Integrated Transcriptomics and Metabolomics Analysis Promotes the Understanding of Adventitious Root Formation in Eucommia ulmoides Oliver.

As a primary approach to nutrient propagation for many woody plants, cutting roots is essential for the breeding and production of Eucommia ulmoides Oliver. In this study, hormone level, transcriptomics, and metabolomics analyses were performed on two E. ulmoides varieties with different adventitious root (AR) formation abilities. The higher JA level on the 0th day and the lower JA level on the 18th day promoted superior AR development. Several hub genes executed crucial roles in the crosstalk regulation of JA and other hormones, including F-box protein (EU012075), SAUR-like protein (EU0125382), LOB protein (EU0124232), AP2/ERF transcription factor (EU0128499), and CYP450 protein (EU0127354). Differentially expressed genes (DEGs) and metabolites of AR formation were enriched in phenylpropanoid biosynthesis, flavonoid biosynthesis, and isoflavonoid biosynthesis pathways. The up-regulated expression of PAL, CCR, CAD, DFR, and HIDH genes on the 18th day could contribute to AR formation. The 130 cis-acting lncRNAs had potential regulatory functions on hub genes in the module that significantly correlated with JA and DEGs in three metabolism pathways. These revealed key molecules, and vital pathways provided more comprehensive insight for the AR formation mechanism of E. ulmoides and other plants.

The chromosome-level genome of Eucommia ulmoides provides insights into sex differentiation and α-linolenic acid biosynthesis.

Eucommia ulmoides Oliver is a typical dioecious plant endemic to China that has great medicinal and economic value. Here, we report a high-quality chromosome-level female genome of E. ulmoides obtained by PacBio and Hi-C technologies. The size of the female genome assembly was 1.01 Gb with 17 pseudochromosomes and 31,665 protein coding genes. In addition, Hi-C technology was used to reassemble the male genome released in 2018. The reassembled male genome was 1.24 Gb with the superscaffold N50 (48.30 Mb), which was increased 25.69 times, and the number of predicted genes increased by 11,266. Genome evolution analysis indicated that E. ulmoides has undergone two whole-genome duplication events before the divergence of female and male, including core eudicot γ whole-genome triplication event (γ-WGT) and a recent whole genome duplication (WGD) at approximately 27.3 million years ago (Mya). Based on transcriptome analysis, EuAP3 and EuAG may be the key genes involved in regulating the sex differentiation of E. ulmoides. Pathway analysis showed that the high expression of ω-3 fatty acid desaturase coding gene EU0103017 was an important reason for the high α-linolenic acid content in E. ulmoides. The genome of female and male E. ulmoides presented here is a valuable resource for the molecular biological study of sex differentiation of E. ulmoides and also will provide assistance for the breeding of superior varieties.

Identifying Influential Nodes in Social Networks: Exploiting Self-Voting Mechanism.

The influence maximization (IM) problem is defined as identifying a group of influential nodes in a network such that these nodes can affect as many nodes as possible. Due to its great significance in viral marketing, disease control, social recommendation, and so on, considerable efforts have been devoted to the development of methods to solve the IM problem. In the literature, VoteRank and its improved algorithms have been proposed to select influential nodes based on voting approaches. However, in the voting process of these algorithms, a node cannot vote for itself. We argue that this voting schema runs counter to many real scenarios. To address this issue, we designed the VoteRank* algorithm, in which we first introduce the self-voting mechanism into the voting process. In addition, we also take into consideration the diversities of nodes. More explicitly, we measure the voting ability of nodes and the amount of a node voting for its neighbors based on the H-index of nodes. The effectiveness of the proposed algorithm is experimentally verified on 12 benchmark networks. The results demonstrate that VoteRank* is superior to the baseline methods in most cases.

Complete chloroplast genome of the oil-bearing shrub Staphylea bumalda DC (Staphyleaceae).

Staphylea bumalda DC, belonging to family Staphyleaceae, is a woody understory tree that is both edible and medicinal and produces oil with high economic value. This study reports the first complete chloroplast genome sequence of S. bumalda. The complete chloroplast genome sequence of S. bumalda is 160,319 bp in length with an overall GC content of 32.79%, which is composed of a large single-copy region (LSC: 89,401 bp), a small single-copy region (SSC: 18,834 bp), and two inverted repeat regions (IR: 26,042 bp). A total of 130 genes were predicted in this genome, including 85 protein-coding genes, 37 tRNA genes, and eight rRNA genes. The phylogenetic analysis based on 14 complete chloroplast sequences from related species revealed that S. bumalda is a sister to S. holocarpa.

