Molecular Systematics of the Nepetoideae (Family Labiatae): Phylogenetic Implications from rbcL Gene Sequences

1994 ◽  
Vol 49 (9-10) ◽  
pp. 635-645 ◽  
Author(s):  
Martina Kaufmann ◽  
Michael Wink
Keyword(s):  
Rbcl Gene ◽  
Character State ◽  
Specific Primers ◽  
Distance Methods ◽  
Phylogenetic Implications ◽  
Viii And Ix ◽  
Total Dna ◽  
Polymerase Chain ◽  
Rbcl Gene Sequences ◽  
Rbcl Sequences

Abstract Total DNA was extracted from 41 species (20 genera) of the subfamily Nepetoideae (family Labiatae). Using rbcL-specific primers, the rbcL gene was amplified by polymerase chain reaction (PCR) and sequenced directly. RbcL sequences were evaluated with character state (maximum parsimony; PAUP) and distance methods (neighbour-joining; MEGA). In agree­ ment with classical systematics all taxa studied cluster within the Nepetoideae and are clearly distinguished from members of the subfamily Lamioideae. A number of distinctive clades are apparent within the Nepetoideae:, and XIII -Perovskia. At least five main branches rep­ resenting the clades I, II, III to VII, VIII, and IX to XIII respectively, can be distinguished within the Nepetoideae studied. They might be considered representing the tribes (according to Cantino, 1992) Elsholtzieae (I), Lavanduleae (II), and Mentheae (III - XIII). The tribe Mentheae needs to be subdivided into at least three main groups (clades III-VII, VIII and IX -XIII). Major ana hortensis which is often classified as Origanum hortensis does not cluster with Origanum and deserves a generic status of its own.

Corrigendum to: Batrachospermum pseudogelatinosum (Batrachospermales, Rhodophyta), a polyecious paraspecies from Australia and New Zealand

2006 ◽  
Vol 19 (1) ◽  
pp. 113
Author(s):  
Timothy J. Entwisle ◽  
Morgan L. Vis ◽  
Hannah McPherson
Keyword(s):  
New Zealand ◽  
Great Variability ◽  
Rbcl Gene ◽  
Taxonomic Character ◽  
Gene Sequences ◽  
Eastern Australia ◽  
Rbcl Gene Sequences ◽  
Rbcl Sequences

New and existing collections of Batrachospermum pseudogelatinosum Entwisle & Vis, and related taxa, from Australia and New Zealand, were analysed to determine whether this morphologically diverse taxon should be further subdivided. In particular, the value of the taxonomic character 'dioecy/monoecy' was assessed with molecular (rbcL gene sequences), morphometric and diagnostic morphology datasets, and its applicability more widely within the genus considered in light of our results. While the rbcL sequences supported our intuitive feeling that there is great variability within this taxon, there was no practical way to subdivide B. pseudogelatinosum. We recommend the acceptance of a broadly circumscribed paraphyletic species (paraspecies), B. pseudogelatinosum, which includes both dioecious and monoecious populations. The value of monoecy/dioecy as a character must be determined on a taxon-by-taxon basis—it is no better or worse than any other taxonomic character. Batrachospermum pseudogelatinosum occurs in eastern Australia and Stewart Island in New Zealand, with implications for the circumscription of B. campyloclonum Skuja ex Entwisle & Foard.

scholarly journals Phytoplasma associated with shoot proliferation in begonia

2006 ◽  
Vol 63 (5) ◽  
pp. 475-477 ◽  
Author(s):  
Luiz Fernando Caldeira Ribeiro ◽  
Ana Paula de Oliveira Amaral Mello ◽  
Ivan Paulo Bedendo ◽  
Ricardo Gioria
Keyword(s):  
Ornamental Plants ◽  
Shoot Proliferation ◽  
Plant Size ◽  
Universal Primers ◽  
Chain Reaction ◽  
Specific Primers ◽  
Nested Polymerase Chain Reaction ◽  
Phytoplasma Infection ◽  
Total Dna ◽  
Polymerase Chain

