Long-read RNA sequencing can probe organelle genome pervasive transcription.

40 years ago, organelle genomes were assumed to be streamlined and, perhaps, unexciting remnants of their prokaryotic past. However, the field of organelle genomics has exposed an unparallel diversity in genome architecture (i.e. genome size, structure, and content). The transcription of these eccentric genomes can be just as elaborate - organelle genomes are pervasively transcribed into a plethora of RNA types. However, while organelle protein-coding genes are known to produce polycistronic transcripts that undergo heavy posttranscriptional processing, the nature of organelle noncoding transcriptomes is still poorly resolved. Here, we review how wet-lab experiments and second-generation sequencing data (i.e. short reads) have been useful to determine certain types of organelle RNAs, particularly noncoding RNAs. We then explain how third-generation (long-read) RNA-Seq data represent the new frontier in organelle transcriptomics. We show that public repositories (e.g. NCBI SRA) already contain enough data for inter-phyla comparative studies and argue that organelle biologists can benefit from such data. We discuss the prospects of using publicly available sequencing data for organelle-focused studies and examine the challenges of such an approach. We highlight that the lack of a comprehensive database dedicated to organelle genomics/transcriptomics is a major impediment to the development of a field with implications in basic and applied science.

Photobiomodulation Treatment with a Home-Use Device for COVID-19: A Randomized Controlled Trial for Efficacy and Safety.

Background: Photobiomodulation therapy (PBMT) using devices to deliver red and/or near-infrared light to tissues has shown promising effects in clinical settings for respiratory diseases, including potential benefits in managing symptoms associated with COVID-19. Objective: To determine if at-home self-administered PBMT for patients with COVID-19 is safe and effective. Methods: This was a randomized controlled trial (RCT) carried out at home during the COVID-19 pandemic (September 2020 to August 2021). The treatment group self-administered the Vielight RX Plus PBMT device (635 nm intranasal and 810 nm chest LEDs) and were monitored remotely. Eligible patients scored 4-7 (out of 7) for severity on the Wisconsin Upper Respiratory Symptom Survey (WURSS-44). Patients were randomized equally to Control group receiving standard-of-care (SOC) only or Treatment group receiving SOC plus PBMT. The device was used for 20 min 2X/day for 5 days and, subsequently, once daily for 30 days. The primary end-point was time-to-recovery (days) based on WURSS-44 question 1, "How sick do you feel today?". Subgroup analysis was performed, and Kaplan-Meier and Cox Proportional Hazards analysis were employed. Results: One hundred and ninety-nine eligible patients (18-65 years old) were divided into two subgroups as follows: 136 patients with 0-7 days of symptoms at baseline and 63 patients with 8-12 days of symptoms. Those with 0-7 days of symptoms at baseline recovered significantly faster with PBMT. The median for Treatment group was 18 days [95% confidence interval (CI), 13-20] versus the Control group 21 days (95% CI, 15-28), p = 0.050. The treatment:control hazard ratio was 1.495 (95% CI, 0.996-2.243), p = 0.054. Patients with symptom duration ≥7 days did not show any significant improvement. No deaths or severe adverse events (SAEs) occurred in the Treatment group, whereas there was 1 death and 3 SAEs requiring hospitalization in the Control group. Conclusions: Patients with ≤7 days of COVID-19 symptoms recovered significantly faster with PBMT compared to SOC. Beyond 7 days, PBMT showed no superiority over SOC. Trial Registration: ClinicalTrials.gov NCT04418505.

Potential distribution and ecological impacts of Acmella radicans (Jacquin) R.K. Jansen (a new Yunnan invasive species record) in China.

