Plastome-wide comparison reveals new SNV resources for the authentication of Dendrobium huoshanense and its corresponding medicinal slice (Huoshan Fengdou)

Acta Pharmaceutica Sinica B - Tập 8 - Trang 466-477 - 2018
Zhitao Niu1, Jiajia Pan1, Qingyun Xue1, Shuying Zhu1, Wei Liu1, Xiaoyu Ding1
1College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China

Tài liệu tham khảo

Wood, 2006 Adams, 2011, Systematics of Dendrobiinae (Orchidaceae), with special reference to Australian taxa, Bot J Linn Soc, 166, 105, 10.1111/j.1095-8339.2011.01141.x Xiang, 2013, Molecular systematics of Dendrobium (Orchidaceae, Dendrobieae) from mainland Asia based on plastid and nuclear sequences, Mol Phylogenet Evol, 69, 950, 10.1016/j.ympev.2013.06.009 Bao, 2001 Xu, 2012, Detecting adulteration of Dendrobium officinale by real-time PCR coupled with ARMS, Int J Food Sci Tech, 47, 1695, 10.1111/j.1365-2621.2012.03023.x Paul, 2005, Current approaches for the authentication of medicinal Dendrobium species and its products, Plant Genet Resour, 3, 144, 10.1079/PGR200578 Zha, 2009, Identification and classification of Dendrobium candidum species by fingerprint technology with capillary electrophoresis, S Afr J Bot, 75, 276, 10.1016/j.sajb.2009.02.002 Yang, 2006, Simultaneous determination of phenols (bibenzyl, phenanthrene, and fluorenone) in Dendrobium species by high-performance liquid chromatography with diode array detection, J Chromatogr A, 1104, 230, 10.1016/j.chroma.2005.12.012 Yue, 2006, Development of simple sequence repeat (SSR) markers and their use in identification of Dendrobium varieties, Mol Ecol Notes, 6, 832, 10.1111/j.1471-8286.2006.01361.x Shen, 2006, Inter simple sequence repeats (ISSR) molecular fingerprinting markers for authenticating populations of Dendrobium officinale Kimura et Migo, Biol Pharm Bull, 29, 420, 10.1248/bpb.29.420 Li, 2008, Genetic diversity analysis and conservation of the endangered Chinese endemic herb Dendrobium officinale Kimuraet Migo (Orchidaceae) based on AFLP, Genetica, 133, 159, 10.1007/s10709-007-9196-8 Teixeira da Silva, 2016, Advances in Dendrobium molecular research: applications in genetic variation, identification and breeding, Mol Phylogenet Evol, 95, 196, 10.1016/j.ympev.2015.10.012 Asahina, 2010, Identification of medicinal Dendrobium species by phylogenetic analyses using matK and rbcL sequences, J Nat Med, 64, 133, 10.1007/s11418-009-0379-8 Feng, 2015, Molecular identification of Dendrobium species (Orchidaceae) based on the DNA barcode ITS2 region and its application for phylogenetic study, Int J Mol Sci, 16, 21975, 10.3390/ijms160921975 Xu, 2015, Evaluation of the DNA barcodes in Dendrobium (Orchidaceae) from mainland Asia, PLoS One, 10, e0115168, 10.1371/journal.pone.0115168 Zhang, 2009, Authentication of three valuable Dendrobium species by adapter ligation-mediated allele-specific amplification, Eur Food Res Technol, 229, 1, 10.1007/s00217-009-1019-y Yan, 2016, Combination of SYBR Green II and TaqMan Probe in the adulteration detection of Dendrobium devonianum by fluorescent quantitative PCR, Int J Food Sci Tech, 50, 2572, 10.1111/ijfs.12925 Paun, 2016, Processes driving the adaptive radiation of a tropical tree (Diospyros, Ebenaceae) in New Caledonia, a biodiversity hotspot, Syst Biol, 10.1093/sysbio/syv076 Wang, 2013, Identification of SNP