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We de novo assembled and analysed the chloroplast genomes of Capsella bursa-pastoris, Descurainia sophia, and Lepidium apetalum of the plant family Brassicaceae. These chloroplast genomes exhibited a quadripartite structure characterised by inverted repeat regions (26,268–26,460 bp) separating large single copy (83,771–83,870 bp) and small single copy (17,570–18,014 bp) regions. Genetic analysis revealed 112 unique genes, comprising 78 protein-coding genes, 30 transfer RNA (tRNA) genes, and 4 ribosomal RNA (rRNA) genes. Notably, phylogenetic analysis of 21 species revealed close relationships between C. bursa-pastoris and C. orientalis, D. sophia and D. erodiifolia, and L. apetalum and L. cordatum, with 100% bootstrap support. In conclusion, the analysis of these genomes will contribute to the growing knowledge of chloroplast genomes in the Brassicaceae family and of the specific genera Capsella, Descurainia, and Lepidium.

The shift from outcrossing to self-fertilization is one of the main evolutionary transitions in plants and has broad effects on evolutionary trajectories. In Brassicaceae, the ability to inhibit self-fertilization is controlled by 2 genes, SCR and SRK , tightly linked within the S -locus. A series of small non-coding RNAs also encoded within the S -locus regulates the transcriptional activity of SCR alleles, resulting in a linear dominance hierarchy between them. In Brassicaceae, natural allopolyploid species are often self-compatible (SC) even when one of the progenitor species is self-incompatible, but the reason why polyploid lineages tend to lose self-incompatibility (SI) and the timing of the loss of SI (immediately after ancestral hybridization between the progenitor species, or at a later stage after the formation of allopolyploid lineages) have generally remained elusive. We used a series of synthetic diploid and tetraploid hybrids obtained between self-fertilizing Capsella orientalis and outcrossing Capsella grandiflora to test whether the breakdown of SI could be observed immediately after hybridization, and whether the occurrence of SC phenotypes could be explained by the dominance interactions between S -haplotypes inherited from the parental lineages. We used RNA-sequencing data from young inflorescences to measure allele-specific expression of the SCR gene and infer dominance interactions in the synthetic hybrids. We then evaluated the seed set from autonomous self-pollination in the synthetic hybrids. Our results demonstrate that self-compatibility of the hybrids depends on the relative dominance between S -alleles inherited from the parental species, confirming that SI can be lost instantaneously upon formation of the ancestral allopolyploid lineage. They also confirm that the epigenetic regulation that controls dominance interactions between S -alleles can function between subgenomes in allopolyploids. Together, our results illustrate how a detailed knowledge of the mechanisms controlling SI can illuminate our understanding of the patterns of co-variation between the mating system and changes in ploidy. [ABSTRACT FROM AUTHOR]

Premise: Floral scent, usually consisting of multiple compounds, is a complex trait, and its role in pollinator attraction has received increasing attention. However, disentangling the effect of individual floral scent compounds is difficult due to the complexity of isolating the effect of single compounds by traditional methods. Methods: Using available quasi‐isogenic lines (qILs) that were generated as part of the original mapping of the floral scent volatile‐related loci CNL1 (benzaldehyde) and TPS2 (β‐ocimene) in Capsella, we generated four genotypes that should only differ in these two compounds. Plants of the four genotypes were introduced into a common garden outside the natural range of C. rubella or C. grandiflora, with individuals of a self‐compatible C. grandiflora line as pollen donors, whose different genetic background facilitates the detection of outcrossing events. Visitors to flowers of all five genotypes were compared, and the seeds set during the common‐garden period were collected for high‐throughput amplicon‐based sequencing to estimate their outcrossing rates. Results: Benzaldehyde and β‐ocimene emissions were detected in the floral scent of corresponding genotypes. While some pollinator groups showed specific visitation preferences depending on scent compounds, the outcrossing rates in seeds did not vary among the four scent‐manipulated genotypes. Conclusions: The scent‐manipulated Capsella materials constructed using qILs provide a powerful system to study the ecological effects of individual floral scent compounds under largely natural environments. In Capsella, individual benzaldehyde and β‐ocimene emission may act as attractants for different types of pollinators. [ABSTRACT FROM AUTHOR]

Premise: Researchers often use ecological niche models to predict where species might establish and persist under future or novel climate conditions. However, these predictive methods assume species have stable niches across time and space. Furthermore, ignoring the time of occurrence data can obscure important information about species reproduction and ultimately fitness. Here, we assess compare ecological niche models generated from full‐year averages to seasonal models. Methods: In this study, we generate full‐year and monthly ecological niche models for Capsella bursa‐pastoris in Europe and North America to see if we can detect changes in the seasonal niche of the species after long‐distance dispersal. Results: We find full‐year ecological niche models have low transferability across continents and there are continental differences in the climate conditions that influence the distribution of C. bursa‐pastoris. Monthly models have greater predictive accuracy than full‐year models in cooler seasons, but no monthly models can predict North American summer occurrences very well. Conclusions: The relative predictive ability of European monthly models compared to North American monthly models suggests a change in the seasonal timing between the native range to the non‐native range. These results highlight the utility of ecological niche models at finer temporal scales in predicting species distributions and unmasking subtle patterns of evolution. [ABSTRACT FROM AUTHOR]

Genetic drift is expected to remove polymorphism from populations over long periods of time, with the rate of polymorphism loss being accelerated when species experience strong reductions in population size. Adaptive forces that maintain genetic variation in populations, or balancing selection, might counteract this process. To understand the extent to which natural selection can drive the retention of genetic diversity, we document genomic variability after two parallel species-wide bottlenecks in the genus Capsella. We find that ancestral variation preferentially persists at immunity related loci, and that the same collection of alleles has been maintained in different lineages that have been separated for several million years. By reconstructing the evolution of the disease-related locus MLO2b, we find that divergence between ancient haplotypes can be obscured by referenced based re-sequencing methods, and that trans-specific alleles can encode substantially diverged protein sequences. Our data point to long-term balancing selection as an important factor shaping the genetics of immune systems in plants and as the predominant driver of genomic variability after a population bottleneck.

