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With the development of high-throughput sequencing techniques, transcriptome sequencing projects which provide valuable resources for designing simple sequence repeat (SSR) primers have been carried out for many plants. However, the utility of SSRs for molecular breeding depends on genome-wide distribution and coverage, as well as moderately high allelic variability, in the available SSR library. In this study, we characterized the exonic SSRs developed from the publicly available Populus genome as a case study to determine their value for molecular breeding. As expected, our results confirmed that microsatellites occurred approximately three times less often in coding regions than in non-coding regions. Mutability test also showed that exonic SSRs contained less allelic variability than intronic SSRs. More importantly, exonic SSRs were unevenly distributed both among and within chromosomes. Large exonic SSRs deserts were observed on several chromosomes. Differential selection between paralogous chromosomes, at the gene level, appears to be responsible for these SSR deserts, though the mechanisms that cause chromosome-specific SSR deserts are not known. This work provides ample evidence that the candidate gene approach based on unigenes identified from transcribed sequences may not be the best strategy to identify highly polymorphic SSRs. [ABSTRACT FROM AUTHOR]

The capacity to root from cuttings is a key factor for the mass deployment of superior genotypes in clonal forestry. We studied the genetic basis of rooting capacity by mapping quantitative trait loci (QTLs) that control growth rate and form of root traits in a full-sib family of 93 hybrids derived from an interspecific cross between two Populus species, P. deltoides and P. euramericana. The hybrid family was typed for different marker systems (including SSRs, AFLPs, RAPDs, ISSRs, and SNPs), leading to the construction of two linkage maps based on the female P. deltoides (D map) and male P. euramericana (E map) with a pseudotestcross mapping strategy. The two maps were scanned by functional mapping to detect QTLs that control early growth trajectories of two rooting traits, maximal single-root length and the total number of roots per cutting, measured at five time points in water culture. Of the six QTLs detected for these two growth traits, only one is segregating in P. deltoides with poor rooting capacity, while the other five are segregating in P. euramericana showing good rooting capacity. Tests with functional mapping suggest different developmental patterns of the genetic effects of these root QTLs in time course. Five QTLs were detected to change their effects on root growth trajectories with time, whereas one detected to affect root growth consistently in time course. Knowledge about the genetic and developmental control mechanisms of root QTLs will have important implications for the genetic improvement of vegetative propagation traits in Populus. [ABSTRACT FROM AUTHOR]

Almost all plants in the genus Populus are dioecious (i.e. trees are either male or female), but it is unknown whether dioecy evolved in a common ancestor or independently in different subgenera. Here, we sequence the small peritelomeric X- and Y-linked regions of P. deltoides chromosome XIX. Two genes are present only in the Y-linked region. One is a duplication of a non-Y-linked, female-specifically expressed response regulator, which produces siRNAs that block this gene's expression, repressing femaleness. The other is an LTR/Gypsy transposable element family member, which generates long non-coding RNAs. Overexpression of this gene in A. thaliana promotes androecium development. We also find both genes in the sex-determining region of P. simonii, a different poplar subgenus, which suggests that they are both stable components of poplar sex-determining systems. By contrast, only the duplicated response regulator gene is present in the sex-linked regions of P. davidiana and P. tremula. Therefore, findings in our study suggest dioecy may have evolved independently in different poplar subgenera. Dioecy has evolved independently from hermaphroditic ancestors in different plant lineages. Here, the authors assemble Populus deltoides male and female genomes, and show the putative roles of a femaleness gene and a maleness gene in sex determination, which suggests independent evolution in different poplar species. [ABSTRACT FROM AUTHOR]

Populus (poplars) and Salix (willows) are sister genera in the Salicaceae family that arise from a common tetraploid ancestor. The karyotypes of these two lineages are distinguished by two major interchromosomal and some minor intrachromosomal rearrangements, but which one is evolutionarily more primitive remains debatable. In this study, we compare the selection pressure acting on the paralogous genes resulting from salicoid duplication (PGRS) within and between the genomes of the two lineages. Purifying selection was determined to act more strongly on the PGRS in willow than on those in poplar, which would cause a faster loss of paralogous duplicates in willow. Therefore, Salix species are supposed to evolve faster than Populus species, which is consistent with the observation that the former are taxonomically and morphologically more diverse than the latter. In these two lineages, different autosomes were found to have been evolving into sex chromosomes. Examining the ω ratio and the PGRS in the sex determination regions in willow and poplar revealed higher convergent selection pressure and a faster loss of PGRS in the sex determination regions of both lineages. At the chromosome level, the sex chromosome in poplar is characterized by the lowest gene density among all chromosome members, while this feature is not observed on the sex chromosome in willow, suggesting that Populus species may inherit the more incipient sex chromosome from their progenitor. Taken together, Salix is supposed to be the nascent lineage arising from the additional round of genome reorganization that distinguishes the karyotypes of the two sister genera. In this study, assessment of ω ratios also detected a list of paralogous genes under unusual selection pressure, which could have special consequences for the adaptive evolution of Salicaceae species. In conclusion, the results of this study provide unique information for better understanding the genetic mechanism accelerating the divergence of these two closely related lineages. Genomics: Salicaceae family members under different selection pressures Different selection pressure on duplicate genes explains how willow and poplar diverged from a common progenitor with four copies of their genome. A study by Tongming Yin and colleagues at Nanjing Forestry University in China compared the genomes of these two fast-growing trees to shed light on how they lost ancestral genes to retain only two copies of their genome. They found an uneven selection pressure on different genomic regions and a faster loss of duplicated genes in willow. This could explain why willow evolved more nascent and gave rise to over 300 species, whereas there are only about 29 species of poplar. Differences in gene density in the sex chromosomes are also key to the divergent evolution of these two sister lineages. [ABSTRACT FROM AUTHOR]

Understanding the underlying mechanisms and links between genome evolution and adaptive innovations stands as a key goal in evolutionary studies. Poplars, among the world's most widely distributed and cultivated trees, exhibit extensive phenotypic diversity and environmental adaptability. In this study, we present a genus-level super-pangenome comprising 19 Populus genomes, revealing the likely pivotal role of private genes in facilitating local environmental and climate adaptation. Through the integration of pangenomes with transcriptomes, methylomes, and chromatin accessibility mapping, we unveil that the evolutionary trajectories of pangenes and duplicated genes are closely linked to local genomic landscapes of regulatory and epigenetic architectures, notably CG methylation in gene-body regions. Further comparative genomic analyses have enabled the identification of 142 202 structural variants across species that intersect with a significant number of genes and contribute substantially to both phenotypic and adaptive divergence. We have experimentally validated a ∼180-bp presence/absence variant affecting the expression of the CUC2 gene, crucial for leaf serration formation. Finally, we developed a user-friendly web-based tool encompassing the multi-omics resources associated with the Populus super-pangenome (http://www.populus-superpangenome.com). Together, the present pioneering super-pangenome resource in forest trees not only aids in the advancement of breeding efforts of this globally important tree genus but also offers valuable insights into potential avenues for comprehending tree biology. A Populus super-pangenome is reconstructed from whole-genome assemblies for forest trees in this study. Based on this super-pangenome this study offers novel insights into the evolution of genomic landscape that underlies the widespread adaptation and high phenotypic diversity of long-lived trees, which advance our comprehension of tree biology and breeding. [ABSTRACT FROM AUTHOR]

