scholarly journals Population Genetic Analysis ofLobelia rhynchopetalumHemsl. (Campanulaceae) Using DNA Sequences fromITSand Eight Chloroplast DNA Regions

2012 ◽  
Vol 2012 ◽  
pp. 1-10 ◽  
Author(s):  
Mulatu Geleta ◽  
Tomas Bryngelsson
Keyword(s):  
Chloroplast Dna ◽  
Dna Sequences ◽  
Population Genetic ◽  
Sequence Data ◽  
Gene Diversity ◽  
Nuclear Ribosomal Dna ◽  
Bootstrap Support ◽  
Population Genetic Analysis ◽  
Mountain Systems ◽  
Chloroplast Dna Regions

DNA sequence data from the internal transcribed spacer of nuclear ribosomal DNA and eight chloroplast DNA regions were used to investigate haplotypic variation and population genetic structure of the Afroalpine giant lobelia,Lobelia rhynchopetalum.The study was based on eight populations sampled from two mountain systems in Ethiopia. A total of 20 variable sites were obtained, which resulted in 13 unique haplotypes and an overall nucleotide diversity (ND) of 0.281 ± 0.15 and gene diversity (GD) of 0.85 ± 0.04. Analysis of molecular variance (AMOVA) revealed a highly significant variation (P<0.001) among populations (FST), and phylogenetic analysis revealed that populations from the two mountain systems formed their own distinct clade with >90% bootstrap support. Each population should be regarded as a significant unit for conservation of this species. The primers designed for this study can be applied to anyLobeliaand other closely related species for population genetics and phylogenetic studies.

Molecular phylogeny of the genus Hordeum using three chloroplast DNA sequences

Genome ◽  
2002 ◽  
Vol 45 (6) ◽  
pp. 1157-1166 ◽  
Author(s):  
Tomotaro Nishikawa ◽  
Björn Salomon ◽  
Takao Komatsuda ◽  
Roland von Bothmer ◽  
Koh-ichi Kadowaki
Keyword(s):  
Chloroplast Dna ◽  
Dna Sequences ◽  
Sequence Data ◽  
Genetic Relationships ◽  
Closely Related Species ◽  
Dna Phylogeny ◽  
Molecular Phylogenetic ◽  
Hordeum Jubatum ◽  
Chloroplast Dna Sequences ◽  
Chloroplast Dna Regions

The genus Hordeum consists of three cytotypes (2x, 4x, and 6x). Its reproductive isolation has been incomplete between closely related species and hence the genetic relationship is reticulate and complex. We used 32 taxa of Hordeum and three chloroplast DNA sequences, matK, atpB–rbcL, and trnL–trnF, in the current study. Molecular phylogenetic analysis based on sequence data of the three chloroplast DNA regions clearly demonstrated genetic relationships among taxa and origin of polypoids. The formation of H. secalinum likely involved hybridization between Hordeum marinum subsp. marinum and a Eurasian diploid possessing the H genome. The formation of hexaploid Hordeum brachyantherum involved hybridization between tetraploid H. brachyantherum and diploid H. marinum subsp. gussoneanum. The formation of three tetraploids, H. brachyantherum, Hordeum jubatum, and Hordeum guatemalense, probably involved hybridization between H. brachyantherum subsp. californicum and an altered H genome diploid. The formation of Hordeum arizonicum involved the two taxa Hordeum pusillum and H. jubatum.Key words: chloroplast DNA, phylogeny, Hordeum, barley.

Understanding taxonomic position of local endemic Agropyron deweyi (Poaceae) using morphological characters and sequences of nuclear and chloroplast DNA regions

Biologia ◽  
2015 ◽  
Vol 70 (10) ◽  
Author(s):  
Mesut S. Pinar ◽  
Ayten Dizkirici ◽  
Oktay Yigit
Keyword(s):  
Chloroplast Dna ◽  
Dna Sequences ◽  
Morphological Characters ◽  
Molecular Techniques ◽  
Taxonomic Position ◽  
Nuclear Ribosomal Dna ◽  
Trnl Intron ◽  
Internal Transcribed Spacer Region ◽  
Local Endemic ◽  
Chloroplast Dna Regions