Summary: The shift from outcrossing to selfing is one of the main evolutionary transitions in plants. It is accompanied by profound effects on reproductive traits, the so‐called selfing syndrome. Because the transition to selfing also implies deep genomic and ecological changes, one also expects to observe a genomic selfing syndrome.We took advantage of the three independent transitions from outcrossing to selfing in the Capsella genus to characterize the overall impact of mating system change on RNA expression, in flowers but also in leaves and roots. We quantified the extent of both selfing and genomic syndromes, and tested whether changes in expression corresponded to adaptation to selfing or to relaxed selection on traits that were constrained in outcrossers.Mating system change affected gene expression in all three tissues but more so in flowers than in roots and leaves. Gene expression in selfing species tended to converge in flowers but diverged in the two other tissues. Hence, convergent adaptation to selfing dominates in flowers, whereas genetic drift plays a more important role in leaves and roots.The effect of mating system transition is not limited to reproductive tissues and corresponds to both adaptation to selfing and relaxed selection on previously constrained traits. [ABSTRACT FROM AUTHOR]

Studying the independent evolution of similar traits provides valuable insights into the ecological and genetic factors driving phenotypic evolution. 1 The transition from outcrossing to self-fertilization is common in plant evolution 2 and is often associated with a reduction in floral attractive features such as display size, chemical signals, and pollinator rewards. 3 These changes are believed to result from the reallocation of the resources used for building attractive flowers, as the need to attract pollinators decreases. 2,3 We investigated the similarities in the evolution of flower fragrance following independent transitions to self-fertilization in Capsella. 4,5,6,7,8,9 We identified several compounds that exhibited similar changes in different selfer lineages, such that the flower scent composition reflects mating systems rather than evolutionary history within this genus. We further demonstrate that the repeated loss of β -ocimene emission, one of the compounds most strongly affected by these transitions, was caused by mutations in different genes. In one of the Capsella selfing lineages, the loss of its emission was associated with a mutation altering subcellular localization of the ortholog of TERPENE SYNTHASE 2. This mutation appears to have been fixed early after the transition to selfing through the capture of variants segregating in the ancestral outcrossing population. The large extent of convergence in the independent evolution of flower scent, together with the evolutionary history and molecular consequences of a causal mutation, suggests that the emission of specific volatiles evolved as a response to changes in ecological pressures rather than resource limitation. [Display omitted] • Flower scent evolved similarly in the independent selfing lineages of Capsella • β -ocimene emission is highly reduced in both lineages • This reduction is attributed to distinct mutations in each selfing species • In C. rubella , it is linked to a decrease in chloroplastic levels of TPS02 Flower scent serves as chemical signals to attract pollinators in many plants. Wozniak et al. describe a very similar evolution of floral volatile emission after independent transitions to autogamy in the genus Capsella , emphasizing its ecological importance even when animal pollination is not required. [ABSTRACT FROM AUTHOR]

The taxonomic history of Capsella Medik., one of the genera with the highest phenotypic plasticity, and thus the highest synonym number relative to the recognized species number, was reviewed. The current systematics of the genus was discussed and the exact number of taxa was determined. In light of the molecular and nomenclatural data, it was decided that the genus was represented around the world by five species and one hybrid. Considering the molecular studies that have been conducted over the 30 years it was concluded that the species of this genus are typical examples of the concept of cryptic species. The classification and nomenclature of such genetically different, morphologically similar species should be one of the most current discussion topics of modern systematic science. Capsella is one of the best examples to examine this situation; hence, this feature was discussed herein. It was decided that C. thracica and C. x abortiva are conspecific and the correct naming should be C. abortiva (pro hybr.). Lectotype assignments were performed for the names of 5 taxa, mainly C. rubella, C. x abortiva, and C. thracica. Also, the missing type specimen of the Turkish endemic C. lycia was found, the lectotype was assigned and it was determined to be a synonym of C. bursa-pastoris. Various errors in the type sample references, especially in the holotype of C. grandiflora, were thus corrected. Their distribution around the world was checked and then corrected, and an identification key is given for the taxa of the genus. [ABSTRACT FROM AUTHOR]

Accurate estimates of genome-wide rates and fitness effects of new mutations are essential for an improved understanding of molecular evolutionary processes. Although eukaryotic genomes generally contain a large noncoding fraction, functional noncoding regions and fitness effects of mutations in such regions are still incompletely characterized. A promising approach to characterize functional noncoding regions relies on identifying accessible chromatin regions (ACRs) tightly associated with regulatory DNA. Here, we applied this approach to identify and estimate selection on ACRs in Capsella grandiflora , a crucifer species ideal for population genomic quantification of selection due to its favorable population demography. We describe a population-wide ACR distribution based on ATAC-seq data for leaf samples of 16 individuals from a natural population. We use population genomic methods to estimate fitness effects and proportions of positively selected fixations (α) in ACRs and find that intergenic ACRs harbor a considerable fraction of weakly deleterious new mutations, as well as a significantly higher proportion of strongly deleterious mutations than comparable inaccessible intergenic regions. ACRs are enriched for expression quantitative trait loci (eQTL) and depleted of transposable element insertions, as expected if intergenic ACRs are under selection because they harbor regulatory regions. By integrating empirical identification of intergenic ACRs with analyses of eQTL and population genomic analyses of selection, we demonstrate that intergenic regulatory regions are an important source of nearly neutral mutations. These results improve our understanding of selection on noncoding regions and the role of nearly neutral mutations for evolutionary processes in outcrossing Brassicaceae species. [ABSTRACT FROM AUTHOR]