Effects of Applying Different Doses of Selenite to Soil and Foliar at Different Growth Stage on Selenium Content and Yield of Different Oat Varieties.

(1) Background: With the increase in people's consumption of processed oat products, the production of selenium (Se)-enriched oat has become a possibility to supplement the human body with Se. Therefore, the effects of various factors on the Se-enriched ability and yield of different oat varieties were comprehensively studied. (2) Methods: cv."Pinyan 5" and cv."Bayou 18" were applied at the stem-elongation stage and heading stage in the Jinzhong (JZ), and cv."Bayou 1" and cv."Jinyan 18" were applied at the heading stage and flowering stage in the northwestern Shanxi (JXB) with different doses of Na2SeO3 (0, 5.48, 10.96, 21.92, 43.84, 65.76, 98.64, 0, 5.48, 10.96, 21.92, 43.84, 65.76, 98.64, 147.96 g hm-2) by soil application and foliar spraying. (3) Results: The grain Se content and yield of oat were affected by the variety, Se application dose, stage and method of Se supplementation. Additionally, the Se content in oat grain was positively correlated with the Se application dose while the yield of oat first increased and then decreased with the Se application dose. (4) Conclusions: In the JZ and JXB, 21.92 g hm-2 and 43.84 g hm-2 Se was sprayed on the leaves of cv."Bayou 18" and cv."Bayou 1" at the heading stage, respectively, was the most effective Se biofortification program.

Effects of selenium application concentration, period and method on the selenium content and grain yield of Tartary buckwheat of different varieties.

BACKGROUND: As a potential selenium-enriched crop, it is of great significance to study the selenium application of Tartary buckwheat. Therefore, to study the effects of selenium application concentration, variety, selenium application period and method on the grain selenium content and yield of Tartary buckwheat, an orthogonal experimental design was used to carry out field experiments in the Jinzhong and Northwest Shanxi ecological regions at the same time. Heifeng 1 and Jinqiao 2 were applied at the branching stage and flowering stage in the Jinzhong, and Heifeng 1 and Jinqiao 6 were applied at the early flowering stage and peak flowering stage in the Northwest Shanxi with different concentrations of sodium selenite (0, 1.37, 2.74, 5.48, 8.22, 12.33, 18.495, 27.7425 g hm-2 ) by foliar spraying and soil application. RESULTS: The results showed that the selenium content in Tartary buckwheat grains was positively correlated with the selenium application concentration and increased with increasing selenium application concentration, while the yield of Tartary buckwheat first increased and then decreased with the selenium application concentration. The grain selenium content and yield of Tartary buckwheat were affected by the selenium application concentration, variety and application method. CONCLUSION: The most effective selenium biofortification program was spraying 2.32 g hm-2 sodium selenite on the leaves of Heifeng 1 at the early flowering stage in the Jinzhong. In the Northwest Shanxi, spraying 11.01 g hm-2 sodium selenite on the leaves of Jinqiao 6 at the flowering stage was the most effective selenium biofortification program. © 2022 Society of Chemical Industry.

Whole genome re-sequencing reveals the genetic diversity and evolutionary patterns of Eucommia ulmoides.

Eucommia ulmoides (E. ulmoides) is a deciduous perennial tree belonging to the order Garryales, and is known as "living fossil" plant, along with ginkgo (Ginkgo biloba), metaspaca (Metasequoia glyptostroboides) and dove tree (Davidia involucrata Baill). However, the genetic diversity and population structure of E. ulmoides are still  ambiguous nowdays. In this study, we re-sequenced the genomes of 12 E. ulmoides accessions from different major climatic geography regions in China to elucidate the genetic diversity, population structure and evolutionary pattern. By integration of phylogenetic analysis, principal component analysis and population structure analysis based on a number of high-quality SNPs, a total of 12 E. ulmoides accessions were clustered into four different groups. This result is consistent with their geographical location except for group samples from Shanghai and Hunan province. E. ulmoides accessions from Hunan province exhibited a closer genetic relationship with E. ulmoides accessions from Shanghai in China compared with other regions, which is also supported by the result of population structure analyses. Genetic diversity analysis further revealed that E. ulmoides samples in Shanghai and Hunan province were with higher genetic diversity than those in other regions in this study. In addition, we treated the E. ulmoides materials from Shanghai and Hunan province as group A, and the other materials from other places as group B, and then analyzed the evolutionary pattern of E. ulmoides. The result showed the significant differentiation (Fst = 0.1545) between group A and group B. Some candidate highly divergent genome regions were identified in group A by selective sweep analyses, and the function analysis of candidate genes in these regions showed that biological regulation processes could be correlated with the Eu-rubber biosynthesis. Notably, nine genes were identified from selective sweep regions. They were involved in the Eu-rubber biosynthesis and expressed in rubber containing tissues. The genetic diversity research and evolution model of E. ulmoides were preliminarily explored in this study, which laid the foundation for the protection of germplasm resources and the development and utilization of multipurpose germplasm resources in the future.

