De novo assembly and annotation of the transcriptome of the agricultural weed Ipomoea purpurea uncovers gene expression changes associated with herbicide resistance

Weed biology and management in the multi-omics era: Progress and perspectives

Weeds pose a significant threat to crop production, resulting in substantial yield reduction. In addition, they possess robust weedy traits that enable them to survive in extreme environments and evade human control. In recent years, the application of multi-omics biotechnologies has helped to reveal the molecular mechanisms underlying these weedy traits. In this review, we systematically describe diverse applications of multi-omics platforms for characterizing key aspects of weed biology, including the origins of weed species, weed classification, and the underlying genetic and molecular bases of important weedy traits such as crop-weed interactions, adaptability to different environments, photoperiodic flowering responses, and herbicide resistance. In addition, we discuss limitations to the application of multi-omics techniques in weed science, particularly compared with their extensive use in model plants and crops. In this regard, we provide a forward-looking perspective on the future application of multi-omics technologies to weed science research. These powerful tools hold great promise for comprehensively and efficiently unraveling the intricate molecular genetic mechanisms that underlie weedy traits. The resulting advances will facilitate the development of sustainable and highly effective weed management strategies, promoting greener practices in agriculture.

Yeast of Eden: microbial resistance to glyphosate from a yeast perspective

First marketed as RoundUp, glyphosate is history's most popular herbicide because of its low acute toxicity to metazoans and broad-spectrum effectiveness across plant species. The development of glyphosate-resistant crops has led to increased glyphosate use and consequences from the use of glyphosate-based herbicides (GBH). Glyphosate has entered the food supply, spurred glyphosate-resistant weeds, and exposed non-target organisms to glyphosate. Glyphosate targets EPSPS/AroA/Aro1 (orthologs across plants, bacteria, and fungi), the rate-limiting step in the production of aromatic amino acids from the shikimate pathway. Metazoans lacking this pathway are spared from acute toxicity and acquire their aromatic amino acids from their diet. However, glyphosate resistance is increasing in non-target organisms. Mutations and natural genetic variation discovered in Saccharomyces cerevisiae illustrate similar types of glyphosate resistance mechanisms in fungi, plants, and bacteria, in addition to known resistance mechanisms such as mutations in Aro1 that block glyphosate binding (target-site resistance (TSR)) and mutations in efflux drug transporters non-target-site resistance (NTSR). Recently, genetic variation and mutations in an amino transporter affecting glyphosate resistance have uncovered potential off-target effects of glyphosate in fungi and bacteria. While glyphosate is a glycine analog, it is transported into cells using an aspartic/glutamic acid (D/E) transporter. The size, shape, and charge distribution of glyphosate closely resembles D/E, and, therefore, glyphosate is a D/E amino acid mimic. The mitochondria use D/E in several pathways and mRNA-encoding mitochondrial proteins are differentially expressed during glyphosate exposure. Mutants downstream of Aro1 are not only sensitive to glyphosate but also a broad range of other chemicals that cannot be rescued by exogenous supplementation of aromatic amino acids. Glyphosate also decreases the pH when unbuffered and many studies do not consider the differences in pH that affect toxicity and resistance mechanisms.

A high diversity of non-target site resistance mechanisms to acetolactate-synthase (ALS) inhibiting herbicides has evolved within and among field populations of common ragweed (Ambrosia artemisiifolia L.)

BACKGROUND

Non-target site resistance (NTSR) to herbicides is a polygenic trait that threatens the chemical control of agricultural weeds. NTSR involves differential regulation of plant secondary metabolism pathways, but its precise genetic determinisms remain fairly unclear. Full-transcriptome sequencing had previously been implemented to identify NTSR genes. However, this approach had generally been applied to a single weed population, limiting our insight into the diversity of NTSR mechanisms. Here, we sought to explore the diversity of NTSR mechanisms in common ragweed (Ambrosia artemisiifolia L.) by investigating six field populations from different French regions where NTSR to acetolactate-synthase-inhibiting herbicides had evolved.

RESULTS

A de novo transcriptome assembly (51,242 contigs, 80.2% completeness) was generated as a reference to seek genes differentially expressed between sensitive and resistant plants from the six populations. Overall, 4,609 constitutively differentially expressed genes were identified, of which none were common to all populations, and only 197 were shared by several populations. Similarly, population-specific transcriptomic response was observed when investigating early herbicide response. Gene ontology enrichment analysis highlighted the involvement of stress response and regulatory pathways, before and after treatment. The expression of 121 candidate constitutive NTSR genes including CYP71, CYP72, CYP94, oxidoreductase, ABC transporters, gluco and glycosyltransferases was measured in 220 phenotyped plants. Differential expression was validated in at least one ragweed population for 28 candidate genes. We investigated whether expression patterns at some combinations of candidate genes could predict phenotype. Within populations, prediction accuracy decreased when applied to an additional, independent plant sampling. Overall, a wide variety of genes linked to NTSR was identified within and among ragweed populations, of which only a subset was captured in our experiments.

CONCLUSION

Our results highlight the complexity and the diversity of NTSR mechanisms that can evolve in a weed species in response to herbicide selective pressure. They strongly point to a non-redundant, population-specific evolution of NTSR to ALS inhibitors in ragweed. It also alerts on the potential of common ragweed for rapid adaptation to drastic environmental or human-driven selective pressures.

