) Methods: We predict the anti-inflammatory mechanism by pharmacology. LPS was added to 264.7 cell medium to induce an inflammatory state, and the safe action range of corilagin was screened using CCK-8. The Griess method was used to determine NO content. The presence of TNF-α, IL-6, IL-1β, and IL-10 was determined by ELISA to evaluate the effect of corilagin on the secretion of inflammatory factors, while that of reactive oxygen species was detected by flow cytometry. The gene expression levels of TNF-α, IL-6, COX-2, and iNOS were determined using qRT-PCR. qRT-PCR and Western blot were used to detect the mRNA and expression of target genes in the network pharmacologic prediction pathway. (3) Results: Network pharmacology analysis revealed that the anti-inflammatory effect of corilagin may be related to MAPK and TOLL-like receptor signaling pathways. The results demonstrated the presence of an anti-inflammatory effect, as indicated by the reduction in the level of NO, TNF-α, IL-6, IL-1β, IL-10, and ROS in Raw264.7 cells induced by LPS. The results suggest that corilagin reduced the expression of TNF-α, IL-6, COX-2, and iNOS genes in Raw264.7 cells induced by LPS. The downregulation of the phosphorylation of IκB-α protein related to the toll-like receptor signaling pathway and upregulation of the phosphorylation of key proteins in the MAPK signaling pathway, P65 and JNK, resulted in reduced tolerance toward lipopolysaccharide, allowing for the exertion of the immune response. (4) Conclusions: The results demonstrate the significant anti-inflammatory effect of corilagin from Euryale ferox Salisb shell. This compound regulates the tolerance state of macrophages toward lipopolysaccharide through the NF-κB signaling pathway and plays an immunoregulatory role. The compound also regulates the expression of iNOS through the MAPK signaling pathway, thereby alleviating the cell damage caused by excessive NO release.

Euryale Small Auxin Up RNA62 promotes cell elongation and seed size by altering the distribution of indole-3-acetic acid under the light

Euryale (Euryale ferox Salisb.) is an aquatic crop used as both food and drug in Asia, but its utilization is seriously limited due to low yield. Previously, we hypothesized that Euryale small auxin up RNAs (EuSAURs) regulate seed size, but the underlying biological functions and molecular mechanisms remain unclear. Here, we observed that the hybrid Euryale lines (HL) generate larger seeds with higher indole-3-acetic acid (IAA) concentrations than those in the North Gordon Euryale (WT). Histological analysis suggested that a larger ovary in HL is attributed to longer cells around. Overexpression of EuSAUR62 in rice (Oryza sativa L.) resulted in larger glumes and grains and increased the length of glume cells. Immunofluorescence and protein interaction assays revealed that EuSAUR62 modulates IAA accumulation around the rice ovary by interacting with the rice PIN-FORMED 9, an auxin efflux carrier protein. Euryale basic region/leucine zipper 55 (EubZIP55), which was highly expressed in HL, directly binds to the EuSAUR62 promoter and activated the expression of EuSAUR62. Constant light increased the expression of both EubZIP55 and EuSAUR62 with auxin-mediated hook curvature in HL seedlings. Overall, we proposed that EuSAUR62 is a molecular bridge between light and IAA and plays a crucial role in regulating the size of the Euryale seed.

Proteomic analysis of Euryale ferox Salisb seeds at different developmental stages

The development of plant seeds is accompanied by changes in their internal substances. The edible part of E. ferox is the seed, and starch and flavonoids are the storage substances and functional substances in E. ferox seeds respectively. Herein, four time points of seed development, including after flowering T10 (10 days), T20 (20 days), T30 (30 days) and T40 (40 days), were investigated by using iTRAQ technology. A total of 2809 differential proteins were identified. The enrichment analysis of differential proteins found that they were mainly enriched in starch synthesis pathways and flavonoid biosynthesis pathways. The key candidate enzymes for starch synthesis, APS (c54069), APL (c55730), SBE (c56416), SSS (c54912) and GBSS (c53181), were identified. At the same time,PAL (c50934), CHS (c49212), F3H (c35949) and ANS (c54610) may be key enzymes in flavonoid biosynthesis. In addition, the ABA signal transduction pathway was analyzed and it was identified that PYL3 (c54854) and ABI5 (c56122) are up-regulated from T10 to T40, and it is speculated that they play an important regulatory role in the development of E. ferox seeds. Together, these results reveals the dynamic changes during the development of E. ferox seeds, which will provide guidance for the study of the molecular mechanism of starch and flavonoids.