Analysis of chemotypes and their markers in leaves of core collections of Eucommia ulmoides using metabolomics.

The leaves of Eucommia ulmoides contain various active compunds and nutritional components, and have successively been included as raw materials in the Chinese Pharmacopoeia, the Health Food Raw Material Catalogue, and the Feed Raw Material Catalogue. Core collections of E. ulmoides had been constructed from the conserved germplasm resources basing on molecular markers and morphological traits, however, the metabolite diversity and variation in this core population were little understood. Metabolite profiles of E. ulmoides leaves of 193 core collections were comprehensively characterized by GC-MS and LC-MS/MS based non-targeted metabolomics in present study. Totally 1,100 metabolites were identified and that belonged to 18 categories, and contained 120 active ingredients for traditional Chinese medicine (TCM) and 85 disease-resistant metabolites. Four leaf chemotypes of the core collections were established by integrated uses of unsupervised self-organizing map (SOM), supervised orthogonal partial least squares discriminant analysis (OPLS-DA) and random forest (RF) statistical methods, 30, 23, 43, and 23 chemomarkers were screened corresponding to the four chemotypes, respectively. The morphological markers for the chemotypes were obtained by weighted gene co-expression network analysis (WGCNA) between the chenomarkers and the morphological traits, with leaf length (LL), chlorophyll reference value (CRV), leaf dentate height (LDH), and leaf thickness (LT) corresponding to chemotypes I, II, III, and IV, respectively. Contents of quercetin-3-O-pentosidine, isoquercitrin were closely correlated to LL, leaf area (LA), and leaf perimeter (LP), suggesting the quercetin derivatives might influence the growth and development of E. ulmoides leaf shape.

Genome-wide identification and expression pattern analysis of the ribonuclease T2 family in Eucommia ulmoides.

The 2',3'-cycling ribonuclease (RNase) genes are catalysts of RNA cleavage and include the RNase T2 gene family. RNase T2 genes perform important roles in plants and have been conserved in the genome of eukaryotic organisms. In this study we identified 21 EURNS genes in Eucommia ulmoides Oliver (E. ulmoides) and analyzed their structure, chromosomal location, phylogenetic tree, gene duplication, stress-related cis-elements, and expression patterns in different tissues. The length of 21 predicted EURNS proteins ranged from 143 to 374 amino acids (aa), their molecular weight (MW) ranged from 16.21 to 42.38 kDa, and their isoelectric point (PI) value ranged from 5.08 to 9.09. Two classifications (class I and class III) were obtained from the conserved domains analysis and phylogenetic tree. EURNS proteins contained a total of 15 motifs. Motif 1, motif 2, motif 3, and motif 7 were distributed in multiple sequences and were similar to the conserved domain of RNase T2. EURNS genes with similar structure and the predicted EURNS proteins with conserved motif compositions are in the same group in the phylogenetic tree. The results of RT-PCR and transcription data showed that EURNS genes have tissue-specific expression and exhibited obvious trends in different developmental stages. Gene duplication analysis results indicated that segment duplication may be the dominant duplication mode in this gene family. This study provides a theoretical basis for research on the RNase T2 gene family and lays a foundation for the further study of EURNS genes.

Chemotype classification and biomarker screening of male Eucommia ulmoides Oliv. flower core collections using UPLC-QTOF/MS-based non-targeted metabolomics.

