| Literature DB >> 26649268 |
Corinna Schmiderer1, Brigitte Lukas1, Joana Ruzicka1, Johannes Novak1.
Abstract
PREMISE OF THE STUDY: For the economically important species Calendula officinalis, a fast identification assay based on high-resolution melting curve analysis was designed. This assay was developed to distinguish C. officinalis from other species of the genus and other Asteraceae genera, and to detect C. officinalis as an adulterant of saffron samples. METHODS ANDEntities:
Keywords: Asteraceae; Calendula; Calendula officinalis; high-resolution melting curve analysis (HRM); molecular phylogeny
Year: 2015 PMID: 26649268 PMCID: PMC4651632 DOI: 10.3732/apps.1500069
Source DB: PubMed Journal: Appl Plant Sci ISSN: 2168-0450 Impact factor: 1.936
Base composition of PCR, sequencing(*), and HRM primers used in this study.
| Forward primer | Sequence (5′–3′) | Reverse primer | Sequence (5′–3′) | References |
| ITS5* | GGAAGGAGAAGTCGTAACAAGG | ITS4* | TCCTTCCGCTTATTGATATGC | |
| Cal_trnK_2F* | CCCCCAAATCCTCTACCTTTC | 12 matK-1506R | TTCCATAGAAATATATTCG | |
| Cal_trnK_2F* | CCCCCAAATCCTCTACCTTTC | 13 matK-1848R | TATCGAACTTCTTAATAGC | |
| matKf1 | ATACTCCTGAAAGATAAGTGG | ccmp1r* | CCGAAGTCAAAAGAGCGATT | |
| trnL-trnF e* | GGTTCAAGTCCCTCTATCCC | trnL-trnF f | ATTTGAACTGGTGACACGAG | |
| psbA3′f* | GTTATGCATGAACGTAATGCTC | trnHf | CGCGCATGGTGGATTCACAATCC | |
| rbcLa_F | ATGTCACCACAAACAGAGACTAAAGC | rbcL_ajf634R* | GAAACGGTCTCTCCAACGCAT | |
| Cal_trnK_2F | CCCCCAAATCCTCTACCTTTC | Cal_trnK_2R | TCTAGCCCTAAATAGCTTTGGAATT | This study |
| Cal_trnL-F_1F | TAAAAATGAACATCTTTGAGCAAGAA | Cal_trnL-F_1R | GAACGTGGGTCTATGTCAATTG | This study |
Amplicon size: Cal_trnK_2F&R = 71 bp; Cal_trnL-F_1F&R = 126 bp.
Diagnostic nucleotide candidates to distinguish individual species.
| Species | ITS | |||||
| 7 | 0 | 0 | 0 | 0 | 0 | |
| 1 | 0 | 0 | 1149 (C/A) | 0 | 0 | |
| 1166 (T/C) | ||||||
| 1 | 513 (T/C) | 254 (C/A) | 1199 (T/G) | 0 | 0 | |
| 1 | 104 (T/C) | 0 | 0 | 0 | 0 | |
| 1 | 0 | 0 | 0 | 0 | 2260 (A/C) | |
| 1 | 0 | 855 (C/T) | 0 | 0 | 2327 (A/G) | |
| 2 | 0 | 211 (A/C) | 0 | 0 | 0 | |
| 2 | 0 | 0 | 0 | 0 | 0 | |
| 3 | 0 | 0 | 0 | 0 | 0 | |
| 2 | 0 | 0 | 0 | 0 | 0 |
Note: n = number of individuals.
Nucleotide position is given, with diagnostic nucleotides in parentheses; the first is the species-specific nucleotide.