Transcriptomic analysis of Amaranthus retroflex resistant to PPO-inhibitory herbicides

Amaranthus retroflexus L. is one of the malignant weeds which can cause a reduction in the soybean yield. We found a population of A. retroflexus (R-Q) resistant to fomesafen through the initial screening of whole-plant dose response bioassay in the research. The resistance index of the population (R-Q) was 183 times of the sensitive population (S-N). The resistant and sensitive populations were used as experimental materials in the paper. Strand-specific RNA-Seq analyses of R‒Q and S‒N populations obtained from herbicide-treated and mock-treated leaf samples after treatment were conducted to generate a full-length transcriptome database. We analyzed differentially expressed genes (DEGs) among the R-Q and S‒N A. retroflexus populations treated with recommended dose and mock-treated on the 1st (24 h) and 3rd (72 h) days to identify genes involved in fomesafen resistance. All 82,287 unigenes were annotated by Blastx search with E-value < 0.00001 from 7 databases. A total of 94,815 DEGs among the three group comparisons were identified. Two nuclear genes encoding PPO (PPX1 and PPX2) and five unigenes belonging to the AP2-EREBP, GRAS, NAC, bHLH and bZIP families exhibited different expression patterns between individuals of S‒N and R-Q populations. The A. retroflexus transcriptome and specific transcription factor families which can respond to fomesafen in resistant and susceptible genotypes were reported in this paper. The PPX1 and PPX2 genes of the target enzyme were identified. The study establishes the foundation for future research and provides opportunities to manage resistant weeds better.

Integrated omic techniques and their genomic features for invasive weeds

Many emerging invasive weeds display rapid adaptation against different stressful environments compared to their natives. Rapid adaptation and dispersal habits helped invasive populations have strong diversity within the population compared to their natives. Advances in molecular marker techniques may lead to an in-depth understanding of the genetic diversity of invasive weeds. The use of molecular techniques is rapidly growing, and their implications in invasive weed studies are considered powerful tools for genome purposes. Here, we review different approach used multi-omics by invasive weed studies to understand the functional structural and genomic changes in these species under different environmental fluctuations, particularly, to check the accessibility of advance-sequencing techniques used by researchers in genome sequence projects. In this review-based study, we also examine the importance and efficiency of different molecular techniques in identifying and characterizing different genes, associated markers, proteins, metabolites, and key metabolic pathways in invasive and native weeds. Use of these techniques could help weed scientists to further reduce the knowledge gaps in understanding invasive weeds traits. Although these techniques can provide robust insights about the molecular functioning, employing a single omics platform can rarely elucidate the gene-level regulation and the associated real-time expression of weedy traits due to the complex and overlapping nature of biological interactions. We conclude that different multi-omic techniques will provide long-term benefits in launching new genome projects to enhance the understanding of invasive weeds' invasion process.

Evolution of weedy giant ragweed (Ambrosia trifida): Multiple origins and gene expression variability facilitates weediness

Agricultural weeds may originate from wild populations, but the origination patterns and genetics underlying this transition remain largely unknown. Analysis of weedy-wild paired populations from independent locations may provide evidence to identify key genetic variation contributing to this adaptive shift. We performed genetic variation and expression analyses on transcriptome data from 67 giant ragweed samples collected from different locations in Ohio, Iowa, and Minnesota and found geographically separated weedy populations likely originated independently from their adjacent wild populations, but subsequent spreading of weedy populations also occurred locally. By using eight closely related weedy-wild paired populations, we identified thousands of unique transcripts in weedy populations that reflect shared or specific functions corresponding, respectively, to both convergently evolved and population-specific weediness processes. In addition, differential expression of specific groups of genes was detected between weedy and wild giant ragweed populations using gene expression diversity and gene co-expression network analyses. Our study suggests an integrated route of weedy giant ragweed origination, consisting of independent origination combined with the subsequent spreading of certain weedy populations, and provides several lines of evidence to support the hypothesis that gene expression variability plays a key role in the evolution of weedy species.

On the hidden temporal dynamics of plant adaptation

Adaptation to a wide range of environments is a major driver of plant diversity. It is now possible to catalog millions of potential adaptive genomic differences segregating between environments within a plant species in a single experiment. Understanding which of these changes contributes to adaptive phenotypic divergence between plant populations is a major goal of evolutionary biologists and crop breeders. In this review, we briefly highlight the approaches frequently used to understand the genetic basis of adaptive phenotypes in plants, and we discuss some of the limitations of these methods. We propose that direct observation of the process of adaptation using multigenerational studies and whole genome sequencing is a crucial missing component of recent studies of plant adaptation because it complements several shortcomings of sampling-based techniques.