EfABI4 Transcription Factor Is Involved in the Regulation of Starch Biosynthesis in Euryale ferox Salisb Seeds

Starch is the final product of photosynthesis and the main storage form in plants. Studies have shown that there is a close synergistic regulatory relationship between ABA signal transduction and starch biosynthesis. In this study, we employed RNA sequencing (RNA-Seq) to investigate transcriptomic changes of the Euryale ferox seeds treated by exogenous ABA. The differentially expressed genes engaged in the “Starch and sucrose” and “TCA cycle” pathway. Furthermore, the key transcription factor EfABI4 in ABA signaling pathway and the key genes of starch biosynthesis (EfDBE1, EfSBE2, EfSS1, EfSS2, EfSS3, EfSS4 and EfGBSS1) were significantly up-regulated. Further, the Euryale ferox plant was treated with ABA, it was found that the total starch content of Euryale ferox seeds at different development stages was significantly higher than that of the control, and the key genes of starch synthesis in Euryale ferox seeds were also significantly up-regulated. Finally, yeast one-hybrid and dual luciferase assay proved that EfABI4 can promote the expression of EfSS1 by directly binding to its promoter. Subcellular localization results showed that EfABI4 protein was located at the nucleus and EfSS1 protein was located in the cytomembrane. These findings revealed that ABA promotes starch synthesis and accumulation by mediating EfABI4 to directly promote EfSS1 gene expression, which is helpful for understanding starch synthesis in seeds.

Multi-functional topology optimization of Victoria cruziana veins

The growth and development of biological tissues and organs strongly depend on the requirements of their multiple functions. Plant veins yield efficient nutrient transport and withstand various external loads. Victoria cruziana, a tropical species of the Nymphaeaceae family of water lilies, has evolved a network of three-dimensional and rugged veins, which yields a superior load-bearing capacity. However, it remains elusive how biological and mechanical factors affect their unique vein layout. In this paper, we propose a multi-functional and large-scale topology optimization method to investigate the morphomechanics of Victoria cruziana veins, which optimizes both the structural stiffness and nutrient transport efficiency. Our results suggest that increasing the branching order of radial veins improves the efficiency of nutrient delivery, and the gradient variation of circumferential vein sizes significantly contributes to the stiffness of the leaf. In the present method, we also consider the optimization of the wall thickness and the maximum layout distance of circumferential veins. Furthermore, biomimetic leaves are fabricated by using the three-dimensional printing technique to verify our theoretical findings. This work not only gains insights into the morphomechanics of Victoria cruziana veins, but also helps the design of, for example, rib-reinforced shells, slabs and dome skeletons.

Genome-Wide Analysis of NBS-LRR Genes From an Early-Diverging Angiosperm Euryale ferox

NBS-LRR genes are the largest gene family in plants conferring resistance to pathogens. At present, studies on the evolution of NBS-LRR genes in angiosperms mainly focused on monocots and eudicots, while studies on NBS-LRR genes in the basal angiosperms are limited. Euryale ferox represents an early-diverging angiosperm order, Nymphaeales, and confronts various pathogens during its lifetime, which can cause serious economic losses in terms of yield and quality. In this study, we performed a genome-wide identification and analysis of NBS-LRR genes in E. ferox. All 131 identified NBS-LRR genes could be divided into three subclasses according to different domain combinations, including 18 RNLs, 40 CNLs, and 73 TNLs. The E. ferox NBS-LRR genes are unevenly distributed on 29 chromosomes; 87 genes are clustered at 18 multigene loci, and 44 genes are singletons. Gene duplication analysis revealed that segmental duplications acted as a major mechanism for NBS-LRR gene expansions but not for RNL genes, because 18 RNL genes were scattered over 11 chromosomes without synteny loci, indicating that the expansion of RNL genes could have been caused by ectopic duplications. Ancestral gene reconciliation based on phylogenetic analysis revealed that there were at least 122 ancestral NBS-LRR lineages in the common ancestor of the three Nymphaeaceae species, suggesting that NBS-LRR genes expanded slightly during speciation in E. ferox. Transcriptome analysis showed that the majority of NBS-LRR genes were at a low level of expression without pathogen stimulation. Overall, this study characterized the profile of NBS-LRR genes in E. ferox and should serve as a valuable resource for disease resistance breeding in E. ferox.