Fig. 1.HRM analysis based on two chloroplast markers. A. = Anthemis, Ad. = Adenostyles, C. = Calendula, Ci. = Cichorium, L. = Leucanthemum, T. perfor. = Tripleurospermum perforatum. (A) HRM analysis with the primer pair Cal_trnK_2F&R amplifying one species-specific SNP (A/C) located in the trnK 5′ intron, distinguishing Calendula officinalis samples from all other analyzed samples of the genus. (B) HRM analysis of outgroup samples with the primers Cal_trnK_2F&R. (C) HRM analysis with the primer pair Cal_trnL-F_1F&R of a 126-bp part of the trnL-trnF intergenic spacer including several SNPs. The Calendula samples were divided in three groups. Group I: C. maroccana and C. lanzae, group II: C. eckerleinii and C. meuselii, group III: C. officinalis and all other Calendula samples. (D) HRM analysis of outgroup samples with the primers Cal_trnL-F_1F&R. Group IV: Adenostyles glabra, Eupatorium cannabinum, E. perfoliatum, Matricaria nigellifolia, Scorzonera sp., Senecio sp. Group V: E. purpureum, Helianthus annuus. Group VI: Tanacetum vulgare. Group VII: Anthemis spp., Ci. intybus, Dimorphotheca pluvialis, Helianthus tuberosus, Leucanthemum vulgare, Matricaria spp., Tanacetum parthenium, Tripleurospermum perforatum. HRM curves of other Tanacetum samples appeared between V and VI (data not shown).
Fig. 2.Analysis of artificial admixtures of Calendula officinalis in saffron. All properly amplified admixture samples showed an equivalent HRM curve like the C. officinalis references. (A) HRM analysis with the primer pair Cal_trnK_2F&R. (B) Amplification plot of the qPCR corresponding to A. (C) HRM analysis with the primer pair Cal_trnL-F_1F&R. (D) Amplification plot of the qPCR corresponding to B. %-Values mean proportion of C. officinalis DNA in saffron DNA of each sample. NTC = no template control.
Locality and specimen information of reference samples used in this study.
| Species | Herbarium ID no. (Laboratory code) | Collection locality (Collection date) | |
| 1 | Cal104 | Cultivated | |
| 1 | WU082667 (Cal119) | WU: Turkey (5.4.2002) | |
| 1 | WU082668 (Cal120) | WU: Jordan (9.3.1992) | |
| 1 | WU082669 (Cal121) | WU: Italy (14.4.2004) | |
| 1 | WU082670 (Cal125) | WU: Greece, Crete (24.4.1914) | |
| 1 | WU082671 (Cal126) | WU: Greece, Crete (24.4.1914) | |
| 1 | WU082672 (Cal128) | WU: Iran (24.4.1885) | |
| 3 | IPK-CAL 38 | Morocco, ACCID: 50036 | |
| 6 | IPK-CAL 75 | Spain, ACCID: 98773 | |
| 7 | IPK-CAL 82 | Egypt, ACCID: 247372 | |
| 9 | IPK-CAL 27 | Italy, ACCID: 80458 | |
| 10 | IPK-CAL 13 | Spain, ACCID: 77842 | |
| 10 | IPK-CAL 40 | Morocco, ACCID: 50038 | |
| 10 | IPK-CAL 42 | Greece, ACCID: 50040 | |
| 12 | IPK-CAL 17 | Libya, ACCID: 82082 | |