Functional study of CYP90A1 and ALDH3F1 gene obtained by transcriptome sequencing analysis of Brassica napus seedlings treated with brassinolide

Sclerotinia disease and weeds of Brassica napus greatly reduce crop yields. However, brassinolides can improve the resistance of plants to sclerotinia diseases and herbicides. In this study, we investigated the effects of brassinolide on the occurrence, physiological indices, yield, and gene expression of Fanming No. 1 seeds under sclerotinia and glufosinate stress. The results showed that soaking of the seeds in 0.015% brassinolide for 6 h reduced the incidence of sclerotinia by 10%. Additionally, in response to glufosinate stress at the seedling stage, the enzyme activities of catalase and superoxide dismutase increased by 9.6 and 19.0 U/gFW/min, respectively, and the soluble sugar content increased by 9.4 mg/g, increasing the stress resistance of plants and yield by 2.4%. LHCB1, fabF, psbW, CYP90A1, ALDH3F1, ACOX1, petF, and ACSL were screened by transcriptome analysis. ALDH3F1 and CYP90A1 were identified as key genes. Following glufosinate treatment, transgenic plants overexpressing ALDH3F1 and CYP90A1 were found to be resistant to glufosinate, and the expression levels of the ALDH3F1 and CYP90A1 were 1.03-2.37-fold as high as those in the control. The expression level of ATG3, which is an antibacterial gene related to sclerotinia disease, in transgenic plants was 2.40-2.37-fold as high as that in the control. Our results indicate that these two key genes promote plant resistance to sclerotinia and glufosinate. Our study provides a foundation for further studies on the molecular mechanisms of rapeseed resistance breeding and selection of new resistant varieties.

Repeated origins, widespread gene flow, and allelic interactions of target-site herbicide resistance mutations

Causal mutations and their frequency in agricultural fields are well-characterized for herbicide resistance. However, we still lack understanding of their evolutionary history: the extent of parallelism in the origins of target-site resistance (TSR), how long these mutations persist, how quickly they spread, and allelic interactions that mediate their selective advantage. We addressed these questions with genomic data from 19 agricultural populations of common waterhemp (Amaranthus tuberculatus), which we show to have undergone a massive expansion over the past century, with a contemporary effective population size estimate of 8 x 10⁷. We found variation at seven characterized TSR loci, two of which had multiple amino acid substitutions, and three of which were common. These three common resistance variants show extreme parallelism in their mutational origins, with gene flow having shaped their distribution across the landscape. Allele age estimates supported a strong role of adaptation from de novo mutations, with a median age of 30 suggesting that most resistance alleles arose soon after the onset of herbicide use. However, resistant lineages varied in both their age and evidence for selection over two different timescales, implying considerable heterogeneity in the forces that govern their persistence. Two such forces are intra- and inter-locus allelic interactions; we report a signal of extended haplotype competition between two common TSR alleles, and extreme linkage with genome-wide alleles with known functions in resistance adaptation. Together, this work reveals a remarkable example of spatial parallel evolution in a metapopulation, with important implications for the management of herbicide resistance.

The genetic architecture and population genomic signatures of glyphosate resistance in Amaranthus tuberculatus

Much of what we know about the genetic basis of herbicide resistance has come from detailed investigations of monogenic adaptation at known target-sites, despite the increasingly recognized importance of polygenic resistance. Little work has been done to characterize the broader genomic basis of herbicide resistance, including the number and distribution of genes involved, their effect sizes, allele frequencies and signatures of selection. In this work, we implemented genome-wide association (GWA) and population genomic approaches to examine the genetic architecture of glyphosate (Round-up) resistance in the problematic agricultural weed Amaranthus tuberculatus. A GWA was able to correctly identify the known target-gene but statistically controlling for two causal target-site mechanisms revealed an additional 250 genes across all 16 chromosomes associated with non-target-site resistance (NTSR). The encoded proteins had functions that have been linked to NTSR, the most significant of which is response to chemicals, but also showed pleiotropic roles in reproduction and growth. Compared to an empirical null that accounts for complex population structure, the architecture of NTSR was enriched for large effect sizes and low allele frequencies, suggesting the role of pleiotropic constraints on its evolution. The enrichment of rare alleles also suggested that the genetic architecture of NTSR may be population-specific and heterogeneous across the range. Despite their rarity, we found signals of recent positive selection on NTSR-alleles by both window- and haplotype-based statistics, and an enrichment of amino acid changing variants. In our samples, genome-wide single nucleotide polymorphisms explain a comparable amount of the total variation in glyphosate resistance to monogenic mechanisms, even in a collection of individuals where 80% of resistant individuals have large-effect TSR mutations, indicating an underappreciated polygenic contribution to the evolution of herbicide resistance in weed populations.

Novel Candidate Genes Differentially Expressed in Glyphosate-Treated Horseweed (Conyza canadensis)

The evolution of herbicide-resistant weed species is a serious threat for weed control. Therefore, we need an improved understanding of how gene regulation confers herbicide resistance in order to slow the evolution of resistance. The present study analyzed differentially expressed genes after glyphosate treatment on a glyphosate-resistant Tennessee ecotype (TNR) of horseweed (Conyza canadensis), compared to a susceptible biotype (TNS). A read size of 100.2 M was sequenced on the Illumina platform and subjected to de novo assembly, resulting in 77,072 gene-level contigs, of which 32,493 were uniquely annotated by a BlastX alignment of protein sequence similarity. The most differentially expressed genes were enriched in the gene ontology (GO) term of the transmembrane transport protein. In addition, fifteen upregulated genes were identified in TNR after glyphosate treatment but were not detected in TNS. Ten of these upregulated genes were transmembrane transporter or kinase receptor proteins. Therefore, a combination of changes in gene expression among transmembrane receptor and kinase receptor proteins may be important for endowing non-target-site glyphosate-resistant C. canadensis.

