New insight into the rapid growth of the Mikania micrantha stem based on DIA proteomic and RNA-Seq analysis

Unveiling the resistance of native weed communities: insights for managing invasive weed species in disturbed environments

Weed communities influence the dynamics of ecosystems, particularly in disturbed environments where anthropogenic activities often result in higher pollution. Understanding the dynamics existing between native weed communities and invasive species in disturbed environments is crucial for effective management and normal ecosystem functioning. Recognising the potential resistance of native weed communities to invasion in disturbed environments can help identify suitable native plants for restoration operations. This review aims to investigate the adaptations exhibited by native and non-native weeds that may affect invasions within disturbed environments. Factors such as ecological characteristics, altered soil conditions, and adaptations of native weed communities that potentially confer a competitive advantage relative to non-native or invasive weeds in disturbed environments are analysed. Moreover, the roles of biotic interactions such as competition, mutualistic relationships, and allelopathy in shaping the invasion resistance of native weed communities are described. Emphasis is given to the consideration of the resistance of native weeds as a key factor in invasion dynamics that provides insights for conservation and restoration efforts in disturbed environments. Additionally, this review underscores the need for further research to unravel the underlying mechanisms and to devise targeted management strategies. These strategies aim to promote the resistance of native weed communities and mitigate the negative effects of invasive weed species in disturbed environments. By delving deeper into these insights, we can gain an understanding of the ecological dynamics within disturbed ecosystems and develop valuable insights for the management of invasive species, and to restore long-term ecosystem sustainability.

Plant Adaptation to Flooding Stress under Changing Climate Conditions: Ongoing Breakthroughs and Future Challenges

Climate-change-induced variations in temperature and rainfall patterns are a serious threat across the globe. Flooding is the foremost challenge to agricultural productivity, and it is believed to become more intense under a changing climate. Flooding is a serious form of stress that significantly reduces crop yields, and future climatic anomalies are predicted to make the problem even worse in many areas of the world. To cope with the prevailing flooding stress, plants have developed different morphological and anatomical adaptations in their roots, aerenchyma cells, and leaves. Therefore, researchers are paying more attention to identifying developed and adopted molecular-based plant mechanisms with the objective of obtaining flooding-resistant cultivars. In this review, we discuss the various physiological, anatomical, and morphological adaptations (aerenchyma cells, ROL barriers (redial O2 loss), and adventitious roots) and the phytohormonal regulation in plants under flooding stress. This review comprises ongoing innovations and strategies to mitigate flooding stress, and it also provides new insights into how this knowledge can be used to improve productivity in the scenario of a rapidly changing climate and increasing flood intensity.

Laser-optics-based method to suppress Mikania micrantha growth

Mikania micrantha is an exotic and aggressive species that can reproduce asexually and sexually through its germinative stem and its featherlike seeds. Present weeding methods cannot effectively or economically control the spread of Mikania micrantha. In this article, we propose a method to suppress the growth and spread of Mikania micrantha by applying a high-energy laser beam to penetrate its stem. The threshold penetrating optical intensity is 3.1 W/mm². To optimize the damage to the inner tissue of the stem, which includes the vascular bundle and medulla for transporting organic nutrients, water, and inorganic salt, the absorption spectrum of the tissue and laser beam size are analyzed. According to the absorption spectrum of the tissue and growth mechanism of Mikania micrantha, a 455 nm blue laser is used as an irradiated light source. A single beam with two different beam sizes or two laser beams with the same beam size is used to optimize the stem damage. By the time the cumulative energy reaches 15 Joules for a single laser beam with dimensions of 0.81 mm × 0.74 mm, the inner tissue will be damaged 97.5%. We perform laser irradiation on the fresh Mikania micrantha grown hydroponically, with the result that all samples withered in 30 days. Therefore, using the method before the flowering season of Mikania micrantha can effectively inhibit its reproduction.

Differentially expressed genes related to plant height and yield in two alfalfa cultivars based on RNA-seq

Background

Alfalfa (Medicago sativa L.) is a kind of forage with high relative feeding value in farming and livestock breeding, and is of great significance to the development of animal husbandry. The growth of the aboveground part of alfalfa is an important factor that limits crop yield. Clarifying the molecular mechanisms that maintain vigorous growth in alfalfa may contribute to the development of molecular breeding for this crop.

Methods

Here, we evaluated the growth phenotypes of five cultivars of alfalfa (WL 712, WL 525HQ, Victoria, Knight 2, and Aohan). Then RNA-seq was performed on the stems of WL 712, chosen as a fast growing cultivar, and Aohan, chosen as a slow growing cultivar. GO enrichment analysis was conducted on all differentially expressed genes (DEGs).