Abstract Background The outcrossing rate is a key determinant of the population-genetic structure of species and their long-term evolutionary trajectories. However, determining the outcrossing rate using current methods based on PCR-genotyping individual offspring of focal plants for multiple polymorphic markers is laborious and time-consuming. Results We have developed an amplicon-based, high-throughput enabled method for estimating the outcrossing rate and have applied this to an example of scented versus non-scented Capsella (Shepherd’s Purse) genotypes. Our results show that the method is able to robustly capture differences in outcrossing rates. They also highlight potential biases in the estimates resulting from differential haplotype sharing of the focal plants with the pollen-donor population at individual amplicons. Conclusions This novel method for estimating outcrossing rates will allow determining this key population-genetic parameter with high-throughput across many genotypes in a population, enabling studies into the genetic determinants of successful pollinator attraction and outcrossing.

In the vineyards of Rhineland-Palatinate (Germany), two different types of Shepherd’s Purse (Capsella bursa-pastoris) coexist: (1) the common type called ‘wild type’, and (2) the decandric type called Capsella apetala or ‘Spe’ with four stamens in place of the four petals. In this study, we compare the anatomical and physiological characters of rosette leaves of the respective types. Progeny of individual plants was cultivated in growth chambers under low- and high-light conditions. Under low-light conditions, the stomata densities of the adaxial and abaxial epidermis did not differ between the two types. When grown under high-light conditions, wild type and Spe, both exhibited increased stomata densities compared to low-light conditions, but Spe to a lesser extent than the wild type. The maximal photosynthetic capacity of Spe was lower in both, low-light and high-light conditions compared to wild-type plants. Under all CO2 concentrations, Spe seemed to be less productive. The less effective CO2 assimilation of the Spe mutant C. apetala was accompanied by later flowering. This fact prolonged the vegetative phase of Spe by about two weeks and was sufficient for the maintenance of both populations stably over years.

In the vineyards of Rhineland-Palatinate (Germany), two different types of Shepherd's Purse (Capsella bursa-pastoris) coexist: (1) the common type called 'wild type', and (2) the decandric type called Capsella apetala or 'Spe' with four stamens in place of the four petals. In this study, we compare the anatomical and physiological characters of rosette leaves of the respective types. Progeny of individual plants was cultivated in growth chambers under low- and high-light conditions. Under low-light conditions, the stomata densities of the adaxial and abaxial epidermis did not differ between the two types. When grown under high-light conditions, wild type and Spe, both exhibited increased stomata densities compared to low-light conditions, but Spe to a lesser extent than the wild type. The maximal photosynthetic capacity of Spe was lower in both, low-light and high-light conditions compared to wild-type plants. Under all CO2 concentrations, Spe seemed to be less productive. The less effective CO2 assimilation of the Spe mutant C. apetala was accompanied by later flowering. This fact prolonged the vegetative phase of Spe by about two weeks and was sufficient for the maintenance of both populations stably over years. [ABSTRACT FROM AUTHOR]

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Shepherin I is a glycine- and histidine-rich antimicrobial peptide from the root of a shepherd's purse, whose antimicrobial activity was suggested to be enhanced by the presence of Zn(II) ions. We describe Zn(II) and Cu(II) complexes of this peptide, aiming to understand the correlation between their metal binding mode, structure, morphology, and biological activity. We observe a logical sequence of phenomena, each of which is the result of the previous one: (i) Zn(II) coordinates to shepherin I, (ii) causes a structural change, which, in turn, (iii) results in fibril formation. Eventually, this chain of structural changes has a (iv) biological consequence: The shepherin I-Zn(II) fibrils are highly antifungal. What is of particular interest, both fibril formation and strong anticandidal activity are only observed for the shepherin I-Zn(II) complex, linking its structural rearrangement that occurs after metal binding with its morphology and biological activity.

Phytochemical investigation of 70% EtOH extract of the seeds of Capsella bursa-pastoris led to the isolation of a new cyclobutane organic acid (1), and fourteen known compounds, including two organosulfur compounds (2, 3), two quinonoids (4, 5), five flavonoids (6-10), three sterols (11-13) and two other types (14, 15). The structures of the compounds were elucidated by extensive spectroscopic analyses as well as comparison of their spectroscopic data with those reported in the literature. The antioxidant capacities of all compounds and extractive fractions were evaluated by the 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical-scavenging test and ferric reducing antioxidant power (FRAP) assay. Then the antioxidative substances were evaluated for their neuroprotective effects against H 2 O 2 -induced HT22 cell injury. The results indicated the strong scavenging ability to free radical of the extractive fractions and compounds 1-3, 8-10 and 13, and the ferric reducing antioxidant power of the extractive fractions and compounds 1-3, 8 and 10, which were close to or higher than that of the positive control trolox. The EtOAc fraction, n-BuOH fraction, and compounds 1, 3 and 8 can protect HT-22 cells from oxidative damage., (© 2023. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)