Adaptive and maladaptive expression plasticity underlying herbicide resistance in an agricultural weed

Plastic phenotypic responses to environmental change are common, yet we lack a clear understanding of the fitness consequences of these plastic responses. Here, we use the evolution of herbicide resistance in the common morning glory (Ipomoea purpurea) as a model for understanding the relative importance of adaptive and maladaptive gene expression responses to herbicide. Specifically, we compare leaf gene expression changes caused by herbicide to the expression changes that evolve in response to artificial selection for herbicide resistance. We identify a number of genes that show plastic and evolved responses to herbicide and find that for the majority of genes with both plastic and evolved responses, plastic responses appear to be adaptive. We also find that selection for herbicide response increases gene expression plasticity. Overall, these results show the importance of adaptive plasticity for herbicide resistance in a common weed and that expression changes in response to strong environmental change can be adaptive.

The Genetic Architecture of Emerging Fungicide Resistance in Populations of a Global Wheat Pathogen

Containing fungal diseases often depends on the application of fungicidal compounds. Fungicides can rapidly lose effectiveness due to the rise of resistant individuals in populations. However, the lack of knowledge about resistance mutations beyond known target genes challenges investigations into pathways to resistance. We used whole-genome sequencing data and association mapping to reveal the multilocus genetic architecture of fungicide resistance in a global panel of 159 isolates of Parastagonospora nodorum, an important fungal pathogen of wheat. We found significant differences in azole resistance among global field populations. The populations evolved distinctive combinations of resistance alleles which can interact when co-occurring in the same genetic background. We identified 34 significantly associated single nucleotide polymorphisms located in close proximity to genes associated with fungicide resistance in other fungi, including a major facilitator superfamily transporter. Using fungal colony growth rates and melanin production at different temperatures as fitness proxies, we found no evidence that resistance was constrained by genetic trade-offs. Our study demonstrates how genome-wide association studies of a global collection of pathogen strains can recapitulate the emergence of fungicide resistance. The distinct complement of resistance mutations found among populations illustrates how the evolutionary trajectory of fungicide adaptation can be complex and challenging to predict.

Parallel and nonparallel genomic responses contribute to herbicide resistance in Ipomoea purpurea, a common agricultural weed

The repeated evolution of herbicide resistance has been cited as an example of genetic parallelism, wherein separate species or genetic lineages utilize the same genetic solution in response to selection. However, most studies that investigate the genetic basis of herbicide resistance examine the potential for changes in the protein targeted by the herbicide rather than considering genome-wide changes. We used a population genomics screen and targeted exome re-sequencing to uncover the potential genetic basis of glyphosate resistance in the common morning glory, Ipomoea purpurea, and to determine if genetic parallelism underlies the repeated evolution of resistance across replicate resistant populations. We found no evidence for changes in 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS), glyphosate's target protein, that were associated with resistance, and instead identified five genomic regions that showed evidence of selection. Within these regions, genes involved in herbicide detoxification-cytochrome P450s, ABC transporters, and glycosyltransferases-are enriched and exhibit signs of selective sweeps. One region under selection shows parallel changes across all assayed resistant populations whereas other regions exhibit signs of divergence. Thus, while it appears that the physiological mechanism of resistance in this species is likely the same among resistant populations, we find patterns of both similar and divergent selection across separate resistant populations at particular loci.

Herbicide resistant weeds: A call to integrate conventional agricultural practices, molecular biology knowledge and new technologies

Herbicide resistant (HR) weeds are of major concern in modern agriculture. This situation is exacerbated by the massive adoption of herbicide-based technologies along with the overuse of a few active ingredients to control weeds over vast areas year after year. Also, many other anthropological, biological, and environmental factors have defined a higher rate of herbicide resistance evolution in numerous weed species around the world. This review focuses on two central points: 1) how these factors have affected the resistance evolution process; and 2) which cultural practices and new approaches would help to achieve an effective integrated weed management. We claim that global climate change is an unnoticed factor that may be acting on the selection of HR weeds, especially those evolving into non-target-site resistance mechanisms. And we present several new tools -such as Gene Drive and RNAi technologies- that may be adopted to cope with herbicide resistance spread, as well as discuss their potential application at field level. This is the first review that integrates agronomic and molecular knowledge of herbicide resistance. It covers not only the genetic basis of the most relevant resistance mechanisms but also the strengths and weaknesses of traditional and forthcoming agricultural practices.

Evolutionary and ecological insights from herbicide-resistant weeds: what have we learned about plant adaptation, and what is left to uncover?

The evolution of herbicide resistance in crop weeds presents one of the greatest challenges to agriculture and the production of food. Herbicide resistance has been studied for more than 60 yr, in the large part by researchers seeking to design effective weed control programs. As an outcome of this work, various unique questions in plant adaptation have been addressed. Here, I collate recent research on the herbicide-resistant problem in light of key questions and themes in evolution and ecology. I highlight discoveries made on herbicide-resistant weeds in three broad areas - the genetic basis of adaptation, evolutionary constraints, experimental evolution - and similarly discuss questions left to be answered. I then develop how one would use herbicide-resistance evolution as a model for studying eco-evolutionary dynamics within a community context. My overall goals are to highlight important findings in the weed science literature that are relevant to themes in plant adaptation and to stimulate the use of herbicide-resistant plants as models for addressing key questions within ecology and evolution.

Non-target site-based resistance to tribenuron-methyl and essential involved genes in Myosoton aquaticum (L.)