AbstractIn this study, both morphological characters and molecular techniques were used to determine the taxonomic position of the local endemic Agropyron deweyi within the genus. Plant length, inflorescence type, flower, leaf, spike, spikelet, indumentum and lemma structures were studied as morphological characters. DNA sequences of the nuclear ribosomal DNA internal transcribed spacer region (nrDNA ITS) and four chloroplast DNA regions [trnT-trnL intergenic spacer (IGS), trnL intron, trnL-trnF IGS and matK gene] were analyzed as part of molecular investigations. The results demonstrated that no remarkable morphological differences exist among studied specimens of A. deweyi and A. cristatum complex. Based on 12 sequences of 4 Agropyron taxa produced from the current study and different numbers of sequences obtained from GenBank, our results support the conclusion that the taxonomic status of Agropyron deweyi is synonymous to that of the species A. cristatum. Sequence divergences were estimated using Kimura two-parameter model, and the phylogenetic analyses were performed using the maximum parsimony (MP) and maximum likelihood (ML) methods. No genetic variation was observed among samples of native A. deweyi and A. cristatum complex regardless of the analyzed region. Agropyron deweyi was especially very similar to A. cristatum subsp. pectinatum var. pectinatum in terms of morphological characters such as inflorescence rachis tough at maturity, spikelets with distinct gaps, indumentum glabrous, and lemma glabrous. Therefore, when all morphological and molecular results are taken into account, A. deweyi and A. cristatum subsp. pectinatum var. pectinatum should be considered as synonym.

A review of the fern genus Pellaea (Pteridaceae) in Australasia

2020 ◽  
Author(s):  
Patrick J. Brownsey ◽  
Daniel J. Ohlsen ◽  
Lara D. Shepherd ◽  
Whitney L. M. Bouma ◽  
Erin L. May ◽  
...  
Keyword(s):  
New Zealand ◽  
Chloroplast Dna ◽  
Dna Sequences ◽  
Sequence Data ◽  
Indigenous Species ◽  
Ploidy Levels ◽  
Dna Sequence Data ◽  
Australian Species ◽  
The Status ◽  
Chloroplast Dna Sequences

Five indigenous species of Pellaea in Australasia belong to section Platyloma. Their taxonomic history is outlined, morphological, cytological and genetic evidence for their recognition reviewed, and new morphological and chloroplast DNA-sequence data provided. Australian plants of P. falcata (R.Br.) Fée are diploid and have longer, narrower pinnae than do New Zealand plants previously referred to P. falcata, which are tetraploid. Evidence indicates that P. falcata does not occur in New Zealand, and that collections so-named are P. rotundifolia (G.Forst.) Hook. Chloroplast DNA sequences are uninformative in distinguishing Australian P. falcata from New Zealand P. rotundifolia, but show that Australian P. nana is distinct from both. Sequence data also show that Australian and New Zealand populations of P. calidirupium Brownsey &amp; Lovis are closely related, and that Australian P. paradoxa (R.Br.) Hook. is distinct from other Australian species. Although P. falcata is diploid and P. rotundifolia tetraploid, P. calidirupium, P. nana (Hook.) Bostock and P. paradoxa each contain multiple ploidy levels. Diploid populations of Pellaea species are confined to Australia, and only tetraploids are known in New Zealand. Evolution of the group probably involved hybridisation, autoploidy, alloploidy, and possibly apomixis. Further investigation is required to resolve the status of populations from Mount Maroon, Queensland and the Kermadec Islands.

scholarly journals Population structure in the Neisseria , and the biological significance of fuzzy species

2011 ◽  
Vol 9 (71) ◽  
pp. 1208-1215 ◽  
Author(s):  
Jukka Corander ◽  
Thomas R. Connor ◽  
Clíona A. O'Dwyer ◽  
J. Simon Kroll ◽  
William P. Hanage
Keyword(s):  
Population Structure ◽  
Genetic Analysis ◽  
Population Genetic ◽  
Vaccine Development ◽  
Sequence Data ◽  
Genetic Material ◽  
Biological Significance ◽  
Population Genetic Analysis ◽  
Uniform Manner ◽  
Complex Forms