BACKGROUND ACMELLA RADICANS: (Jacquin) R.K. Jansen is a new invasive species record for Yunnan Province, China. Native to Central America, it has also been recently recorded invading other parts of Asia. To prevent this weed from becoming a serious issue, an assessment of its ecological impacts and potential distribution is needed. We predicted the potential distribution of A. radicans in China using the MaxEnt model and its ecological impacts on local plant communities and soil nutrients were explored. RESULTS: Simulated training using model parameters produced an area under curve value of 0.974, providing a high degree of confidence in model predictions. Environmental variables with the greatest predictive power were precipitation of wettest month, isothermality, topsoil TEB (total exchangeable bases), and precipitation seasonality, with a cumulative contribution of more than 72.70% and a cumulative permutation importance of more than 69.20%. The predicted potential suitable area of A. radicans in China is concentrated in the southern region. Projected areas of A. radicans ranked as high and moderately suitable comprised 5425 and 26,338 km2, accounting for 0.06 and 0.27% of the Chinese mainland area, respectively. Over the 5 years of monitoring, the population density of A. radicans increased while at the same time the population density and importance values of most other plant species declined markedly. Community species richness, diversity, and evenness values significantly declined. Soil organic matter, total N, total P, available N, and available P concentrations decreased significantly with increasing plant cover of A. radicans, whereas pH, total K and available K increased. CONCLUSION: Our study was the first to show that A. radicans is predicted to expand its range in China and may profoundly affect plant communities, species diversity, and the soil environment. Early warning and monitoring of A. radicans must be pursued with greater vigilance in southern China to prevent its further spread.

Pervasive transcription of plant organelle genomes: functional noncoding transcriptomes?

Plant mitochondrial and plastid genomes typically show pervasive, genome-wide transcription. Little is known, however, about the utility of organelle noncoding RNAs, which often make up most of the transcriptome. Here, we suggest that long-read sequencing data combined with dedicated RNA databases could help identify putative functional organelle noncoding transcripts.

Experience and severity of menopause symptoms and effects on health-seeking behaviours: a cross-sectional online survey of community dwelling adults in the United Kingdom.

BACKGROUND: Almost all women will experience menopause, and the symptoms can have a severely detrimental impact on their quality of life. However, there is limited research exploring health-seeking behaviours and alternative service design or consultation formats. Group consultations have been successfully deployed in perinatal and diabetic care, improving accessibility and outcomes. This cross-sectional online survey was conducted to explore women's personal experiences of menopause, including perspectives on group consultations. METHODS: An online survey investigated the experiences of individuals at all stages of menopause and their receptiveness towards group consultations for menopause. Respondents were categorised by menopause stage according to the STRAW + 10 staging system. Associations between menopause stage, acceptability of group consultations and participant demographics were assessed using logistic regression. RESULTS: Respondents experienced an average of 10.7 menopausal symptoms, but only 47% of respondents felt they had the knowledge and tools to manage their symptoms. Advice on menopause was sought from a healthcare professional (HCP) by 61% of respondents, the largest trigger for this being severity of symptoms and the main barrier for this was the perception that menopause wasn't a valid enough reason to seek help. Of the respondents seeking advice from HCPs, 32% were prescribed transdermal HRT, 29% received oral HRT, 19% were offered antidepressants, 18% received local oestrogen and 6% were prescribed testosterone. Over three quarters (77%) of respondents indicated that they would join a group consultation for menopause and would be comfortable sharing their experiences with others (75%). Logistic regression indicated premenopausal respondents were 2.84 times more likely than postmenopausal women to be interested in a group consultation where they can meet or learn from others' experiences. CONCLUSIONS: This study highlighted a strong willingness of women aged 35-70 to participate in group consultations for menopause, with motivation being strongest amongst premenopausal women. Low awareness of self-management and lifestyle interventions to manage the symptoms of menopause highlight the need for greater outreach, research and interventions to build knowledge and confidence in the general population at scale. Future studies should focus on investigating the effectiveness and economic impact of menopause group consultations and the lived experience of individuals participating in group consultations.

Sweet potato (Ipomoea batatas) and hyacinth bean (Lablab purpureus) in combination provide greater suppression of mile-a-minute (Mikania micrantha) than either crop alone.