Willow (Salix spp.), a woody plant in forms of tree, sub-tree, or shrub, has long been cultivated as an important fiber resource and for environmental protection. To manage commercial willow plantations, there is an increasing demand for the genetic discrimination of willow cultivars based on molecular markers. In this study, based on the genomic sequences of Salix suchowensis, a core set of 16 highly polymorphic simple sequence repeat (SSR) primer pairs were selected for the molecular discrimination of different willow cultivars. Using these primer pairs, DNA fingerprints of a collection of 25 elite willow cultivars were generated and their genetic identities were analyzed based on the SSR genotyping profiles and the UPGMA clustering. Subsequently, we examined the ploidy levels of these cultivars by combining SSR marker genotyping with flow cytometry measurements. It was found that, in this collection, the shrub cultivars were mainly presented as diploids, while cultivars in tree form mainly existed as polyploids. This study established a reference DNA fingerprinting database for managing the commercial willow cultivars, and the determination of their ploidy levels provided critical information for aiding the polyploid breeding programs in willows. [ABSTRACT FROM AUTHOR]

Shrub willows are widely planted for landscaping, soil remediation, and biomass production, due to their rapid growth rates. Identification of regulatory genes in wood formation would provide clues for genetic engineering of willows for improved growth traits on marginal lands. Here, we conducted an expression quantitative trait locus (eQTL) analysis, using a full sibling F1 population of Salix suchowensis, to explore the genetic mechanisms underlying wood formation. Based on variants identified from simplified genome sequencing and gene expression data from RNA sequencing, 16,487 eQTL blocks controlling 5505 genes were identified, including 2148 cis-eQTLs and 16,480 trans-eQTLs. eQTL hotspots were identified, based on eQTL frequency in genomic windows, revealing one hotspot controlling genes involved in wood formation regulation. Regulatory networks were further constructed, resulting in the identification of key regulatory genes, including three transcription factors (JAZ1, HAT22, MYB36) and CLV1, BAM1, CYCB2;4, CDKB2;1, associated with the proliferation and differentiation activity of cambium cells. The enrichment of genes in plant hormone pathways indicates their critical roles in the regulation of wood formation. Our analyses provide a significant groundwork for a comprehensive understanding of the regulatory network of wood formation in S. suchowensis. [ABSTRACT FROM AUTHOR]

Despite the economic, ecological, and scientific importance of the genera Salix L. (willows) and Populus L. (poplars, cottonwoods, and aspens) Salicaceae, we know little about the sources of differences in species diversity between the genera and of the phylogenetic conflict that often confounds estimating phylogenetic trees. Salix subgenera and sections, in particular, have been difficult to classify, with one recent attempt termed a "spectacular failure" due to a speculated radiation of the subgenera Vetrix and Chamaetia. Here, we use targeted sequence capture to understand the evolutionary history of this portion of the Salicaceae plant family. Our phylogenetic hypothesis was based on 787 gene regions and identified extensive phylogenetic conflict among genes. Our analysis supported some previously described subgeneric relationships and confirmed the polyphyly of others. Using an f branch analysis, we identified several cases of hybridization in deep branches of the phylogeny, which likely contributed to discordance among gene trees. In addition, we identified a rapid increase in diversification rate near the origination of the Vetrix–Chamaetia clade in Salix. This region of the tree coincided with several nodes that lacked strong statistical support, indicating a possible increase in incomplete lineage sorting due to rapid diversification. The extraordinary level of both recent and ancient hybridization in both Salix and Populus have played important roles in the diversification and diversity in these two genera. [ABSTRACT FROM AUTHOR]

Colorectal cancer is a common malignancy and the second leading cause of cancer-related death. Emerging evidence suggests that the Wnt/β-catenin pathway has a significant role in cancer development. Shikonin is one of the main bioactive components of the plant, Lithospermum erythrorhizon, which possesses various biological properties. In this study, we identified a shikonin derivative, E5, as a novel suppressor of colorectal carcinoma that acted by inhibiting cell proliferation and migration, and promoting apoptosis. Mechanistically, the drug activated caspase-dependent pathways, negatively regulating the Wnt/β-catenin pathway, and inhibited epithelial–mesenchymal transition. The findings suggest the potential of β-catenin as a molecular target in colon carcinoma and propose E5 as a promising therapeutic strategy for targeting Wnt/β-catenin [Display omitted] ● A novel thioether shikonin derivative (E5), modified form of shikonin, acts as a novel inhibitor of β-catenin. ● E5 suppressed cancer cell proliferation and migration and promoted cell apoptosis via caspase-dependent pathways. ● E5 can be a drug candidate and has the potential to inhibit Wnt/β-catenin signaling pathway in the colon carcinoma. [ABSTRACT FROM AUTHOR]

3-hydroxy-3-methylglutaryl-CoA reductase (HMGR), as the rate-limiting enzyme in the mevalonate pathway, is essential for the biosynthesis of shikonin in Lithospermum erythrorhizon. However, in the absence of sufficient data, the principles of a genome-wide in-depth evolutionary exploration of HMGR family members in plants, as well as key members related to shikonin biosynthesis, remain unidentified. In this study, 124 HMGRs were identified and characterized from 36 representative plants, including L. erythrorhizon. Vascular plants were found to have more HMGR family genes than nonvascular plants. The phylogenetic tree revealed that during lineage and species diversification, the HMGRs evolved independently and intronless LerHMGRs emerged from multi-intron HMGR in land plants. Among them, Pinus tabuliformis and L. erythrorhizon had the most HMGR gene duplications, with 11 LerHMGRs most likely expanded through WGD/segmental and tandem duplications. In seedling roots and M9 cultured cells/hairy roots, where shikonin biosynthesis occurs, LerHMGR1 and LerHMGR2 were expressed significantly more than other genes. The enzymatic activities of LerHMGR1 and LerHMGR2 further supported their roles in catalyzing the conversion of HMG-CoA to mevalonate. Our findings provide insight into the molecular evolutionary properties and function of the HMGR family in plants and a basis for the genetic improvement of efficiently produced secondary metabolites in L. erythrorhizon. [ABSTRACT FROM AUTHOR]

