Using full chloroplast genomes of 'red' and 'yellow' Bixa orellana (achiote) for kmer based identification and phylogenetic inference.
ABSTRACT: BACKGROUND:Full chloroplast genomes provide high resolution taxonomic discrimination between closely related plant species and are quickly replacing single and multi-locus barcoding regions as reference materials of choice for DNA based taxonomic annotation of plants. Bixa orellana, commonly known as "achiote" and "annatto" is a plant used for both human and animal foods and was thus identified for full chloroplast sequencing for the Center for Veterinary Medicine (CVM) Complete Chloroplast Animal Feed database. This work was conducted in collaboration with the Instituto de Medicina Tradicional (IMET) in Iquitos, Peru. There is a wide range of color variation in pods of Bixa orellana for which genetic loci that distinguish phenotypes have not yet been identified. Here we apply whole chloroplast genome sequencing of "red" and "yellow" individuals of Bixa orellana to provide high quality reference genomes to support kmer database development for use identifying this plant from complex mixtures using shotgun data. Additionally, we describe chloroplast gene content, synteny and phylogeny, and identify an indel and snp that may be associated with seed pod color. RESULTS:Fully assembled chloroplast genomes were produced for both red and yellow Bixa orellana accessions (158,918 and 158,823?bp respectively). Synteny and gene content was identical to the only other previously reported full chloroplast genome of Bixa orellana (NC_041550). We observed a 17 base pair deletion at position 58,399-58,415 in both accessions, relative to NC_041550 and a 6?bp deletion at position 75,531-75,526 and a snp at position 86,493 in red Bixa orellana. CONCLUSIONS:Our data provide high quality reference genomes of individuals of red and yellow Bixa orellana to support kmer based identity markers for use with shotgun sequencing approaches for rapid, precise identification of Bixa orellana from complex mixtures. Kmer based phylogeny of full chloroplast genomes supports monophylly of Bixaceae consistent with alignment based approaches. A potentially discriminatory indel and snp were identified that may be correlated with the red phenotype.
Project description:<i>Bixa orellana</i> is a small tree known for its red, oil-soluble pigment contained in the seed coat that is used as a natural dye and food coloring. In this study, we assembled and characterized the complete chloroplast genome of <i>B. orellana</i> as a resource for future genetic studies. With a total length of 159,825?bp, the chloroplast genome comprised of a large single-copy (LSC) region of 89,476?bp, a small single-copy (SSC) region of 19,617?bp, and two inverted repeat (IR) regions of 25,356?bp each. A total of 127 genes were predicted, consisting of 83 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. Phylogenetic analysis confirmed the position of <i>B. orellana</i> within the order Malvales.
Project description:Bixa orellana L., popularly known as "urucum," has been used by indigenous communities in Brazil and other tropical countries for several biological applications, which indicates its potential use as an active ingredient in pharmaceutical products. The aim of this work was to report the main evidence found in the literature, concerning the ethnopharmacology, the biological activity, and the phytochemistry studies related to Bixa orellana L. Therefore, this work comprises a systematic review about the use of Bixa orellana in the American continent and analysis of the data collected. This study shows the well-characterized pharmacological actions that may be considered relevant for the future development of an innovative therapeutic agent.
Project description:<h4>Background</h4>The antimicrobial activity and Minimal Inhibitory Concentration (MIC) of the extracts of Bidens pilosa L., Bixa orellana L., Cecropia peltata L., Cinchona officinalis L., Gliricidia sepium H.B. & K, Jacaranda mimosifolia D.Don, Justicia secunda Vahl., Piper pulchrum C.DC, P. paniculata L. and Spilanthes americana Hieron were evaluated against five bacteria (Staphylococcus aureus, Streptococcus beta hemolític, Bacillus cereus, Pseudomonas aeruginosa, and Escherichia coli), and one yeast (Candida albicans). These plants are used in Colombian folk medicine to treat infections of microbial origin.<h4>Methods</h4>Plants were collected by farmers and traditional healers. The ethanol, hexane and water extracts were obtained by standard methods. The antimicrobial activity was found by using a modified agar well diffusion method. All microorganisms were obtained from the American Type Culture Collection (ATCC). MIC was determined in the plant extracts that showed some efficacy against the tested microorganisms. Gentamycin sulfate (1.0 microg/ml), clindamycin (0.3 microg/ml) and nystatin (1.0 microg/ml) were used as positive controls.<h4>Results</h4>The water extracts of Bidens pilosa L., Jacaranda mimosifolia D.Don, and Piper pulchrum C.DC showed a higher activity against Bacillus cereus and Escherichia coli than gentamycin sulfate. Similarly, the ethanol extracts of all species were active against Staphylococcus aureus except for Justicia secunda. Furthermore, Bixa orellana L, Justicia secunda Vahl. and Piper pulchrum C.DC presented the lowest MICs against Escherichia coli (0.8, 0.6 and 0.6 microg/ml, respectively) compared to gentamycin sulfate (0.9 8 g/ml). Likewise, Justicia secunda and Piper pulchrum C.DC showed an analogous MIC against Candida albicans (0.5 and 0.6 microg/ml, respectively) compared to nystatin (0.6 microg/ml). Bixa orellana L, exhibited a better MIC against Bacillus cereus (0.2 microg/ml) than gentamycin sulfate (0.5 microg/ml).<h4>Conclusion</h4>This in vitro study corroborated the antimicrobial activity of the selected plants used in folkloric medicine. All these plants were effective against three or more of the pathogenic microorganisms. However, they were ineffective against Streptococcus beta hemolytic and Pseudomonas aeruginosa. Their medicinal use in infections associated with these two species is not recommended. This study also showed that Bixa orellana L, Justicia secunda Vahl. and Piper pulchrum C.DC could be potential sources of new antimicrobial agents.