Summary: The transition from pollinator‐mediated outbreeding to selfing has occurred many times in angiosperms. This is generally accompanied by a reduction in traits attracting pollinators, including reduced emission of floral scent. In Capsella, emission of benzaldehyde as a main component of floral scent has been lost in selfing C. rubella by mutation of cinnamate‐CoA ligase CNL1. However, the biochemical basis and evolutionary history of this loss remain unknown, as does the reason for the absence of benzaldehyde emission in the independently derived selfer Capsella orientalis.We used plant transformation, in vitro enzyme assays, population genetics and quantitative genetics to address these questions.CNL1 has been inactivated twice independently by point mutations in C. rubella, causing a loss of enzymatic activity. Both inactive haplotypes are found within and outside of Greece, the centre of origin of C. rubella, indicating that they arose before its geographical spread. By contrast, the loss of benzaldehyde emission in C. orientalis is not due to an inactivating mutation in CNL1.CNL1 represents a hotspot for mutations that eliminate benzaldehyde emission, potentially reflecting the limited pleiotropy and large effect of its inactivation. Nevertheless, even closely related species have followed different evolutionary routes in reducing floral scent. [ABSTRACT FROM AUTHOR]

Summary: A crucial step in the transition from outcrossing to self‐fertilization is the loss of genetic self‐incompatibility (SI). In the Brassicaceae, SI involves the interaction of female and male specificity components, encoded by the genes SRK and SCR at the self‐incompatibility locus (S‐locus). Theory predicts that S‐linked mutations, and especially dominant mutations in SCR, are likely to contribute to loss of SI. However, few studies have investigated the contribution of dominant mutations to loss of SI in wild plant species.Here, we investigate the genetic basis of loss of SI in the self‐fertilizing crucifer species Capsella orientalis, by combining genetic mapping, long‐read sequencing of complete S‐haplotypes, gene expression analyses and controlled crosses.We show that loss of SI in C. orientalis occurred < 2.6 Mya and maps as a dominant trait to the S‐locus. We identify a fixed frameshift deletion in the male specificity gene SCR and confirm loss of male SI specificity. We further identify an S‐linked small RNA that is predicted to cause dominance of self‐compatibility.Our results agree with predictions on the contribution of dominant S‐linked mutations to loss of SI, and thus provide new insights into the molecular basis of mating system transitions. [ABSTRACT FROM AUTHOR]

The mustard family Brassicaceae, which includes the model plant Arabidopsis thaliana, exhibits morphological stasis and significant uniformity of floral plan. Nonetheless, there is untapped diversity in almost every aspect of floral morphology in the family that lends itself to comparative study, including organ number, shape, form, and color. Studies on the genetic basis of morphological diversity, enabled by extensive genetic tools and genomic resources and the close phylogenetic distance among mustards, have revealed a mosaic of conservation and divergence in numerous floral traits. Here I review the morphological diversity of the flowers of Brassicaceae and discuss studies addressing the underlying genetic and developmental mechanisms shaping floral diversity. To put flowers in the context of the floral display, I describe diversity in inflorescence morphology and the variation that exists in the structures preceding the floral organs. Reconstructing the floral morphospace in Brassicaceae coupled with next-generation sequencing data and unbiased approaches to interrogate gene function in species throughout the mustard phylogeny offers promising ways to understand how developmental mechanisms originate and diversify. [ABSTRACT FROM AUTHOR]

Crucihimalaya himalaica, a close relative of Arabidopsis and Capsella, grows on the Qinghai–Tibet Plateau (QTP) about 4,000 m above sea level and represents an attractive model system for studying speciation and ecological adaptation in extreme environments. We assembled a draft genome sequence of 234.72 Mb encoding 27,019 genes and investigated its origin and adaptive evolutionary mechanisms. Phylogenomic analyses based on 4,586 single-copy genes revealed that C. himalaica is most closely related to Capsella (estimated divergence 8.8 to 12.2 Mya), whereas both species form a sister clade to Arabidopsis thaliana and Arabidopsis lyrata, from which they diverged between 12.7 and 17.2 Mya. LTR retrotransposons in C. himalaica proliferated shortly after the dramatic uplift and climatic change of the Himalayas from the Late Pliocene to Pleistocene. Compared with closely related species, C. himalaica showed significant contraction and pseudogenization in gene families associated with disease resistance and also significant expansion in gene families associated with ubiquitin-mediated proteolysis and DNA repair. We identified hundreds of genes involved in DNA repair, ubiquitin-mediated proteolysis, and reproductive processeswith signs of positive selection. Gene families showing dramatic changes in size and genes showing signs of positive selection are likely candidates for C. himalaica’s adaptation to intense radiation, low temperature, and pathogen-depauperate environments in the QTP. Loss of function at the S-locus, the reason for the transition to selffertilization of C. himalaica, might have enabled its QTP occupation. Overall, the genome sequence of C. himalaica provides insights into the mechanisms of plant adaptation to extreme environments. [ABSTRACT FROM AUTHOR]