Introduction: In natural systems, diverse plant communities tend to prevent a single species from dominating. Similarly, management of invasive alien plants may be achieved through various combinations of competing species. Methods: We used a de Wit replacement series to compare different combinations of sweet potato (Ipomoea batatas (L.) Lam), hyacinth bean (Lablab purpureus (L.) Sweet) and mile-a-minute (Mikania micrantha Kunth) through measures of photosynthesis, plant growth, nutrient levels in plant tissue and soil, and competitive ability. Results: Cultured alone sweet potato and hyacinth beans exhibited higher total biomass, leafstalk length, and leaf area than mile-a-minute. In mixed culture, either sweet potato or hyacinth bean or both together significantly suppressed the mile-a-minute parameters, i.e., plant height, branch, leaf, adventitious root, and biomass (P<0.05). Based on a significantly lower than 1.0 relative yield of the three plant species in mixed culture, we showed intraspecific competition to be less than interspecific competition. Calculated indices (relative yield, relative yield total, competitive balance index, and change in contribution) demonstrated a higher competitive ability and higher influence of either crop compared to mile-a-minute. The presence of sweet potato and hyacinth bean, especially with both species in combination, significantly reduced (P<0.05) mile-a-minute's net photosynthetic rate (Pn), antioxidant enzyme activities (superoxide dismutase, peroxidase, catalase, and malondialdehyde), chlorophyll content, and nutrient content (N, P, and K). In soil with mile-a-minute in monoculture soil organic matter, total and available N, total and available K, and available P were significantly greater (P<0.05) than in soil with sweet potato grown in monoculture, but less than in soil with hyacinth bean grown in monoculture soil. Nutrient soil content was comparatively reduced for plant mixtures. Plant height, leaf, biomass, Pn, antioxidant enzyme activities, and plant and soil nutrient contents of sweet potato and hyacinth bean tended to be much greater when grown with two crops compared to in mixture with just sweet potato or hyacinth bean. Discussion: Our results suggest that the competitive abilities of both sweet potato and hyacinth bean were greater than that of mile-a-minute, and also that mile-a-minute suppression was significantly improved via a combination of the two crops compared to either sweet potato or hyacinth bean alone.

HSDatabase-a database of highly similar duplicate genes from plants, animals, and algae.

Gene duplication is an important evolutionary mechanism capable of providing new genetic material, which in some instances can help organisms adapt to various environmental conditions. Recent studies, for example, have indicated that highly similar duplicate genes (HSDs) are aiding adaptation to extreme conditions via gene dosage. However, for most eukaryotic genomes HSDs remain uncharacterized, partly because they can be hard to identify and categorize efficiently and effectively. Here, we collected and curated HSDs in nuclear genomes from various model animals, land plants and algae and indexed them in an online, open-access sequence repository called HSDatabase. Currently, this database contains 117 864 curated HSDs from 40 distinct genomes; it includes statistics on the total number of HSDs per genome as well as individual HSD copy numbers/lengths and provides sequence alignments of the duplicate gene copies. HSDatabase also allows users to download sequences of gene copies, access genome browsers, and link out to other databases, such as Pfam and Kyoto Encyclopedia of Genes and Genomes. What is more, a built-in Basic Local Alignment Search Tool option is available to conveniently explore potential homologous sequences of interest within and across species. HSDatabase has a user-friendly interface and provides easy access to the source data. It can be used on its own for comparative analyses of gene duplicates or in conjunction with HSDFinder, a newly developed bioinformatics tool for identifying, annotating, categorizing and visualizing HSDs. Database URL: http://hsdfinder.com/database/.

An overview of online resources for intra-species detection of gene duplications.

Gene duplication plays an important role in evolutionary mechanism, which can act as a new source of genetic material in genome evolution. However, detecting duplicate genes from genomic data can be challenging. Various bioinformatics resources have been developed to identify duplicate genes from single and/or multiple species. Here, we summarize the metrics used to measure sequence identity among gene duplicates within species, compare several computational approaches that have been used to predict gene duplicates, and review recent advancements of a Basic Local Alignment Search Tool (BLAST)-based web tool and database, allowing future researchers to easily identify intra-species gene duplications. This article is a quick reference guide for research tools used for detecting gene duplicates.

The evolution of extremely diverged plastomes in Selaginellaceae (lycophyte) is driven by repeat patterns and the underlying DNA maintenance machinery.

Two factors are proposed to account for the unusual features of organellar genomes: the disruptions of organelle-targeted DNA replication, repair, and recombination (DNA-RRR) systems in the nuclear genome and repetitive elements in organellar genomes. Little is known about how these factors affect organellar genome evolution. The deep-branching vascular plant family Selaginellaceae is known to have a deficient DNA-RRR system and convergently evolved organellar genomes. However, we found that the plastid genome (plastome) of Selaginella sinensis has extremely accelerated substitution rates, a low GC content, pervasive repeat elements, a dynamic network structure, and it lacks direct or inverted repeats. Unexpectedly, its organelle DNA-RRR system is short of a plastid-targeted Recombinase A1 (RecA1) and a mitochondrion-targeted RecA3, in line with other explored Selaginella species. The plastome contains a large collection of short- and medium-sized repeats. Given the absence of RecA1 surveillance, we propose that these repeats trigger illegitimate recombination, accelerated mutation rates, and structural instability. The correlations between repeat quantity and architectural complexity in the Selaginella plastomes support these conclusions. We, therefore, hypothesize that the interplay of the deficient DNA-RRR system and the high repeat content has led to the extraordinary divergence of the S. sinensis plastome. Our study not only sheds new light on the mechanism of plastome divergence by emphasizing the power of cytonuclear integration, but it also reconciles the longstanding contradiction on the effects of DNA-RRR system disruption on genome structure evolution.