Project description:Bixin or annatto is a commercially important natural orange-red pigment derived from lycopene that is produced and stored in seeds of Bixa orellana L. An enzymatic pathway for bixin biosynthesis was inferred from homology of putative proteins encoded by differentially expressed seed cDNAs. Some activities were later validated in a heterologous system. Nevertheless, much of the pathway remains to be clarified. For example, it is essential to identify the methylerythritol phosphate (MEP) and carotenoid pathways genes.In order to investigate the MEP, carotenoid, and bixin pathways genes, total RNA from young leaves and two different developmental stages of seeds from B. orellana were used for the construction of indexed mRNA libraries, sequenced on the Illumina HiSeq 2500 platform and assembled de novo using Velvet, CLC Genomics Workbench and CAP3 software. A total of 52,549 contigs were obtained with average length of 1,924 bp. Two phylogenetic analyses of inferred proteins, in one case encoded by thirteen general, single-copy cDNAs, in the other from carotenoid and MEP cDNAs, indicated that B. orellana is closely related to sister Malvales species cacao and cotton. Using homology, we identified 7 and 14 core gene products from the MEP and carotenoid pathways, respectively. Surprisingly, previously defined bixin pathway cDNAs were not present in our transcriptome. Here we propose a new set of gene products involved in bixin pathway.The identification and qRT-PCR quantification of cDNAs involved in annatto production suggest a hypothetical model for bixin biosynthesis that involve coordinated activation of some MEP, carotenoid and bixin pathway genes. These findings provide a better understanding of the mechanisms regulating these pathways and will facilitate the genetic improvement of B. orellana.
Project description:BACKGROUND: This paper is based on ethnobotanical interviews conducted from 1996-2000 in Trinidad and Tobago with thirty male and female respondents. METHODS: A non-experimental validation was conducted on the plants used for urinary problems and diabetes mellitus: This is a preliminary step to establish that the plants used are safe or effective, to help direct clinical trials, and to inform Caribbean physicians of the plants' known properties to avoid counter-prescribing. RESULTS: The following plants are used to treat diabetes: Antigonon leptopus, Bidens alba, Bidens pilosa, Bixa orellana, Bontia daphnoides, Carica papaya, Catharanthus roseus, Cocos nucifera, Gomphrena globosa, Laportea aestuans, Momordica charantia, Morus alba, Phyllanthus urinaria and Spiranthes acaulis. Apium graviolens is used as a heart tonic and for low blood pressure. Bixa orellana, Bontia daphnoides, Cuscuta americana and Gomphrena globosa are used for jaundice. The following plants are used for hypertension: Aloe vera, Annona muricata, Artocarpus altilis, Bixa orellana, Bidens alba, Bidens pilosa, Bonta daphnoides, Carica papaya, Cecropia peltata, Citrus paradisi, Cola nitida, Crescentia cujete, Gomphrena globosa, Hibiscus sabdariffa, Kalanchoe pinnata, Morus alba, Nopalea cochinellifera, Ocimum campechianum, Passiflora quadrangularis, Persea americana and Tamarindus indicus. The plants used for kidney problems are Theobroma cacao, Chamaesyce hirta, Flemingia strobilifera, Peperomia rotundifolia, Petiveria alliacea, Nopalea cochinellifera, Apium graveolens, Cynodon dactylon, Eleusine indica, Gomphrena globosa, Pityrogramma calomelanos and Vetiveria zizanioides. Plants are also used for gall stones and for cooling. CONCLUSION: Chamaesyce hirta, Cissus verticillata, Kalanchoe pinnata, Peperomia spp., Portulaca oleraceae, Scoparia dulcis, and Zea mays have sufficient evidence to support their traditional use for urinary problems, "cooling" and high cholesterol. Eggplant extract as a hypocholesterolemic agent has some support but needs more study. The plants used for hypertension, jaundice and diabetes that may be safe and justify more formal evaluation are Annona squamosa, Aloe vera, Apium graveolens, Bidens alba, Carica papaya, Catharanthus roseus, Cecropia peltata, Citrus paradisi, Hibsicus sabdariffa, Momordica charantia, Morus alba, Persea americana, Phyllanthus urinaria, Tamarindus indicus and Tournefortia hirsutissima. Several of the plants are used for more than one condition and further trials should take this into account.