Rapid phenotypic changes in traits of adaptive significance are crucial for organisms to thrive in changing environments. How such phenotypic variation is achieved rapidly, despite limited genetic variation in species that experience a genetic bottleneck is unknown. Capsella rubella, an annual and inbreeding forb (Brassicaceae), is a great system for studying this basic question. Its distribution is wider than those of its congeneric species, despite an extreme genetic bottleneck event that severely diminished its genetic variation. Here, we demonstrate that transposable elements (TEs) are an important source of genetic variation that could account for its high phenotypic diversity. TEs are (i) highly enriched in C. rubella compared with its outcrossing sister species Capsella grandiflora, and (ii) 4.2% of polymorphic TEs in C. rubella are associated with variation in the expression levels of their adjacent genes. Furthermore, we show that frequent TE insertions at FLOWERING LOCUS C (FLC) in natural populations of C. rubella could explain 12.5% of the natural variation in flowering time, a key life history trait correlated with fitness and adaptation. In particular, we show that a recent TE insertion at the 3′ UTR of FLC affects mRNA stability, which results in reducing its steady-state expression levels, to promote the onset of flowering. Our results highlight that TE insertions can drive rapid phenotypic variation, which could potentially help with adaptation to changing environments in a species with limited standing genetic variation. [ABSTRACT FROM AUTHOR]

Capsella bursa-pastoris is a highly nutritious and medicinal plant very popular among Asian and Middle Eastern countries. The plant is patronized for its essential mineral components, vitamins, proteins and its medicinal properties including coagulant, anticancer and wound healing potentials. In this study, a metabolic study wasperformed with the ethanolic extract obtained from dried powdered plant to analyze its effect on some biochemical parameters of mice. The experiment revealed that treatment of mice with 150-300mg/kg ethanol extract of Capsella bursa-pastoris did not produced any significant alteration on hepatic biomarker enzymes ALT, AST, Alkaline phosphatase as well as blood urea nitrogen. Although, at a higher dose, a considerable increase in serum glucose, HDL cholesterol and AST enzymes was observed. The elevated level of serum transaminase enzymes observed may be as a result of hepatic impairment caused by the plant extract. This increase may be due to the chemical content of the plant, that result in increased metabolism and activity of the cells ultimately resulting in increased efficiency of liver in the production of enzymes. On the whole, this study was able to demonstrate that ethanolic extract of Capsella bursa pastoris doesn't exert toxic effects to normal liver function in mice. Hence, it's antibacterial, anticancer, and diuretic as well as other useful applications should be harnessed adequately without fear of severe adverse effect. It also support that notion that the plant can be used in the development of novel drugs for the treatment of many human diseases due to its safety and effectiveness. [ABSTRACT FROM AUTHOR]

Abstract Acetolactate synthase (ALS) inhibitor-resistant biotypes are the fastest growing class of herbicide-resistant weeds. Shepherd's purse (Capsella bursa-pastoris (L.) Medik.), a tetraploid species and one of the most troublesome weeds in wheat production, has evolved ALS inhibitor resistance. To confirm and characterize the resistance of shepherd's purse populations to ALS-inhibiting herbicides, whole-plant bioassays were conducted. To investigate the molecular basis of resistance in shepherd's purse, the ALS gene was sequenced and compared between susceptible (S) and resistant (R) biotypes. Two partial intronless ALS genes (ALS-1 and ALS-2) were identified, and two heterozygous mutations (CCT to TCT in ALS-1 and CCT to CAT in ALS-2) at position 197 (Pro197Ser and Pro197His) providing resistance were simultaneously found in a single plant in a resistant population. Our results confirmed that the resistant shepherd's purse population showed high-level resistance to tribenuron-methyl (RI = 59.8), pyroxsulam (RI = 38.7) and flucarbazone-Na (RI = 88.0). Quantitative reverse transcription-polymerase chain reaction (RT-qPCR) results suggested that the difference in ALS gene expression was small between S and R populations, which may be insufficient to cause herbicide resistance, and according to the results of in vitro ALS activity, insensitivity of ALS may be the main mechanism of high resistance to tribenuron-methyl in resistant populations. Graphical abstract Unlabelled Image Highlights • Two partial intronless ALS genes were identified in shepherd's purse. • Two heterozygous mutations at position 197 were simultaneously found in a single shepherd's purse plant. • The increased ALS gene expression levels in resistant population may be insufficient to cause resistance. • The insensitivity of ALS is likely involved in the resistance to tribenuron-methyl in the resistant populations. [ABSTRACT FROM AUTHOR]

Summary: Following allopolyploid formation, extensive genome evolution occurs, with the eventual loss of many homeologous gene copies. Although this process of diploidization has occurred many times independently, the evolutionary forces determining the probability and rate of gene loss remain poorly understood. Here, we conduct genome and transcriptome sequencing in a broad sample of Chinese accessions of Capsella bursa‐pastoris, a recently formed allotetraploid. Our whole genome data reveal three groups of these accessions: an Eastern group from low‐altitude regions, a Western group from high‐altitude regions, and a much more differentiated Northwestern group. Population differentiation in total expression was limited among closely related populations; by contrast, the relative expression of the two homeologous copies closely mirrors the genome‐wide SNP divergence. Consistent with this, we observe a negative correlation between expression changes in the two homeologues. However, genes showing population genomic evidence for adaptive evolution do not show an enrichment for expression divergence between homeologues, providing no clear evidence for adaptive shifts in relative gene expression. Overall, these patterns suggest that neutral drift may contribute to the population differentiation in the expression of the homeologues, and drive eventual gene loss over longer periods of time. [ABSTRACT FROM AUTHOR]