| 12 | IPK-CAL 9 | Morocco, ACCID: 49196 | |
| 1 | WU082676 (Cal132) | WU: Tunisia (12.4.1913) | |
| 1 | WU082677 (Cal133) | WU: Tunisia (12.4.1913) | |
| 1 | WU082673 (Cal122) | WU: Portugal (12.8.1968) | |
| 2 | WU082674 (Cal123), WU082675 (Cal124) | WU: Portugal (8.4.1971) | |
| 1 | IPK-CAL 41 | Morocco, ACCID: 50039 | |
| 4 | IPK-CAL 95 | Morocco, ACCID: 236458 | |
| 10 | IPK-CAL 29 | Cultivated, ACCID: 49214 | |
| 9 | IPK-CAL 8 | Morocco, ACCID: 49195 | |
| 1 | Cal101 | Cultivated at VMU | |
| 1 | Cal102 | Cultivated at VMU | |
| 1 | Cal103 | Cultivated | |
| 1 | WU08267 (Cal127) | WU: cultivated at HBV | |
| 5 | Cal105-9 | Cultivated | |
| 12 | IPK-CAL 16 | Libya, ACCID: 81928 | |
| 1 | Cal118 | Cultivated at VMU | |
| 5 | IPK-CAL 54 | Morocco, ACCID: 50052 | |
| 6 | IPK-CAL 53 | Morocco, ACCID: 50051 | |
| 1 | WU082679 (Cal129) | WU: Morocco (17.4.2003) | |
| 5 | IPK-CAL 45 | Morocco, ACCID: 50043 | |
| 5 | IPK-CAL 51 | Morocco, ACCID: 50049 | |
| 7 | IPK-CAL 98 | Morocco, ACCID: 236450 | |
| 6 | IPK-CAL 63 | Tunisia, ACCID: 59220 | |
| 6 | IPK-CAL 94 | Portugal, ACCID: 259716 | |
| 6 | IPK-CAL 96 | Italy, ACCID: 259717 | |
| 7 | IPK-CAL 44 | Algeria, ACCID: 50042 | |
| 8 | IPK-CAL 22 | Italy, ACCID: 80066 | |
| 9 | IPK-CAL 33 | Cultivated, ACCID: 50034 | |
| 12 | IPK-CAL 15 | Algeria, ACCID: 49202 | |
| 1 | WU027733 (Cal131) | WU: Spain (9.3.2002) | |
| 1 | WU082680 (Cal130) | WU: Morocco (21.4.2003) | |
| 1 | IPK-CAL 49 | Morocco, ACCID: 50047 | |
| 2 | WU082681 (Cal134-5) | WU: Morocco (22.4.2003) | |
| 1 | Ast 06 | Austria, LA, Hohe Wand; 47°51′07″N, 16°02′31″E (5.5.2011) | |
| 1 | IPK-ANTHE 18 | Cultivated, ACCID: 49159 | |
| 1 | IPK-ANTHE 7 | Cultivated, ACCID: 49154 | |
| 1 | Anth 01 | Austria, LA, Bisamberg; 48°19′00″N, 16°21′40″E (11.5.2015) | |
| 1 | IPK-ANTHE 17 | Cultivated, ACCID: 49158 | |
| 1 | IPK-ANTHE 10 | Cultivated, ACCID: 49156 | |
| 1 | IPK-ANTHE 25 | Armenia, ACCID: 57847 | |
| 1 | IPK-ANTHE 33 | Cultivated, ACCID: 236444 | |
| 1 | Rühl-Ant05x | Trade sample | |
| 2 | Anth 14 | Austria, LA, Kamptal; 48°37′51″N, 15°36′51″E (6.8.2011) | |
| 3 | Ast 03-5 | Austria, V, J. Baumann Gasse; 48°15′15″N, 16°25′54″E (23.6.2011) | |
| 1 | Cal138 | Trade sample (Kotany) | |
| 1 | Cal139 | Trade sample (Iran) | |
| 1 | Cal142 | Trade sample (Greece) | |
| 1 | IPK-DIM 3 | Cultivated, ACCID: 86120 | |
| 7 | IPK-DIM 17 | Cultivated, ACCID: 258980 | |
| 1 | Ast 01 | Austria, V, Lainzer Tiergarten; 48°10′01″N, 16°15′15″E (5.5.2011) | |
| 1 | Ast 02 | Austria, V, Wienerwald; 48°14′00″N, 16°16′16″E (7.5.2011) | |
| 1 | Ast 07 | Austria, LA, Hohe Wand; 47°51′07″N, 16°02′31″E (21.6.2011) | |
| 1 | Ast 08 | Austria, ST, Spielberg; 47°14′18″N, 14°47′06″E (10.7.2011) | |