Chloroplast thylakoid ascorbate peroxidase PtotAPX plays a key role in chloroplast development by decreasing hydrogen peroxide in Populus tomentosa

Chloroplast development is a complex process that is critical to the growth and development of plants. However, the detailed mechanism of chloroplast development in woody plants remains unclear. In this study, we showed that chloroplasts with elaborate thylakoids could develop from proplastids in the cells of calli derived from leaf tissues of Populus tomentosa upon exposure to light. Chloroplast development was confirmed at the molecular and cellular levels. Transcriptome analysis revealed that genes related to photoreceptors and photosynthesis were significantly up-regulated during chloroplast development in a time-dependent manner. In light-induced chloroplast development, a key process was the removal of hydrogen peroxide, in which thylakoid-localized PtotAPX played a major role; light-induced chloroplast development was enhanced in PtotAPX-overexpressing transgenic P. tomentosa callus with lower levels of hydrogen peroxide, but was suppressed in PtotAPX antisense transgenic callus with higher levels of hydrogen peroxide. Moreover, the suppression of light-induced chloroplast development in PtotAPX antisense transgenic callus was relieved by the exogenous reactive oxygen species scavenging agent N,N'-dimethylthiourea (DMTU). Based on these results, we propose that PtotAPX-mediated removal of reactive oxygen species plays a key role in chloroplast development from proplastids upon exposure to light in P. tomentosa.

Metabolomics and transcriptome analysis of the biosynthesis mechanism of flavonoids in the seeds of Euryale ferox Salisb at different developmental stages

Flavonoids belong to polyphenolic compounds, which are widely distributed in plants and have rich functions. Euryale ferox Salisb is an important medicinal and edible homologous plant, and flavonoids are its main functional substances. However, the biosynthesis mechanism of flavonoids in E. ferox is still poorly understood. To explore the dynamic changes of flavonoid biosynthesis during the development of E. ferox seeds, the targeted flavonoid metabolome was determined. A total of 129 kinds of flavonoid metabolites were characterized in the seeds of E. ferox, including 11 flavanones, 8 dihydroflavanols, 16 flavanols, 29 flavones, 3 isoflavones, 12 anthocyanins, 29 flavonols, 6 flavonoid carbonosides, 3 chalcones and 13 proanthocyanidins. The relative content of flavonoid metabolites accumulated continuously during the development of E. ferox seeds, and reached the highest at T30. In transcriptome, the expression of key genes in the flavonoid pathway, such as PAL, CHS, F3H, FLS, ANS, was highest in T30, which was consistent with the trend of metabolites. Six candidate transcription factors (R2R3MYBs and bHLHs) may affect the biosynthesis of flavonoids by regulating the expression of structural genes. Furthermore, transcriptome analysis and exogenous ABA and SA treatment demonstrated that ABA (PYR1, PP2Cs, SnRK2s) and SA (NPR1) are involved in the positive regulation of flavonoid biosynthesis. This study clarified the differential changes of flavonoid metabolites during the development of E. ferox seeds, confirmed that ABA and SA promote the synthesis of flavonoids, and found key candidate genes that are involved in the regulation of ABA and SA in the positive regulation of flavonoid biosynthesis.

Comprehensive Analysis of Evolutionary Characterization and Expression for Monosaccharide Transporter Family Genes in Nelumbo nucifera

Sugar transporters, an important class of transporters for sugar function, regulate many processes associated with growth, maturation, and senescence processes in plants. In this study, a total of 35 NuMSTs were identified in the Nelumbo nucifera genome and grouped by conserved domains and phylogenetic analysis. Additionally, we identified 316 MST genes in 10 other representative plants and performed a comparative analysis with Nelumbo nucifera genes, including evolutionary trajectory, gene duplication, and expression pattern. A large number of analyses across plants and algae indicated that the MST family could have originated from STP and Glct, expanding to form STP and SFP by dispersed duplication. Finally, a quantitative real-time polymerase chain reaction and cis-element analysis showed that some of them may be regulated by plant hormones (e.g., abscisic acid), biotic stress factors, and abiotic factors (e.g., drought, excessive cold, and light). We found that under the four abiotic stress conditions, only NuSTP5 expression was upregulated, generating a stress response, and ARBE and LTR were present in NuSTP5. In summary, our findings are significant for understanding and exploring the molecular evolution and mechanisms of NuMSTs in plants.

Bulk segregant analysis identifies SSR markers associated with leaf- and seed-related traits in Perilla crop (Perilla frutescens L.)