Phenotypic and genetic variation in bacteria can take bewilderingly complex forms even within a single genus. One of the most intriguing examples of this is the genus Neisseria , which comprises both pathogens and commensals colonizing a variety of body sites and host species, and causing a range of disease. Complex relatedness among both named species and previously identified lineages of Neisseria makes it challenging to study their evolution. Using the largest publicly available collection of bacterial sequence data in combination with a population genetic analysis and experiment, we probe the contribution of inter-species recombination to neisserial population structure, and specifically whether it is more common in some strains than others. We identify hybrid groups of strains containing sequences typical of more than one species. These groups of strains, typical of a fuzzy species, appear to have experienced elevated rates of inter-species recombination estimated by population genetic analysis and further supported by transformation experiments. In particular, strains of the pathogen Neisseria meningitidis in the fuzzy species boundary appear to follow a different lifestyle, which may have considerable biological implications concerning distribution of novel resistance elements and meningococcal vaccine development. Despite the strong evidence for negligible geographical barriers to gene flow within the population, exchange of genetic material still shows directionality among named species in a non-uniform manner.

scholarly journals Mitochondrial cytochrome b sequence data are not an improvement for species identification in Scleractinian corals

2014 ◽  
Author(s):  
John Wares
Keyword(s):  
Population Genetics ◽  
Population Genetic ◽  
Sequence Data ◽  
Mitochondrial Gene ◽  
Gene Region ◽  
Mitochondrial Genomes ◽  
Mitochondrial Cytochrome ◽  
Species Delineation ◽  
Population Genetic Analysis ◽  
Mitochondrial Cytochrome B

There are well-known difficulties in using the cytochrome oxidase I (COI) mitochondrial gene region for population genetics and DNA barcoding in corals. A recent study of species divergence in the endemic Caribbean genus Agaricia reinforced such knowledge. However, the growing availability of whole mitochondrial genomes may help indicate more promising gene regions for species delineation. I assembled the whole mitochondrial genome for Agaricia fragilis from Illumina single-end 250bp reads and compared this sequence to that of the congener A. humilis. Although these data suggest that the cytochrome b (CYB) gene region is more promising, comparison of all available Scleractinian CYB sequence data indicates that multilocus approaches are still probably necessary for phylogenetic and population genetic analysis of recently-diverged coral taxa.

scholarly journals Contribution to Globularia phylogeny based on nuclear ribosomal spacer and two chloroplast DNA regions

2017 ◽  
Vol 118 (4) ◽  
Author(s):  
Kroata Hazler Pilepić ◽  
Maja Friščić ◽  
Ahmet Duran ◽  
Semir Maslo ◽  
Rade Garić ◽  
...  
Keyword(s):  
Chloroplast Dna ◽  
Maximum Parsimony ◽  
Nuclear Dna ◽  
Sequence Data ◽  
Leaf Tissue ◽  
Molecular Data ◽  
Rbcl Gene ◽  
Nuclear Its ◽  
Cellular Dna ◽  
Chloroplast Dna Regions

Background and Purpose: Molecular approach has a major impact on phylogenetic studies of plants, considering that it gives useful information about evolutionary events and relations on all taxonomic levels. The sequence data of the nuclear ITS and of two chloroplast regions, trnL-trnF spacer and rbcL gene, obtained from thirteen Globularia L. taxa, including five Anatolian endemics, representing six sections altogether, were analyzed in order to determine the relations between the European and the Anatolian species and get a better insight into the phylogeny of several closely related Globularia taxa.  Materials and Methods: Total cellular DNA was extracted from fresh or frozen leaf tissue of thirteen Globularia samples. The ITS regions of nuclear DNA and two chloroplast DNA regions were amplified and sequenced. Obtained nuclear and combined plastid data matrices were subjected to Maximum Parsimony analyses. Results and Conclusions: Molecular data that were obtained in this study indicate the existence of separate centers of diversification for the European and the Anatolian Globularia. The results provide support for relationships among the studied Anatolian endemic species and indications for a redefinition of affinities of some of the European species. The results presented herein are discussed along with available morphological, karyological, phytogeographical and molecular data. Keywords: Globularia, ITS, trnL-trnF, rbcL, Maximum Parsimony, Quaternary

scholarly journals A novel Arabidopsis phyllosphere resident Protomyces species and a re-examination of genus Protomyces based on genome sequence data

