Nucleotide sequences of rbcL confirm the capparalean affinity of the Australian endemis Gyrostemonaceae

1994 ◽  
Vol 7 (1) ◽  
pp. 57 ◽  
Author(s):  
JE Rodman ◽  
KG Karol ◽  
RA PRice ◽  
E Conti ◽  
KJ Systma
Keyword(s):  
Sequence Data ◽  
Stop Codon ◽  
Large Subunit ◽  
Cladistic Analysis ◽  
Sister Group ◽  
Nucleotide Sequences ◽  
Mustard Oil ◽  
Rbcl Gene ◽  
Bisphosphate Carboxylase ◽  
Weak Support

Nucleotide sequences (1452 base pairs) from the chloroplast gene for the large subunit of ribulose-1, 5-bisphosphate carboxylase/oxygenase (rbcL) were obtained for three species of Gyrostemon and Tersonia of the Australian endemic family Gyrostemonaceae. Phylogenetic reconstruction based on parsimony robustly allies the family with other mustard oil-producing plants in Dahlgren's expanded order Capparales. Within this clade, Gyrostemonaceae are the sister group to Resedaceae, but the sequence data provide only weak support for this particular linkage. The new molecular data corroborate recent embryological and ultrastructural findings for Gyrosternonaceae and confirm results from Rodman's cladistic analysis of traditional morphological features of these plants. The rbcL sequences for the three species of Gyrostemonaceae were consistent in possessing a stop codon ending at position 1452, well beyond the usual 1428 site for many dicots. An extended terminus for the rbcL gene appears to be a marker within the expanded order Capparales for a derived clade that comprises the traditional core Capparales (Brassicaceae, Capparaceae, Resedaceae and Tovariaceae) plus Gyrostemonaceae, the sister taxa Batis + Koeberlinia, and Limnanthaceae.

scholarly journals Molecular phylogenies support taxonomic revision of three species of Laurencia (Rhodomelaceae, Rhodophyta), with the description of a new genus

2017 ◽  
Author(s):  
Florence Rousseau ◽  
Delphine Gey ◽  
Akira Kurihara ◽  
Christine A. Maggs ◽  
Julie Martin-Lescanne ◽  
...  
Keyword(s):  
New Genus ◽  
Large Subunit ◽  
Taxonomic Revision ◽  
Sister Group ◽  
Rbcl Gene ◽  
Data Sets ◽  
Cortical Cells ◽  
Data Set ◽  
Bisphosphate Carboxylase ◽  
Rich Data

The systematics of the Laurencia complex was investigated using a taxon-rich data set including the chloroplast ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (rbcL) gene only and a character-rich data set combining mitochondrial cytochrome oxidase 1 (COI-5P), the rbcL marker, and the nuclear large subunit of the ribosomal operon (LSU). Bayesian and ML analyses of these data sets showed that three species hitherto placed in the genus Laurencia J.V.Lamour. were not closely related to Laurencia s. str. Laurencia caspica Zinova & Zaberzhinskaya was the sister group of the remaining Osmundea Stackh. species, L. crustiformans McDermid joined Palisada and L. flexilis Setch. consisted of an independent lineage. In light of these results a new genus, Ohelopapa F.Rousseau, Martin-Lescanne, Payri & L.Le Gall gen. nov., is proposed to accommodate L. flexilis. This new genus is morphologically characterized by four pericentral cells in each vegetative axial segment; however, it lacks ‘corps en cerise’ in cortical cells and secondary pit connections between cortical cells, which are characteristic of Laurencia. Three novel combinations are proposed to render the classification closer to a natural system: Ohelopapa flexilis (Setch.) F.Rousseau, Martin-Lescanne, Payri & L.Le Gall comb. nov., Osmundea caspica (Zinova & Zaberzhinskaya) Maggs & L.M.McIvor comb. nov. and Palisada crustiformans (McDermid) A.R.Sherwood, A.Kurihara & K.W.Nam comb. nov.

scholarly journals The perspectives for DNA barcoding of Rhaponticum carthamoides (Willd.) Iljin using rbcL gene sequence

2021 ◽  
Vol 908 (1) ◽  
pp. 012030
Author(s):  
M V Protopopova ◽  
N A Shvetsova ◽  
V V Pavlichenko
Keyword(s):  
Dna Barcoding ◽  
Large Subunit ◽  
Dna Barcode ◽  
Natural Populations ◽  
Rbcl Gene ◽  
Ribulose Bisphosphate Carboxylase ◽  
Bisphosphate Carboxylase ◽  
Rhaponticum Carthamoides ◽  
South Siberia ◽  
Illegal Harvesting