BACKGROUND

Water chickweed (Myosoton aquaticum (L.)) is a dicot broadleaf weed that is widespread in winter fields in China, and has evolved serious resistance to acetolactate synthase (ALS) inhibiting herbicides.

RESULTS

We identified a M. aquaticum population exhibiting moderate (6.15-fold) resistance to tribenuron-methyl (TM). Target-site ALS gene sequencing revealed no known resistance mutations in these plants, and the in vitro ALS activity assays showed no differences in enzyme sensitivity between susceptible and resistant populations; however, resistance was reversed by pretreatment with the cytochrome P450 (CYP) monooxygenase inhibitor malathion. An RNA sequencing transcriptome analysis was performed to identify candidate genes involved in metabolic resistance, and the unigenes obtained by de novo transcriptome assembly were annotated across seven databases. In total, 34 differentially expressed genes selected by digital gene expression analysis were validated by quantitative real-time (qRT)-PCR. Ten consistently overexpressed contigs, including four for CYP, four for ATP-binding cassette (ABC) transporter, and two for peroxidase were further validated by qRT-PCR using additional plants from resistant and susceptible populations. Three CYP genes (with homology to CYP734A1, CYP76C1, and CYP86B1) and one ABC transporter gene (with homology to ABCC10) were highly expressed in all resistant plants.

CONCLUSION

The mechanism of TM resistance in M. aquaticum is controlled by NTSR rather than TSR. Four genes, CYP734A1, CYP76C1, CYP86B1, and ABCC10 could play essential role in metabolic resistance to TM and justify further functional studies. To our knowledge, this is the first large-scale transcriptome analysis of genes associated with NTSR in M. aquaticum using the Illumina platform. Our data provide resource for M. aquaticum biology, and will facilitate the study of herbicide resistance mechanism at the molecular level in this species as well as in other weeds.

Optimizing RNA-seq studies to investigate herbicide resistance

Transcriptomic profiling, specifically via RNA sequencing (RNA-seq), is becoming one of the more commonly used methods for investigating non-target site resistance (NTSR) to herbicides due to its high throughput capabilities and utility in organisms with little to no previous sequence information. A review of the weed science RNA-seq literature revealed some basic principles behind generating quality data from these types of studies. First, studies that included more replicates per biotype and took steps to control for genetic background had significantly better control of false positives and, consequently, shorter lists of potential resistance genes to sift through. Pooling of biological replicates prior to sequencing was successful in some cases, but likely contributed to an overall increase in the false discovery rate. Although the inclusion of herbicide-treated samples was common across most of the studies, it ultimately introduced difficulties in interpretation of the final results due to challenges in capturing the right sampling window after treatment and to the induction of stress responses in the injured herbicide-sensitive plants. RNA-seq is an effective tool for NTSR gene discovery, but careful consideration should be given to finding the most powerful and cost-effective balance between replicate number, sequencing depth and treatment number. © 2017 Society of Chemical Industry.

Gene expression in response to glyphosate treatment in fleabane (Conyza bonariensis) - glyphosate death response and candidate resistance genes

BACKGROUND

This study takes a whole-transcriptome approach to assess gene expression changes in response to glyphosate treatment in glyphosate-resistant fleabane. We assessed gene expression changes in both susceptible and resistant lines so that the glyphosate death response could be quantified, and constitutively expressed candidate resistance genes identified. There are three copies of the glyphosate target site (5-enolpyruvylshikimate-3-phosphate; EPSPS) gene in Conyza and because Conyza bonariensis is allohexaploid, there is a baseline nine copies of the gene in any individual.

RESULTS

Many genes were differentially expressed in response to glyphosate treatment. Known resistance mutations are present in EPSPS2 but they are present in a glyphosate-susceptible line as well as resistant lines and therefore not sufficient to confer resistance. EPSPS1 is expressed four times more than EPSPS2, further reducing the overall contribution of these mutations.

CONCLUSION

We demonstrate that glyphosate resistance in C. bonariensis is not the result of EPSPS mutations or overexpression, but due to a non-target-site mechanism. A large number of genes are affected by glyphosate treatment. We present a list of candidate non-target-site-resistance (NTSR) genes in fleabane for future studies into these mechanisms. © 2017 Society of Chemical Industry.

Transcriptomic changes in Echinochloa colona in response to treatment with the herbicide imazamox

Presented here is the first Echinochloa colona leaf transcriptome. Analysis of gene expression before and after herbicide treatment reveals that E. colona mounts a stress response upon exposure to herbicide. Herbicides are the most frequently used means of controlling weeds. For many herbicides, the target site is known; however, it is considerably less clear how plant gene expression changes in response to herbicide exposure. In this study, changes in gene expression in response to herbicide exposure in imazamox-sensitive (S) and- resistant (R) junglerice (Echinochloa colona L.) biotypes was examined. As no reference genome is available for this weed, a reference leaf transcriptome was generated. Messenger RNA was isolated from imazamox-treated- and untreated R and S plants and the resulting cDNA libraries were sequenced on an Illumina HiSeq2000. The transcriptome was assembled, annotated, and differential gene expression analysis was performed to identify transcripts that were upregulated or downregulated in response to herbicide exposure for both biotypes. Differentially expressed transcripts included transcription factors, protein-modifying enzymes, and enzymes involved in metabolism and signaling. A literature search revealed that members of the families represented in this analysis were known to be involved in abiotic stress response in other plants, suggesting that imazamox exposure induced a stress response. A time course study examining a subset of transcripts showed that expression peaked within 4-12 h and then returned to untreated levels within 48 h of exposure. Testing of plants from two additional biotypes showed a similar change in gene expression 4 h after herbicide exposure compared to the resistant and sensitive biotypes. This study shows that within 48 h junglerice mounts a stress response to imazamox exposure.

