Invasive alien plants are phylogenetically distinct from other alien species across spatial and taxonomic scales in China

IntroductionPhylogenetic relatedness is one of the important factors in the community assembly process. Here, we aimed to understand the large-scale phylogenetic relationship between alien plant species at different stages of the invasion process and how these relationships change in response to the environmental filtering process at multiple spatial scales and different phylogenetic extents.MethodsWe identified the alien species in three invasion stages, namely invasive, naturalized, and introduced, in China. The occurrence records of the species were used to quantify two abundance-based phylogenetic metrics [the net relatedness index (NRI) and the nearest taxon index (NTI)] from a highly resolved phylogenetic tree. The metrics were compared between the three categories of alien species. Generalized linear models were used to test the effect of climate on the phylogenetic pattern. All analyses were conducted at four spatial scales and for three major angiosperm families.ResultsWe observed significantly higher NRI and NTI values at finer spatial scales, indicating the formation of more clustered assemblages of phylogenetically closely related species in response to the environmental filtering process. Positive NTI values for the invasive and naturalized aliens suggested that the presence of a close relative in the community may help the successful naturalization and invasion of the introduced alien species. In the two-dimensional phylogenetic space, the invasive species communities significantly differed from the naturalized and introduced species, indicating that established alien species need to be phylogenetically different to become invasive. Positive phylogenetic measures for the invasive aliens across the spatial scales suggested that the presence of invasive aliens could facilitate the establishment of other invasive species. Phylogenetic relatedness was more influenced by temperature than precipitation, especially at a finer spatial scale. With decreased temperature, the invasive species showed a more clustered assemblage, indicating conservatism of their phylogenetic niche. The phylogenetic pattern was different at the family level, although there was a consistent tendency across families to form more clustered assemblages.DiscussionOverall, our study showed that the community assemblage became more clustered with the progression of the invasion process. The phylogenetic measures varied at spatial and taxonomic scales, thereby highlighting the importance of assessing phylogenetic patterns at different gradients of the community assembly process

Genome-Wide RNAi Screen in IFN-γ-Treated Human Macrophages Identifies Genes Mediating Resistance to the Intracellular Pathogen Francisella tularensis

Interferon-gamma (IFN-γ) inhibits intracellular replication of Francisella tularensis in human monocyte-derived macrophages (HMDM) and in mice, but the mechanisms of this protective effect are poorly characterized. We used genome-wide RNA interference (RNAi) screening in the human macrophage cell line THP-1 to identify genes that mediate the beneficial effects of IFN-γ on F. tularensis infection. A primary screen identified ∼200 replicated candidate genes. These were prioritized according to mRNA expression in IFN-γ-primed and F. tularensis-challenged macrophages. A panel of 20 top hits was further assessed by re-testing using individual shRNAs or siRNAs in THP-1 cells, HMDMs and primary human lung macrophages. Six of eight validated genes tested were also found to confer resistance to Listeria monocytogenes infection, suggesting a broadly shared host gene program for intracellular pathogens. The F. tularensis-validated hits included ‘druggable’ targets such as TNFRSF9, which encodes CD137. Treating HMDM with a blocking antibody to CD137 confirmed a beneficial role of CD137 in macrophage clearance of F. tularensis. These studies reveal a number of important mediators of IFN-γ activated host defense against intracellular pathogens, and implicate CD137 as a potential therapeutic target and regulator of macrophage interactions with Francisella tularensis

Interspecific variation and phylogenetic relationship between mangrove and non-mangrove species of a same family (Meliaceae)—insights from comparative analysis of complete chloroplast genome

