An acyltransferase gene that putatively functions in anthocyanin modification was horizontally transferred from Fabaceae into the genus Cuscuta

The Role of MbEGS1 and MbEGS2 in Methyleugenol Biosynthesis by Melaleuca bracteata

Many aromatic plant volatile compounds contain methyleugenol, which is an attractant for insect pollination and has antibacterial, antioxidant, and other properties. The essential oil of Melaleuca bracteata leaves contains 90.46% methyleugenol, which is an ideal material for studying the biosynthetic pathway of methyleugenol. Eugenol synthase (EGS) is one of the key enzymes involved in the synthesis of methyleugenol. We recently reported two eugenol synthase genes (MbEGS1 and MbEGS2) present in M. bracteata, where MbEGS1 and MbEGS2 were mainly expressed in flowers, followed by leaves, and had the lowest expression levels in stems. In this study, the functions of MbEGS1 and MbEGS2 in the biosynthesis of methyleugenol were investigated using transient gene expression technology and virus-induced gene silencing (VIGS) technology in M. bracteata. Here, in the MbEGSs genes overexpression group, the transcription levels of the MbEGS1 gene and MbEGS2 gene were increased 13.46 times and 12.47 times, respectively, while the methyleugenol levels increased 18.68% and 16.48%. We further verified the function of the MbEGSs genes by using VIGS, as the transcript levels of the MbEGS1 and MbEGS2 genes were downregulated by 79.48% and 90.35%, respectively, and the methyleugenol content in M. bracteata decreased by 28.04% and 19.45%, respectively. The results indicated that the MbEGS1 and MbEGS2 genes were involved in the biosynthesis of methyleugenol, and the transcript levels of the MbEGS1 and MbEGS2 genes correlated with the methyleugenol content in M. bracteata.

Dynamics of Zea mays transcriptome in response to a polyphagous herbivore, Spodoptera litura

Zea mays defense response is well-crafted according to the physical and chemical weapons utilized by their invaders during the coevolutionary period. Maize plants employ diversified defense strategies and alter the spatiotemporal distribution of several classes of defensive compounds to affect insect herbivore performance. However, only little knowledge is available about the defense orchestration of maize in response to Spodoptera litura, a voracious Noctuidae pest. In order to decipher the defense status of Zea mays (African tall variety) against S. litura, a comparative feeding bioassay was executed, which revealed reduced performance of the herbivore on maize. In order to understand the molecular mechanism behind maize tolerance against S. litura, a microarray-based genome-wide expression analysis was performed. The comparative analysis displayed 792 differentially expressed genes (DEGs), wherein 357 genes were upregulated and 435 genes were downregulated at fold change ≥ 2 and p value ≤ 0.05. The upregulated genes were identified and categorized as defense-related, oxidative stress-related, transcription regulatory genes, protein synthesis genes, phytohormone-related, and primary and secondary metabolism-related. In contrast, downregulated genes were mainly associated with plant growth and development, indicating a balance of growth and defense response and utilization of a highly evolved C-diversion response were noticed. Maize plants showed better tolerance against herbivory and maintained its fitness using a combinatorial strategy. This peculiar response of Zea mays against S. litura offers an excellent possibility of managing polyphagous pests by spicing up the plant's defensive response with tolerance mechanism.

Diversity in flower colorations of Ranunculus asiaticus L. revealed by anthocyanin biosynthesis pathway in view of gene composition, gene expression patterns, and color phenotype

Anthocyanin biosynthesis is one of the best studied secondary metabolisms. However, related pathways were generally concluded based on anthocyanin components; most studies focused on the backbone forming of anthocyanidins (cyanidin, delphinidin, and pelargonidin) of model or commercial plants, while anthocyanin modification was less discussed, and non-model plants with abundant colorations were less researched either. Ranunculus asiaticus L. has great diversity in flower colorations, not only indicating its value in researching anthocyanin biosynthesis but also implying it is unique in this regard. Based on transcriptome sequencing and gene annotation of three varieties (10 samples) of Ranunculus asiaticus L., 176 unigenes from 151,136 unigenes were identified as involved in anthocyanin biosynthesis, among which, 74 unigenes were related to anthocyanin modification; 61 unigenes were responsible for glycosylation at C3 and C5 with 3-monosaccharides of glucose, 3-biosides of rutinose, sophorose, or sambubiose to form 3Gly-, 3Gly5Gly-, 3Gly3'Gly-, 3Gly2''Gly-, 3Gly2''Xly-, 3Gly2''Rly-glycosylated anthocyanins, etc.; 2 unigenes transferred -CH₃; 11 unigenes of BAHD family catalyzd the aromatic or malonyl acylation at 6'' / 6''''position of 3/5-O-glucoside. Based on gene composition, a putative pathway was established. The pathway was validated by flower colorations, and gene expression patterns where F3H, F3'H, 3GT, 5GT, and FMT2 were highly expressed in varieties colored as lateritious and carmine, while variety with purple flowers had high expression of F3'5'H and 3MAT. In view of anthocyanin biosynthesis pathway of Ranunculus asiaticus L., great diversity in its flower colorations was illustrated via the complete branches (F3H, F3'H and F3'5'H) as well as complete modifications (glycosylation, methylation, and acylation), and besides, via the higher percentage of C3 glycosylation than C5 glycosylation.