markers for inferring phylogeny in temperate bamboos (Poaceae: bambusoideae) using RAD sequencing, Mol Ecol Resour, 13, 938, 10.1111/1755-0998.12136 Lu, 2010, Confirming the genetic identity of Dendrobium fimbriatum using an amplification refractory mutation system (arms), Plant Mol Biol Rep, 28, 712, 10.1007/s11105-010-0190-4 Qian, 2008, Molecular authentication of Dendrobium loddigesii rolfe by amplification refractory mutation system (arms), Planta Med, 74, 470, 10.1055/s-2008-1034360 Sonnante, 2009, DNA microsatellite region for a reliable quantification of soft wheat adulteration in durum wheat-based foodstuffs by real-time PCR, J Agr Food Chem, 57, 10199, 10.1021/jf902624z Brod, 2009, Quantification of roundup Ready (TM) soybean in Brazilian soy-derived foods by real-time PCR, Int J Food Sci Tech, 43, 1027, 10.1111/j.1365-2621.2007.01556.x Gambino, 2015, Multiplex RT-PCR method for the simultaneous detection of nine grapevine viruses, Methods Mol Biol, 1236, 39, 10.1007/978-1-4939-1743-3_4 CBOL Plant Working Group, 2009, A DNA barcode for land plants, Proc Natl Acad Sci U S A, 106, 12794, 10.1073/pnas.0905845106 Kress, 2005, Use of DNA barcodes to identify flowering plants, Proc Natl Acad Sci U S A, 102, 8369, 10.1073/pnas.0503123102 Kress, 2007, A two-locus global DNA barcode for land plants: the coding rbcL gene complements the non-coding trnH-psbA spacer region, PLoS One, 2, e508, 10.1371/journal.pone.0000508 Niu, 2017, The complete plastome sequences of four orchid species: insights into the evolution of the Orchidaceae and the utility of plastomic mutational hotspots, Front Plant Sci, 8, 715, 10.3389/fpls.2017.00715 Luo, 2014, Comparative chloroplast genomes of photosynthetic orchids: insights into evolution of the Orchidaceae and development of molecular markers for phylogenetic applications, PLoS One, 9, e99016, 10.1371/journal.pone.0099016 Niu, 2017, Comparative analysis of Dendrobium plastomes and utility of plastomic mutational hotspots, Sci Rep, 7, 2073, 10.1038/s41598-017-02252-8 Tsi, 1999 Wyman, 2004, Automatic annotation of organellar genomes with DOGMA, Bioinformatics, 20, 3252, 10.1093/bioinformatics/bth352 Schattner, 2005, The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs, Nucleic Acids Res, 33, W686, 10.1093/nar/gki366 Edgar, 2004, MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Res, 32, 1792, 10.1093/nar/gkh340 Tamura, 2011, MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods, Mol Biol Evol, 28, 2731, 10.1093/molbev/msr121 Librado, 2009, DnaSP v5: a software for comprehensive analysis of DNA polymorphism data, Bioinformatics, 25, 1451, 10.1093/bioinformatics/btp187 Geng, 2015, Applylication of new type combined fragments: nr DNA ITS+ nad 1-intron 2 for identification of Dendrobium species of Fengdous, Acta Pharm Sin, 50, 1060 Wolfe, 1987, Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs, Proc Natl Acad Sci U S A, 84, 9054, 10.1073/pnas.84.24.9054 Drouin, 2008, Relative rates of synonymous substitutions in the mitochondrial, chloroplast and nuclear genomes of seed plants, Mol Phylogenet Evol, 49, 827, 10.1016/j.ympev.2008.09.009 Shaw, 2014, Chloroplast DNA sequence utility for the lowest phylogenetic and phylogeographic inferences in angiosperms: the tortoise and the hare IV, Am J Bot, 101, 1987, 10.3732/ajb.1400398 Morris, 1996, Vegetative