De novo transcriptome assembly analysis of weed Apera spica-venti from seven tissues and growth stages

BACKGROUND

Loose silky bentgrass (Apera spica-venti) is an important weed in Europe with a recent increase in herbicide resistance cases. The lack of genetic information about this noxious weed limits its biological understanding such as growth, reproduction, genetic variation, molecular ecology and metabolic herbicide resistance. This study produced a reference transcriptome for A. spica-venti from different tissues (leaf, root, stem) and various growth stages (seed at phenological stages 05, 07, 08, 09). The de novo assembly was performed on individual and combined dataset followed by functional annotations. Individual transcripts and gene families involved in metabolic based herbicide resistance were identified.

RESULTS

Eight separate transcriptome assemblies were performed and compared. The combined transcriptome assembly consists of 83,349 contigs with an N50 and average contig length of 762 and 658 bp, respectively. This dataset contains 74,724 transcripts consisting of total 54,846,111 bp. Among them 94% had a homologue to UniProtKB, 73% retrieved a GO mapping, and 50% were functionally annotated. Compared with other grass species, A. spica-venti has 26% proteins in common to Brachypodium distachyon, and 41% to Lolium spp. Glycosyltransferases had the highest number of transcripts in each tissue followed by the cytochrome P450s. The GSTF1 and CYP89A2 transcripts were recovered from the majority of tissues and aligned at a maximum of 66 and 30% to proven herbicide resistant allele from Alopecurus myosuroides and Lolium rigidum, respectively.

CONCLUSIONS

De novo transcriptome assembly enabled the generation of the first reference transcriptome of A. spica-venti. This can serve as stepping stone for understanding the metabolic herbicide resistance as well as the general biology of this problematic weed. Furthermore, this large-scale sequence data is a valuable scientific resource for comparative transcriptome analysis for Poaceae grasses.

Transcriptome Profiling to Identify Genes Involved in Mesosulfuron-Methyl Resistance in Alopecurus aequalis

Non-target-site resistance (NTSR) to herbicides is a worldwide concern for weed control. However, as the dominant NTSR mechanism in weeds, metabolic resistance is not yet well-characterized at the genetic level. For this study, we have identified a shortawn foxtail (Alopecurus aequalis Sobol.) population displaying both TSR and NTSR to mesosulfuron-methyl and fenoxaprop-P-ethyl, yet the molecular basis for this NTSR remains unclear. To investigate the mechanisms of metabolic resistance, an RNA-Seq transcriptome analysis was used to find candidate genes that may confer metabolic resistance to the herbicide mesosulfuron-methyl in this plant population. The RNA-Seq libraries generated 831,846,736 clean reads. The de novo transcriptome assembly yielded 95,479 unigenes (averaging 944 bp in length) that were assigned putative annotations. Among these, a total of 29,889 unigenes were assigned to 67 GO terms that contained three main categories, and 14,246 unigenes assigned to 32 predicted KEGG metabolic pathways. Global gene expression was measured using the reads generated from the untreated control (CK), water-only control (WCK), and mesosulfuron-methyl treatment (T) of R and susceptible (S). Contigs that showed expression differences between mesosulfuron-methyl-treated R and S biotypes, and between mesosulfuron-methyl-treated, water-treated and untreated R plants were selected for further quantitative real-time PCR (qRT-PCR) validation analyses. Seventeen contigs were consistently highly expressed in the resistant A. aequalis plants, including four cytochrome P450 monooxygenase (CytP450) genes, two glutathione S-transferase (GST) genes, two glucosyltransferase (GT) genes, two ATP-binding cassette (ABC) transporter genes, and seven additional contigs with functional annotations related to oxidation, hydrolysis, and plant stress physiology. These 17 contigs could serve as major candidate genes for contributing to metabolic mesosulfuron-methyl resistance; hence they deserve further functional study. This is the first large-scale transcriptome-sequencing study to identify NTSR genes in A. aequalis that uses the Illumina platform. This work demonstrates that NTSR is likely driven by the differences in the expression patterns of a set of genes. The assembled transcriptome data presented here provide a valuable resource for A. aequalis biology, and should facilitate the study of herbicide resistance at the molecular level in this and other weed species.