| 1 | Ast 15 | Austria, LA, Kamptal; 48°37′55″N, 15°36′49″E (6.8.2011) | |
| 1 | Rühl-Eup02 | Trade sample | |
| 1 | Rühl-Eup03 | Trade sample | |
| 1 | Cal111 | Cultivated, V, Siebensterngasse | |
| 1 | Cal110 | Cultivated | |
| 1 | Anth 05 | Austria, LA, Hohe Wand; 47°50′08″N, 16°03′26″E (21.6.2011) | |
| 1 | IPK-TRIP 7 | Cultivated, ACCID: 49972 | |
| 1 | Anth 09-10 | Austria, ST, Spielberg; 47°13′10″N, 14°47′20″E (10.7.2011) | |
| 1 | IPK-MAT 13 | Cultivated, ACCID: 49705 | |
| 1 | IPK-MAT 30 | Cultivated, ACCID: 87870 | |
| 1 | IPK-MAT 10 | Cultivated, ACCID: 49703 | |
| 1 | IPK-MAT 16 | Cultivated, ACCID: 49707 | |
| 1 | IPK-MAT 17 | Germany, ACCID: 49708 | |
| 1 | IPK-MAT 20 | Italy, ACCID: 81538 | |
| 1 | IPK-TRIP 8 | Bulgaria, ACCID: 50939 | |
| 2 | Ast 11-2 | Austria, ST, Spielberg; 47°13′50″N, 14°46′39″E (24.4.2011) | |
| 1 | Ast 13 | Austria, ST, Spielberg; 47°14′05″N, 14°46′35″E (24.4.2011) | |
| 1 | Ast 14 | Austria, LA, Groß Enzersdorf; 48°11′57″N, 16°33′45″E (15.5.2011) | |
| 1 | Sen 01 | Austria, V, Baumgartner Höhe; 48°12′24″N, 16°16′50″E (7.5.2011) | |
| 6 | Cal112-7 | Cultivated, V, Siebensterngasse | |
| 1 | Rühl-Bal01 | Trade sample | |
| 1 | Rühl-Bal02 | Trade sample | |
| 1 | Anth 02 | Austria, ST, Spielberg; 47°14′18″N, 14°47′6″E (10.7.2011) | |
| 1 | Anth 03 | Austria, LA, Würnitz; 48°25′25″N, 16°26′18″E (22.6.2011) | |
| 1 | Anth 11 | Austria, LA, Hollabrunn; 48°32′40″N, 16°06′11″E (12.7.2011) | |
| 1 | Rühl-Chr02 | Trade sample | |
| 1 | Anth 12 | Austria, LA, Kaltenleutgeben; 48°06′51″N, 16°12′50″E (16.7.2011) | |
| 1 | Anth 13 | Austria, LA, Kamptal; 48°37′51″N, 15°36′51″E (6.8.2011) | |
| 1 | Anth 04 | Austria, LA, Hollabrunn; 48°35′05″N, 16°03′55″E (25.6.2011) | |
| 2 | Anth 16-7 | Austria, LA, Kamptal; 48°37′51″N, 15°36′51″E (6.8.2011) |
Note: n = number of individuals.
Voucher specimens (excluding those from WU) are stored at the herbarium of the Institute for Animal Nutrition and Functional Plant Compounds under the given herbarium ID numbers.
HBV = Botanical Garden of the University of Vienna, Austria; IPK = Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben, Germany. Accessions were received as seeds, which were raised in the University’s greenhouse in 2012. GPS coordinates of the specimen origins are not known.
ACCID = accession identification number (assigned by IPK); LA = Province Lower Austria; Rühl = Rühlemann’s Kräuter und Duftpflanzen, Horstedt, Germany; ST = Province Styria; V = Province Vienna; VMU = University of Veterinary Medicine, Vienna, Austria; WU = Herbarium of the University of Vienna, Austria. Collection dates are presented in the format: day.month.year. GPS coordinates of the specimen origins are not known.