Molecular Mechanisms behind Safranal's Toxicity to HepG2 Cells from Dual Omics.

The spice saffron (Crocus sativus) has anticancer activity in several human tissues, but the molecular mechanisms underlying its potential therapeutic effects are poorly understood. We investigated the impact of safranal, a small molecule secondary metabolite from saffron, on the HCC cell line HepG2 using untargeted metabolomics (HPLC-MS) and transcriptomics (RNAseq). Increases in glutathione disulfide and other biomarkers for oxidative damage contrasted with lower levels of the antioxidants biliverdin IX (139-fold decrease, p = 5.3 × 105), the ubiquinol precursor 3-4-dihydroxy-5-all-trans-decaprenylbenzoate (3-fold decrease, p = 1.9 × 10-5), and resolvin E1 (-3282-fold decrease, p = 45), which indicates sensitization to reactive oxygen species. We observed a significant increase in intracellular hypoxanthine (538-fold increase, p = 7.7 × 10-6) that may be primarily responsible for oxidative damage in HCC after safranal treatment. The accumulation of free fatty acids and other biomarkers, such as S-methyl-5'-thioadenosine, are consistent with safranal-induced mitochondrial de-uncoupling and explains the sharp increase in hypoxanthine we observed. Overall, the dual omics datasets describe routes to widespread protein destabilization and DNA damage from safranal-induced oxidative stress in HCC cells.

Allelochemicals Identified From Sweet Potato (Ipomoea batatas) and Their Allelopathic Effects on Invasive Alien Plants.

Sweet potato [Ipomoea batatas (L.) Lam] is grown as important cash and food crop worldwide and has been shown to exhibit allelopathic effects on other plants. However, its metabolome has not been studied extensively, particularly with respect to the production of phytotoxic bioactive secondary products. In this study, the chemical composition of petroleum ether extract of sweet potato was characterized, and the morphological and physiological effects of some individual components against four invasive alien weeds Bidens pilosa L., Galinsoga parviflora Cav., Lolium multiflorum Lam., and Phalaris minor Retz. were determined. Twenty-one components were identified by GS-MS, constituting 96.08% of petroleum ether extract in sweet potato. The major components were palmitic acid (PA) (17.48%), ethyl linoleate (EL) (13.19%), linoleic acid (LA) (12.55%), ethyl palmitate (EP) (11.77%), ethyl linolenate (ELL) (8.29%) oleic acid (5.82%), ethyl stearate (4.19%), and 3-methylphenol acetate (3.19%). The five most abundant compounds exhibited strong inhibition activity against the four invasive weeds tested. The highest inhibition rates were seen for LA, followed by PA and EP, respectively. Catalase (CAT), malondialdehyde (MDA), and peroxidase (POD) content of L. multiflorum were increased by the three allelochemicals, i.e., LA, PA and EP, but superoxide dismutase (SOD), chlorophyll-a and chlorophyll-b levels declined. Overall, the combined impact of all five compounds could be quite effective in suppressing the invasive weeds of concern.

Genome evolution: Minicircular mtDNA and unusual heteroplasmy in a parasitic plant.

Minicircular organelle genomes exist in diverse species but have never been observed in plants - that is, until now. The mitochondrial genome of the holoparasite Rhopalocnemis phalloides comprises 21 minicircles, which are extremely heteroplasmic, providing an exceptional example of convergent organelle evolution across disparate lineages.

Simple Matching Using QIIME 2 and RDP Reveals Misidentified Sequences and an Underrepresentation of Fungi in Reference Datasets.

