The emergence of the hyperinvasive vine, Mikania micrantha (Asteraceae), via admixture and founder events inferred from population transcriptomics

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.

Comparative transcriptome analyses of three Gentiana species provides signals for the molecular footprints of selection effects and the phylogenetic relationships

Species in Gentiana section Cruciata are important alpine plants with a center of diversity and speciation in Qinghai-Tibet Plateau (QTP), and some of these species are sympatrically distributed in northeastern QTP. Studies on genome features and natural selection signatures of sympatric species in section Crucata have been impeded by a lack of genomic resources. Here, we showed transcript characterizations and molecular footprints of selection effects on G. straminea, G. dahurica and G. officinalis based on the comparative transcriptome. A total of 62.97 Gb clean reads were obtained with unigene numbers per species ranging from 141,819 to 236,408 after assembly. We found that these three species had similar distribution of functional categories in different databases, and key enzyme-encoding genes involved in the iridoids biosynthesis were also obtained. The selective pressure analyses indicated that most paired orthologs between these three species were subject to negative selection, and only a low proportion of the orthologs that underwent positive selection were detected. We found that some positive selected genes were involved in "catalytic activity", "metabolic process", "response to stimulus" and "response to stress". Besides, large numbers of SSR primer pairs with transferabilities were successfully designed based on the available transcriptome datasets of three Gentiana species. The phylogenetic relationships reconstructed based on 352 single-copy nuclear genes provided a rough phylogenetic framework for this genus and confirmed the monophyly of section Cruciata. Our study not only provides insights for the natural selection effects on sympatric Gentiana species, but also enhances future genetic breeding or evolutionary studies on Qinjiao species.

Integrated Analysis of Transcriptome and Small RNAome Reveals the Regulatory Network for Rapid Growth in Mikania micrantha

M. micrantha has caused huge ecological damage and economic losses worldwide due to its rapid growth and serious invasion. However, the underlying molecular mechanisms of its rapid growth and environmental adaption remain unclear. Here, we performed transcriptome and small RNA sequencing with five tissues of M. micrantha to dissect miRNA-mediated regulation in M. micrantha. WGCNA and GO enrichment analysis of transcriptome identified the gene association patterns and potential key regulatory genes for plant growth in each tissue. The genes highly correlated with leaf and stem tissues were mainly involved in the chlorophyll synthesis, response to auxin, the CAM pathway and other photosynthesis-related processes, which promoted the fast growth of M. micrantha. Importantly, we identified 350 conserved and 192 novel miRNAs, many of which displayed differential expression patterns among tissues. PsRNA target prediction analysis uncovered target genes of both conserved and novel miRNAs, including GRFs and TCPs, which were essential for plant growth and development. Further analysis revealed that miRNAs contributed to the regulation of tissue-specific gene expression in M. micrantha, such as mmi-miR396 and mmi-miR319. Taken together, our study uncovered the miRNA-mRNA regulatory networks and the potential vital roles of miRNAs in modulating the rapid growth of M. micrantha.

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.

High genetic and epigenetic variation of transposable elements: Potential drivers to rapid adaptive evolution for the noxious invasive weed Mikania micrantha

Why invasive species can rapidly adapt to novel environments is a puzzling question known as the genetic paradox of invasive species. This paradox is explainable in terms of transposable elements (TEs) activity, which are theorized to be powerful mutational forces to create genetic variation. Mikania micrantha, a noxious invasive weed, in this sense provides an excellent opportunity to test the explanation. The genetic and epigenetic variation of 21 invasive populations of M. micrantha in southern China have been examined by using transposon display (TD) and transposon methylation display (TMD) techniques to survey 12 TE superfamilies. Our results showed that M. micrantha populations maintained an almost equally high level of TE-based genetic and epigenetic variation and they have been differentiated into subpopulations genetically and epigenetically. A similar positive spatial genetic and epigenetic structure pattern was observed within 300 m. Six and seven TE superfamilies presented significant genetic and epigenetic isolation by distance (IBD) pattern. In total, 59 genetic and 86 epigenetic adaptive TE loci were identified. Of them, 51 genetic and 44 epigenetic loci were found to correlate with 25 environmental variables (including precipitation, temperature, vegetation coverage, and soil metals). Twenty-five transposon-inserted genes were sequenced and homology-based annotated, which are found to be involved in a variety of molecular and cellular functions. Our research consolidates the importance of TE-associated genetic and epigenetic variation in the rapid adaptation and invasion of M. micrantha.