Cytokinins have vital effects on various plant development-related processes. Type-A response regulators (RRs) are among the most important regulators in the cytokinin signaling pathway. Specifically, RR genes are the primary cytokinin-responsive genes, encode negative regulators of cytokinin signaling. Similar sex-determining mechanisms involving a type-A RR homolog have recently been identified in sister genera Populus and Salix. Here, we aimed to identify and characterize type-A RR gene family members in Populus deltoides. On the basis of the conserved receiver domain and phylogenetic analysis, we identified 9, 11, and 14 type-A RR genes were identified in P. deltoides , Populus trichocarpa , and Salix suchowensis , respectively. The exon-intron organization and chromosomal locations of these genes in P. deltoides as well as the characteristics of the encoded proteins were analyzed in detail. Gene duplication events, molecular evolution, and phylogenetic relationships were analyzed for all identified type-A RR genes along with 10 Arabidopsis thaliana homologs. These results indicated that the expansion of the type-A RR gene family was primarily due to whole-genome and segmental duplication events. The collinear type-A ARR pairs in A. thaliana were all derived from the α-whole-genome duplication (WGD) event, whereas those in the three Salicaceae species were divided into two groups, one comprising 10 pairs derived from the p -WGD event and the other consisting of 11 pairs derived from the γ-WGD event or a more ancient duplication event. All of the duplicated paralogous gene pairs had undergone purifying selection. Although different type-A RR paralogs experienced different selection pressures, convergent evolution was detected within the receiver domain-encoding sequence, indicative of the importance of this domain for the phosphorelay-related function of the encoded proteins. Three type-A RR genes (PdRR9 , PtRR11 , and SsRR12) associated with sex determination in Salicaceae species formed a small subclade that lacked A. thaliana counterparts. Evaluation of gene expression in vegetative tissues and at different floral developmental stages in P. deltoides revealed the specific spatiotemporal expression of each PdRR gene, with two (PdRR8 and PdRR9) of the nine PdRR genes exhibiting the opposite sex-biased expression patterns. Diverse expression levels were detected between all eight paralogous PdRR pairs. These findings support future research to elucidate the functional divergence of type-A RR genes. • Systematic genome-wide analysis of type-A RR genes was conducted in P. deltoides. • Expansion of the type-A RR gene family was primarily due to the WGD/segmental duplication events. • The PdRRs exhibited distinct developmental stage- and tissue-specific expression patterns. • This study will provide critical information to further elucidate the functional divergence of type-A RR genes. [ABSTRACT FROM AUTHOR]

Expansins are a group of cell wall enzyme proteins that help to loosen cell walls by breaking hydrogen bonds between cellulose microfibrils and hemicellulose. Expansins are essential plant proteins that are involved in several key processes, including seed germination, the growth of pollen tubes and root hairs, fruit ripening and abscission processes. Currently, there is a lack of knowledge concerning the role of expansins in woody plants. In this study, we analyzed expansin genes using Populus genome as the study target. Thirty-six members of the expansin gene family were identified in Populus that were divided into four subfamilies (EXPA, EXPB, EXLA and EXLB). We analyzed the molecular structure, chromosome localization, evolutionary relationships and tissue specificity of these genes and investigated expression changes in responses to phytohormone and abiotic stresses of the expansin genes of Populus tremula L. (PtEXs). Molecular structure analysis revealed that each PtEX protein had several conserved motifs and all of the PtEXs genes had multiple exons. Chromosome structure analysis showed that the expansin gene family is distributed on 14 chromosomes. The PtEXs gene family expansion patterns showed segmental duplication. Transcriptome data of Populus revealed that 36 PtEXs genes were differently expressed in different tissues. Cis-element analysis showed that the PtEXs were closely associated with plant development and responses to phytohormone and abiotic stress. Quantitative real-time PCR showed that abscisic acid (ABA) and low-temperature treatment affected the expression of some PtEXs genes, suggesting that these genes are involved in responses to phytohormone and abiotic stress. This study provides a further understanding of the expansin gene family in Populus and forms a basis for future functional research studies. [ABSTRACT FROM AUTHOR]

Fasciclin-like arabinogalactan proteins (FLAs) are a subclass of arabinogalactan proteins (AGPs) containing both AGP-like glycated domains and fasciclin (FAS) domains, which are involved in plant growth and development and synthesis of the cell wall. However, these proteins have not been identified or analyzed in willow, Salix, the sister genus of Populus. In this study, we performed a whole genome study of the FLA gene family of Salix suchowensis and compared it with the FLA gene family of Populus deltoides. The results showed the presence of 40 and 46 FLA genes in P. deltoides and S. suchowensis, distributed on 17 and 16 chromosomes, respectively. Four pairs of tandem repeat genes were found in willow, while poplar had no tandem repeat genes. Twelve and thirteen pairs of duplicated gene fragments were identified in poplar and willow, respectively. The multispecies phylogenetic tree showed that the FLA gene family could be divided into four groups (I–IV), with Group 1 showing significant expansion in woody plants. A gene expression analysis showed that PdeFLA19/27 in Group I of poplar was highly expressed, specifically during the secondary growth period of the stem and the rapid elongation of seed hairs. In the Group I genes of S. suchowensis, SsuFLA25/26/28 was also highly expressed during the secondary growth period, whereas increased expression of SsuFLA35 was associated with seed hair tissue. These results provide important clues about the differences in the FLA gene family during the evolution of herbs and woody plants, and suggest that the FLA gene family may play an essential role in regulating the secondary growth of woody plants. It also provides a reference for further studies on the regulation of secondary growth and seed hair development by FLA genes in poplar and willow. [ABSTRACT FROM AUTHOR]

Plant roots significantly influence soil microbial diversity, and soil microorganisms play significant roles in both natural and agricultural ecosystems. Although the genetically modified (GM) crops with enhanced insect and herbicide resistance are thought to have unmatched yield and stress resistance advantages, thorough and in‐depth case studies still need to be carried out in a real‐world setting due to the potential effects of GM plants on soil microbial communities. In this study, three treatments were used: a recipient soybean variety Jack, a triple transgenic soybean line JD321, and the glyphosate‐treated JD321 (JD321G). Three sampling stages (flowering, seed filling and maturing), as well as three host niches of soybean rhizosphere [intact roots (RT), rhizospheric soil (RS) and surrounding soil (SS)] were established. In comparison to Jack, the rhizospheric soil of JD321G had higher urease activity and lower nitrite reductase at the flowering stage. Different treatments and different sampling stages existed no significant effects on the compositions of microbial communities at different taxonomic levels. However, at the genus level, the relative abundance of three plant growth‐promoting fungal genera (i.e. Mortierella, Chaetomium and Pseudombrophila) increased while endophytic bacteria Chryseobacterium and pathogenic bacteria Streptomyces decreased from the inside to the outside of the roots (i.e. RT → RS → SS). Moreover, two bacterial genera, Bradyrhizobium and Ensifer were more abundant in RT than in RS and SS, as well as three species, Agrobacterium radiobacter, Ensifer fredii and Ensifer meliloti, which are closely related to nitrogen‐fixation. Furthermore, five clusters of orthologous groups (COGs) associated to nitrogen‐fixation genes were higher in RT than in RS, whereas only one COG annotated as dinitrogenase iron‐molybdenum cofactor biosynthesis protein was lower. Overall, the results imply that the rhizosphere host niches throughout the soil–plant continuum largely control the composition and function of the root‐associated microbiome of triple transgenic soybean. [ABSTRACT FROM AUTHOR]