BACKGROUND

Bulk segregant analysis (BSA) is another method of identifying significant molecular markers linked to the target gene or region for specific traits. BSA is easier and less expensive than other methods; it does not require genetic map construction and needs fewer markers than the number needed to construct a genetic map for QTL mapping.

OBJECTIVES

The purpose of our study was to identify simple sequence repeat (SSR) markers linked with leaf- and seed-related traits in Perilla crop, and to allow the selection of better accessions in Perilla breeding programs with marker-assisted selection (MAS).

METHODS

The genotypes of the 25 SSR markers and phenotypic data for the eight qualitative traits were used to confirm significant marker-trait associations (SMTAs) using TASSEL software. To detect SSR markers associated with leaf color, the 16 individuals of the F₃ population were divided into three bulk groups based on the colors of the surface and reverse sides of the leaf, respectively: six in the green/green group, five in the green/purple group and five in the purple/purple group.

RESULTS

This study detected 18 significant marker-trait associations (SMTAs) involving 12 SSR markers associated with six agronomic traits. The SSR markers KNUPF15, KNUPF21, KNUPF29, and KNUPF60 were associated with leaf surface color, and KNUPF11, KNUPF15, KNUPF21, and KNUPF60 were associated with leaf reverse side color. In addition, five SSR markers were associated with seed-related traits. KNUPF11 and KNUPF29 were associated with seed coat color, while KNUPF29 was associated with seed size. KNUPF12, KNUPF16, and KNUPF42 were associated with seed hardness. To verify the selected significant SSR markers associated with leaf color and seed-related traits, a UPGMA dendrogram for 11 individuals in the F₃ population, which formed two bulk groups consisting of 6 green/green and 5 purple/purple individuals, was constructed using six SSR marker-related LC and RLC traits.

CONCLUSION

These results are very important for understanding the characteristics of Perilla leaves and seeds; they may also support opportunities to effectively preserve and utilize existing accessions and to allow Perilla breeders to improve crop quality by mean of MAS.

Bacillus pumilus LZP02 Promotes Rice Root Growth by Improving Carbohydrate Metabolism and Phenylpropanoid Biosynthesis

Elucidation of the underlying mechanisms of plant growth promotion of rhizobacteria is very important. This study explored the mechanism by which Bacillus pumilus LZP02 promotes growth in rice roots through proteomic, transcriptomic, and metabolomic techniques. The results showed that B. pumilus LZP02 promoted the absorption of phosphorous, calcium, and magnesium ions by colonization of rice roots and enhanced peroxidase, catalase, superoxide dismutase, and Ca²⁺Mg²⁺ adenosine triphosphatase activities and chlorophyll contents in rice. The proteomic results showed that most of the differentially expressed proteins were involved in carbohydrate metabolism and that the biosynthesis of other secondary metabolites was also increased. According to RNA-seq and reverse transcription-quantitative PCR analyses, expression of some genes involved in carbohydrate metabolism and phenylpropanoid biosynthesis was upregulated in rice roots. Regarding metabolomics, phenylpropanoid biosynthesis, starch and sucrose metabolism, the pentose phosphate pathway, and glyoxylate and dicarboxylate metabolism were increased. The results indicated that B. pumilus LZP02 promoted the growth of rice roots by enhancing carbohydrate metabolism and phenylpropanoid biosynthesis.

Small Auxin Up RNAs influence the distribution of indole-3-acetic acid and play a potential role in increasing seed size in Euryale ferox Salisb

BACKGROUND

Aquatic Euryale ferox Salisb. is an economically important crop in China and India. Unfortunately, low yield limitations seriously hinder market growth. Unveiling the control of seed size is of remarkable importance in improvement of crops. Here, we generated a new hybrid line (HL) with larger seeds by crossing South Gordon Euryale and North Gordon Euryale (WT) which hasn't been reported before. However, the functional genes and molecular mechanisms controlling the seed size in Euryale ferox Salisb. remain unclear. In this study, we focused on the differentially expressed genes in the auxin signal transduction pathway during fruit development between HL and WT to explore candidate regulatory genes participated in regulating seed size.

RESULTS

Both concentration and localization of indole-3-acetic acid (IAA) at two growth stages of fruits of WT and HL were detected by LC-MS and immunofluorescence. Although IAA content between the two lines did not differ, IAA distribution was significantly different. To elucidate the mechanism and to seek the key genes underlying this difference, RNA-seq was performed on young fruits at the two selected growth stages, and differentially expressed genes related to the auxin transduction pathway were selected for further analysis.