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.

Going with the flow: analysis of population structure reveals high gene flow shaping invasion pattern and inducing range expansion of Mikania micrantha in Asia

BACKGROUND AND AIMS

Mikania micrantha, a climbing perennial weed of the family Asteraceae, is native to Latin America and is highly invasive in the tropical belt of Asia, Oceania and Australia. This study was framed to investigate the population structure of M. micrantha at a large spatial scale in Asia and to identify how introduction history, evolutionary forces and landscape features influenced the genetic pattern of the species in this region.

METHODS

We assessed the genetic diversity and structure of 1052 individuals from 46 populations for 12 microsatellite loci. The spatial pattern of genetic variation was investigated by estimating the relationship between genetic distance and geographical, climatic and landscape resistances hypothesized to influence gene flow between populations.

KEY RESULTS

We found high genetic diversity of M. micrantha in this region, as compared with the genetic diversity parameters of other invasive species. Spatial and non-spatial clustering algorithms identified the presence of multiple genetic clusters and admixture between populations. Most of the populations showed heterozygote deficiency, primarily due to inbreeding, and the founder populations showed evidence of a genetic bottleneck. Persistent gene flow throughout the invasive range caused low genetic differentiation among populations and provided beneficial genetic variation to the marginal populations in a heterogeneous environment. Environmental suitability was found to buffer the detrimental effects of inbreeding at the leading edge of range expansion. Both linear and non-linear regression models demonstrated a weak relationship between genetic distance and geographical distance, as well as bioclimatic variables and environmental resistance surfaces.

CONCLUSIONS

These findings provide evidence that extensive gene flow and admixture between populations have influenced the current genetic pattern of M. micrantha in this region. High gene flow across the invaded landscape may facilitate adaptation, establishment and long-term persistence of the population, thereby indicating the range expansion ability of the species.

Genetic admixture accelerates invasion via provisioning rapid adaptive evolution

Genetic admixture, the intraspecific hybridization among divergent introduced sources, can immediately facilitate colonization via hybrid vigor and profoundly enhance invasion via contributing novel genetic variation to adaption. As hybrid vigor is short-lived, provisioning adaptation is anticipated to be the dominant and long-term profit of genetic admixture, but the evidence for this is rare. We employed the 30 years' geographic-scale invasion of the salt marsh grass, Spartina alterniflora, as an evolutionary experiment and evaluated the consequences of genetic admixture by combining the reciprocal transplant experiment with quantitative and population genetic surveys. Consistent with the documentation, we found that the invasive populations in China had multiple origins from the southern Atlantic coast and the Gulf of Mexico in the US. Interbreeding among these multiple sources generated a "hybrid swarm" that spread throughout the coast of China. In the northern and mid-latitude China, natural selection greatly enhanced fecundity, plant height and shoot regeneration compared to the native populations. Furthermore, genetic admixture appeared to have broken the negative correlation between plant height and shoot regeneration, which was genetically-based in the native range, and have facilitated the evolution of super competitive genotypes in the invasive range. In contrast to the evolved northern and mid-latitude populations, the southern invasive populations showed slight increase of plant height and shoot regeneration compared to the native populations, possibly reflecting the heterotic effect of the intraspecific hybridization. Therefore, our study suggests a critical role of genetic admixture in accelerating the geographic invasion via provisioning rapid adaptive evolution.