Project description:BACKGROUND:Halitosis is an unpleasant breath odour that can interfere with the professional life, social life and quality of life of people who suffer from it. A modality of treatment that has been increasing in dentistry is antimicrobial photodynamic therapy (aPDT). Bixa orellana, popularly known as "urucum" is a plant native to Brazil. The seeds are used to produce a dye that is largely used in the food, textile, paint and cosmetic industries. The aim of this study is to verify whether aPDT with Bixa orellana extract and blue light-emitting diodes (LEDs) is effective in reducing halitosis. This method will also be compared with tongue scraping, the most commonly used conventional method for tongue coating removal, and the association of both methods will be evaluated. METHODS/DESIGN:A randomized clinical trial will be conducted at the dental clinic of the Universidade Nove de Julho. Thirty-nine patients will be divided by block randomization into three groups (n?=?13) according to the treatment to be performed. In Group 1, tongue scraping will be performed by the same operator in all patients for analysis of the immediate results. Patients will also be instructed on how to use the scraper at home. Group 2 will be treated with aPDT with Bixa orellana extract and the LED light curing device: Valo Cordless Ultradent®. Six points in the tongue dorsum with a distance of 1 cm between them will be irradiated. The apparatus will be pre-calibrated at wavelength 395-480 nm for 20 s and 9.6 J per point. In Group 3, patients will be submitted to the tongue scraping procedure, as well as to the previously explained aPDT. Oral air collection with the Oral Chroma™ and microbiological collections of the tongue coating shall be done before, immediately after and 7 days after treatment for comparison. DISCUSSION:Halitosis treatment is a topic that still needs attention. The results of this trial could support decision-making by clinicians regarding aPDT using blue LEDs for treating halitosis on a daily basis, as most dentists already have this light source in their offices. TRIAL REGISTRATION:ClinicalTrials.gov, NCT03346460 . Registered on 17 November 2017.
Project description:The chloroplast genomic information was obtained from three wild <i>Solanum</i> and four hybrids by chloroplast genome sequencing. The chloroplast genomes of the seven samples comprise of a circular structure and sizes from 155,581 to 155,612 bp and composed of 130 genes. The genome structures of the two hybrids were identical, while the other two hybrids showed 2 bp differences in the LSC when compared with their maternal parent. The total sites of SNP and InDel were 39-344 and 54-90, respectively. With the exception of one hybrid with two additional sites, the other hybrids were identical to their maternal.
Project description:Data presents the chloroplast genome sequences of the five sunflower alloplasmic cytoplasmic male sterility (CMS) lines obtained with using the Illumina MiSeq, HiSeq and NextSeq platforms. The sunflower alloplasmic CMS lines has the same nuclear genome from line HA89, but they differ in cytoplasmic genomes, inherited from annual (PET1, PET2 - H. petiolaris, ANN2 - H. annuus) and perennial (MAX1 - H. maximilliani) species of the genus Helianthus L. The chloroplast genomes were annotated. Also presented is a dataset of variable sites such as single nucleotide polymorphism (SNP), simple sequence repeat (SSR), insertion and deletion (INDEL) in the chloroplast genome of the sequenced alloplasmic lines. The raw reads are available in FIGSHARE (https://doi.org/10.6084/m9.figshare.7520183). The complete chloroplast genome sequences for the sunflower alloplasmic lines are available in GenBank NCBI under the accessions MK341448.1-MK341452.1; the remaining data are provided with this article.
Project description:There is a colossal demand for natural pigments and its applications in recent times. In the study, a novel lactone pigment was isolated from a predominant endophytic fungus residing in <i>Bixa orellana</i> L. (Bixaceae) leaves. The endophyte was identified as <i>Fusarium verticillioides</i> through morphological and molecular investigations. The optimum growth parameters of the endophyte for pigment production were at 33 ºC with pH 6.5 in dark. Through comprehensive spectroscopic studies, the structure of the isolated lactone was resolved and identified as (<i>E</i>)-3, 3-dimethyl-4-(pent-1-en-1-yl)-4-propyldihydrofuran-2(3<i>H</i>)-one. The acute oral toxicity study of the pigment investigated upon female Wistar rats indicated the median lethal dose (LD<sub>50</sub>) value above 1000 mg/kg body weight affirming safety. Thus, the red pigment from the isolated endophyte may be employed as a sustainable source for natural colorant in industries owing to its non-toxicity.<h4>Supplementary information</h4>The online version contains supplementary material available at 10.1007/s13205-020-02566-x.