Abstract The methods of biological species identification using nucleotide sequences of short genome regions (DNA barcoding) are actively developed. The universal DNA barcode for plants remains to be discovered, and one of the leading candidates is the plastid gene of the large subunit of ribulose-bisphosphate carboxylase gene (rbcL). In our study, we estimated the part of rbcL gene as a possible marker for molecular identification of Rhaponticum carthamoides (Willd.) Iljin. Due to its officinal properties, the species is susceptible to uncontrolled and illegal harvesting from natural populations. Today, the species needs to be protected and therefore is included into the Red Data Books of the Russian Federation and certain regions. The study was carried out using plants from the natural populations sampled from the Khamar-Daban Ridge (South Siberia) and considering now as Rh. carthamoides var. chamarense (Peschkova) O S Zhirova. It was shown that rbcL gene can be used to identify Rh. carthamoides at least from the populations of the Khamar-Daban Ridge using a fragment of the maximum length or its 3’ region. Apparently, the 5’ region of the gene (rbcLa) most often used as DNA barcode for plants may be of lesser importance for Rh. carthamoides. The rbcL gene sequences can be also used for the development of approaches for Rh. carthamoides identification in the medicinal preparations and products containing dried tissues to prevent their falsification and illegal harvesting of this species. The combination of rbcL gene with additional markers seems to be highly desirable to create effective DNA barcodes for Rhaponticum species.

scholarly journals Phylogeny of Opisthokonta and the evolution of multicellularity and complexity in Fungi and Metazoa

2003 ◽  
Vol 2 (3) ◽  
pp. 203-211 ◽  
Author(s):  
Mónica Medina ◽  
Allen G. Collins ◽  
John W. Taylor ◽  
James W. Valentine ◽  
Jere H. Lipps ◽  
...  
Keyword(s):  
Ribosomal Dna ◽  
Special Interest ◽  
Sequence Data ◽  
Large Subunit ◽  
Sister Group ◽  
Ssu Rdna ◽  
Lsu Rdna ◽  
Evolutionary Transitions ◽  
Stephanoeca Diplocostata ◽  
Paraphyletic Assemblage

While early eukaryotic life must have been unicellular, multicellular lifeforms evolved multiple times from protistan ancestors in diverse eukaryotic lineages. The origins of multicellularity are of special interest because they require evolutionary transitions towards increased levels of complexity. We have generated new sequence data from the nuclear large subunit ribosomal DNA gene (LSU rDNA) and the SSU rDNA gene of several unicellular opisthokont protists – a nucleariid amoeba (Nuclearia simplex) and four choanoflagellates (Codosiga gracilis, Choanoeca perplexa, Proterospongia choanojuncta and Stephanoeca diplocostata) to provide the basis for re-examining relationships among several unicellular lineages and their multicellular relatives (animals and fungi). Our data indicate that: (1) choanoflagellates are a monophyletic rather than a paraphyletic assemblage that independently gave rise to animals and fungi as suggested by some authors and (2) the nucleariid filose amoebae are the likely sister group to Fungi. We also review published information regarding the origin of multicellularity in the opisthokonts.

Systematics and biogeography of the family Scorpionidae (Chelicerata : Scorpiones), with a discussion on phylogenetic methods

2003 ◽  
Vol 17 (2) ◽  
pp. 185 ◽  
Author(s):  
Lorenzo Prendini ◽  
Timothy M. Crowe ◽  
Ward C. Wheeler
Keyword(s):  
Mitochondrial Genome ◽  
Sequence Data ◽  
Conservation Status ◽  
Phylogenetic Reconstruction ◽  
Cladistic Analysis ◽  
Nuclear Genome ◽  
Sister Group ◽  
Dna Sequence Data ◽  
Phylogenetic Methods ◽  
The Family

A cladistic analysis of relationships among the genera of Scorpionidae Latreille, 1802—Heterometrus Ehrenberg, 1828; Opistophthalmus C. L. Koch, 1837; Pandinus Thorell, 1876; and Scorpio Linnaeus, 1758—based on morphology and DNA sequence data from loci of three genes in the mitochondrial genome (12S ribosomal DNA (rDNA), 16S rDNA and cytochrome oxidase I) and one gene in the nuclear genome (28S rDNA) is presented. The analysis makes use of exemplar species, specifically selected to test the monophyly of the genera, rather than supraspecific terminal taxa. Other methods used in the analysis are justified in the context of a discussion of current methods for phylogenetic reconstruction. Relationships among the scorpionid genera are demonstrated to be as follows: (Opistophthalmus (Scorpio (Heterometrus + Pandinus))). This reconstruction identifies Opistophthalmus as the basal lineage of the Scorpionidae, rather than the sister-group of Scorpio. Revised descriptions, diagnoses and a key to identification of the four scorpionid genera are provided, together with a summary of what is known about their ecology, distribution and conservation status.