IMA Fungus ◽  
2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Kai Wang ◽  
Timo Sipilä ◽  
Kirk Overmyer
Keyword(s):  
Dna Sequences ◽  
Internal Transcribed Spacer ◽  
Host Plants ◽  
Sequence Data ◽  
Nuclear Gene ◽  
Molecular Data ◽  
Rapid Identification ◽  
Nuclear Ribosomal Dna ◽  
Species Relationships ◽  
Internal Transcribed Spacer Sequences

AbstractProtomyces is an understudied genus of yeast-like fungi currently defined as phytopathogens of only Umbelliferae and Compositae. Species relationships and boundaries remain controversial and molecular data are lacking. Of the 82 named Protomyces, we found few recent studies and six available cultures. We previously isolated Protomyces strains from wild Arabidopsis thaliana, a member of Brassicaceae, a family distant from accepted Protomyces hosts. We previously sequenced the genomes of all available Protomyces species, and P. arabidopsidicola sp. nov. strain C29, from Arabidopsis. Phylogenomics suggests this new species occupied a unique position in the genus. Genomic, morphological, and physiological characteristics distinguished P. arabidopsidicola sp. nov. from other Protomyces. Nuclear gene phylogenetic marker analysis suggests actin1 gene DNA sequences could be used with nuclear ribosomal DNA internal transcribed spacer sequences for rapid identification of Protomyces species. Previous studies demonstrated P. arabidopsidicola sp. nov. could persist on the Arabidopsis phyllosphere and Protomyces sequences were discovered on Arabidopsis at multiple sites in different countries. We conclude that the strain C29 represents a novel Protomyces species and propose the name of P. arabidopsidicola sp. nov. Consequently, we propose that Protomyces is not strictly associated only with the previously recognized host plants.

Phylogeny and biogeography of Apiaceae tribe Oenantheae inferred from nuclear rDNA ITS and cpDNA psbI–5′trnK(UUU) sequences, with emphasis on the North American Endemics clade

Botany ◽  
2008 ◽  
Vol 86 (9) ◽  
pp. 1039-1064 ◽  
Author(s):  
Stephen R. Downie ◽  
Deborah S. Katz-Downie ◽  
Feng-Jie Sun ◽  
Chang-Shook Lee
Keyword(s):  
Dna Sequences ◽  
North American ◽  
Maximum Parsimony ◽  
Nuclear Dna ◽  
Sequence Data ◽  
Sister Group ◽  
Nuclear Ribosomal Dna ◽  
Intergenic Spacers ◽  
Rdna Its ◽  
The North

Intergeneric phylogenetic relationships within Apiaceae tribe Oenantheae were investigated using sequence data from the chloroplast DNA psbI–5′trnK(UUU) and nuclear ribosomal DNA internal transcribed spacer regions. One hundred and thirty-one accessions were examined, representing all 17 genera of the tribe and approximately one-half of its species. The cpDNA region includes four intergenic spacers and the rps16 intron and these noncoding loci were analyzed separately to assess their relative utility for resolving relationships. Separate maximum parsimony analyses of the entire psbI–5′trnK(UUU) and ITS regions, each with and without scored indels, yielded concordant trees. Phylogenies derived from maximum parsimony, Bayesian, or maximum likelihood analyses of combined chloroplast and nuclear DNA sequences for 82 accessions were highly resolved, well supported, and consistent. Among the five noncoding loci examined, the trnQ(UUG)–5′rps16 and 3′rps16–5′trnK(UUU) intergenic spacers are the most variable, with the latter contributing the greatest total number of parsimony informative characters relative to its size. The North American genera Atrema , Cynosciadium , Daucosma , Limnosciadium , Neogoezia , Oxypolis , Ptilimnium , and Trepocarpus ally with the western hemispheric and Australasian genus Lilaeopsis in a strongly supported North American Endemics clade that is a sister group to a clade composed primarily of Old World taxa ( Berula sensu lato, Cryptotaenia , Helosciadium , and Sium ). Oxypolis and Ptilimnium are not monophyletic, with the rachis-leaved members of each comprising a clade separate from their compound-leaved congeners. Dispersal-vicariance analysis suggests that the ancestors of the North American Endemics clade probably originated in Canada and the USA or in a broader ancestral area including Mexico and South America.

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