(A) The structural maps of pBI121-LeBAHD1/LeSAT1-eGFP overexpression vector and pYLCRISPR/Cas9-LeBAHD1/LeSAT1 knockout vectors. However, not all members of the BAHD acyltransferase gene family could be screened out from the I L. erythrorhizon i genome by only using AAT/SAT amino acid sequences as a query. Identification and Characterization of LeBAHD Genes in L. erythrorhizon Genome In order to have a comprehensive understanding of the characteristics and functions of BAHD family genes in I L. erythrorhizon i , 104 members were initially screened out from the I L. erythrorhizon i genome based on sequences homology and the conserved BAHD superfamily feature domain (Pfam: PF02458). [Extracted from the article]

Abiotic stresses such as drought and high salinity inhibit plant growth and productivity. NAC transcription factors play a variety of important roles in plant development and abiotic stress responses. To date, the transformation of NAC genes into poplar plants has not been reported. In this study, we introduced the CarNAC3 and CarNAC6 salinity and drought tolerant genes from Cicer arietinum (chickpea) into Populus deltoides × Populus euramericana 'Nanlin895' (poplar) plants using Agrobacterium tumefaciens-mediated transformation . We verified the integration of the two genes into the poplar genome using polymerase chain reaction (PCR) and their stable expression was confirmed at the transcript level using real-time (RT)-PCR. The growth rates of roots and shoots and the clawed root rate increased in transformed plants grown in agar medium or in soil and increased in response to drought and salt stress conditions. Proline and photoprotectant pigment accumulation and antioxidant enzyme activities increased in response to abiotic stress, but the accumulation of photosynthetic pigments and malondialdehyde (MDA) decreased in transgenic lines relative to wild-type control plants. The CarNAC3 transgene was expressed at higher levels than the CarNAC6 transgene. Our results showed that the CarNAC3 and CarNAC6 genes enhanced the capacity for osmotic adjustment and increased antioxidant enzyme activity and suggest that these genes could play a significant role in improving drought and salt tolerance when expressed in poplar plants. [ABSTRACT FROM AUTHOR]

Compared to linear discriminant analysis (LDA), its orthogonalized version is a more effective statistical learning tool for dimension reduction, which devotes to better separating the data points from different classes in the lower-dimensional subspace. However, existing orthogonalized LDA techniques suffer from various drawbacks, including the requirement for expensive computing time. This paper develops an efficient orthogonal dimension reduction approach, referred to as fast orthogonal linear discriminant analysis (FOLDA), which is based on existing orthogonal linear discriminant analysis (OLDA) algorithms. However, different from previous efforts, the new approach applies the QR decomposition and the regression to solve for a new orthogonal projection vector at each iteration, leading to the by far cheaper computational cost. FOLDA achieves comparable recognition rate to existing OLDA algorithms due to the incorporation of the idea and spirit behind the latter ones. Experimental results on image databases, such as MINST, COIL20, MEPG-7 and OUTEX, show the effectiveness and efficiency of our algorithm. [ABSTRACT FROM AUTHOR]

12-Oxophytodienoate reductase (OPR) enzymes in dicots are categorized as flavin mononucleotide (FMN)–dependent oxidoreductases and are divided into two subgroups. Although subgroup II OPRs have been identified as being involved in a critical step in the production of jasmonic acid (JA), the functions of subgroup I OPRs are uncertain. In this study, we cloned a potential subgroup I OPR gene, EpOPR1, from Echium plantagineum using comparative transcriptome analysis. EpOPR1 expression was found to be significantly increased in root samples containing secondary metabolites such as shikonin and its derivatives. Using a transgenic hairy root system, we further explored the role of EpOPR1 in the production of these secondary metabolites. The results indicated that although the chemical profile of EpOPR1 overexpressing hairy roots (OPRO) is similar to that of the empty vector hairy roots (EV), the EpOPR1 overexpressing line considerably increased the yield of acetylshikonin by around two-fold. Our findings shed light on the potential role of subgroup I OPRs in E. plantagineum secondary metabolism regulation. [ABSTRACT FROM AUTHOR]

Elucidating the genetic factors underlying long-term biological processes remains challenging since the relevant genes and their effects may vary across different developmental stages. In this study, we carried out a large-scale field trial of the progeny of an F1 full-sib pedigree of Salix suchowensis and measured plant height and ground diameter periodically over a time course of 240 days. With the obtained data, we characterized plant growth rhythms and performed time-sequential analyses of quantitative trait loci underlying the dynamic growth of the plants. The dynamic mapping of quantitative trait loci revealed that stem height and ground diameter were under the control of four quantitative trait loci, and the effects of these quantitative trait loci varied greatly throughout the growth process, in which two quantitative trait loci were found to exert a pleiotropic effect determining the correlation between stem height and ground diameter. The analysis of candidate genes in the target genetic intervals showed that the pleiotropic effect of the two quantitative trait loci arises from the colocalization of genes with independent effects on stem height and ground diameter. Further examination of the expression patterns of the candidate genes indicated that height and circumference growth involve different activities of leaf and cambium tissues. This study provides unprecedented information to help us understand the dynamic growth of plants and presents an applicable strategy for elucidating the genetic mechanism underlying a long-term biological process by using plant growth as an example. [ABSTRACT FROM AUTHOR]

Shikonin and its derivatives are the main components of traditional Chinese medicine, Zicao. The pharmacological potential of shikonin and its derivatives have been extensively studied. Yet, less is known about the microbial assemblages associated with shikonin producing Borage plants. We studied microbial profiles of two Borage species, Echium plantagineum (EP) and Lithospermum erythrorhizon (LE), to identify the dynamics of microbial colonization pattern within three rhizo-compatments and two distinct soil types. Results of α and β-diversity via PacBio sequencing revealed significantly higher microbial richness and diversity in the natural soil along with a decreasing microbial gradient across rhizosphere to endosphere. Our results displayed genotype and soil type–dependent fine-tuning of microbial profiles. The host plant was found to exert effects on the physical and chemical properties of soil, resulting in reproducibly different micro-biota. Analysis of differentially abundant microbial OTUs displayed Planctomycetes and Bacteroidetes to be specifically enriched in EP and LE rhizosphere while endosphere was mostly prevailed by Cyanobacteria. Network analysis to unfold co-existing microbial species displayed different types of positive and negative interactions within different communities. The data provided here will help to identify microbes associated with different rhizo-compartments of potential host plants. In the future, this might be helpful for manipulating the keystone microbes for ecosystem functioning. [ABSTRACT FROM AUTHOR]