Background and Aims Capsella is a model genus for studying the transition from outcrossing to selfing, with or without change in ploidy levels. The genomic consequences and changes in reproductive traits (selfing syndrome) associated with these shifts have been studied in depth. However, potential ecological divergence among species of the genus has not been determined. Among ecological traits, competitive ability could be relevant for selfing evolution, as selfing has been shown to be statistically associated with reduced competitiveness in a recent meta-analysis. Methods We assessed the effect of competition on three Capsella species differing in their mating system and ploidy level. We used an experimental design where fitness related traits were measured in focal individuals with and without competitors. Key Results The diploid selfer (C. rubella) was most sensitive to competition, whereas the tetraploid selfer (C. bursa-pastoris) performed the best, with the diploid outcrosser (C. grandiflora) being intermediate. Conclusions These results add to the detailed characterization of Capsella species and highlight the possible roles of ecological context and ploidy in the evolutionary trajectories of selfing species. [ABSTRACT FROM AUTHOR]

Gene duplication is a major driver for the increase of biological complexity. The divergence of newly duplicated paralogs may allow novel functions to evolve, while maintaining the ancestral one. Alternatively, partitioning the ancestral function among paralogs may allow parts of that role to follow independent evolutionary trajectories. We studied the REDUCED COMPLEXITY (RCO) locus, which contains three paralogs that have evolved through two independent events of gene duplication, and which underlies repeated events of leaf shape evolution within the Brassicaceae. In particular, we took advantage of the presence of three potentially functional paralogs in Capsella to investigate the extent of functional divergence among them. We demonstrate that the RCO copies control growth in different areas of the leaf. Consequently, the copies that are retained active in the different Brassicaceae lineages contribute to define the leaf dissection pattern. Our results further illustrate how successive gene duplication events and subsequent functional divergence can increase trait evolvability by providing independent evolutionary trajectories to specialized functions that have an additive effect on a given trait. [ABSTRACT FROM AUTHOR]

Rapid advances in short-read DNA sequencing technologies have revolutionized population genomic studies, but there are genomic regions where this technology reaches its limits. Limitations mostly arise due to the difficulties in assembly or alignment to genomic regions of high sequence divergence and high repeat content, which are typical characteristics for loci under strong long-term balancing selection. Studying genetic diversity at such loci therefore remains challenging. Here, we investigate the feasibility and error rates associated with targeted long-read sequencing of a locus under balancing selection. For this purpose, we generated bacterial artificial chromosomes (BACs) containing the Brassicaceae S-locus, a region under strong negative frequency-dependent selection which has previously proven difficult to assemble in its entirety using short reads. We sequence S-locus BACs with single-molecule long-read sequencing technology and conduct de novo assembly of these S-locus haplotypes. By comparing repeated assemblies resulting from independent long-read sequencing runs on the same BAC clone we do not detect any structural errors, suggesting that reliable assemblies are generated, but we estimate an indel error rate of 5.7×10-5. A similar error rate was estimated based on comparison of Illumina short-read sequences and BAC assemblies. Our results show that, until de novo assembly of multiple individuals using long-read sequencing becomes feasible, targeted long-read sequencing of loci under balancing selection is a viable option with low error rates for single nucleotide polymorphisms or structural variation. We further find that short-read sequencing is a valuable complement, allowing correction of the relatively high rate of indel errors that result from this approach. [ABSTRACT FROM AUTHOR]

Plants respond to cold stress by modulating biochemical pathways and array of molecular events. Plant morphology is also affected by the onset of cold conditions culminating at repression in growth as well as yield reduction. As a preventive measure, cascades of complex signal transduction pathways are employed that permit plants to endure freezing or chilling periods. The signaling pathways and related events are regulated by the plant hormonal activity. Recent investigations have provided a prospective understanding about plant response to cold stress by means of developmental pathways e.g., moderate growth involved in cold tolerance. Cold acclimation assays and bioinformatics analyses have revealed the role of potential transcription factors and expression of genes like CBF, COR in response to low temperature stress. Capsella bursa-pastoris is a considerable model plant system for evolutionary and developmental studies. On different occasions it has been proved that C. bursa-pastoris is more capable of tolerating cold than A. thaliana. But, the mechanism for enhanced low or freezing temperature tolerance is still not clear and demands intensive research. Additionally, identification and validation of cold responsive genes in this candidate plant species is imperative for plant stress physiology and molecular breeding studies to improve cold tolerance in crops. We have analyzed the role of different genes and hormones in regulating plant cold resistance with special reference to C. bursa-pastoris. Review of collected data displays potential ability of Capsella as model plant for improvement in cold stress regulation. Information is summarized on cold stress signaling by hormonal control which highlights the substantial achievements and designate gaps that still happen in our understanding.

To avoid negative effects of transposable element (TE) proliferation, plants epigenetically silence TEs using a number ofmechanisms, including RNA-directed DNA methylation. These epigenetic modifications can extend outside the boundaries of TE insertions and lead to silencing of nearby genes, resulting in a trade-off between TE silencing and interference with nearby gene regulation. Therefore, purifyingselection is expectedtoremove silencedTE insertions near genesmore efficiently andprevent their accumulation within a population. To explore howeffects of TE silencing on gene regulation shapes purifying selection on TEs,we analyzedwhole genome sequencing data from166 individuals of a large population of the outcrossing species Capsella grandiflora.We found that most TEs are rare, and in chromosome arms, silenced TEs are exposed to stronger purifying selection than those that are not silenced by 24-nucleotide small RNAs, especially with increasing proximity to genes. An age-of-allele test of neutrality on a subset of TEs supports our inference of purifying selection on silenced TEs, suggesting that our results are robust to varying transposition rates.Our results provide newinsights into the processes affecting the accumulation of TEs in an outcrossing species and support the viewthat epigenetic silencing of TEs results in a trade-off between preventing TE proliferation and interference with nearby gene regulation. We also suggest that in the centromeric and pericentromeric regions, the negative aspects of epigenetic TE silencing are missing. [ABSTRACT FROM AUTHOR]

