An analysis of Echinacea chloroplast genomes: Implications for future botanical identification

Zhang, Ning; Erickson, David L.; Ramachandran, Padmini; Ottesen, Andrea; Timme, Ruth; Funk, Vicki A.; Luo, Yan; Handy, Sara M.

doi:10.1038/s41598-017-00321-6

Cited by 53 publications

(52 citation statements)

References 51 publications

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“…Chen et al [14] reported that there were no barcode gaps for Curcuma L. Zingiberaceae species with four chloroplast barcoding regions (matK, rbcL, trnH-psbA, and trnL-F). Recently this issue was also encountered with closely related Echinacea species in our own study [15].…”

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confidence: 66%

“…Both the consensus sequence from the reference-guided assembly and the contigs from the de novo assembly were imported into Geneious Pro 9.1.4 [25], and then those contigs were mapped onto the consensus sequence. The mapped contigs were manually checked to align them with the consensus sequence obtained using referenced-guided assembly [15,26]. The final sequence of the chloroplast genome of each species is the ordered sequence of those mapped contigs.…”

Section: Genome Assembly and Annotationmentioning

confidence: 99%

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Development of a Reference Standard Library of Chloroplast Genome Sequences, GenomeTrakrCP

et al. 2017

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Precise, species-level identification of plants in foods and dietary supplements is difficult. While the use of DNA barcoding regions (short regions of DNA with diagnostic utility) has been effective for many inquiries, it is not always a robust approach for closely related species, especially in highly processed products. The use of fully sequenced chloroplast genomes, as an alternative to short diagnostic barcoding regions, has demonstrated utility for closely related species. The U. S. Food and Drug Administration (FDA) has also developed species-specific DNA-based assays targeting plant species of interest by utilizing chloroplast genome sequences. Here, we introduce a repository of complete chloroplast genome sequences called GenomeTrakrCP, which will be publicly available at the National Center for Biotechnology Information (NCBI). Target species for inclusion are plants found in foods and dietary supplements, toxin producers, common contaminants and adulterants, and their close relatives. Publicly available data will include annotated assemblies, raw sequencing data, and voucher information with each NCBI accession associated with an authenticated reference herbarium specimen. To date, 40 complete chloroplast genomes have been deposited in GenomeTrakrCP (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA325670/), and this will be expanded in the future.

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confidence: 66%

Section: Genome Assembly and Annotationmentioning

confidence: 99%

Development of a Reference Standard Library of Chloroplast Genome Sequences, GenomeTrakrCP

et al. 2017

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“…The most variable noncoding regions included trnH-GUG-psbA, trnR-UCU-atpA, trnC-GCA-petN, ycf3-trnS-GGA, and trnL-UAA-trnF-GAA in six Adoxaceae chloroplast genomes 32 ; and TrnN-GUU-ndhF is the hotspot region in Capsicum 36 . The regions with the highest percentage of sequence variation were ccs-trnL-UAG, psbI-trnS-GCU, rpl32-ndhF, trnT-UGU-TrnL-UAA and petN-psbM in Echinacea 19 . In three closely related East Asian wild roses, matK-trnK, psbI-trnS-trnG, rps16-trnG, rpoB-trnC and rps4-trnT were the most divergent intergenic regions, with Pi values exceeding 0.006 28 .…”

Section: Genetic Diversity In Different Chloroplast Regions the Genementioning

confidence: 99%

“…The evolution rate or genetic diversity of different regions of the chloroplast genome varies greatly, and the successful development of common primers in those high-variability regions make these loci widely used in the study of phylogenetic relationships among species; among these loci, matK and rbcL are most commonly used 16,17 . With the application of high-throughput sequencing technology, the cost of sequencing has been greatly reduced, which makes it possible to reveal the phylogenetic relationships among species by using the genetic information of the whole chloroplast genome in many plant groups 15,[18][19][20] . The abundant genetic variation information and maternal genetic characteristics of the chloroplast genome are particularly suitable for reconstructing the phylogeny of low-level taxonomic hierarchies with complex relationships.…”

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Comparison of the complete plastomes and the phylogenetic analysis of Paulownia species

