CAPG: comprehensive allopolyploid genotyper.

MOTIVATION: Genotyping by sequencing is a powerful tool for investigating genetic variation in plants, but many economically important plants are allopolyploids, where homoeologous similarity obscures the subgenomic origin of reads and confounds allelic and homoeologous SNPs. Recent polyploid genotyping methods use allelic frequencies, rate of heterozygosity, parental cross or other information to resolve read assignment, but good subgenomic references offer the most direct information. The typical strategy aligns reads to the joint reference, performs diploid genotyping within each subgenome, and filters the results, but persistent read misassignment results in an excess of false heterozygous calls. RESULTS: We introduce the Comprehensive Allopolyploid Genotyper (CAPG), which formulates an explicit likelihood to weight read alignments against both subgenomic references and genotype individual allopolyploids from whole-genome resequencing data. We demonstrate CAPG in allotetraploids, where it performs better than Genome Analysis Toolkit's HaplotypeCaller applied to reads aligned to the combined subgenomic references. AVAILABILITY AND IMPLEMENTATION: Code and tutorials are available at https://github.com/Kkulkarni1/CAPG.git. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Genome-wide associations and epistatic interactions for internode number, plant height, seed weight and seed yield in soybean.

BACKGROUND: Breeding programs benefit from information about marker-trait associations for many traits, whether the goal is to place those traits under active selection or to maintain them through background selection. Association studies are also important for identifying accessions bearing potentially useful alleles by characterizing marker-trait associations and allelic states across germplasm collections. This study reports the results of a genome-wide association study and evaluation of epistatic interactions for four agronomic and seed-related traits in soybean. RESULTS: Using 419 diverse soybean accessions, together with genotyping data from the SoySNP50K Illumina Infinium BeadChip, we identified marker-trait associations for internode number (IN), plant height (PH), seed weight (SW), and seed yield per plant (SYP). We conducted a genome-wide epistatic study (GWES), identifying candidate genes that show evidence of SNP-SNP interactions. Although these candidate genes will require further experimental validation, several appear to be involved in developmental processes related to the respective traits. For IN and PH, these include the Dt1 determinacy locus (a soybean meristematic transcription factor), as well as a pectinesterase gene and a squamosa promoter binding gene that in other plants are involved in cell elongation and the vegetative-to-reproductive transition, respectively. For SW, candidate genes include an ortholog of the AP2 gene, which in other species is involved in maintaining seed size, embryo size, seed weight and seed yield. Another SW candidate gene is a histidine phosphotransfer protein - orthologs of which are involved in cytokinin-mediated seed weight regulating pathways. The SYP association loci overlap with regions reported in previous QTL studies to be involved in seed yield. CONCLUSIONS: This study further confirms the utility of GWAS and GWES approaches for identifying marker-trait associations and interactions within a diverse germplasm collection.

Evaluation of linkage disequilibrium, population structure, and genetic diversity in the U.S. peanut mini core collection.

BACKGROUND: Due to the recent domestication of peanut from a single tetraploidization event, relatively little genetic diversity underlies the extensive morphological and agronomic diversity in peanut cultivars today. To broaden the genetic variation in future breeding programs, it is necessary to characterize germplasm accessions for new sources of variation and to leverage the power of genome-wide association studies (GWAS) to discover markers associated with traits of interest. We report an analysis of linkage disequilibrium (LD), population structure, and genetic diversity, and examine the ability of GWA to infer marker-trait associations in the U.S. peanut mini core collection genotyped with a 58 K SNP array. RESULTS: LD persists over long distances in the collection, decaying to r2 = half decay distance at 3.78 Mb. Structure within the collection is best explained when separated into four or five groups (K = 4 and K = 5). At K = 4 and 5, accessions loosely clustered according to market type and subspecies, though with numerous exceptions. Out of 107 accessions, 43 clustered in correspondence to the main market type subgroup whereas 34 did not. The remaining 30 accessions had either missing taxonomic classification or were classified as mixed. Phylogenetic network analysis also clustered accessions into approximately five groups based on their genotypes, with loose correspondence to subspecies and market type. Genome wide association analysis was performed on these lines for 12 seed composition and quality traits. Significant marker associations were identified for arachidic and behenic fatty acid compositions, which despite having low bioavailability in peanut, have been reported to raise cholesterol levels in humans. Other traits such as blanchability showed consistent associations in multiple tests, with plausible candidate genes. CONCLUSIONS: Based on GWA, population structure as well as additional simulation results, we find that the primary limitations of this collection for GWAS are a small collection size, significant remaining structure/genetic similarity and long LD blocks that limit the resolution of association mapping. These results can be used to improve GWAS in peanut in future studies - for example, by increasing the size and reducing structure in the collections used for GWAS.