The mahogany family, Meliaceae, contains 58 genera with only one mangrove genus: Xylocarpus. Two of the three species of the genus Xylocarpus are true mangroves (X. granatum and X. moluccensis), and one is a non-mangrove (X. rumphii). In order to resolve the phylogenetic relationship between the mangrove and non-mangrove species, we sequenced chloroplast genomes of these Xylocarpus species along with two non-mangrove species of the Meliaceae family (Carapa guianensis and Swietenia macrophylla) and compared the genome features and variations across the five species. The five Meliaceae species shared 130 genes (85 protein-coding genes, 37 tRNA, and eight rRNA) with identical direction and order, with a few variations in genes and intergenic spacers. The repetitive sequences identified in the rpl22 gene region only occurred in Xylocarpus, while the repetitive sequences in accD were found in X. moluccensis and X. rumphii. The TrnH-GUG and rpl32 gene regions and four non-coding gene regions showed high variabilities between X. granatum and the two non-mangrove species (S. macrophylla and C. guianensis). In addition, among the Xylocarpus species, only two genes (accD and clpP) showed positive selection. Carapa guianensis and S. macrophylla owned unique RNA editing sites. The above genes played an important role in acclimation to different stress factors like heat, low temperature, high UV light, and high salinity. Phylogenetic analysis with 22 species in the order Sapindales supported previous studies, which revealed that the non-mangrove species X. rumphii is closer to X. moluccensis than X. granatum. Overall, our results provided important insights into the variation of genetic structure and adaptation mechanism at interspecific (three Xylocarpus species) and intergeneric (mangrove and non-mangrove genera) levels

The Cry1Ab Protein Has Minor Effects on the Arbuscular Mycorrhizal Fungal Communities after Five Seasons of Continuous Bt Maize Cultivation.

The cultivation of genetically modified plants (GMP) has raised concerns regarding the plants' ecological safety. A greenhouse experiment was conducted to assess the impact of five seasons of continuous Bt (Bacillus thuringiensis) maize cultivation on the colonisation and community structure of the non-target organisms arbuscular mycorrhizal fungi (AMF) in the maize roots, bulk soils and rhizospheric soils using the terminal restriction fragment length polymorphism (T-RFLP) analysis of the 28S ribosomal DNA and sequencing methods. AMF colonisation was significantly higher in the two Bt maize lines that express Cry1Ab, 5422Bt1 (event Bt11) and 5422CBCL (MON810) than in the non-Bt isoline 5422. No significant differences were observed in the diversity of the AMF community between the roots, bulk soils and rhizospheric soils of the Bt and non-Bt maize cultivars. The AMF genus Glomus was dominant in most of the samples, as detected by DNA sequencing. A clustering analysis based on the DNA sequence data suggested that the sample types (i.e., the samples from the roots, bulk soils or rhizospheric soils) might have greater influence on the AMF community phylotypes than the maize cultivars. This study indicated that the Cry1Ab protein has minor effects on the AMF communities after five seasons of continuous Bt maize cultivation

Effects of Exogenous Salicylic Acid Application to Aboveground Part on the Defense Responses in Bt (Bacillus thuringiensis) and Non-Bt Corn (Zea mays L.) Seedlings

Bt (Bacillus thuringiensis) corn is one of the top three large-scale commercialized anti-insect transgenic crops around the world. In the present study, we tested the Bt protein content, defense chemicals contents, and defense enzyme activities in both the leaves and roots of Bt corn varieties 5422Bt1 and 5422CBCL, as well as their conventional corn 5422 seedlings, with two fully expanded leaves which had been treated with 2.5 mM exogenous salicylic acid (SA) to the aboveground part for 24 h. The result showed that the SA treatment to the aboveground part could significantly increase the polyphenol oxidase activity of conventional corn 5422, the Bt protein content, and peroxidase activities of Bt corn 5422Bt1, as well as the polyphenol oxidase and peroxidase activity of Bt corn 5422CBCL in the leaves. In the roots, the polyphenol oxidase and peroxidase activity of conventional corn 5422, the polyphenol oxidase and superoxide dismutase activities of Bt corn 5422Bt1, the DIMBOA (2,4-dihydroxy-7-methoxy-2H, 1, 4-benzoxazin-3 (4H)-one) content, and four defense enzymes activities of Bt corn 5422CBCL were systematically increased. These findings suggest that the direct effect of SA application to aboveground part on the leaf defense responses in Bt corn 5422CBCL is stronger than that in non-Bt corn. Meanwhile, the systemic effect of SA on the root defense responses in Bt corn 5422CBCL is stronger than that in conventional corn 5422 and Bt corn 5422Bt1. It can be concluded that the Bt gene introduction and endogenous chemical defense responses of corns act synergistically during the SA-induced defense processes to the aboveground part. Different transformation events affected the root defense response when the SA treatment was applied to the aboveground part

Effects of Salicylic Acid Concentration and Post-Treatment Time on the Direct and Systemic Chemical Defense Responses in Maize (Zea mays L.) Following Exogenous Foliar Application