A few north Appalachian populations are the source of European black locust

The role of evolution in biological invasion studies is often overlooked. In order to evaluate the evolutionary mechanisms behind invasiveness, it is crucial to identify the source populations of the introduction. Studies in population genetics were carried out on Robinia pseudoacacia L., a North American tree which is now one of the worst invasive tree species in Europe. We realized large-scale sampling in both the invasive and native ranges: 63 populations were sampled and 818 individuals were genotyped using 113 SNPs. We identified clonal genotypes in each population and analyzed between and within range population structure, and then, we compared genetic diversity between ranges, enlarging the number of SNPs to mitigate the ascertainment bias. First, we demonstrated that European black locust was introduced from just a limited number of populations located in the Appalachian Mountains, which is in agreement with the historical documents briefly reviewed in this study. Within America, population structure reflected the effects of long-term processes, whereas in Europe it was largely impacted by human activities. Second, we showed that there is a genetic bottleneck between the ranges with a decrease in allelic richness and total number of alleles in Europe. Lastly, we found more clonality within European populations. Black locust became invasive in Europe despite being introduced from a reduced part of its native distribution. Our results suggest that human activity, such as breeding programs in Europe and the seed trade throughout the introduced range, had a major role in promoting invasion; therefore, the introduction of the missing American genetic cluster to Europe should be avoided.

Evolutionary and ecological functional genomics, from lab to the wild

Plant phenotypes are the result of both genetic and environmental forces that act to modulate trait expression. Over the last few years, numerous approaches in functional genomics and systems biology have led to a greater understanding of plant phenotypic variation and plant responses to the environment. These approaches, and the questions that they can address, have been loosely termed evolutionary and ecological functional genomics (EEFG), and have been providing key insights on how plants adapt and evolve. In particular, by bringing these studies from the laboratory to the field, EEFG studies allow us to gain greater knowledge of how plants function in their natural contexts.

Comparative transcriptome analysis of the invasive weed Mikania micrantha with its native congeners provides insights into genetic basis underlying successful invasion

Background

Mikania micrantha H.B.K. (Asteraceae) is one of the world’s most invasive weeds which has been rapidly expanding in tropical Asia, including China, while its close relative M. cordata, the only Mikania species native to China, shows no harm to the local ecosystems. These two species are very similar in morphology but differ remarkably in several ecological and physiological traits, representing an ideal system for comparative analysis to investigate the genetic basis underlying invasion success. In this study, we performed RNA-sequencing on the invader M. micrantha and its native congener M. cordata in China, to unravel the genetic basis underlying the strong invasiveness of M. micrantha. For a more robust comparison, another non-invasive congener M. cordifolia was also sequenced and compared.

Results

A total of 52,179, 55,835, and 52,983 unigenes were obtained for M. micrantha, M. cordata, and M. cordifolia, respectively. Phylogenetic analyses and divergence time dating revealed a relatively recent split between M. micrantha and M. cordata, i.e., approximately 4.81 million years ago (MYA), after their divergence with M. cordifolia (8.70 MYA). Gene ontology classifications, pathway assignments and differential expression analysis revealed higher representation or significant up-regulation of genes associated with photosynthesis, energy metabolism, protein modification and stress response in M. micrantha than in M. cordata or M. cordifolia. Analysis of accelerated evolution and positive selection also suggested the importance of these related genes and processes to the adaptability and invasiveness of M. micrantha. Particularly, most (77 out of 112, i.e. 68.75%) positively selected genes found in M. micrantha could be classified into four groups, i.e., energy acquisition and utilization (10 genes), growth and reproduction (13 genes), protection and repair (34 genes), and signal transduction and expression regulation (20 genes), which may have contributed to the high adaptability of M. micrantha to various new environments and the capability to occupy a wider niche, reflected in its high invasiveness.

Conclusions

We characterized the transcriptomes of the invasive species M. micrantha and its non-invasive congeners, M. cordata and M. cordifolia. A comparison of their transcriptomes provided insights into the genetic basis of the high invasiveness of M. micrantha.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4784-9) contains supplementary material, which is available to authorized users.