scholarly journals Chloroplast Genome Evolution in the Genus Avena

Genetics ◽  
1987 ◽  
Vol 116 (4) ◽  
pp. 613-621
Author(s):  
Koji Murai ◽  
Koichiro Tsunewaki
Keyword(s):  
Chloroplast Genome ◽  
Restriction Site ◽  
Physical Map ◽  
Fragment Size ◽  
Large Subunit ◽  
Single Copy ◽  
Rbcl Gene ◽  
Type I ◽  
Bisphosphate Carboxylase ◽  
Chloroplast Genomes

ABSTRACT The genus Avena contains five different chloroplast genomes, I-V. A physical map of chloroplast (ct) DNA of Avena sativa (type I chloroplast genome) was constructed using three restriction endonucleases, PstI, SalI and SmaI. This genome is ca. 135.5 kbp in size, and contains two inverted repeats of ca. 22.5 kbp each, separated by a large (ca. 79.0 kbp) and small (ca. 12.5 kbp) single copy region. The rbcL gene which codes for the large subunit of ribulose 1,5-bisphosphate carboxylase, was located in the map. Restriction fragment patterns of all five chloroplast genomes were compared, and among them five fragment size and five restriction site mutations were disclosed. Four site mutations were found in two or more chloroplast genomes, the other site and five fragment size mutations were specific to one or another of the chloroplast genomes. A dendrogram showing phylogenetic relationships among the five chloroplast genomes, based on the distribution of the common and specific mutations among them, indicates that chloroplast genome divergence characterized by three restriction site mutations occurred first between two diploid groups, each carrying A and C genome (nuclear), respectively, followed by further speciation in each group.

Further phylogenetic studies of the Polychaeta using 18S rDNA sequence data

2004 ◽  
Vol 84 (5) ◽  
pp. 949-960 ◽  
Author(s):  
Kathryn A. Hall ◽  
Pat A. Hutchings ◽  
Donald J. Colgan
Keyword(s):  
Dna Sequences ◽  
Sequence Data ◽  
Cladistic Analysis ◽  
Sister Group ◽  
Morphological Data ◽  
Phylogenetic Studies ◽  
Rdna Sequence Data ◽  
Substantial Progress ◽  
18S Rdna Sequence

The integration of molecular and morphological approaches has produced substantial progress in understanding the higher classification of most major invertebrate groups. The striking exception to this is the Polychaeta. Neither the membership nor the higher classification of this group has been robustly established. Major inconsistencies exist between the only comprehensive cladistic analysis of Polychaeta using morphological data and the DNA sequence studies covering all or part of the taxon.We have compiled a dataset of available nearly complete 18S ribosomal DNA sequences and collected an additional 22 sequences (20 Polychaeta in 19 taxa, one Myzostomida and one Phoronida) to obtain more comprehensive coverage of polychaete diversity for this gene. Analyses of the data do not resolve all inconsistencies among current hypotheses of polychaete phylogeny. They do support the recognition (in whole or part) of some clades such as the Eunicida, Phyllodocida and Terebellida that have been proposed on morphological grounds. Our analyses contradict the Canalipalpata and the Scolecida. Although the polychaete sister-group to the Clitellata is not clearly resolved in our analyses, the clitellates are always recovered as a derived clade within the Polychaeta. Increased taxon sampling is required to elucidate further the phylogeny of the Polychaeta.

Molecular systematics of the Hypocreales: a teleomorph gene phylogeny and the status of their anamorphs

1995 ◽  
Vol 73 (S1) ◽  
pp. 816-823 ◽  
Author(s):  
Stephen A. Rehner ◽  
Gary J. Samuels
Keyword(s):  
Sequence Data ◽  
Large Subunit ◽  
Cladistic Analysis ◽  
Verticillium Lecanii ◽  
Acremonium Chrysogenum ◽  
Phylogenetic Placement ◽  
The Status ◽  
Molecular Phylogenetic ◽  
Comprehensive Classification