Salicylic acid (SA) plays a critical role in allergic reactions of plants to pathogens and acquired systemic resistance. Thus far, although some research has been conducted on the direct effects of different concentrations of SA on the chemical defense response of treated plant parts (leaves) after at multiple post-treatments times, few research has reported on the systematic effects of non-treated parts (roots). Therefore, we examined direct and systemic effects of SA concentration and time following foliar application on chemical defense responses in maize variety 5422 with two fully expanded leaves. In the experiments, maize leaves were treated with different SA concentrations of 0.1, 0.5, 1.0, 2.5, 5.0 mM, and then, the presence of defense chemicals and enzymes in treated leaves and non-treated roots was measured at different time points of 3, 12, 24, 48, 72 h following SA foliar application. The results showed that direct and systemic effects of SA treatment to the leaf on chemical defense responses were related to SA concentration and time of measurement after spraying SA. In treated leaves, total phenolics content increased directly by 28.65% at the time point of 12 h following foliar application of 0.5 mM SA. DIMBOA (2,4-dihydroxy-7-methoxy-2H, 1, 4-benzoxazin-3 (4H)-one) content was directly enhanced by 80.56~551.05% after 3~72 h following 0.5~5.0 mM SA treatments. Polyphenol oxidase and superoxide dismutase activities were directly enhanced after 12~72 h following 0.5~5.0 mM SA treatments, whereas peroxidase and catalase activities were increased after 3~24 h following application of 1.0~5.0 mM SA. In non-treated roots, DIMBOA content and polyphenol oxidase activity were enhanced systematically after 3~48 h following 1.0~5.0 mM SA foliar treatments. Superoxide dismutase activities were enhanced after 3~24 h following 0.5~2.5 mM SA applications, but total phenolics content, peroxidase and catalase activity decreased in some particular concentrations or at the different times of measurement in the SA treatment. It can be concluded that SA foliar application at 1.0 and 2.5 mM produces strong chemical defense responses in maize, with the optimal induction time being 24 h following the foliar application

High-Precision Detection for Sandalwood Trees via Improved YOLOv5s and StyleGAN

An algorithm model based on computer vision is one of the critical technologies that are imperative for agriculture and forestry planting. In this paper, a vision algorithm model based on StyleGAN and improved YOLOv5s is proposed to detect sandalwood trees from unmanned aerial vehicle remote sensing data, and this model has excellent adaptability to complex environments. To enhance feature expression ability, a CA (coordinate attention) module with dimensional information is introduced, which can both capture target channel information and keep correlation information between long-range pixels. To improve the training speed and test accuracy, SIOU (structural similarity intersection over union) is proposed to replace the traditional loss function, whose direction matching degree between the prediction box and the real box is fully considered. To achieve the generalization ability of the model, StyleGAN is introduced to augment the remote sensing data of sandalwood trees and to improve the sample balance of different flight heights. The experimental results show that the average accuracy of sandalwood tree detection increased from 93% to 95.2% through YOLOv5s model improvement; then, on that basis, the accuracy increased by another 0.4% via data generation from the StyleGAN algorithm model, finally reaching 95.6%. Compared with the mainstream lightweight models YOLOv5-mobilenet, YOLOv5-ghost, YOLOXs, and YOLOv4-tiny, the accuracy of this method is 2.3%, 2.9%, 3.6%, and 6.6% higher, respectively. The size of the training sandalwood tree model is 14.5 Mb, and the detection time is 17.6 ms. Thus, the algorithm demonstrates the advantages of having high detection accuracy, a compact model size, and a rapid processing speed, making it suitable for integration into edge computing devices for on-site real-time monitoring

Characterization of the complete chloroplast genome of Trailliaedoxa gracilis (Rubiaceae)

Trailliaedoxa gracilis (Rubiaceae) is a Chinese endemic monotypic genus distributed in southwestern China. This study reported the complete chloroplast genome of T. gracilis assembled from Illumina sequencing reads. The chloroplast genome size is 152,407 bp, containing a single large copy (LSC) region of 82,957 bp, a short single copy (SSC) region of 17,936 bp, and a pair of inverted repeats (IRs) of 25,757 bp. A total of 127 genes were found, including 82 protein-coding genes, 37 tRNA genes, and eight rRNA genes. A phylogenetic analysis using the maximum likelihood algorithm revealed that T. gracilis belonged to the subfamily Ixoroideae and had the closest relationship with Scyphiphora hydrophyllacea