Short-rotation coppice willows, which are commonly propagated with cuttings, are promising bioenergy resource crops. In this study, a field trial with a completely randomized block design was carried out with 787 clones from three full-sib pedigrees involving two shrub willow species. A total of 7083 cuttings were planted in the field, and the mass of each cutting was recorded correspondingly. The mortality rate, growth traits, and wood property traits of each cutting-propagated plant were measured throughout a complete growing season. The obtained data showed that heavier cuttings produced shoots with lower mortality rate, higher height, thicker ground diameter, and larger biomass production than lighter cuttings. The cutting mass significantly improved plant performance, especially at the early developmental stages. However, the cutting mass had no effect on the basic density and the main chemical composition (i.e., cellulose, hemicellulose, and lignin) of willow wood. This study provided essential information for improving the establishment of short-rotation coppice willow plantations. [ABSTRACT FROM AUTHOR]

Summary: Phylogenetic analysis is complicated by interspecific gene flow and the presence of shared ancestral polymorphisms, particularly those maintained by balancing selection. In this study, we aimed to examine the prevalence of these factors during the diversification of Populus, a model tree genus in the Northern Hemisphere.We constructed phylogenetic trees of 29 Populus taxa using 80 individuals based on re‐sequenced genomes. Our species tree analyses recovered four main clades in the genus based on consensus nuclear phylogenies, but in conflict with the plastome phylogeny. A few interspecific relationships remained unresolved within the multiple‐species clade because of inconsistent gene trees. Our results indicated that gene flow has been widespread within each clade and also occurred among the four clades during their early divergence.We identified 45 candidate genes with ancient polymorphisms maintained by balancing selection. These genes were mainly associated with mating compatibility, growth and stress resistance.Both gene flow and selection‐mediated ancient polymorphisms are prevalent in the genus Populus. These are potentially important contributors to adaptive variation. Our results provide a framework for the diversification of model tree genus that will facilitate future comparative studies. [ABSTRACT FROM AUTHOR]

[Display omitted] • A novel series of dual-target benzenesulfonyl shikonin derivative has been designed and synthesized. • Z10 could activate activity of PKM2 and inhibit activity against PDK1 by direct intereaction. • Z10 showed significant anticancer activity in colorectal cancer in comparison with shikonin, PKM2 or PDK1 target agent. • Z10 exhibited lower toxicity than shikonin at 4 μM in vitro and at a dosage of 4.2 mg/kg in vivo. • Z10 could significantly induce apoptosis in colorectal cells and in xenograft mice models. Warburg effect provides energy and material essential for tumor proliferation, the reverse of Warburg effect provides insights into the development of a novel anti-cancer strategy. Pyruvate kinase 2 (PKM2) and pyruvate dehydrogenase kinase 1 (PDK1) are two key enzymes in tumor glucose metabolism pathway that not only contribute to the Warburg effect through accelerating aerobic glycolysis, but also serve as druggable target for colorectal cancer (CRC). Considering that targeting PKM2 or PDK1 alone does not seem to be sufficient to remodel abnormal glucose metabolism and achieve significant antitumor activity, a series of novel benzenesulfonyl shikonin derivatives were designed to regulate PKM2 and PDK1 simultaneously. By means of molecular docking and antiproliferative screen, we found that compound Z10 could act as the combination of PKM2 activator and PDK1 inhibitor, thereby significantly inhibited glycolysis that reshaping tumor metabolism. Moreover, Z10 could inhibit proliferation, migration and induce apoptosis in CRC cell HCT-8. Finally, the in vivo anti-tumor activity of Z10 was evaluated in a colorectal cancer cell xenograft model in nude mice and the results demonstrated that Z10 induced tumor cell apoptosis and inhibited tumor cell proliferation with lower toxicity than shikonin. Our findings indicated that it is feasible to alter tumor energy metabolism through multi-target synergies, and the dual-target benzenesulfonyl shikonin derivative Z10 could be a potential anti-CRC agent. [ABSTRACT FROM AUTHOR]

The SnRK (sucrose non-fermenting-1 related protein kinase) families respond to salt tolerance, nutritional stress, disease stress, and carbon metabolic regulation. In this study, the SnRK2.8 gene was cloned from Arabidopsis thaliana and nominated AtSnRK2.8. Bioinformatics characterization of AtSnRK2.8 showed that it contained an ATP binding site and a serine/threonine protein kinase binding site at the N-terminal catalytic domain. In addition, the AtSnRK2.8 protein contained special domain I at the C-terminal catalytic domain. Real-time polymerase chain reaction (PCR) results showed that the AtSnRK2.8 gene was expressed in all tested tissues and was highly expressed in seeds. Our analyses proved that the AtSnRK2.8 gene expression was upregulated by salt and drought stresses. The recombinant AtSnRK2.8 protein was expressed using a pET-28a system and purified with HisTrap HP affinity columns. The recombinant AtSnRK2.8 protein has the properties of a protein kinase. The results of overexpressing AtSnRK2.8 in Nanlin895 poplar showed that the transgenic poplar plants had a better ability to resist drought and salt stress compared to the wild type, and adapted well to drought and a high-salt environment. [ABSTRACT FROM AUTHOR]

The placenta in fruits of most plants either desiccate and shrink as the fruits mature or develop further to form the fleshy tissues. In poplars, placental epidermal cells protrude collectively to produce catkin fibers. In this study, three carpel limited MIXTA genes, PdeMIXTA02, PdeMIXTA03, PdeMIXTA04 , were find to specifically expressed in carpel immediately after pollination. Heterologous expression of the three genes in Arabidopsis demonstrated that PdeMIXTA04 significantly promoted trichomes density and could restore trichomes in the trichomeless mutant. By contrast, such functions were not observed with PdeMIXTA02, PdeMIXTA03. In situ hybridization revealed that PdeMIXTA04 was explicitly expressed in poplar placental epidermal cells. We also confirmed trichome-specific expression of the PdeMIXTA04 promoter. Multiple experimental proofs have confirmed the interaction between PdeMIXTA04, PdeMYC and PdeWD40, indicating PdeMIXTA04 functioned through the MYB-bHLH-WD40 ternary complex. Our work provided distinctive understanding of the molecular mechanism triggering differentiation of poplar catkins. [ABSTRACT FROM AUTHOR]