Begonia is a very appreciated genus of ornamental plants, of economic relevancy, having species of flowers and foliage. In commercial croppings, plants exhibiting characteristic symptoms of phytoplasma infection have been observed, such as shoot proliferation, reduced plant, size small leaves and flowers, and phyllody. Leaves were sampled and total DNA was extracted to be used in nested Polymerase Chain Reaction (PCR), in order to detect and identify an expected phytoplasma. The results confirmed consistently the presence of a phytoplasma associated with symptomatic plants through the amplification of a typical genomic fragment of 1.2 kb by using the universal primers R16mF2/mR1 and R16F2n/R2. The use of specific primers R16(III)F2/R1 allowed to identify the phytoplasma detected as a representative of the group 16SrIII. This information is very expressive, because different diseases caused by fungus, bacteria, virus and nematodes have been reported for begonia, however, reports have not been found for begonia diseases associated with phytoplasmas.

scholarly journals Species diversity and phylogenetic analysis of Heliconia spp. collections of Purwodadi Botanic Garden (East Java, Indonesia) inferred by rbcL gene sequences

2019 ◽  
Vol 20 (5) ◽  
Author(s):  
LIA HAPSARI ◽  
TRIMANTO TRIMANTO ◽  
DIDIK WAHYUDI
Keyword(s):  
Phylogenetic Analysis ◽  
Species Diversity ◽  
Genetic Variability ◽  
Morphological Characteristics ◽  
Pairwise Distance ◽  
Rbcl Gene ◽  
Gene Sequences ◽  
Botanic Garden ◽  
Rbcl Gene Sequences ◽  
Rbcl Sequences

Abstract. Hapsari L, Trimanto, Wahyudi D. 2019. Species diversity and phylogenetic analysis of Heliconia spp. collections of Purwodadi Botanic Garden (East Java, Indonesia) inferred by rbcL gene sequences. Biodiversitas 20: 1266-1283. Heliconia L. is a single genus in the family Heliconiaceae, with approximate consists of 200 species. It has wide morphological variations among and within species which led to problems in species identification. Species diversity and phylogenetic analysis using morphology and rbcL marker subjected to 17 Heliconia spp. living collections of Purwodadi Botanic Garden (PBG) have been conducted. The rbcL gene located in chloroplast genome is one of appropriate proposed marker for plant barcoding assessment. This study aimed to study morphology and genetic variability of the PBG Heliconiaceae collections, to confirms the species name for a more accurate identity record and to reveal the diversity and phylogenetics of the species. Morphological characterization showed high variability among Heliconia species, which included 3 subgenera (Heliconia, Stenochlamys, and Griggsia) and 1 hybrid. Each species possessed unique morphological characteristics. The common morphological characters which distinguished among and within Heliconia species includes leaf form, inflorescence type, and bract characteristics. Key to the Heliconia species examined is presented in this paper. However, molecular confirmation using rbcL sequences showed high conservation level (0.932) and low genetic variability. About 656 nucleotides were monomorphic and 33 positions were polymorphic which comprised 18 singleton variable sites and 15 parsimony informative sites. Twelve haplotypes were produced with haplotype diversity value 0.8952. Pairwise distance analysis shows that they were shared high similarity of rbcL sequences with very low genetic distance (0.022 to 0.000). The topology of phylogenetic tree resulted by Neighbour-Joining algorithm has the best grouping and be able to explain the relationship among species of Heliconia, although supported by low bootstrap (65). It was separated into two clades following its subgen. classification. Clade 1 consists of subgen. Heliconia and Griggsia; while clade 2 consists of subgen. Heliconia and Stenochlamys; also hybrid species. Further, separation of deeper branchings (section) was inconsistent and unclear. Upon this study, rbcL marker was considered too conserved thus less valuable for phylogenetic analysis at lower taxa among and within Heliconia spp. However, rbcL was suggested to distinguish at higher level taxa between closely related genus and above.