Main conclusion : The contribution of variations in coding regions or promoters to the changes in FAE1 expression levels have be quantified and compared in parallel by specifically designed swapping constructs. FATTY ACID ELONGATION1 ( FAE1) is a key gene in control of erucic acid synthesis in plant seeds. The expression of FAE1 genes in Brassica oleracea and Capsella rubella, representatives of high and low erucic acid species, respectively, was characterized to provide insight into the regulation of very long-chain fatty-acid biosynthesis in seeds. Virtually, no methylation was detected either in B. oleracea or in C. rubella, suggesting that modification of promoter methylation might not be a predominant mechanism. Swapping constructs were specifically designed to quantify and compare the contribution of variations in coding regions or promoters to the changes in FAE1 expression levels in parallel. A significantly higher fold change in erucic acid content was observed when swapping coding regions rather than when swapping promoters, indicating that the coding region is a major determinant of the catalytic power of β-ketoacyl-CoA synthase proteins. Common motifs have been proposed as essential for the preservation of basic gene expression patterns, such as seed-specific expression. However, the occurrence of variation in common cis-elements or the presence of species-specific cis-elements might be plausible mechanisms for changes in the expression levels in different organisms. In addition, conflicting observations in previous reports associated with FAE1 expression are discussed, and we suggest that caution should be taken when selecting a plant transformation vector and in interpreting the results obtained from vectors carrying the CaMV 35S promoter. [ABSTRACT FROM AUTHOR]

Cold stress is one of the major limitations to crop productivity worldwide. We investigated the effects of multiple gene expression from cold tolerant Capsella bursa-pastoris in transgenic tobacco ( Nicotiana tabaccum) plants. We combined CblCE53 and CbCBF into a reconstruct vector by isocaudomers. Plant overexpression of CbICE53 under the stress inducible CbCOR15b promoter and CbCBF under a constitutive promoter showed increased tolerance to both chilling and freezing temperatures in comparison to wild-type plants, according to the electrolyte leakage and relative water content. The expressions of endogenous cold-responsive genes in transgenic tobacco ( NtDREB1, NtDREB3, NtERD10a and NtERD10b) were obviously upregulated under normal and low temperature conditions. These results suggest that the CbICE53 + CbCBF transgenic plants showed a much greater cold tolerance as well as no dwarfism and delayed flowering. Thus they can be considered as a potential candidate for transgenic engineering for cold tolerant tobacco. [ABSTRACT FROM AUTHOR]

Plants respond to cold stress by modulating biochemical pathways and array of molecular events. Plant morphology is also affected by the onset of cold conditions culminating at repression in growth as well as yield reduction. As a preventive measure, cascades of complex signal transduction pathways are employed that permit plants to endure freezing or chilling periods. The signaling pathways and related events are regulated by the plant hormonal activity. Recent investigations have provided a prospective understanding about plant response to cold stress by means of developmental pathways e.g., moderate growth involved in cold tolerance. Cold acclimation assays and bioinformatics analyses have revealed the role of potential transcription factors and expression of genes like CBF, COR in response to low temperature stress. Capsella bursa-pastoris is a considerable model plant system for evolutionary and developmental studies. On different occasions it has been proved that C. bursa-pastoris is more capable of tolerating cold than A. thaliana. But, the mechanism for enhanced low or freezing temperature tolerance is still not clear and demands intensive research. Additionally, identification and validation of cold responsive genes in this candidate plant species is imperative for plant stress physiology and molecular breeding studies to improve cold tolerance in crops. We have analyzed the role of different genes and hormones in regulating plant cold resistance with special reference to C. bursa-pastoris. Review of collected data displays potential ability of Capsella as model plant for improvement in cold stress regulation. Information is summarized on cold stress signaling by hormonal control which highlights the substantial achievements and designate gaps that still happen in our understanding. [ABSTRACT FROM AUTHOR]

The CAX (Calcium Exchanger) genes constitute a set of signal transductors that are important for plant growth and adaptation to environmental stresses, especially to low temperature. CbCAX51, a Ca2+/H+ exchanger was cloned form Capsella bursa-pastoris, has been reported as a cold inducible gene. Here we showed that the transcriptional level of CbCAX51 in leaf and stem was higher than that in roots. Transcript of CbCAX51 was continuously up-regulated by Ca2+ and Cu2+, and transiently up-regulated by Zn2+ and Li+, cold stress, GA and ABA. The CbCAX51 protein was predicted to be localized in vacuolar by PSORT to Plant-mPLos, which was further confirmed by the subcellular detection of CbCAX51-GFP fusion protein. When CbCAX51 was transformed into the cold-sensitive plant tobacco, it conferred cold tolerance in tobacco seedlings based on physiological studies. Likewise, overexpression of CbCAX51 can activated some cold responsive genes in transgenic tobacco. Taken together, CbCAX51 is involved in the cold signal transduction and modulation of downstream components to enhance cold tolerance in tobacco. [ABSTRACT FROM AUTHOR]