Gene knockdown and gene-silencing pathways in eukaryotic organisms are associated with small RNAs 20 to 25 nucleotides in length, which include microRNAs (miRNAs) and small interfering RNAs (siRNAs). These small RNAs are recruited to repress gene expression upstream or downstream of the transcription pathway. RNA interference (RNAi) is a biological inhibitor of gene expression that results in the destruction of messenger RNAs (mRNAs), leading to the inhibition of protein production. Indeed, RNA silencing plays a key role in plant development in terms of the plant’s response to both biotic and abiotic stresses. Conversely, Viral Suppressors of RNA silencing (VSRs) are proteins that hamper antiviral RNAi activation in plants, lead to suppress plant RNA-silencing. These VSR proteins prevent the induction of the plant antiviral RNAi immune response. This review focuses on small RNAs in plants and their roles in the responses of plants to biotic and abiotic stresses. [ABSTRACT FROM AUTHOR]

There are concerns that the innovation of genetically modified herbicide-tolerant (GMHT) plants, as well as the application of herbicide to such GMHT plants, could have an impact on ecological interactions and unintentionally harm non-targeted organisms. Consequently, we intend to use full-length 16 S rDNA amplicon sequencing to examine changes in the bacterial community in the rhizosphere of GMHT soybean (Z106) harboring 5-enolpyruvylshikimate-3-phosphate synthase and Glyphosate N-acetyltransferase genes and GMHT soybean treated with glyphosate (Z106G). Glyphosate application significantly impacted bacterial alpha diversity (species richness, and Shannon diversity). Permutational multivariate analysis of variance of beta diversity demonstrated that soil compartments and growth stages had a substantial impact on soybean rhizobacterial communities (soil compartments, growth stages, P = 0.001). Community composition revealed that Z106G soils were abundant in Taibaiella and Arthrobacter pascens at maturity, while Chryseobacterium joostei and Stenotrophomonas maltophilia predominated in Z106 soils during flowering. Nitrogen-fixing and phosphate-solubilizing microbes were found in higher proportions in the rhizosphere than in bulk soil, with Sinorhizobium being more abundant in Z106 and Bacillus and Stenotrophomonas being more prevalent in Z106G rhizosphere soils. Collectively, our findings suggest glyphosate application and glyphosate-tolerant soybean as potential regulators of soybean rhizobacterial composition. [Display omitted] • Glyphosate application had an impact on bacterial alpha diversity (species richness, and Shannon diversity). • Sinorhizobium fredii, a nitrogen fixer, was more abundant in the glyphosate-tolerant soybean line. • Neither glyphosate nor transgenic soybean line affected the relative abundance of the pathogenic fungus Fusarium. • Glyphosate spraying and soybean carrying EPSPS and GAT transgenes both positively regulate rhizobacterial composition. [ABSTRACT FROM AUTHOR]

Pyruvate kinase 2 (PKM2) and pyruvate dehydrogenase kinase 1 (PDK1) are two key enzymes in tumor glucose metabolism pathway that not only promote tumor growth and proliferation through accelerating aerobic glycolysis, but also contribute to drug resistance of non-small cell lung cancer (NSCLC). Considering that targeting PKM2 or PDK1 alone seems insufficient to remodel abnormal glucose metabolism to achieve significant antitumor activity, we proposed a "two-step approach" that regulates PKM2 and PDK1 synchronously. Firstly, we found that the combination of ML265 (PKM2 activator) and AZD7545 (PDK1 inhibitor) could synergistically inhibit proliferation and induce apoptosis in H1299 cells. Base on this, we designed a series of novel shikonin (SK) thioether derivatives as PKM2/PDK1 dual-target agents, among which the most potent compound E5 featuring a 2-methyl substitution on the benzene ring exerted significantly increased inhibitory activity toward EGFR mutant NSCLC cell H1975 (IC 50 = 1.51 μmol/L), which was 3 and 17-fold more active than the lead compound SK (IC 50 = 4.56 μmol/L) and the positive control gefitinib (IC 50 = 25.56 μmol/L), respectively. Additionally, E5 also showed good anti-tumor activity in xenografted mouse models, with significantly lower toxicity side effects than SK. Moreover, E5 also inhibited the entry of PKM2 into nucleus to regulate the transcriptional activation of oncogenes, thus restoring the sensitivity of H1975 cell to gefitinib. Collectively, these data demonstrate that E5 , a dual inhibitor of PKM2/PDK1, may be a promising adjunct to gefitinib in the treatment of EGFR-TKIs resistant NSCLC, deserving further investigation. [Display omitted] • A synergistic effect of PKM2 activation and PDK1 inhibition was first demonstrated. • A series of PKM2/PDK1 dual-target shikonin thioether derivatives were developed. • The most active compound E5 significantly inhibit tumor growth in vitro and in vivo. • The most active compound E5 enhance the sensitivity of H1975 cells to gefitinib. [ABSTRACT FROM AUTHOR]

Unlike two-class (multi-class) support vector machines, massive targets and few outliers are available in one-class support vector machine. The strategies to select useful data for two-class (multi-class) support vector machines are not suitable for one-class support vector machine. In this paper, relative density degree is introduced to select useful data for one-class support vector machine. These data would become support vectors after training and locate near the boundary of the data distribution. The relative density degree of the data near the boundary of the training set is smaller than that of the data in the interior of the training set. Thus, the data near the boundary of training set can be preserved and the others can be disposed through relative density degree. Experimental results show that merely preserving about 20 % of the training set, the performance will not decrease and be better than previous related method. But the model is simpler and the training process is faster. [ABSTRACT FROM AUTHOR]

PDK1 is one of the key enzymes in the glucose metabolism pathway, which is abnormally high expressed in breast cancer tissues and can promote tumor proliferation and metastasis. PDK1 and the PDHC/PDK axis are important targets for regulating glucose metabolism and anti-tumor activity. In this study, we evaluated the anti-tumor activities of a series of semi-synthesized shikonin (SK) derivatives against human breast cancer cells. The anti-proliferation activity of SK derivatives against human breast cancer cell lines was tested by CCK-8 and EdU assay. Flow cytometry was utilized to evaluate cell apoptosis, reactive oxygen species and cell cycle distribution. Cell migration ability was determined by wound healing and trans-well assay. PDK1 targeting effect was confirmed by western bolting, molecular docking, bio-layer interferometry and PDK1 enzyme activity assay. Nude-mouse transplanted tumor model was used to evaluate their anti-tumor effect in vivo. Findings revealed that SK derivatives had good anti-proliferation ability against MDA-MB-231 cell. They induced cell apoptosis by regulating the mitochondrial apoptosis and death receptor pathway. They also inhibited cell migration by suppressing EMT progression. Molecular docking, PDK1 affinity and enzyme activity demonstrated their PDK1 targeting. In vivo antitumor experiment showed that E2 could significantly inhibit tumor growth with lower side-effect on mice than SK. In conclusion, the novel SK derivatives E2 and E5 inhibited tumor glycolysis by targeting PDK1 and ultimately induced apoptosis. Our data demonstrated that E2 would be a good lead compound for the treatment of human TNBC as a novel PDK1 inhibitor. [ABSTRACT FROM AUTHOR]