High-resolution transcript profiling reveals shoot abscission process of spruce dwarf mistletoe Arceuthobium sichuanense in response to ethephon

Arceuthobium (dwarf mistletoes) are hemiparasites that may cause great damage to infected trees belonging to Pinaceae and Cupressaceae. Currently, dwarf mistletoe control involves the use of the ethylene-producing product ethephon (ETH), which acts by inducing dwarf mistletoe shoot abscission. However, the process by which ETH functions is mostly unknown. Therefore, the transcriptome of the ETH-exposed plants was compared to non-exposed controls to identify genes associated with the response to ethephon. In this study, the reference transcriptome was contained 120,316 annotated unigenes, with a total of 21,764 ETH-responsive differentially expressed unigenes were identified. These ETH-associated genes clustered into 20 distinctly expressed pattern groups, providing a view of molecular events with good spatial and temporal resolution. As expected, the greatest number of unigenes with changed expression were observed at the onset of abscission, suggesting induction by ethylene. ETH also affected genes associated with shoot abscission processes including hormone biosynthesis and signaling, cell wall hydrolysis and modification, lipid transference, and more. The comprehensive transcriptome data set provides a wealth of genomic resources for dwarf mistletoe communities and contributes to a better understanding of the molecular regulatory mechanism of ethylene-caused shoots abscission.

De novo assembly and transcriptome characterization of spruce dwarf mistletoe Arceuthobium sichuanense uncovers gene expression profiling associated with plant development

Background

The parasitic flowering plant dwarf mistletoe (Arceuthobium spp., Viscaceae) is one of the most destructive forest pests, posing a major threat to numerous conifer species worldwide. Arceuthobium sichuanense (spruce dwarf mistletoe, SDM) infects Qinghai spruce (Picea crassifolia) and causes severe damage to spruce forests in Northwest China. SDM is a Chinese native parasitic plant and acquires carbohydrates and mineral nutrition from its hosts. However, underlying molecular basis of the physiological development is largely unknown. Investigations of these physiological traits have been hampered by the lack of genomic resources for this species.

Results

In this study, to investigate the transcriptomic processes underlying physiological traits and development in SDM, we used RNA from four major tissues (i.e., shoots, flowers, fruits, and seeds) for de novo assembly and to annotate the transcriptome of this species. We uncovered the annotated transcriptome and performed whole genome expression profiling to uncover transcriptional dynamics during physiological development, and we identified key gene categories involved in the process of sexual development. The assembled SDM transcriptome reported in this work contains 331,347 assembled transcripts; 226,687 unigenes were functionally annotated by Gene Ontology analysis. RNA-Seq analysis using this reference transcriptome identified 22,641 differentially expressed genes from shoots, flowers, fruits, and seeds. These genes are enriched in processes including organic substance metabolism, cellular metabolism, biosynthesis, and cellular component. In addition, genes related to transport, transcription, hormone biosynthesis and signaling, carbohydrate metabolism, and photosynthesis were differentially expressed between tissues.

Conclusion

This work reveals tissue-specific gene expression patterns and pathways of SDM and implied to a difference between photosynthetic and non-photosynthetic tissues in plants. The data can potentially be used for future investigations on endophytic parasitism and SDM-spruce interaction, and it dramatically increases the available genomic resources for Arceuthobium and dwarf mistletoe communities. This preliminary study of the Arceuthobium transcriptome provides excellent opportunities for characterizing plant parasitic genes with unknown functions.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-3127-y) contains supplementary material, which is available to authorized users.

Fitness costs of herbicide resistance across natural populations of the common morning glory, Ipomoea purpurea

Although fitness costs associated with plant defensive traits are widely expected, they are not universally detected, calling into question their generality. Here, we examine the potential for life-history trade-offs associated with herbicide resistance by examining seed germination, root growth, and above-ground growth across 43 naturally occurring populations of Ipomoea purpurea that vary in their resistance to RoundUp®, the most commonly used herbicide worldwide. We find evidence for life-history trade-offs associated with all three traits; highly resistant populations had lower germination, shorter roots, and smaller above-ground size. A visual exploration of the data indicated that the type of trade-off may differ among populations. Our results demonstrate that costs of adaptation may be present at stages other than simply the production of progeny in this agricultural weed. Additionally, the cumulative effect of costs at multiple life cycle stages can result in severe consequences to fitness when adapting to novel environments.

Genome-Wide Transcriptional Profiling and Metabolic Analysis Uncover Multiple Molecular Responses of the Grass Species Lolium perenne Under Low-Intensity Xenobiotic Stress

Lolium perenne, which is a major component of pastures, lawns, and grass strips, can be exposed to xenobiotic stresses due to diffuse and residual contaminations of soil. L. perenne was recently shown to undergo metabolic adjustments in response to sub-toxic levels of xenobiotics. To gain insight in such chemical stress responses, a de novo transcriptome analysis was carried out on leaves from plants subjected at the root level to low levels of xenobiotics, glyphosate, tebuconazole, and a combination of the two, leading to no adverse physiological effect. Chemical treatments influenced significantly the relative proportions of functional categories and of transcripts related to carbohydrate processes, to signaling, to protein-kinase cascades, such as Serine/Threonine-protein kinases, to transcriptional regulations, to responses to abiotic or biotic stimuli and to responses to phytohormones. Transcriptomics-based expressions of genes encoding different types of SNF1 (sucrose non-fermenting 1)-related kinases involved in sugar and stress signaling or encoding key metabolic enzymes were in line with specific qRT-PCR analysis or with the important metabolic and regulatory changes revealed by metabolomic analysis. The effects of pesticide treatments on metabolites and gene expression strongly suggest that pesticides at low levels, as single molecule or as mixture, affect cell signaling and functioning even in the absence of major physiological impact. This global analysis of L. perenne therefore highlighted the interactions between molecular regulation of responses to xenobiotics, and also carbohydrate dynamics, energy dysfunction, phytohormones and calcium signaling.