Batrachospermum pseudogelatinosum (Batrachospermales, Rhodophyta), a polyecious paraspecies from Australia and New Zealand

2004 ◽  
Vol 17 (1) ◽  
pp. 17 ◽  
Author(s):  
Timothy J. Entwisle ◽  
Morgan L. Vis ◽  
Hannah McPherson
Keyword(s):  
New Zealand ◽  
Great Variability ◽  
Rbcl Gene ◽  
Taxonomic Character ◽  
Gene Sequences ◽  
Eastern Australia ◽  
Rbcl Gene Sequences ◽  
Rbcl Sequences

New and existing collections of Batrachospermum pseudogelatinosum Entwisle & Vis, and related taxa, from Australia and New Zealand, were analysed to determine whether this morphologically diverse taxon should be further subdivided. In particular, the value of the taxonomic character 'dioecy/monoecy' was assessed with molecular (rbcL gene sequences), morphometric and diagnostic morphology datasets, and its applicability more widely within the genus considered in light of our results. While the rbcL sequences supported our intuitive feeling that there is great variability within this taxon, there was no practical way to subdivide B. pseudogelatinosum. We recommend the acceptance of a broadly circumscribed paraphyletic species (paraspecies), B. pseudogelatinosum, which includes both dioecious and monoecious populations. The value of monoecy/dioecy as a character must be determined on a taxon-by-taxon basis—it is no better or worse than any other taxonomic character. Batrachospermum pseudogelatinosum occurs in eastern Australia and Stewart Island in New Zealand, with implications for the circumscription of B. campyloclonum Skuja ex Entwisle & Foard.

scholarly journals Characterization of Xanthomonas axonopodis pv. phaseoli isolates

2008 ◽  
Vol 34 (3) ◽  
pp. 228-231 ◽  
Author(s):  
Willian Mário de Carvalho Nunes ◽  
Maria Júlia Corazza ◽  
Silvana Aparecida Crestes Dias de Souza ◽  
Siu Mui Tsai ◽  
Eiko Eurya Kuramae
Keyword(s):  
Xanthomonas Campestris ◽  
Random Amplified Polymorphic Dna ◽  
Hypersensitive Reaction ◽  
Chain Reaction ◽  
Xanthomonas Axonopodis ◽  
Paulo State ◽  
Total Dna ◽  
Polymerase Chain ◽  
Bacterial Plant Pathogen

A simple, quick and easy protocol was standardized for extraction of total DNA of the bacteria Xanthomonas axonopodis pv. phaseoli. The DNA obtained by this method had high quality and the quantity was enough for the Random Amplified Polymorphic DNA (RAPD) reactions with random primers, and Polymerase Chain Reaction (PCR) with primers of the hypersensitivity and pathogenicity gene (hrp). The DNA obtained was free of contamination by proteins or carbohydrates. The ratio 260nm/380nm of the DNA extracted ranged from 1.7 to 1.8. The hrp gene cluster is required by bacterial plant pathogen to produce symptoms on susceptible hosts and hypersensitive reaction on resistant hosts. This gene has been found in different bacteria as well as in Xanthomonas campestris pv. vesicatoria (9). The primers RST21 and RST22 (9) were used to amplify the hrp gene of nine different isolates of Xanthomonas axonopodis pv. phaseoli from Botucatu, São Paulo State, Brazil, and one isolate, "Davis". PCR amplified products were obtained in all isolates pathogenic to beans.

scholarly journals Easy and Efficient DNA Extraction from Woody Plants for the Detection of Phytoplasmas by Polymerase Chain Reaction

Plant Disease ◽  
1999 ◽  
Vol 83 (5) ◽  
pp. 482-485 ◽  
Author(s):  
Margaret J. Green ◽  
Dan A. Thompson ◽  
Donald J. MacKenzie
Keyword(s):  
Polymerase Chain Reaction ◽  
Plant Material ◽  
Woody Plant ◽  
Leaf Roll ◽  
Chain Reaction ◽  
Efficient Procedure ◽  
Identical Manner ◽  
Total Dna ◽  
Polymerase Chain ◽  
Selection Of

A simple and efficient procedure for the extraction of high-quality DNA from phytoplasma-infected woody and herbaceous plants for polymerase chain reaction (PCR) detection is described. This procedure does not require phenol, chloroform, or alcohol for the precipitation of nucleic acids. Herbaceous and woody plant material are extracted in an identical manner with no additional purification or enrichment steps required. The method utilizes commercially available microspin-column matrices, and the extraction of total DNA can be achieved in less than 1 h. The method has been used to successfully purify phytoplasma DNA from whole leaves, leaf petioles and midribs, roots, and dormant wood from a diverse selection of plant material. The phytoplasmas detected by PCR include pear decline, western X-disease, peach yellow leaf roll, peach rosette, apple proliferation, Australian grapevine yellows, and Vaccinium witches'-broom.