A new sesquilignan glycoside 1, together with seven known phenolic glycosides 2-8 were isolated from the aerial parts of Capsella bursa-pastoris. The chemical structure of the new compound 1 was elucidated by extensive nuclear magnetic resonance (NMR) data (1H- and 13C-NMR, 1H-1H correlation spectroscopy (1H-1H COSY), heteronuclear single-quantum correlation (HSQC), heteronuclear multiple bond correlation (HMBC), and nuclear overhauser effect spectroscopy (NOESY)) and HR-FABMS analysis. The anti-inflammatory effects of 1-8 were evaluated in lipopolysaccharide (LPS)-stimulated murine microglia BV-2 cells. Compounds 4 and 7 exhibited moderate inhibitory effects on nitric oxide production in LPS-activated BV-2 cells, with IC50 values of 17.80 and 27.91 μM, respectively. [ABSTRACT FROM AUTHOR]

The tribe Camelineae (Brassicaceae) contains eight genera:Arabidopsis,Camelina,Capsella,Catolobus,Chrysochamela,Neslia,NoccidiumandPseudoarabidopsis. Little is known about pollen morphology in these taxa, and this limits research on gene flow, aerobiology, reproductive biology, systematics and palaeobotany. In this study, pollen from 13 taxa representing all of the genera in the tribe Camelineae were examined using light and scanning electron microscopy. Measurements of pollen size inCamelina(mean 26.4 µm) andArabidopsis(mean 30.4 µm) showed that these genera contain taxa with relatively large pollen that could be classified as medium-sized pollen. The largest pollen were fromCamelina microcarpa(mean 37.6 µm) andC. sativa(mean 35.6 µm). Conversely,Pseudoarabidopsishad the smallest pollen (mean 18.4 µm) in the Camelineae.Capsella bursa-pastoriswas distinct in the tribe in having tectum discontinuities.CatolobusandNesliashared a similar pollen shape that tended to be subspheroidal and less prolate than others in the tribe.Noccidiumhad distinct microverrucate elements on its colpus membrane. WithinCamelina, variations in pollen size and stratification were observed among the five species studied. The pollen morphology ofChrysochameladeviated from that of other members of the tribe, and it was distinct in having a homobrochate reticulum and the thickest exine, sexine and infratectum. These results support research on diverse topics including pollen dispersal and gene flow inCamelina, pollen development inArabidopsis thalianaand phylogenetic studies in the Brassicaceae. [ABSTRACT FROM PUBLISHER]

Interactions between genes can have important consequences for how selection shapes sequence variation at these genes. Specifically, genes that have pleiotropic effects by affecting the expression level of many other genesmay be under stronger selective constraint. We used coexpression networks to measure connectivity between genes and investigated the relationship between gene connectivity and selection in a natural population of the plant Capsella grandiflora. We observed that network connectivity was negatively correlated with genetic divergence due to stronger negative selection on highly-connected genes even when controlling for variation in gene expression level. However, the presence of local regulatory variation for a gene's expression level was also associated with reduced negative selection and lower gene connectivity. While it is difficult to disentangle the causal relationships between these factors, our results show that both connectivity and local regulatory variation are important factors for explaining variation in selection between genes. [ABSTRACT FROM AUTHOR]

Shepherd's purse (Capsella bursa-pastoris [L.] Medik.) is a troublesome dicot weed that occurs in major wheat (Triticum aestivum L.) production areas in China. Tribenuron-methyl failed to control shepherd's purse in some fields in Runan County, Henan Province. This study aimed to establish the cross-resistance pattern of a resistant (R) population and explore the potential targetsite and non-target-site based resistance mechanisms. Acetohydroxyacid synthase (AHAS) gene sequencing revealed a single nucleotide change of CCT to CGT resulting in the Pro to Arg substitution at amino acid position 197 in resistant individuals. Compared with the susceptible (S) population, R population displayed high level resistance to tribenuron-methyl. Cross resistance patterns showed that the R population was high resistant to flucarbazone-Na; moderately resistant to florasulam; low resistant to pyrithiobac sodium and pyroxsulam, and sensitive to imazethapyr. The pretreatment of malathion reduced the 50% growth reduction (GR50) value of tribenuron-methyl by 29% in the R population, suggesting that target-site resistance and non-target-site resistance mechanisms were both present in tribenuronmethyl -resistance of shepherd's purse. This is the first report of the acetolactate synthase Pro197Arg mutation in shepherd's purse. [ABSTRACT FROM AUTHOR]

Summary The enormous species richness of flowering plants is at least partly due to floral diversification driven by interactions between plants and their animal pollinators [ 1, 2 ]. Specific pollinator attraction relies on visual and olfactory floral cues [ 3–5 ]; floral scent can not only attract pollinators but also attract or repel herbivorous insects [ 6–8 ]. However, despite its central role for plant-animal interactions, the genetic control of floral scent production and its evolutionary modification remain incompletely understood [ 9–13 ]. Benzenoids are an important class of floral scent compounds that are generated from phenylalanine via several enzymatic pathways [ 14–17 ]. Here we address the genetic basis of the loss of floral scent associated with the transition from outbreeding to selfing in the genus Capsella . While the outbreeding C. grandiflora emits benzaldehyde as a major constituent of its floral scent, this has been lost in the selfing C. rubella . We identify the Capsella CNL1 gene encoding cinnamate:CoA ligase as responsible for this variation. Population genetic analysis indicates that CNL1 has been inactivated twice independently in C. rubella via different novel mutations to its coding sequence. Together with a recent study in Petunia [ 18 ], this identifies cinnamate:CoA ligase as an evolutionary hotspot for mutations causing the loss of benzenoid scent compounds in association with a shift in the reproductive strategy of Capsella from pollination by insects to self-fertilization. [ABSTRACT FROM AUTHOR]