[Display omitted] • SK and acetyl-SK relieve colonic injuries inAOM / DSS -induced colitis-associated colorectal cancer (CAC) model of C57BL/6J mice. • SK and acetyl-SK remodel the gut microbial communities of CAC mice models. • SK and acetyl-SK rescued the increased Ileibacterium valens and g_norank_f_norank_o_Clostridia_UCG-014 in CAC mice. • SK downregulated the expression of ACTN2, FGG and PKM2 in CAC mice. • SK upregulated the expression of Aldh1a1 and Aldh1b1 which involved in the Wnt/ β -catenin pathway in CAC mice. Colorectal cancer (CRC) and inflammatory bowel disease (IBD) are the most common diseases of human digestive system. Nowadays, the influence of the inflammatory microenvironment on tumorigenesis has become a new direction, and the exploration of relative molecular mechanism will facilitate the discovery and identification of novel potential anti-cancer molecules. Natural shikonin (SK) and acetyl-shikonin (acetyl-SK) was administered to azoxymethane (AOM)/dextran sodium sulphate (DSS)-induced colitis-associated colorectal cancer (CAC) mice model by gavage to investigate their therapeutic effects. Moreover, fresh feces and colon tissues were collected for determining the function of SK and acetyl-SK on the gut microbes and protein expression, respectively. Both SK and acetyl-SK decreased AOM/DSS-induced CAC, and regulated the intestinal flora structure in CAC mouse model. They, especially SK, improved species richness, evenness and diversity of intestinal flora, recovered the upregulated ratio of Firmicutes to Bacteroidota (F/B ratio) which symbolizes gut microbiota dysbiosis. SK and its derivative increased the beneficial bacteria g__norank_f__Muribaculaceae, Lactobacillus, Lachnospiraceae_NK4A136_Group, and reduced those harmful ones including Ileibacterium and Coriobacteriaceae UCG–002. Notably, AOM/DSS caused significant increase in the abundance of Ileibaterium valens and g__norank_f__norank_o__Clostridia_UCG-014 , which were not previously reported in studies of colonic inflammation or cancer, and the disorder was reversed by 20 mg/kg of SK. In our current study, the action of SK and acetyl-SK is dose-dependent, and 20 mg/kg SK exhibited the most effective functions, even better than the positive drug mesalazine. Moreover, differential proteomics and ELISA results showed that SK could recover the increase of pro-inflammatory cytokines (including IL-1β, IL-6 and TNF-α), the upregulation of pyruvate kinase isozyme type M2 (PKM2) and some other proteins (mainly concentrated in transcriptional mis-regulation in cancer and IL-17 signaling pathways), and the downregulation of Aldh1b1-Acc3-Maoa and Μgt2b34-Aldh1a1-Aldh1a7 involved in Wnt/ β -catenin signaling pathway. Our study identified SK and acetyl-SK, especially SK, as potential preventive agents for CAC through regulating both gut microbes and pathways involved in inflammation and cancer such as Wnt/ β -catenin signaling pathway. [ABSTRACT FROM AUTHOR]

In plants, many small interfering RNAs (siRNAs) direct de novo methylation by DNA methyltransferase. DNA methylation typically occurs by RNA-directed DNA methylation (RdDM), which directs transcriptional gene silencing of transposons and endogenous transgenes. RdDM is driven by non-coding RNAs (ncRNAs) produced by DNA-dependent RNA polymerases IV and V (PolIV and PolV). The production of siRNAs is initiated by PolIV and ncRNAs produced by PolIV are precursors of 24-nucleotide siRNAs. In contrast, ncRNAs produced by PolV are involved in scaffolding RNAs. In this review, we summarize recent studies of RdDM. In particular, we focus on the mechanisms involved in chromatin remodeling by PolIV and PolV. [ABSTRACT FROM AUTHOR]

The increasing resistance of bacteria and fungi to currently available antibiotics is a major concern worldwide, leading to enormous efforts to develop new antibiotics with new modes of actions. In this paper, cDNA encoding cecropin A was amplified from drury ( Hyphantria cunea ) ( dHC ) pupa fatbody total RNA using RT-PCR. The full-length dHC -cecropin A cDNA encoded a protein of 63 amino acids with a predicted 26-amino acid signal peptide and a 37-amino acid functional domain. We synthesized the antibacterial peptide (ABP) from the 37-amino acid functional domain (ABP- dHC -cecropin A), and amidated it via the C-terminus. Time-of-flight mass spectrometry showed its molecular weight to be 4058.94. The ABP- dHC -cecropin A was assessed in terms of its protein structure using bioinformatics and CD spectroscopy. The protein's secondary structure was predicted to be α-helical. In an antibacterial activity analysis, the ABP- dHC -cecropin A exhibited strong antibacterial activity against E. coli K12D31 and Agrobacterium EHA105. [ABSTRACT FROM AUTHOR]

The antimicrobial peptide ABP-dHC-cecropin A is a small cationic peptide with potent activity against a wide range of bacterial species. Evidence of antifungal activity has also been suggested; however, testing of this peptide has been limited due to the low expression of cecropin proteins in Escherichia coli . To improve expression of this peptide in E. coli , ABP-dHC-cecropin A was cloned into a pSUMO vector and transformed into E. coli , resulting in the production of a pSUMO-ABP-dHC-cecropin A fusion protein. The soluble form of this protein was then purified by Ni-IDA chromatography, yielding a total of 496-mg protein per liter of fermentation culture. The SUMO-ABP-dHC-cecropin A fusion protein was then cleaved using a SUMO protease and re-purified by Ni-IDA chromatography, yielding a total of 158-mg recombinant ABP-dHC-cecropin A per liter of fermentation culture at a purity of ≥94%, the highest yield reported to date. Antifungal activity assays performed using this purified recombinant peptide revealed strong antifungal activity against both Candida albicans and Neurospora crassa , as well as Rhizopus , Fusarium , Alternaria , and Mucor species. Combined with previous analyses demonstrating strong antibacterial activity against a number of important bacterial pathogens, these results confirm the use of ABP-dHC-cecropin A as a broad-spectrum antimicrobial peptide, with significant therapeutic potential. [ABSTRACT FROM AUTHOR]