Phylogenetic relationships among 40 species in the Hypocreales and Clavicipitales were inferred from sequence data obtained from the nuclear large-subunit ribosomal DNA. Cladistic analysis of these data support the monophyly of the Hypocreales, with the Clavicipitales derived from within the Hypocreales. Four groupings were resolved and are informally designated as the Hypocrea, Claviceps, Bionectria, and Nectria groups. Phylogenetic placement of teleomorphs including Melanospora and cleistothecial taxa, such as Heleococcum, Mycoarachis, and Roumegueriella, demonstrate the facility of molecular phylogenies to accommodate taxa with highly modified morphologies. Similarly, the hypocrealean origins of the anamorph species Verticillium lecanii and Acremonium chrysogenum illustrate the potential of the molecular phylogenetic approach to accommodate anamorph isolates within the context of a teleomorph phylogeny. Together these results suggest that a comprehensive classification of the Hypocreales, inclusive of teleomorph and anamorph states, is attainable through a molecular phylogenetic approach. Key words: Ascomycotina, Clavicipitaceae, Hypocreales, phylogeny, pyrenomycete, rDNA.

scholarly journals Can Biomarkers Respond Upon Freshwater Pollution?—A Moss-Bag Approach

Biology ◽  
2020 ◽  
Vol 10 (1) ◽  
pp. 3
Author(s):  
Gana Gecheva ◽  
Ivelin Mollov ◽  
Galina Yahubyan ◽  
Mariyana Gozmanova ◽  
Elena Apostolova ◽  
...  
Keyword(s):  
Large Subunit ◽  
Cell Number ◽  
Total Phenolic ◽  
Rbcl Gene ◽  
Leaf Cell ◽  
Fontinalis Antipyretica ◽  
Bisphosphate Carboxylase ◽  
Freshwater Pollution ◽  
Aquatic Mosses ◽  
Moss Bags

Moss-bags were applied to study the effect of contamination in three standing water bodies in Bulgaria (Kardzhali, Studen Kladenets and Zhrebchevo Reservoirs), the first two with old industrial contamination and the last polluted with short-chain chlorinated paraffins (SCCPs). Fontinalis antipyretica Hedw. collected from background (unpolluted) site was placed in cages for a period of 30 days. The present study examined whether inorganic and organic pollution detected with moss-bags resulted in corresponding differences in molecular, chemical and micromorphological markers. Suppressed large subunit of ribulose-1,5-bisphosphate carboxylase (rbcL) expression was assessed in moss-bags from two of the reservoirs, contaminated with heavy metals. There was a decrease of the total phenolic content (TPC) in the moss-bags, which provides a basis for further studies of the chemical content of aquatic mosses. Fontinalis antipyretica also showed a response through leaf micromorphological characteristics. In the all three reservoirs, an increase of the twig leaf cell number was recorded (p ≤ 0.01 for Kardzhali and p ≤ 0.001 for Studen Kladenets and Zhrebchevo reservoirs), as well as of the stem leaf cell number in Zhrebchevo Reservoir (p ≤ 0.001). On the contrary, the width of the cells decreased in the studied anthropogenically impacted reservoirs. All three studied groups of biomarkers (molecular, chemical and micromorphological) appeared to be sensitive to freshwater pollution. The results achieved indicated that rbcL gene expression, TPC, cell number and size are promising biomonitoring tools.

scholarly journals Analysis of Adaptive Evolution and Coevolution of rbcL Gene in the Genus Hildenbrandia (Rhodophyta)

2020 ◽  
Vol 16 ◽  
pp. 117693432097786
Author(s):  
Nan Fangru ◽  
Han Yuxin ◽  
Liu Xudong ◽  
Feng Jia ◽  
Lv Junping ◽  
...  
Keyword(s):  
Adaptive Evolution ◽  
Evolutionary History ◽  
Large Subunit ◽  
Purifying Selection ◽  
Dimensional Structure ◽  
Rbcl Gene ◽  
Bisphosphate Carboxylase ◽  
3 Dimensional ◽  
Grand Average ◽  
Tree Construction

The adaptive evolution and coevolution of the ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit ( rbcL) gene in the genus Hildenbrandia were studied based on phylogenetic tree construction and the physicochemical properties and the secondary structures of protein encoded by rbcL (Rubisco large subunit) were analyzed. The amino acids compositions and grand average of hydropathicity of freshwater H. rivularis and marine H. rubra were similar. Rubisco large subunit of Hildenbrandia was hydrophilic and the secondary structure was primarily composed of α-helixes and β-sheets, revealing the relatively stable structure of this protein. The predicted phosphorylation sites in H. rivularis and H. rubra were 33 and 36, respectively. No positive selection sites were detected in the genus Hildenbrandia, implying that rbcL gene evolved either neutrally or under purifying selection. A total of 41 coevolutionary groups were detected in the Rubisco large subunit of Hildenbrandia and the coevolving sites are in closer proximity in 3-dimensional structure of the protein. Despite the long evolutionary history, rbcL gene in genus Hildenbrandia under different environments is rather conservative.

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