Caffeoyl glucosides from Nandina domestica inhibit LPS-induced endothelial inflammatory responses.

Endothelial dysfunction is a key pathological feature of many inflammatory diseases, including sepsis. In the present study, a new caffeoyl glucoside (1) and two known caffeoylated compounds (2 and 3) were isolated from the fruits of Nandina domestica Thunb. (Berberidaceae). The compounds were investigated for their effects against lipopolysaccharide (LPS)-mediated endothelial inflammatory responses. At 20 µM, 1 and 2 inhibited LPS-induced hyperpermeability, adhesion, and migration of leukocytes across a human endothelial cell monolayer in a dose-dependent manner suggesting that 1 and 2 may serve as potential scaffolds for the development of therapeutic agents to treat vascular inflammatory disorders.

Steroidal Alkaloids from Veratrum nigrum Enhance Glucose Uptake in Skeletal Muscle Cells.

Veratrum nigrum is recognized as a medicinal plant used for the treatment of hypertension, stroke, and excessive phlegm. Chemical investigation of the roots and rhizomes led to the isolation of five new steroidal alkaloids, jervine-3-yl formate (1), veramarine-3-yl formate (2), jerv-5,11-diene-3ß,13ß-diol (3), (1ß,3ß,5ß)-1,3-dihydroxyjervanin-12(13)-en-11-one (4), and veratramine-3-yl acetate (5). Compounds 1 and 5 exhibited potent inhibitory activity (11.3 and 4.7 µM, respectively) against protein tyrosine phosphatase 1B (PTP1B), which has emerged as a viable target for treatment of type 2 diabetes mellitus. On the basis of their PTP1B inhibitory activity, the compounds were evaluated for their potential to enhance glucose uptake in C2C12 skeletal muscle cells. The insulin-stimulated glucose uptake was enhanced upon treatment with compounds 1 and 5 (10 µM) by 49.9 ± 6.5% and 56.0 ± 9.7%, respectively, in a more potent manner than that with the positive control rosiglitazone (47.3 ± 3.4% at 30 µM). These results suggest that steroidal alkaloids serve as practical antidiabetes mellitus leads capable of enhancing glucose uptake.

Antimycobacterial labdane diterpenes from Leucas stelligera.

Phytochemical investigation of the acetone extract of the aerial parts of Leucas stelligera afforded four new compounds (1-4) belonging to the labdane diterpene series as well as two known flavones, velutin (5) and chrysoeriol (6). Structure elucidation of the new compounds was carried out using 1D and 2D NMR spectroscopic data and single-crystal X-ray crystallography of compound 1. Compounds 1-4 exhibited selective antimycobacterial activity against Mycobacterium tuberculosis with IC50 values in the range 5.02-9.80 µg/mL.

Phyllocladane diterpenes from Anisomeles heyneana.

New phyllocladane diterpene, phyllocladan-16α,17-dihydroxy-19-oic acid (1), together with known phyllocladane diterpene, phyllocladan-16α,19-diol (2), cembrane diterpene ovatodiolide (3), sitosteryl-3-O-ß-D-glucoside (4), and verbascoside (5), were isolated from aerial parts of Anisomeles heyneana. The structure of compound 1 was elucidated by 1D and 2D NMR analyses which included HSQC, HMBC, and nuclear overhauser effect spectroscopy (NOESY) experiments as well as X-ray crystallography. This is the first report of phyllocladane diterpenes from genus Anisomeles. Compounds 1, 3, 4, and 5 were evaluated for inhibition of Mycobacterium tuberculosis and 3 was found to exhibit anti-mycobacterial activity with IC90 6.53 µg/ml. Compounds 1, 3, and 5, at 100 µg/ml, were also evaluated for inhibition of Thp-1 cell lines, and compounds 1 and 3 showed 59.02% and 96.4% inhibitions, respectively.

Use of Targeted Amplicon Sequencing in Peanut to Generate Allele Information on Allotetraploid Sub-Genomes.

The use of molecular markers in plant breeding has become a routine practice, but the cost per accession can be a hindrance to the routine use of Quantitative Trait Loci (QTL) identification in breeding programs. In this study, we demonstrate the use of targeted re-sequencing as a proof of concept of a cost-effective approach to retrieve highly informative allele information, as well as develop a bioinformatics strategy to capture the genome-specific information of a polyploid species. SNPs were identified from alignment of raw transcriptome reads (2 × 50 bp) to a synthetic tetraploid genome using BWA followed by a GATK pipeline. Regions containing high polymorphic SNPs in both A genome and B genomes were selected as targets for the resequencing study. Targets were amplified using multiplex PCR followed by sequencing on an Illumina HiSeq. Eighty-one percent of the SNP calls in diploids and 68% of the SNP calls in tetraploids were confirmed. These results were also confirmed by KASP validation. Based on this study, we find that targeted resequencing technologies have potential for obtaining maximum allele information in allopolyploids at reduced cost.