anatomy and systematics of subtribe Dendrobiinae (Orchidaceae), Bot J Linn Soc, 120, 89, 10.1111/j.1095-8339.1996.tb00483.x Yukawa, 1996, Vegetative diversification and radiation in subtribe Dendrobiinae (Orchidaceae): evidence from chloroplast DNA phylogeny and anatomical characters, Plant Syst Evol, 201, 1, 10.1007/BF00989048 Li, 2005, Accurate identification of closely related Dendrobium species with multiple species-specific gDNA probes, J Biochem Biophys Methods, 62, 111, 10.1016/j.jbbm.2004.10.006 Ding, 2002, Database establishment of the whole rDNA ITS region of Dendrobium species of “Fengdou” and authentication by analysis of their sequences, Acta Pharm Sin, 37, 567 Sharma, 2016, Internal transcribed spacer guided multiplex PCR for species identification of Convolvulus prostratus and Evolvulus alsinoides, Acta Pharm Sin B, 3, 253, 10.1016/j.apsb.2016.02.003 Niu, 2017, Comparative analysis of the complete plastomes of Apostasia wallichii and Neuwiedia singapureana (Apostasioideae) reveals different evolutionary dynamics of IR/SSC boundary among photosynthetic orchids, Front Plant Sci, 8, 1713, 10.3389/fpls.2017.01713 Wang, 2015, Safety issues and new rapid detection methods in traditional Chinese medicinal materials, Acta Pharm Sin B, 1, 38, 10.1016/j.apsb.2014.12.005 Zhang Y, Xu Z, Ji A, Luo H, Song J. Genomic survey of bZIP transcription factor genes related to tanshinone biosynthes is in Salvia miltiorrhiza. Acta Pharm Sin B 2018. Available from: <10.1016/j.apsb.2017.09.002>. Xin T, Xu Z, Jia J, Leon C, Hu S, Lin Y, et al. Biomonitoring for traditional herbal medicinal products using DNA metabarcoding and single molecule, real-times equencing. Acta Pharm Sin B 2018. Available from: <10.1016/j.apsb.2017.10.001>. Li, 2011, Advances in the of resources, constituents and pharmacological effects of Dendrobium officinale, Sci Technol Rev, 29, 74 Weng, 2003, FAAS determination of trace elements in Dendrobium candidum using suspension sampling with ultrasonic agitation, Chin Pharm J, 38, 704 Zhang, 2016, Transcriptome analysis of Dendrobium officinale and its application to the identification of genes associated with polysaccharide synthesis, Front Plant Sci, 7, 5 Newton, 1989, Analysis of any point mutation in DNA. The ampliflcation refractory mutation system (ARMS), Nucleic Acids Res, 17, 2503, 10.1093/nar/17.7.2503 Hayashi, 2004, Development of PCR based SNP markers for rice blast resistance genes at the Piz locus, Theor Appl Genet, 108, 1212, 10.1007/s00122-003-1553-0 Kwok, 1990, Effects of primer-template mismatches on the polymerase chain reaction: human immunodeficiency virus type 1model studies, Nucleic Acids Res, 18, 999, 10.1093/nar/18.4.999 Li, 2006, Molecular authentication of Alisma orientale by PCR-RFLP and ARMS, Planta Med, 72, 1 Park, 2006, Molecular identification of Korean ginseng by amplification refractory mutation system-PCR, Food Res Intern, 39, 568, 10.1016/j.foodres.2005.11.004 D’Andrea, 2009, Development and validation of a SYBR-Green I real-time PCR protocol to detect hazelnut (Corylus avellana L.) in foods through calibration via plasmid reference standard, J Agr Food Chem, 57, 11201, 10.1021/jf902986t Gambino, 2015, Multiplex RT-PCR method for the simultaneous detection of nine grapevine viruses, Methods Mol Biol, 1236, 39, 10.1007/978-1-4939-1743-3_4