BACKGROUND: In the Chinese health care industry, male Eucommia ulmoides Oliv. flowers are newly approved as a raw material of functional food. Core collections have been constructed from conserved germplasm resources based on phenotypic traits and molecular markers. However, little is known about these collections' phytochemical properties. This study explored the chemical composition of male E. ulmoides flowers, in order to provide guidance in the quality control, sustainable cultivation, and directional breeding of this tree species. METHODS: We assessed the male flowers from 22 core collections using ultra-performance liquid chromatography and quadrupole time-of-flight mass spectrometry (UPLC-QTOF/MS) non-targeted metabolomics, and analyzed them using multivariate statistical methods including principal component analysis (PCA), hierarchical cluster analysis (HCA), and orthogonal partial least squares discriminant analysis (OPLS-DA). RESULTS: We annotated a total of 451 and 325 metabolites in ESI+ and ESI- modes, respectively, by aligning the mass fragments of the secondary mass spectra with those in the database. Four chemotypes were well established using the ESI+ metabolomics data. Of the 29 screened biomarkers, 21, 6, 19, and 5 markers corresponded to chemotypes I, II, III, and IV, respectively. More than half of the markers belonged to flavonoid and amino acid derivative classes. CONCLUSION: Non-targeted metabolomics is a suitable approach to the chemotype classification and biomarker screening of male E. ulmoides flower core collections. We first evaluated the metabolite profiles and compositional variations of male E. ulmoides flowers in representative core collections before establishing possible chemotypes and significant biomarkers denoting the variations. We used genetic variations to infer the metabolite compositional variations of male E. ulmoides flower core collections instead of using the geographical origins of the germplasm resources. The newly proposed biomarkers sufficiently classified the chemotypes to be applied for germplasm resource evaluation.

Ectopic expression of EuWRI1, encoding a transcription factor in E. ulmoides, changes the seeds oil content in transgenic tobacco.

The WRINKLED1 (WRI1) gene is a well-established key transcriptional regulator involved in the regulation of fatty acid biosynthesis in developing seeds. In this study, a new WRI1 gene was isolated from seeds of Eucommia ulmoides and named EuWRI1. A close link between gibberellins signaling and EuWRI1 gene expression was suggested in this study. Functional characterization of EuWRI1 was elucidated through seed-specific expression in tobacco. In transgenic tobacco, the expression of EuWRI1 in eight independent transgenic lines was detected by semiquantitative RT-PCR. The relative mRNA accumulation of genes encoding enzymes involved in fatty acid biosynthesis (biotin carboxyl carrier protein and keto-ACP synthase 1) was also assayed in tobacco seeds. Analysis of the seeds oil content and starch content indicated that the transgenic lines showed a significant increase in seeds oil content, whereas starch content decreased significantly. Further analysis of the fatty acid composition revealed that palmitic acid (16:0), linoleic acid (18:2) and linolenic acid (18:3) increased significantly in seeds of transgenic tobacco lines, but stearic acid (18:0) levels significantly declined. © 2018 American Institute of Chemical Engineers Biotechnol. Prog., 34:337-346, 2018.

The Hardy Rubber Tree Genome Provides Insights into the Evolution of Polyisoprene Biosynthesis.

Eucommia ulmoides, also called hardy rubber tree, is an economically important tree; however, the lack of its genome sequence restricts the fundamental biological research and applied studies of this plant species. Here, we present a high-quality assembly of its ∼1.2-Gb genome (scaffold N50 = 1.88 Mb) with at least 26 723 predicted genes for E. ulmoides, the first sequenced genome of the order Garryales, which was obtained using an integrated strategy combining Illumina sequencing, PacBio sequencing, and BioNano mapping. As a sister taxon to lamiids and campanulids, E. ulmoides underwent an ancient genome triplication shared by core eudicots but no further whole-genome duplication in the last ∼125 million years. E. ulmoides exhibits high expression levels and/or gene number expansion for multiple genes involved in stress responses and the biosynthesis of secondary metabolites, which may account for its considerable environmental adaptability. In contrast to the rubber tree (Hevea brasiliensis), which produces cis-polyisoprene, E. ulmoides has evolved to synthesize long-chain trans-polyisoprene via farnesyl diphosphate synthases (FPSs). Moreover, FPS and rubber elongation factor/small rubber particle protein gene families were expanded independently from the H. brasiliensis lineage. These results provide new insights into the biology of E. ulmoides and the origin of polyisoprene biosynthesis.

[Plutella xylostella granulovirus PP31 interacts with two host proteins].

Protein-protein interactions between viruses and hosts are common during viral infection and replication. In this study, a cDNA library from larvae of Plutella xylostella was constructed and used for screening of genes encoding proteins interacting with Plutella xylostella granulovirus (PlxyGV) proteins. Two cDNA clones containing genes encoding proteins interacting with PlxyGV PP31 were identified by yeast two-hybrid assays. Sequence analysis showed that the genes encoded homologues of receptor for activated protein C kinase (RACK) and methionine aminopeptidase 2 (MetAP2), respectively. The P. xylostella rack gene and the PlxyGV pp31 was expressed in an E. coli strain to produce proteins fused with a 6-His or a GST tag. It was shown that the rack was expressed as a 38kD peptide as prospected. The 38kD His-tagged peptide was co-purified with GST-PP31 by GST-bind resin in GST-pulldown assays, confirming interaction between the PlxyGV PP31 and the RACK protein of P. xylostella.