scholarly journals Amplification Refractory Mutation System – Polymerase Chain Reaction for Rapid Detection of rpoB Gene Mutations in Mycobacterium tuberculosis

2017 ◽  
Vol 5 (1) ◽  
pp. 81-85 ◽  
Author(s):  
Hemanta Kumari Chaudhary ◽  
Mitesh Shrestha ◽  
Prakash Chaudhary ◽  
Bal Hari Poudel
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Rpob Gene ◽  
Amplification Refractory Mutation System ◽  
Chain Reaction ◽  
Arms Pcr ◽  
Mutation System ◽  
Mdr Tb ◽  
Total Dna ◽  
Polymerase Chain ◽  
Rifampin Resistance

Multidrug-resistant tuberculosis (MDR-TB) has become a serious worldwide threat including in Nepal. MDR-TB refers to the pathological condition whereby Mycobacterium tuberculosis becomes resistant to the first line of drug treatment i.e. rifampin and isoniazid. Resistance to rifampin (RIF) is mainly caused by the mutations in the rpoB gene which codes for the β-subunit of RNA polymerase. In this study, Amplification Refractory Mutation System – Polymerase Chain Reaction (ARMS – PCR) technique has been used to detect mutations in the rpoB gene of Mycobacterium tuberculosis. Total DNA samples of 34 phenotypic MDR-TB were subjected to ARMS – PCR using three different codon specific primers (516, 526 and 531). These three codons occupy large portion of total mutation responsible for rifampin resistance. Out of the total DNA samples, all were bearing mutation in at least one of the three codons mentioned. Of those bearing mutation, the highest number had mutation in codon 531 (97.05 %) followed by codon 516 (17.64 %) and finally in codon 526 (11.76%) respectively. Hence, ARMS – PCR may be used as an alternative diagnostic technique for detection of rifampin resistance in Mycobacterium tuberculosis strains, especially for a developing country like Nepal.Int. J. Appl. Sci. Biotechnol. Vol 5(1): 81-85

Variation in bacterial endosymbionts associated with the date palm hopper,Ommatissus lybicuspopulations

2017 ◽  
Vol 108 (2) ◽  
pp. 271-281 ◽  
Author(s):  
S. Karimi ◽  
H. Izadi ◽  
M. Askari Seyahooei ◽  
A. Bagheri ◽  
P. Khodaygan
Keyword(s):  
Date Palm ◽  
Multiple Infections ◽  
Infection Frequency ◽  
Pcr Assay ◽  
Specific Primers ◽  
Consensus Sequences ◽  
Pcr Products ◽  
Bacterial Endosymbionts ◽  
Different Populations ◽  
Polymerase Chain

AbstractThe date palm hopper,Ommatissus lybicus, is a key pest of the date palm, which is expected to be comprised of many allopatric populations. The current study was carried out to determine bacterial endosymbiont diversity in the different populations of this pest. Ten date palm hopper populations were collected from the main date palm growing regions in Iran and an additional four samples from Pakistan, Oman, Egypt and Tunisia for detection of primary and secondary endosymbionts using polymerase chain reaction (PCR) assay with their specific primers. The PCR products were directly sequenced and edited using SeqMan software. The consensus sequences were subjected to a BLAST similarity search. The results revealed the presence of ‘CandidatusSulcia muelleri’ (primary endosymbiont) andWolbachia,ArsenophonusandEnterobacter(secondary endosymbionts) in all populations. This assay failed to detect ‘CandidatusNasuia deltocephalinicola’ andSerratiain these populations. ‘Ca. S. muelleri’ exhibited a 100% infection frequency in populations andWolbachia,ArsenophonusandEnterobacterdemonstrated 100, 93.04 and 97.39% infection frequencies, respectively. The infection rate ofArsenophonusandEnterobacterranged from 75 to 100% and 62.5 to 100%, respectively, in different populations of the insect. The results demonstrated multiple infections by ‘Ca. Sulcia muelleri’,Wolbachia,ArsenophonusandEnterobacterin the populations and may suggest significant roles for these endosymbionts on date palm hopper population fitness. This study provides an insight to endosymbiont variation in the date palm hopper populations; however, further investigation is needed to examine how these endosymbionts may affect host fitness.

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