PMMB-302 has an effect on the expression of apoptosis-related proteins such as Bcl2, Bcl-XL, caspase-9, caspase3 and FADD. Moreover, PMMB-302 inhibited expression of telomerase core proteins, dyskerin and NHP2, and telomerase reverse transcriptase RNA. These results suggested that PMMB-302 has tumor suppressive roles in lung cancer cells. [Display omitted] • A small novel molecule modified form of a natural product (shikonin), acts as a novel inhibitor of telomerase. • The small molecule suppresses cancer cell proliferation in vitro via inducing apoptosis and arresting cell cycle at G2/M phase. • This small molecule induces apoptosis in A549 cells through the mitochondrial and death receptor pathways. In this study, a series of novel shikonin N -benzyl matrinic acid ester derivatives (PMMB-299–PMMB-310) were synthesized and tested for their ability to inhibit the proliferation of cancer cells. Compared with shikonin and matrine, some of the ester derivatives were found to exhibit better anti-proliferative activity against seven different cancer cell lines, with less cytotoxicity toward non-cancerous cells. The strongest anti-proliferative activity was exhibited by PMMB-302, which had an IC 50 value of 2.71 μM against A549 cells. The compound caused cell cycle arrest in the G2/M phase and induced apoptosis. Effects on the expression of apoptosis-related molecules such as Bcl2, Bcl-XL, caspase-3, caspase-9 and FADD suggested that PMMB-302 has tumor suppressive roles in lung cancer cells. In addition, PMMB-302 inhibited expression of telomerase core proteins, dyskerin and NHP2, and telomerase reverse transcriptase RNA. Moreover, molecular docking of PMMB-302 was subsequently conducted to determine the probable binding mode with telomerase. Taken together, the results indicate that PMMB-302 acts as a tumor suppressor in lung cancer cells by negatively regulating telomerase expression. [ABSTRACT FROM AUTHOR]

Polyploid breeding is an important means for creating elite varieties for the development of poplar plantations. However, polyploid poplars are rare in natural stands. In this study, we established an analytical toolkit to perform marker-aided selection of polyploid poplars. This toolkit contains 12 SSR primer pairs with sites located in the exonic DNA regions and resulting amplified microsatellites in the intronic/intergenic regions. Highly conserved primer pairs were selected by testing in eight species from four poplar sections. The amplified loci's variability was examined using trees from a germplasm collection of Populus deltoides. Subsequently, copy numbers amplified by the highly variable primers were experimentally determined using progeny of a full-sib diploid pedigree. Based on the above tests, a subset of primers were finally selected and used for marker-aided selection of polyploid poplars from a set of natural Populus tomentosa stands. The reliability of the established analytical toolkit was further verified using a flow cytometer. We established a fast and reliable technique to screen polyploid poplars from natural stands. [ABSTRACT FROM AUTHOR]

Oil camellia trees are important woody plants for the production of high-quality cooking oil. On the contrary to their economic importance, their genetic and genomic resources are very limited, which greatly hamper the genetic studies on oil camellia trees. Microsatellites or simple sequence repeats (SSRs) have great value in many aspects of genetic analyses due to their high polymorphism and codominant inheritance. In this study, we report the large-scale development and characterization of SSR markers derived from genomic sequences of Camellia chekiangoleosa by high-throughput pyrosequencing technology. A total of 1,091,393 genomic shotgun reads were generated using Roche 454 FLX sequencer, the average read length was 319 bp, and the total sequence throughput was 347.9 Mb. These sequences were assembled into 35,315 contigs with total length of 14.8 Mb and the N50 contig size of 770 bp. By analyzing with microsatellite (MISA), a total of 5,844 perfect microsatellites were detected from the assembled sequences. Among them, tetranucleotide repeats were found to be the most frequent microsatellites in the genome of C. chekiangoleosa, and all the dominant repeat motifs for different types of SSRs were detected to be rich in A/T. Experimental analysis with 900 SSR primer pairs revealed that 66 % of them succeeded in PCR amplification. Further investigation with 345 SSR primer pairs showed that a relatively high percentage of primers amplified polymorphic loci (31.9 %). Experimental data also revealed that, overall, long microsatellite repeats (>20 bp) were more variable than the short ones (<20 bp) in the genome of oil camellia tree. [ABSTRACT FROM AUTHOR]

Epidemic outbreaks of rust disease have been observed in most of the black cottonwood ( Populus trichocarpa) plantations in the south of China in recent years. However, the exact pathogens that cause rust disease in this area remain largely unknown. In this study we collected rust fungi from black cottonwood plantations at four different places in the south of China. Examination of these fungi by scanning electron microscope (SEM) and light microscopy (LM) revealed that the morphological characteristics of urediniospores for all the collected fungi were very close to that of Melampsora larici-populina. Using species-specific primers, these pathogens were confirmed to be M. larici-populina. In a survey on the resistance to rust disease for 88 genotypes of black cottonwood, nine potential candidate genotypes were detected that may be free from infection of rust pathogen. The results of this study provide essential information for breeding new rust-resistant black cottonwood cultivars. [ABSTRACT FROM AUTHOR]

[Display omitted] • A series of novel anilide (dicarboxylic acid) shikonin esters were designed and synthesized as potential antitumor agents. • Representative compound M9 displayed potent anti-proliferative activity in vitro. • M9 could significantly induce apoptosis and arrest cell cycle in G2/M phase on MDA-MB-231 cells. • M9 inhibited the migration of MDA-MB-231 cells through Wnt/β-catenin signaling pathway in vitro. • M9 down-regulates PI3K/Akt/mTOR pathway by targeting Akt, thereby inhibiting cell proliferation and migration. Triple-negative breast cancer (TNBC) has an unfavorable prognosis attribute to its low differentiation, rapid proliferation and high distant metastasis rate. PI3K/Akt/mTOR as an intracellular signaling pathway plays a key role in the cell proliferation, migration, invasion, metabolism and regeneration. In this work, we designed and synthesized a series of anilide (dicarboxylic acid) shikonin esters targeting PI3K/Akt/mTOR signaling pathway, and assessed their antitumor effects. Through three rounds of screening by computer-aided drug design method (CADD), we preliminarily obtained sixteen novel anilide (dicarboxylic acid) shikonin esters and identified them as excellent compounds. CCK-8 assay results demonstrated that compound M9 exhibited better antiproliferative activities against MDA-MB-231, A549 and HeLa cell lines than shikonin (SK), especially for MDA-MB-231 (M9: IC 50 = 4.52 ± 0.28 μM; SK: IC 50 = 7.62 ± 0.26 μM). Moreover, the antiproliferative activity of M9 was better than that of paclitaxel. Further pharmacological studies showed that M9 could induce apoptosis of MDA-MB-231 cells and arrest the cell cycle in G2/M phase. M9 also inhibited the migration of MDA-MB-231 cells by inhibiting Wnt/β-catenin signaling pathway. In addition, western blot results showed that M9 could inhibit cell proliferation and migration by down-regulating PI3K/Akt/mTOR signaling pathway. Finally, a three-dimensional quantitative structure–activity relationship (3D-QSAR) model was also constructed to provide a basis for further development of shikonin derivatives as potential antitumor drugs through structure–activity relationship analysis. To sum up, M9 could be a potential candidate for TNBC therapy. [ABSTRACT FROM AUTHOR]