Widely targeted metabolome and transcriptome landscapes of Allium fistulosum-A. cepa chromosome addition lines revealed a flavonoid hot spot on chromosome 5A

Here, we report a comprehensive analysis of the widely targeted metabolome and transcriptome profiles of Allium fistulosum L. (FF) with the single extra chromosome of shallot [A. cepa L. Aggregatum group (AA)] to clarify the novel gene functions in flavonoid biosynthesis. An exhaustive metabolome analysis was performed using the selected reaction monitoring mode of liquid chromatography–tandem quadrupole mass spectrometry, revealing a specific accumulation of quercetin, anthocyanin and flavone glucosides in AA and FF5A. The addition of chromosome 5A from the shallot to A. fistulosum induced flavonoid accumulation in the recipient species, which was associated with the upregulation of several genes including the dihydroflavonol 4-reductase, chalcone synthase, flavanone 3-hydroxylase, UDP-glucose flavonoid-3-O-glucosyltransferase, anthocyanin 5-aromatic acyltransferase-like, pleiotropic drug resistance-like ATP binding cassette transporter, and MYB14 transcriptional factor. Additionally, an open access Allium Transcript Database (Allium TDB, http://alliumtdb.kazusa.or.jp) was generated by using RNA-Seq data from different genetic stocks including the A. fistulosum–A. cepa monosomic addition lines. The functional genomic approach presented here provides an innovative means of targeting the gene responsible for flavonoid biosynthesis in A. cepa. The understanding of flavonoid compounds and biosynthesis-related genes would facilitate the development of noble Allium varieties with unique chemical constituents and, subsequently, improved plant stress tolerance and human health benefits.

Sampling for DUS Test of Flower Colors of Ranunculus asiaticus L. in View of Spatial and Temporal Changes of Flower Colorations, Anthocyanin Contents, and Gene Expression Levels

Sampling for DUS test of flower colors should be fixed at the stages and sites that petals are fully colored, and besides, flower colorations are uniform among individuals and stable for a period of time to allow testers to get consistent results. It remains a problem since spatial and temporal flower colorations are reported a lot but their change traits are little discussed. In this study, expression state, uniformity and stability of color phenotypes, anthocyanin contents, and gene expression levels were taken into account based on measurements at 12 development stages and three layers (inner, middle, and outer petals) of two varieties of Ranunculus asiaticus L. to get their best sampling. Our results showed that, outer petals of L9–L10 (stage 9–stage 10 of variety ‘Jiaoyan zhuanhong’) and C5–C6 (stage 5–stage 6 of variety ‘Jiaoyan yanghong’) were the best sampling, respectively. For DUS test, it is suggested to track flower colorations continuously to get the best sampling as well as representative colors since different cultivars had different change traits, and moreover, full expression of color phenotypes came later and lasted for a shorter duration than those of anthocyanin contents and gene expressions. Our innovation exists in following two points. Firstly, a model of change dynamic was introduced to illustrate the change traits of flower colorations, anthocyanin contents, and gene expressions. Secondly, genes used for expression analysis were screened on account of tentative anthocyanins, which were identified based on comparison between liquid chromatography–mass spectrometry (LC–MS) results and molecular mass and mass fragment pattern (M²) of each putative anthocyanin and their fragments deduced in our previous study. Gene screening in this regard may also be interest for other non-model plant genera with little molecular background.

Alienness: Rapid Detection of Candidate Horizontal Gene Transfers across the Tree of Life

Horizontal gene transfer (HGT) is the transmission of genes between organisms by other means than parental to offspring inheritance. While it is prevalent in prokaryotes, HGT is less frequent in eukaryotes and particularly in Metazoa. Here, we propose Alienness, a taxonomy-aware web application available at http://alienness.sophia.inra.fr. Alienness parses BLAST results against public libraries to rapidly identify candidate HGT in any genome of interest. Alienness takes as input the result of a BLAST of a whole proteome of interest against any National Center for Biotechnology Information (NCBI) protein library. The user defines recipient (e.g., Metazoa) and donor (e.g., bacteria, fungi) branches of interest in the NCBI taxonomy. Based on the best BLAST E-values of candidate donor and recipient taxa, Alienness calculates an Alien Index (AI) for each query protein. An AI > 0 indicates a better hit to candidate donor than recipient taxa and a possible HGT. Higher AI represent higher gap of E-values between candidate donor and recipient and a more likely HGT. We confirmed the accuracy of Alienness on phylogenetically confirmed HGT of non-metazoan origin in plant-parasitic nematodes. Alienness scans whole proteomes to rapidly identify possible HGT in any species of interest and thus fosters exploration of HGT more easily and largely across the tree of life.

Two hAT transposon genes were transferred from Brassicaceae to broomrapes and are actively expressed in some recipients

A growing body of evidence is pointing to an important role of horizontal gene transfer (HGT) in the evolution of higher plants. However, reports of HGTs of transposable elements (TEs) in plants are still scarce, and only one case is known of a class II transposon horizontally transferred between grasses. To investigate possible TE transfers in dicots, we performed transcriptome screening in the obligate root parasite Phelipanche aegyptiaca (Orobanchaceae), data-mining in the draft genome assemblies of four other Orobanchaceae, gene cloning, gene annotation in species with genomic information, and a molecular phylogenetic analysis. We discovered that the broomrape genera Phelipanche and Orobanche acquired two related nuclear genes (christened BO transposase genes), a new group of the hAT superfamily of class II transposons, from Asian Sisymbrieae or a closely related tribe of Brassicaceae, by HGT. The collinearity of the flanking genes, lack of a classic border structure, and low expression levels suggest that BO transposase genes cannot transpose in Brassicaceae, whereas they are highly expressed in P. aegyptiaca.