CONCLUSION

Hybrid Euryale ferox Salisb. expressed significant heterosis, resulting in non-prickly, thin-coated, large seeds, which accounted for the significantly larger yield of HL than that of WT. Our study indicated that Small Auxin Up RNAs (SAURs) -mediated localization of IAA regulates seed size in Euryale ferox Salisb. We found that some SAURs may act as a positive mediator of the auxin transduction pathway, thereby contributing to the observed heterosis.

Characterization the complete chloroplast genome of Euryale ferox (Nymphaeaceae), an medicinal plant species in China

Euryale ferox belongs to the family Nymphaeaceae that has been used as foods and medicines in China. In this study, we had been completed the complete chloroplast genome of Euryale ferox, which is 159,930 bp in length and has four sub-regions. The complete chloroplast genome sequence of Euryale ferox contains 89,678 bp of a large single-copy region (LSC), 22,202 bp of small single-copy region (SSC) and 25,025 bp of two inverted repeat regions (IRs). The complete chloroplast genome of Euryale ferox is also consistent with other chloroplast genomes most plant species. The overall nucleotide composition of chloroplast genome sequence has: A (30.1%), T (30.8%), C (19.9%), G (19.2%) and the total GC content of 39.1%. Its sequence contains 127 genes, including 84 encoding genes, 35 transfer RNA genes and 8 ribosomal RNA genes. As the analysis result, the ML tree presents that Euryale ferox clustered with Nuphar advena belonging to the family Nymphaeaceae in genetic evolution relationship by the maximum likelihood (ML) methods.

Transcriptome Analysis of Jojoba (Simmondsia chinensis) during Seed Development and Liquid Wax Ester Biosynthesis

Jojoba is one of the main two known plant source of natural liquid wax ester for use in various applications, including cosmetics, pharmaceuticals, and biofuel. Due to the lack of transcriptomic and genomic data on lipid biosynthesis and accumulation, molecular marker breeding has been used to improve jojoba oil production and quality. In the current study, the transcriptome of developing jojoba seeds was investigated using the Illunina NovaSeq 6000 system, 100 × 10⁶ paired end reads, an average length of 100 bp, and a sequence depth of 12 Gb per sample. A total of 176,106 unigenes were detected with an average contig length of 201 bp. Gene Ontology (GO) showed that the detected unigenes were distributed in the three GO groups biological processes (BP, 5.53%), cellular component (CC, 6.06%), and molecular functions (MF, 5.88%) and distributed in 67 functional groups. The lipid biosynthesis pathway was established based on the expression of lipid biosynthesis genes, fatty acid (FA) biosynthesis, FA desaturation, FA elongation, fatty alcohol biosynthesis, triacylglycerol (TAG) biosynthesis, phospholipid metabolism, wax ester biosynthesis, and lipid transfer and storage genes. The detection of these categories of genes confirms the presence of an efficient lipid biosynthesis and accumulation system in developing jojoba seeds. The results of this study will significantly enhance the current understanding of wax ester biology in jojoba seeds and open new routes for the improvement of jojoba oil production and quality through biotechnology applications.

Transcriptome analysis reveals important candidate genes involved in grain-size formation at the stage of grain enlargement in common wheat cultivar "Bainong 4199"

Grain-size is one of the yield components, and the first 14 days after pollination (DAP) is a crucial stage for wheat grain-size formation. To understand the mechanism of grain-size formation at the whole gene expression level and to identify the candidate genes related to grain pattern formation, cDNA libraries from immature grains of 5 DAP and 14 DAP were constructed. According to transcriptome analysis, a total of 12,555 new genes and 9,358 differentially expressed genes (DEGs) were obtained. In DEGs, 2,876, 3,357 and 3,125 genes were located on A, B and D subgenome respectively. 9,937 (79.15%) new genes and 9,059 (96.80%) DEGs were successfully annotated. For DEGs, 4,453 were up-regulated and 4,905 were down-regulated at 14 DAP. The Gene Ontology (GO) database indicated that most of the grain-size-related genes were in the same cluster. The Kyoto Encyclopedia of Genes and Genomes (KEGG) database analysis showed that 130, 129 and 20 DEGs were respectively involved in starch and sucrose metabolism, plant hormone signal transduction and ubiquitin-mediated proteolysis. Expression levels of 8 randomly selected genes were confirmed by qRT-PCR, which was consistent with the transcriptome data. The present database will help us understand the molecular mechanisms underlying early grain development and provide the foundation for increasing grain-size and yield in wheat breeding programs.