Lou

Cai

et al. 2020

Sci Rep

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Paulownia species are important ecological, economic and ornamental species, but their phylogenetic relationship remains unclear, which seriously affects the development and utilization of these important resources. the complete chloroplast genomes of six Paulownia species were assembled by next-generation sequencing data. By adding two known Paulownia chloroplast genomes to these six assembled genomes, we performed the comparative analysis and phylogenetic tree reconstruction of Paulownia. the results indicated that the chloroplast genomes of Paulownia species ranged in size from 154,107 to 154,694 bp. These chloroplast genomes contained 117 unique functional genes, including 80 protein-coding genes, four rRNA genes, and 33 tRNA genes. Twelve hotspot regions, five protein-coding genes and seven noncoding regions, were identified in the chloroplast genomes that showed high levels of sequence variation. Additionally, positive selection was observed in three genes, rps2, rbcL and ndhG. the maximum likelihood (ML) and Bayesian (Bi) analysis strongly supported the monophyletic origin of Paulownia species, which clustered into two major clades: one clade included P. coreana, P. tomentosa and P. kawakamii, while the other clade comprised the 5 other species including P. fargesii and P. australis. This study provides useful genetic information for phylogenetic reconstruction, taxonomic discrepancies, and studying species evolution and phylogeography in Paulownia.

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“…Effective means of identifying Bixa for authentication purposes in food and other commercial products is important. Recently, use of whole genomes as references (as opposed to DNA barcodes [12][13][14][15][16] for species identification programs has provided important reference databases and a greater variety of genetic markers that can be applied to identification/authentication protocols [17,18]. Development of species specific markers that confirm the identify of natural products, relies on well curated databases of multiple high quality accessions [16].…”

Section: Introductionmentioning

confidence: 99%

Full chloroplast genome assembly and phylogeny of “red and “yellow” Bixa orellana, “achiote”; popular source of food coloring and traditional medicine.

Villacrés-Vallejo¹,

Ventura²,

Wallis

et al. 2020

Preprint

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BackgroundSeeds from Bixa orellana, commonly known as “achiote” and “annatto” produce bixin and norbixin apocarotenoids which impart bright red and orange colors that have been used for thousands of years for food, medicine and body painting by indigenous Americans, and by Europeans for ~ 500 years as food coloring, especially for cheeses. Use of Bixa colorants continues to grow as synthetic dyes come under increased scrutiny for toxicity to human and environmental systems. There is a wide range of color variation in pods of Bixa orellana for which genetic loci that delineate phenotypes have not yet been identified. Whole chloroplast genomes and raw genome skims provide a wide variety of genetic markers that can be used for identification purposes as well as phylogenetic inference of broad scale evolutionary relationships. Here we apply whole chloroplast genome sequencing of “red” and “yellow” individuals of Bixa orellana for phylogenetic analyses to explore the position of Bixaceae relative to other families within the Malvales as well as to underpin future work that may delineate diverse color phenotypes.ResultsFully 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 58399-58415 in both of our accessions, relative to NC_041550 and a 6 base pair deletion at position 75531-75526 in the accession of “red” Bixa. A phylogeny based on alignment free kmer distance metrics was used to confirm monophylly of Bixa accessions, and to place Bixaceae relative to other families within the Malvales.ConclusionsOur data support Bixaceae as sister to Malvaceae and identified several potentially diagnostic insertion-deletion mutations that may with future work, reliably distinguish between red and yellow phenotypes. In addition to utility for phylogenic questions and development of identity markers, we demonstrate that chloroplast genomes can be used in conjunction with modern bioinformatic search tools (kmer based) to provide rapid and precise identification of Bixa orellana for Next Generation Sequencing approaches to natural product authentication.

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An analysis of Echinacea chloroplast genomes: Implications for future botanical identification

Cited by 53 publications

References 51 publications

Development of a Reference Standard Library of Chloroplast Genome Sequences, GenomeTrakrCP

Development of a Reference Standard Library of Chloroplast Genome Sequences, GenomeTrakrCP

Comparison of the complete plastomes and the phylogenetic analysis of Paulownia species

Full chloroplast genome assembly and phylogeny of “red and “yellow” Bixa orellana, “achiote”; popular source of food coloring and traditional medicine.

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