Array method Species assessed



Дата26.04.2016
Памер53 Kb.
#33868
Additional file 1 - A summary of array-based methods used on the studies of herbal plants.

Array method

Species assessed

Sources of DNA

Substrate

Probes based on

Results

Oligonucleotide microarray

Allocasia nacrorrhiza, Datura innoxia, D. metel,

D. tatula, Pinellia cordata, P. ternata,

P. pedatisecta and Typhonium giganteum.


Dried materials and fresh leaves

Silicon-based microarray

Spacer region of 5S-rRNA gene

D. innoxia, D. metel and T. giganteum were differentiated based on the differences of the hybridizations [17].

Gene-based probe microarray

Dendrobium chrysanthum, D. chrysotoxum,

D. crystallinum, D. densiflorum, D. falconeri,

D. fimbriatum, D. jenkinsii, D. lindleyi,

D. loddigesii, D. lohohense, D. moniliforme,

D. moschatum, D. nobile, D. pendulum,

D. primulinum.

Fresh, medicinal formulation; leaves, stems

Microarray (glass)

Internal transcribed spacer 2 gene


Using the fluorescence-labeled ITS2 sequences as probes, the presence of D. nobile in a Chinese medicinal formulation containing nine herbal components was detected [6].

Suppression Subtraction Hybridization-based array

Dendrobium auriantiacum, D. nobile

D. chrysotoxum, D. fimbriatum and

D. officinale.

Stems of commercially available

samples


Array (nylon)

Fragments from pair-wise subtraction of genomic DNA

Fourteen species-specific probes from five closely related Dendrobium species were used on the array. Various commercial Dendrobium samples and unrelated samples were successfully identified [27].

Suppression Subtraction Hybridization-based array

Dendrobium aurantiacum Kerr, D. officinale Kimura et Migo, D.nobile Lindl., D. chrysotoxum Lindl. and D. fimbriatum Hook.

Fresh leaves

Array (nylon)

Fragments from pair-wise subtraction of genomic DNA

72 samples of Dendrobrium spp. containing 21 samples of D.officinale Kimura et Migo, 11 samples of D.chrysotoxum Lindl. and 40 samples of other Dendrobrium spp. were screened using this array. This array could successfully identify the species used to generate the probes [21].

Diversity Array Technology

Eucalyptus grandis

Fresh leaves

Microarray (glass)

PstI digested genomic DNA

This array was prepared using a partial genomic library from total genomic DNA of 23 E. grandis trees, of which 22 were full siblings. 27% of the 384 fragments screened were found to be polymorphic and allowed identification of all the 17 full-sibling individuals tested [19].

Oligonucleotide array

Aconitum carmichaeli, A. pendulum, Alocasia macrorrhiza, Corton tiglium, Datura inoxia, D. metel, D. tatula, Dysosma versipellis, Euphorbia kansui, Hyoscyamus niger, Pinellia cordata, P. pedatisecta, P. ternate, Rhododendron molle, Stellera chamaejasme, Strychnos nux-vomica, Typhonium divaricatum, T. giganteum.

Fresh leaves

Silicon-based microarray

Spacer region of 5S-rRNA gene

Multiple toxic plant species were successfully identified by parallel genotyping. Datura inoxia, D. metel, D. tatula were identified based on the differences in fluorescent intensities [15].

Oligonucleotide array

Aconitum napellus Herb., Arabidopsis thaliana L., A. absinthium L., A. vulgaris L., Atropa belladonna L., Capsicum annuum var. glabriusculum L. (Dunal) Heiser & Pickersgill, Caulophyllum thalictroides L. Michx., Citrus aurantium L., Datura metel L., Digitalis lanata Ehrh., Echinacea angustifolia, DC., Ephedra viridis Coville, Glycyrrhiza uralensis Fisch. ex DC., Hypericum perforatum L., Lawsonia inermis L., Lobelia inflata L., Mentha pulegium L., Symphytum officinale L., Tanacetum vulgare L., Teucrium canadense L., T. chamaedrys L., Tussilago farfara L.

Fresh leaves

Microarray (glass)

Cytochrome P450 gene

The genes for cytochrome P450 enzymes were cloned and sequenced for probes design in MLPA assays for identification. The probes can detect the presence of their cognate genomic DNA [26].

Suppression Subtraction Hybridization-based array

Dendrobium aurantiacum Kerr, D. officinale Kimura et Migo, D. nobile Lindl., D. chrysotoxum Lindl., D. fimbriatum Hook. and D. densiflorum Lindl. et Wall.

Fresh leaves

Array (nylon)

Fragments from pair-wise subtraction of genomic DNA

A dendrogram of the relatedness of six Dendrobium species was produced according to their polymorphic profiles. The results revealed that the SSH-based array was effective for profiling genomic DNA polymorphisms and dendrograms [14].

Subtracted Diversity Array

A population of 28 angiosperm species (including 25 medicinal herbs) representing the six main clades in angiosperms


Fresh leaves

Microarray (glass)

Fragments from subtracting pooled genomic DNA

Pooled genomic DNA of 5 non-angiosperm species was subtracted from pooled genomic DNA of 49 angiosperm species to obtain 376 probes. Species representing the six angiosperm clades (Asterids, Rosids, Caryophyllids, Ranunculids, Monocots and Eumagnoliids) could be differentiated using the SDA. A polymorphism rate of 68% was obtained for the probes used [24].

Oligonucleotide microarray

P. ginseng C. A. Meyer, P. japonicus C. A. Meyer (Japanese ginseng), P. quinquefolius L. (American ginseng), P. notoginseng (Burk.) F. H. Chen, P. japonicus C. A. Meyer var. angustifolius (Seem.) C. Y. Wu et Feng, P. stipuleanatus H. T. Tsai et K. M. Feng, P. pseudoginseng Wall.

Dried leaf or roots

Microarray (glass)

18S rRNA gene

33 probes corresponding to the species-specific nucleotide substitutions observed at 11 sites in the 18S rRNA gene sequence were used on the array. This array allowed successful authentication of all the Panax plants, drugs and derived health foods tested [18].

Subtracted Diversity Array

34 species belonging to six angiosperm clades and seven different families


Fresh leaves

Microarray (glass)

Fragments from subtracting pooled genomic DNA

This array could correctly genotype species that were not used for initial DNA pooling to generate probes. All species tested correctly clustered at the family level, but minor discrepancies were observed when the fingerprinting was performed at the species level [20].

Каталог: content -> supplementary
supplementary -> X��t��y�i��#�J9�n�����ϗ�q߂�o?#��K9���y��
supplementary -> Additional file 4 The alternative topologies used in statistical tests. The numbers in parentheses indicate the source of alternative topologies
supplementary -> J. Fish. Aquat. Sc. 2004, 4: 111-113. Arkhipkin ai, Laptikhovsky V: Discovery of the fourth species of the enigmatic chiroteuthid squid
supplementary -> Additional file 1
supplementary -> Supplementary Material for
supplementary -> Additional file 2: Major disease categories and associated medicinal plants used by Aboriginal people of boreal Canada
supplementary -> Supplementary Table
supplementary -> Appendix 2: Taxonomic structure of Rhinopomatidae: morphospecies vs molecular phylogenetics
supplementary -> Additional file 1 List of species used, with database accession numbers
supplementary -> Family Subfamily


Поделитесь с Вашими друзьями:




База данных защищена авторским правом ©shkola.of.by 2022
звярнуцца да адміністрацыі

    Галоўная старонка