Simple nucleotide matching identification methods are not as accurate as once thought at identifying environmental fungal sequences. This is largely because of incorrect naming and the underrepresentation of various fungal groups in reference datasets. Here, we explore these issues by examining an environmental metabarcoding dataset of partial large subunit rRNA sequences of Basidiomycota and basal fungi. We employed the simple matching method using the QIIME 2 classifier and the RDP Classifier in conjunction with the latest releases of the SILVA (138.1, 2020) and RDP (11, 2014) reference datasets and then compared the results with a manual phylogenetic binning approach. Of the 71 query sequences tested, 21 and 42% were misidentified using QIIME 2 and the RDP Classifier, respectively. Of these simple matching misidentifications, more than half resulted from the underrepresentation of various groups of fungi in the SILVA and RDP reference datasets. More comprehensive reference datasets with fewer misidentified sequences will increase the accuracy of simple matching identifications. However, we argue that the phylogenetic binning approach is a better alternative to simple matching since, in addition to better accuracy, it provides evolutionary information about query sequences.

Mutational Effects of Mobile Introns on the Mitochondrial Genomes of Metschnikowia Yeasts.

It has been argued that DNA repair by homologous recombination in the context of endonuclease-mediated cleavage can cause mutations. To better understand this phenomenon, we examined homologous recombination following endonuclease cleavage in a native genomic context: the movement of self-splicing introns in the mitochondrial genomes of Metschnikowia yeasts. Self-splicing mitochondrial introns are mobile elements, which can copy and paste themselves at specific insertion sites in mitochondrial DNA using a homing endonuclease in conjunction with homologous recombination. Here, we explore the mutational effects of self-splicing introns by comparing sequence variation within the intron-rich cox1 and cob genes from 71 strains (belonging to 40 species) from the yeast genus Metschnikowia. We observed a higher density of single nucleotide polymorphisms around self-splicing-intron insertion sites. Given what is currently known about the movement of organelle introns, it is likely that their mutational effects result from the high binding affinity of endonucleases and their interference with repair machinery during homologous recombination (or, alternatively, via gene conversion occurring during the intron insertion process). These findings suggest that there are fitness costs to harbouring self-splicing, mobile introns and will help us better understand the risks associated with modern biotechnologies that use endonuclease-mediated homologous recombination, such as CRISPR-Cas9 gene editing.

Protocol for using NoBadWordsCombiner to merge and minimize "bad words" from BLAST hits against multiple eukaryotic gene annotation databases.

Annotating protein-coding genes can be challenging, especially when searching for the best hits against multiple functional databases. This is partly because of "bad words" appearing as top hits, such as hypothetical or uncharacterized proteins. To help alleviate some of these issues, we designed a bioinformatics tool called NoBadWordsCombiner, which efficiently merges the hits from various databases, strengthening gene definitions by minimizing functional descriptions containing "bad words." Unlike other available tools, NoBadWordsCombiner is user friendly, but it does require users to have some general bioinformatics skills, including a basic understanding of the BLAST package and dash shell in Linux/Unix environments. For complete details on the use and execution of this protocol, please refer to Zhang et al. (2021a).

Protocol for HSDFinder: Identifying, annotating, categorizing, and visualizing duplicated genes in eukaryotic genomes.

Although gene duplications have been documented in many species, the precise numbers of highly similar duplicated genes (HSDs) in eukaryotic nuclear genomes remain largely unknown and can be time-consuming to explore. We developed HSDFinder to identify, categorize, and visualize HSDs in eukaryotic nuclear genomes using protein family domains and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. In contrast to existing tools, HSDFinder allows users to compare HSDs among different species and visualize results in different KEGG pathway functional categories via heatmap plotting. For complete details on the use and execution of this protocol, please refer to Zhang et al. (2021).

Adventitious roots support population expansion of the invasive plant Mikania micrantha Kunth.

Mikania micrantha Kunth is a serious invasive alien plant characterized by the formation of an adventitious root system in its prostrate growth form. Unlike the initial roots from seed germination, adventitious roots gradually appear above the stem and branch nodes. Little is known about adventitious roots play on plant growth and population expansion of M. micrantha. We hypothesized that adventitious roots provide an advantage for plant growth and nutrient availability. To test this hypothesis, plant growth, physiology, and nutrition characteristics of M. micrantha were measured under four soil surface conditions allowing various plant parts to touch the soil to stimulate variable adventitious root formation. The results showed that the biomass, stem length, branch number, and adventitious root biomass of M. micrantha were significantly increased (P < 0.05) with increasing nodes bearing adventitious roots. As the number of nodes with adventitious roots increased, the net photosynthetic rate, antioxidant enzyme activities like superoxide dismutase, catalase, peroxidase, and malondialdehyde, chlorophyll content, and plant nutrient contents (N, P, and K) of M. micrantha were increased (P < 0.05), with higher values in main stem leaves than in those of branch leaves. The concentrations of soil organic matter, total N, total P, total K, available N, available P, and available K were greater (P < 0.05) in initial soil (CK) than in treatment soil (with M. micrantha) and were significantly reduced by adventitious roots. Our study was the first to show that plant growth, physiology and nutrition status of M. micrantha were strongly promoted by adventitious roots in the prostrate growth form.

