Molecular phylogeny in Indian Tinospora species by DNA based molecular markers

2005 ◽  
Vol 256 (1-4) ◽  
pp. 75-87 ◽  
Author(s):  
S. M. Ahmed ◽  
V. Verma ◽  
P. H. Qazi ◽  
M. M. Ganaie ◽  
S. K. Bakshi ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Molecular Phylogeny

scholarly journals Molecular Phylogeny and DNA Amplification Fingerprinting of Petunia

HortScience ◽  
1995 ◽  
Vol 30 (4) ◽  
pp. 777F-778
Author(s):  
Teresa A. Cerny ◽  
Terri W. Starman
Keyword(s):  
Molecular Markers ◽  
Molecular Phylogeny ◽  
Phylogenetic Tree ◽  
Leaf Tissue ◽  
Dna Amplification ◽  
Seed Source ◽  
Polymorphic Loci ◽  
Presence And Absence ◽  
Different Sources

Seed of five species of petunia and 10 cultivars of Petunia xhybrida were obtained from several sources and plants were fingerprinted using DNA amplification fingerprinting (DAF). Within some species, variable fingerprints were generated between individual plants from the same seed source and/or different sources. Consistencies were found among DAF profiles by bulking the leaf tissue from 10 different plants, but not five plants. Each of 10 octamer primers used during the study revealed polymorphic loci between the species and cultivars. Among the 201 bands produced, 146 (73%) loci were polymorphic and these could be used to distinguish between each of the species and cultivars. Scoring for presence and absence of the amplified bands was used to generate a phylogenetic tree and to calculate the pairwise distances between each of the taxa using parsimony (PAUP) analysis. The tree generated using DAF molecular markers separated P. axillaris from P. parodii (two white-flowered species), and distinguished between the violet-flowered species, P, inflata, P. integrifolia, and P. violacea.

Taxonomic placement of Tanaecium mutabile (Bignonieae, Bignoniaceae) based on new morphological data and phylogenetic analyses

Phytotaxa ◽  
2020 ◽  
Vol 438 (5) ◽  
pp. 289-300
Author(s):  
ANNELISE FRAZÃO ◽  
LÚCIA G. LOHMANN
Keyword(s):  
Molecular Markers ◽  
Molecular Phylogeny ◽  
Phylogenetic Analyses ◽  
Morphological Data ◽  
New Combination ◽  
Similar Species ◽  
Taxonomic Studies

During ongoing taxonomic studies with Tanaecium, we identified some morphological disparities between Tanaecium mutabile and the remaining species of the genus. Here, we reconstruct a molecular phylogeny of Tanaecium based on two molecular markers (i.e., the chloroplast ndhF and the nuclear pepC), and a broad sampling of members of the Arrabidaea and allies clade, where Tanaecium is included. In the newly constructed phylogeny, T. mutabile is nested within Fridericia, indicating the need for taxonomic arrangements. These findings are further supported by new morphological data (e.g., venation angle, domatia type, and corolla curvature). Based on these results, we formally transfer T. mutabile into Fridericia, and propose the necessary new combination. We further designate a new lectotype for Arrabidaea muehlbergiana, a synonym of T. mutabile. Morphological comparisons between T. mutabile and other morphologically similar species are presented.

A molecular phylogeny of Eragrostis (Poaceae: Chloridoideae: Eragrostideae): making lovegrass monophyletic in Australia

2020 ◽  
Author(s):  
Russell L. Barrett ◽  
Paul M. Peterson ◽  
Konstantin Romaschenko
Keyword(s):  
Molecular Markers ◽  
Molecular Phylogeny ◽  
Arid Zone ◽  
New Combinations ◽  
Rps16 Intron