Whole Transcriptome Analysis Provides Insights into Molecular Mechanisms for Molting in Litopenaeus vannamei

Molting is one of the most important biological processes in shrimp growth and development. All shrimp undergo cyclic molting periodically to shed and replace their exoskeletons. This process is essential for growth, metamorphosis, and reproduction in shrimp. However, the molecular mechanisms underlying shrimp molting remain poorly understood. In this study, we investigated global expression changes in the transcriptomes of the Pacific white shrimp, Litopenaeus vannamei, the most commonly cultured shrimp species worldwide. The transcriptome of whole L. vannamei was investigated by RNA-sequencing (RNA-seq) throughout the molting cycle, including the inter-molt (C), pre-molt (D0, D1, D2, D3, D4), and post-molt (P1 and P2) stages, and 93,756 unigenes were identified. Among these genes, we identified 5,117 genes differentially expressed (log2ratio ≥1 and FDR ≤0.001) in adjacent molt stages. The results were compared against the National Center for Biotechnology Information (NCBI) non-redundant protein/nucleotide sequence database, Swiss-Prot, PFAM database, the Gene Ontology database, and the Kyoto Encyclopedia of Genes and Genomes database in order to annotate gene descriptions, associate them with gene ontology terms, and assign them to pathways. The expression patterns for genes involved in several molecular events critical for molting, such as hormone regulation, triggering events, implementation phases, skelemin, immune responses were characterized and considered as mechanisms underlying molting in L. vannamei. Comparisons with transcriptomic analyses in other arthropods were also performed. The characterization of major transcriptional changes in genes involved in the molting cycle provides candidates for future investigation of the molecular mechanisms. The data generated in this study will serve as an important transcriptomic resource for the shrimp research community to facilitate gene and genome annotation and to characterize key molecular processes underlying shrimp development.

ALOMYbase, a resource to investigate non-target-site-based resistance to herbicides inhibiting acetolactate-synthase (ALS) in the major grass weed Alopecurus myosuroides (black-grass)

Background

Herbicide resistance in agrestal weeds is a global problem threatening food security. Non-target-site resistance (NTSR) endowed by mechanisms neutralising the herbicide or compensating for its action is considered the most agronomically noxious type of resistance. Contrary to target-site resistance, NTSR mechanisms are far from being fully elucidated. A part of weed response to herbicide stress, NTSR is considered to be largely driven by gene regulation. Our purpose was to establish a transcriptome resource allowing investigation of the transcriptomic bases of NTSR in the major grass weed Alopecurus myosuroides L. (Poaceae) for which almost no genomic or transcriptomic data was available.

Results

RNA-Seq was performed from plants in one F2 population that were sensitive or expressing NTSR to herbicides inhibiting acetolactate-synthase. Cloned plants were sampled over seven time-points ranging from before until 73 h after herbicide application. Assembly of over 159M high-quality Illumina reads generated a transcriptomic resource (ALOMYbase) containing 65,558 potentially active contigs (N50 = 1240 nucleotides) predicted to encode 32,138 peptides with 74 % GO annotation, of which 2017 were assigned to protein families presumably involved in NTSR. Comparison with the fully sequenced grass genomes indicated good coverage and correct representation of A. myosuroides transcriptome in ALOMYbase. The part of the herbicide transcriptomic response common to the resistant and the sensitive plants was consistent with the expected effects of acetolactate-synthase inhibition, with striking similarities observed with published Arabidopsis thaliana data. A. myosuroides plants with NTSR were first affected by herbicide action like sensitive plants, but ultimately overcame it. Analysis of differences in transcriptomic herbicide response between resistant and sensitive plants did not allow identification of processes directly explaining NTSR. Five contigs associated to NTSR in the F2 population studied were tentatively identified. They were predicted to encode three cytochromes P450 (CYP71A, CYP71B and CYP81D), one peroxidase and one disease resistance protein.

Conclusions

Our data confirmed that gene regulation is at the root of herbicide response and of NTSR. ALOMYbase proved to be a relevant resource to support NTSR transcriptomic studies, and constitutes a valuable tool for future research aiming at elucidating gene regulations involved in NTSR in A. myosuroides.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1804-x) contains supplementary material, which is available to authorized users.

Possible glyphosate tolerance mechanism in pitted morningglory (Ipomoea lacunosa L.)

Natural tolerance of Ipomoea lacunosa to glyphosate has made it problematic in the southeastern U.S. since the adoption of glyphosate-resistant crops. Experiments were conducted to determine (i) the variability in tolerance to glyphosate among accessions, (ii) if there is any correlation between metabolism of glyphosate to aminomethylphosponic acid (AMPA) or sarcosine and the level of tolerance, and (iii) the involvement of differential translocation in tolerance to glyphosate. Fourteen I. lacunosa accessions had GR50 values ranging from 58 to 151 grams of acid equivalent per hectare (ae/ha) glyphosate, a 2.6-fold variability in tolerance to glyphosate. There was no evidence of the most tolerant (MT) accession metabolizing glyphosate to AMPA more rapidly than the least tolerant (LT) accession. Metabolism to sarcosine was not found. (14)C-glyphosate absorption was similar in the two accessions. LT accession translocated more (14)C-glyphosate than MT accession at 24 and 48 h after treatment. Differential translocation partly explains glyphosate tolerance in MT accession.