Differences in echocardiography interpretation techniques among trainees and expert readers.

BACKGROUND: Trainees learn transthoracic echocardiogram (TTE) interpretation through independently completing and reviewing selected portions of the study with experts. The diagnostic accuracy of novice TTE interpretation is known to be low and schema for reading TTEs systematically are lacking. The purpose of our study is to identify techniques experts use while reading TTEs which could be used to more effectively teach novice readers. METHODS: We performed a prospective qualitative case study to observe how experts and trainees interpret TTEs in an academic institution using a concurrent think aloud (CTA) method. Three TTEs of intermediate complexity were given to 3 advanced imaging fellows, 3 first year fellows and 3 expert TTE readers Participants filled out a report while reading and described aloud their thought processes. Sessions were video and audiotaped for analysis. RESULTS: Experts and advanced fellows used specific techniques that novices did not including: previewing studies, reviewing multiple images simultaneously, having flexibility in image review order and disease coding, and saving hardest elements to code for the end. Direct observation of TTE reading informed trainee inefficiencies and was a well-received educational tool. CONCLUSIONS: In this single centered study we identified several unique approaches experts use to interpret TTEs which may be teachable to novices. Although limited in generalizability the findings of this study suggests that a more systematic approach to TTE interpretation, using techniques found in experts, might be of significant value for trainees. Further study is needed to evaluate teaching practices at other institutions and to assess whether implementation of these techniques by novices improves can improve their diagnostic accuracy and efficiency of reading at an earlier stage in their training.

Potential use of Helianthus tuberosus to suppress the invasive alien plant Ageratina adenophora under different shade levels.

BACKGROUND: An ecological approach for managing biological invasions in agroecosystems is the selection of alternative crop species to manage the infestation of invasive alien plants through competition. In the current study, plant growth, photosynthesis, and competitive ability of the crop Helianthus tuberosus L. (Jerusalem artichoke) and the invasive alien plant Ageratina adenophora (Spreng.) R. M. King and H. Rob were compared under varying shade levels by utilizing a de Wit replacement series method. We hypothesized that H. tuberosus had higher competitive ability than A. adenophora even under shaded conditions. RESULTS: The results showed the main stem, leafstalk length, leaf area, underground biomass, and aboveground biomass of A. adenophora were significantly lower compared to H. tuberosus in monoculture although A. adenophora had a greater number of branches that were longer on average. Under full sunlight, the total shoot length (stem + branch length), main stem length and branch length of A. adenophora were significantly suppressed (P < 0.05) by increasing proportions of H. tuberosus, and the same morphological variables of H. tuberosus were significantly higher with decreasing proportions of H. tuberosus. With increasing shade rates and plant ratios, the plant height, branch, leaf, and biomass of both plants were significantly suppressed, but to a greater degree in the case of A. adenophora. The net photosynthetic rate (Pn) of H. tuberosus and A. adenophora increased gradually from July to September, then decreased in October. The Pn of H. tuberosus was consistently higher than that of A. adenophora. Although the Pn for both species was significantly reduced with increasing shade rates and plant ratios, A. adenophora experienced greater inhibition than H. tuberosus. The relative yield (RY) of A. adenophora was significantly less than 1.0 (P < 0.05) in mixed culture under all shade levels, indicating that the intraspecific competition was less than interspecific competition. The RY of H. tuberosus was significantly less than 1.0 under 40-60% shade and greater than 1.0 (P < 0.05) under 0-20% shade in mixed culture, respectively, showing that intraspecific competition was higher than interspecific competition under low shade, but the converse was true under high shade. The relative yield total (RYT) of A. adenophora and H. tuberosus was less than 1.0 in mixed culture, indicating that there was competition between the two plants. The fact that the competitive balance (CB) index of H. tuberosus was greater than zero demonstrated a higher competitive ability than A. adenophora even at the highest shade level (60%). CONCLUSIONS: Our results suggest that H. tuberosus is a promising replacement control candidate for managing infestations of A. adenophora, and could be widely used in various habitats where A. adenophora invades.