We present a phylogeny based on four DNA molecular markers (rps16–trnK spacer, rps16 intron, rpl32–trnL spacer and ITS) concentrating on species of Eragrostis Wolf in Australia. Two Australian radiations are shown within Eragrostis, one being centred in the arid zone and one in the monsoon tropics. The genus is paraphyletic, with species of Cladoraphis Franch., Ectrosia R.Br., Harpachne Hochst. ex A.Rich., Heterachne Benth., Neeragrostis Bush, Planichloa B.K.Simon, Psammagrostis C.A.Gardner & C.E.Hubb. and Stiburus Stapf together forming a well supported clade mixed with Eragrostis species. The molecular results are consistent with recognition of an expanded Eragrostis and we make the following new combinations for Australian taxa: Eragrostis agrostoides (Benth.) R.L.Barrett & P.M.Peterson, E. anomala (C.E.Hubb.) R.L.Barrett & P.M.Peterson, E. appressa (S.T.Blake) R.L.Barrett & P.M.Peterson, E. baileyi (C.E.Hubb.) R.L.Barrett & P.M.Peterson, E. blakei (C.E.Hubb.) R.L.Barrett & P.M.Peterson, E. confusa (C.E.Hubb.) R.L.Barrett & P.M.Peterson, E. danesii (Domin) R.L.Barrett & P.M.Peterson, E. gulliveri (F.Muell.) R.L.Barrett & P.M.Peterson, E. leporina (R.Br.) R.L.Barrett & P.M.Peterson, E. nervilemma (B.K.Simon) R.L.Barrett & P.M.Peterson, E. ovata (Night.) R.L.Barrett & P.M.Peterson, E. scabrida (C.E.Hubb.) R.L.Barrett & P.M.Peterson, E. wiseana (C.A.Gardner & C.E.Hubb.) R.L.Barrett & P.M.Peterson and Sporobolus ramigerus (F.Muell.) P.M.Peterson, Romasch. & R.L.Barrett, and propose the following new names: E. divergens R.L.Barrett & P.M.Peterson, E. lilliputiana R.L.Barrett & P.M.Peterson and E. nightingaleae R.L.Barrett & P.M.Peterson. Lectotypes are designated for Ectrosia agrostoides Benth., E. anomala C.E.Hubb., E. appressa S.T.Blake, E. baileyi C.E.Hubb., E. blakei C.E.Hubb., E. confusa C.E.Hubb., E. gulliveri F.Muell., E laxa S.T.Blake, E. leporina R.Br, E. leporina var. longiglumis C.E.Hubb., E. schultzii Benth., E. schultzii var. annua C.E.Hubb., E. spadicea R.Br., Glyceria australasica Steud., Heterachne gulliveri Benth., Heterachne gulliveri var. major C.E.Hubb. Poa ramigera F.Muell. and Psammagrostis wiseana C.A.Gardner & C.E.Hubb.

scholarly journals Phylogenetic analysis and development of molecular markers for five medicinal Alpinia species based on complete plastome sequences

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Heyu Yang ◽  
Liqiang Wang ◽  
Haimei Chen ◽  
Mei Jiang ◽  
Wuwei Wu ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Molecular Markers ◽  
Molecular Phylogeny ◽  
Sequence Divergence ◽  
Intergenic Spacer ◽  
Rrna Genes ◽  
Comparative Genomic ◽  
Medicinal Products ◽  
Protein Coding ◽  
Next Generation Sequencing Technology

Abstract Background Alpinia species are widely used as medicinal herbs. To understand the taxonomic classification and plastome evolution of the medicinal Alpinia species and correctly identify medicinal products derived from Alpinia species, we systematically analyzed the plastome sequences from five Alpinia species. Four of the Alpinia species: Alpinia galanga (L.) Willd., Alpinia hainanensis K.Schum., Alpinia officinarum Hance, and Alpinia oxyphylla Miq., are listed in the Chinese pharmacopeia. The other one, Alpinia nigra (Gaertn.) Burtt, is well known for its medicinal values. Results The four Alpinia species: A. galanga, A. nigra, A. officinarum, and A. oxyphylla, were sequenced using the Next-generation sequencing technology. The plastomes were assembled using Novoplasty and annotated using CPGAVAS2. The sizes of the four plastomes range from 160,590 bp for A. galanga to 164,294 bp for A. nigra, and display a conserved quadripartite structure. Each of the plastomes encodes a total of 111 unique genes, including 79 protein-coding, 28 tRNA, and four rRNA genes. In addition, 293–296 SSRs were detected in the four plastomes, of which the majority are mononucleotides Adenine/Thymine and are found in the noncoding regions. The long repeat analysis shows all types of repeats are contained in the plastomes, of which palindromic repeats occur most frequently. The comparative genomic analyses revealed that the pair of the inverted repeats were less divergent than the single-copy region. Analysis of sequence divergence on protein-coding genes showed that two genes (accD and ycf1) had undergone positive selection. Phylogenetic analysis based on coding sequence of 77 shared plastome genes resolves the molecular phylogeny of 20 species from Zingiberaceae. In particular, molecular phylogeny of four sequenced Alpinia species (A. galanga, A. nigra, A. officinarum, and A. oxyphylla) based on the plastome and nuclear sequences showed congruency. Furthermore, a comparison of the four newly sequenced Alpinia plastomes and one previously reported Alpinia plastomes (accession number: NC_048461) reveals 59 highly divergent intergenic spacer regions. We developed and validated two molecular markers Alpp and Alpr, based on two regions: petN-psbM and psaJ-rpl33, respectively. The discrimination success rate was 100 % in validation experiments. Conclusions The results from this study will be invaluable for ensuring the effective and safe uses of Alpinia medicinal products and for the exploration of novel Alpinia species to improve human health.

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