Genotypic Characterization of the U.S. Peanut Core Collection.

Cultivated peanut (Arachis hypogaea) is an important oil, food, and feed crop worldwide. The USDA peanut germplasm collection currently contains 8,982 accessions. In the 1990s, 812 accessions were selected as a core collection on the basis of phenotype and country of origin. The present study reports genotyping results for the entire available core collection. Each accession was genotyped with the Arachis_Axiom2 SNP array, yielding 14,430 high-quality, informative SNPs across the collection. Additionally, a subset of 253 accessions was replicated, using between two and five seeds per accession, to assess heterogeneity within these accessions. The genotypic diversity of the core is mostly captured in five genotypic clusters, which have some correspondence with botanical variety and market type. There is little genetic clustering by country of origin, reflecting peanut's rapid global dispersion in the 18th and 19th centuries. A genetic cluster associated with the hypogaea/aequatoriana/peruviana varieties, with accessions coming primarily from Bolivia, Peru, and Ecuador, is consistent with these having been the earliest landraces. The genetics, phenotypic characteristics, and biogeography are all consistent with previous reports of tetraploid peanut originating in Southeast Bolivia. Analysis of the genotype data indicates an early genetic radiation, followed by regional distribution of major genetic classes through South America, and then a global dissemination that retains much of the early genetic diversity in peanut. Comparison of the genotypic data relative to alleles from the diploid progenitors also indicates that subgenome exchanges, both large and small, have been major contributors to the genetic diversity in peanut.

Antithrombotic and antiplatelet activities of small-molecule alkaloids from Scolopendra subspinipes mutilans.

The aim of this study was to discover small-molecule anticoagulants from Scolopendra subspinipes mutilans (SSM). A new acylated polyamine (1) and a new sulfated quinoline alkaloid (2) were isolated from SSM. Treatment with the new alkaloids 1, 2, and indole acetic acid 4 prolonged the activated partial thromboplastin time and prothrombin time and inhibited the activity and production of thrombin and activated factor X. Furthermore, compounds 1, 2, and 4 inhibited thrombin-catalyzed fibrin polymerization and platelet aggregation. In accordance with these potential in vitro antiplatelet activities, compounds 1, 2, and 4 showed enhanced antithrombotic effects in an in vivo pulmonary embolism and arterial thrombosis model. Compounds 1, 2, and 4 also elicited anticoagulant effects in mice. Collectively, this study may serve as the groundwork for commercializing SSM or compounds 1, 2, and 4 as functional food components for the prevention and treatment of pathogenic conditions and serve as new scaffolds for the development of anticoagulants.

New pimarane diterpenes and other antimycobacterial metabolites from Anisochilus verticillatus.

Phytochemical investigation of the acetone extract of the aerial parts of Anisochilus verticillatus afforded a new 8,9-secopimarane diterpene (1), two new isopimarane diterpenes (2, 3) and the known ursolic acid (4), α-amyrin (5), ß-amyrin (6), stigmast-5-en-3-one (7) and hydroxychavicol (8). Structures of the new compounds were elucidated with the help of 1D and 2D nuclear magnetic resonance spectroscopic data, and single crystal X-ray crystallography of compound 3. Compounds 2 and 8 inhibited Mycobacterium tuberculosis H37Ra with an IC50 of 11.3 (IC90 of 20.0 µg/mL) and 12.5 µg/mL, respectively. Correspondingly, molecular docking studies with Extra Precision Glide revealed a correlation between score and biological activity for these compounds to describe the molecular basis for the most significant SAR results.

Flavanones and Chromones from Salicornia herbacea Mitigate Septic Lethality via Restoration of Vascular Barrier Integrity.

Salicornia herbacea is an annual halophytic glasswort that has been employed as a culinary vegetable, salad, and traditional medicinal resource. Chemical investigation of the aerial parts of S. herbacea led to the isolation of two new (1, 2) and known (3) flavanones as well as a new nature-derived (4) and two known chromone derivatives (5, 6). These purified compounds were evaluated for their suppressive potentials against the release of high-mobility group box 1 protein (HMGB1), which has captured attention as a viable target for alleviating serious septic manifestations or septicemia. The phenolic compounds improved the survival rates of cecal ligation and puncture operation (CLP) in murine models, simulating severe septic shock and its related complications, to 40-60%. These results collectively validate that flavanone- and chromone-based secondary metabolites may serve as prospective prodrugs or food additives that may be commercialized for the control of septic complications and lethality.