Result

Among the differentially expressed genes that were up-regulated in the fast growing cultivar, GO analysis revealed enrichment in the following seven categories: formation of water-conducting tissue in vascular plants, biosynthesis and degradation of lignin, formation of the primary or secondary cell wall, cell enlargement and plant growth, cell division and shoot initiation, stem growth and induced germination, and cell elongation. KEGG analysis showed that differentially expressed genes were annotated as being involved in plant hormone signal transduction, photosynthesis, and phenylpropanoid biosynthesis. KEGG analysis also showed that up-regulated in the fast growing cultivar were members of the WRKY family of transcription factors related to plant growth and development, members of the NAC and MYB gene families related to the synthesis of cellulose and hemicellulose, and the development of secondary cell wall fibres, and finally, MYB family members that are involved in plant growth regulation. Our research results not only enrich the transcriptome database of alfalfa, but also provide valuable information for explaining the molecular mechanism of fast growth, and can provide reference for the production of alfalfa.

Antioxidant Regulation and DNA Methylation Dynamics During Mikania micrantha Seed Germination Under Cold Stress

As a primary goal, adaptation to cold climate could expand an invasion range of exotic plants. Here, we aimed to explore the regulation strategy of M. micrantha seed development under cold stress through molecular physiology and multi-omics analysis. Significant increase of hydrogen peroxide, malondialdehyde, and electrolyte leakage observed under cold stress revealed that oxidative damage within M. micrantha seed cells was induced in the initial germination phase. Proteomic data underscored an activation of antioxidant activity to maintain redox homeostasis, with a cluster of antioxidant proteins identified. Genomic-wide transcriptome, in combination with time-series whole-genome bisulfite sequencing mining, elucidated that seven candidate genes, which were the target of DNA demethylation-dependent ROS scavenging, were possibly associated with an M. micrantha germ break. Progressive gain of CHH context DNA methylation identified in an early germination phrase suggested a role of a DNA methylation pathway, while an active DNA demethylation pathway was also initiated during late seed development, which was in line with the expression trend of methylation and demethylation-related genes verified through qRT-PCR. These data pointed out that cold-dependent DNA demethylation and an antioxidant regulatory were involved together in restoring seed germination. The expression level of total 441 genes presented an opposite trend to the methylation divergence, while the expression of total 395 genes was proved to be negatively associated with their methylation levels. These data provided new insights into molecular reprograming events during M. micrantha seed development.

Full-length transcriptome analysis of multiple organs and identification of adaptive genes and pathways in Mikania micrantha

Mikania micrantha is a notorious invasive weed that has caused huge economic loss and negative ecological consequences in invaded areas. This species can adapt well to invasive environments with various stress factors. The identification of gene families and functional pathways related to environmental adaptability is lack in M. micrantha at the multi-organ full-length transcriptome level. In this study, we sequenced the transcriptomes of five M. micrantha organs using PacBio single-molecule real-time sequencing and Illumina RNA sequencing technologies. Based on the transcriptome data, full-length transcripts were captured and gene expression patterns among the five organs were analyzed. KEGG enrichment analysis of genes with higher expression indicated their special roles in environmental stress response and adversity adaptation in the various five organs. The gene families and pathways related to biotic and abiotic factors, including terpene synthases, glutathione S-transferases, antioxidant defense system, and terpenoid biosynthesis pathway, were characterized. The expression levels of most differentially expressed genes in the antioxidant defense system and terpenoid biosynthesis pathway were higher in root, stem, and leaf than in the other two organs, suggesting that root, stem, and leaf have strong ability to respond to adverse stresses and form the important organs of terpenoid synthesis and accumulation. Additionally, a large number of transcription factors and alternative splicing events were predicted. This study provides a comprehensive transcriptome resource for M. micrantha, and our findings facilitate further research on the adaptive evolution and functional genomics of this species.

Population Genomics Reveals Gene Flow and Adaptive Signature in Invasive Weed Mikania micrantha

A long-standing and unresolved issue in invasion biology concerns the rapid adaptation of invaders to nonindigenous environments. Mikania micrantha is a notorious invasive weed that causes substantial economic losses and negative ecological consequences in southern China. However, the contributions of gene flow, environmental variables, and functional genes, all generally recognized as important factors driving invasive success, to its successful invasion of southern China are not fully understood. Here, we utilized a genotyping-by-sequencing approach to sequence 306 M. micrantha individuals from 21 invasive populations. Based on the obtained genome-wide single nucleotide polymorphism (SNP) data, we observed that all the populations possessed similar high levels of genetic diversity that were not constrained by longitude and latitude. Mikania micrantha was introduced multiple times and subsequently experienced rapid-range expansion with recurrent high gene flow. Using FST outliers, a latent factor mixed model, and the Bayesian method, we identified 38 outlier SNPs associated with environmental variables. The analysis of these outlier SNPs revealed that soil composition, temperature, precipitation, and ecological variables were important determinants affecting the invasive adaptation of M. micrantha. Candidate genes with outlier signatures were related to abiotic stress response. Gene family clustering analysis revealed 683 gene families unique to M. micrantha which may have significant implications for the growth, metabolism, and defense responses of M. micrantha. Forty-one genes showing significant positive selection signatures were identified. These genes mainly function in binding, DNA replication and repair, signature transduction, transcription, and cellular components. Collectively, these findings highlight the contribution of gene flow to the invasion and spread of M. micrantha and indicate the roles of adaptive loci and functional genes in invasive adaptation.