Antimicrobial activity of plant extracts against sexually transmitted pathogens.

Comprehensive management of sexually transmitted infections (STIs) using vaginal or rectal microbicide-based intervention is one of the strategies for prevention of HIV infection. Herbal products have been used for treating STIs traditionally. Herein, we present in vitro activity of 10 plant extracts and their 34 fractions against three sexually transmitted/reproductive tract pathogens - Neisseria gonorrhoeae, Haemophilus ducreyi and Candida albicans. The plant parts were selected; the extracts/fractions were prepared and screened by disc diffusion method. The minimum inhibitory and minimum cidal concentrations were determined. The qualitative phytochemical analysis of selected extracts/fractions showing activity was performed. Of the extracts/fractions tested, three inhibited C. albicans, ten inhibited N. gonorrhoeae and five inhibited H. ducreyi growth. Our study demonstrated that Terminalia paniculata Roth. extracts/fractions inhibited growth of all three organisms. The ethyl acetate fraction of Syzygium cumini Linn. and Bridelia retusa (L.) Spreng. extracts was found to inhibit N. gonorrhoeae at lowest concentrations.

Antifungal dimeric chalcone derivative kamalachalcone E from Mallotus philippinensis.

From the red coloured extract (Kamala) prepared through acetone extraction of the fresh whole uncrushed fruits of Mallotus philippinensis, one new dimeric chalcone (1) along with three known compounds 1-(5,7-dihydroxy-2,2,6-trimethyl-2H-1-benzopyran-8-yl)-3-phenyl-2-propen-1-one (2), rottlerin (3) and 4'-hydroxyrottlerin (4) were isolated. The structure of compound 1 was elucidated by 1D and 2D NMR analyses that included HSQC, HMBC, COSY and ROESY experiments along with the literature comparison. Compounds 1-4 were evaluated for antifungal activity against different human pathogenic yeasts and filamentous fungi. The antiproliferative activity of the compounds was evaluated against Thp-1 cell lines. Compounds 1 and 2 both exhibited IC50 of 8, 4 and 16 µg/mL against Cryptococcus neoformans PRL518, C. neoformans ATCC32045 and Aspergillus fumigatus, respectively. Compound 4, at 100 µg/mL, showed 54% growth inhibition of Thp-1 cell lines.

Complete NMR assignments of undegraded asterosaponins from Asterias amurensis.

Four asterosaponins, thornasteroside A (1), versicoside A (2), anasteroside B (3), and asteronylpentaglycoside sulfate (4), were isolated from the predatory starfish Asterias amurensis Lütken. Unlike previous studies focusing on structure elucidation by degradation of the complex saponin molecules, complete nuclear magnetic resonance (NMR) assignment for the intact molecules was accomplished using 600 MHz high magnetic field NMR. The complete set of NMR assignments can help in the structure elucidation of asterosaponins isolated in low yields without resorting to chemical degradation. Furthermore, this approach can be extended to other complex steroidal saponins, which may accelerate the discovery of bioactive secondary metabolites from this invasive starfish species.

New 2,2-diphenylpropane and ethoxylated aromatic monoterpenes from Lavandula gibsoni (Lamiaceae).

A new substituted 2,2-diphenylpropane (1) and two new ethoxylated aromatic monoterpene alcohols (2 and 4) have been isolated from the acetone extract of the aerial parts of Lavandula gibsoni, along with the known compounds 8-hydroxycarvacrol (3), 8-hydroxythymol (5), coumarin (6), 4-methylresorcinol (7), 7,4'-dimethylapigenin (8), salvigenin (9), ß-sitosteryl-3-O-ß-D-glucopyranosyl-6'-O-palmitate (10) and euscaphic acid D (11). The structures of the isolated compounds were assigned on the basis of their (1)H- and (13)C-NMR spectra and two-dimensional NMR techniques, which included COSY, HSQC, HMBC and NOESY experiments and comparison with the reported literature.

Isobutrin from butea monosperma (flame of the forest): a promising new natural sensitizer belonging to chalcone class.

In this work, "isobutrin", an ecofriendly sensitizer that is extracted from Butea monosperma (commonly known as "Flame of the Forest") flowers, is introduced. It is a bright yellow pigment belonging to the chalcone class and is examined as a sensitizer for optoelectronic applications. It is observed that chelation of this dye with Ti ions results into a strong dye-TiO(2) charge transfer (DTCT) band in the visible region. This Ti-Isobutrin chelate is stable, irreversible and its formation is studied using Benesi-Hildebrand plot. The locations of HOMO-LUMO states of the Ti-isobutrin chelate and the corresponding band alignment with TiO(2) are obtained. Also, a thermal stability test revealed that isobutrin is stable above 100 °C.