scholarly journals Application of the Ribosomal DNA ITS2 Region of Physalis (Solanaceae): DNA Barcoding and Phylogenetic Study

2016 ◽  
Vol 7 ◽  
Author(s):  
Shangguo Feng ◽  
Mengying Jiang ◽  
Yujun Shi ◽  
Kaili Jiao ◽  
Chenjia Shen ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Ribosomal Dna ◽  
Phylogenetic Study ◽  
Its2 Region

Phylogenetic Analysis of Black Peper (Piper Spp.) Population Collected in Different Locations of Vietnam Based on the ITSU1-4 Gene Region

2021 ◽  
Author(s):  
Sonexay Rasphone ◽  
Long Thanh Dang ◽  
Hoan Nguyen ◽  
Ngoc Quang Nguyen ◽  
Oanh Thi Duong ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Ribosomal Dna ◽  
Maximum Likelihood Method ◽  
Dna Barcode ◽  
Population Expansion ◽  
Nuclear Ribosomal Dna ◽  
Likelihood Method ◽  
Gene Region ◽  
Universal Primers ◽  
Intraspecific Distance

Abstract Background: The internal transcribed spacer (ITS) of nuclear ribosomal DNA is one of the most commonly used DNA markers in plant phylogenetic and DNA barcoding analyses, and it has been recommended as a core plant DNA barcode. To compare and find out the analysis genetic diversity difference some pepper individuals collected in different localities in Vietnam when using the ITS of nuclear ribosomal DNA. The ITS gene region from the nuclear genomes were tested for their suitability as DNA barcoding regions of thirty-nine pepper individuals. Universal primers were used, and sequenced products were analyzed using the Maximum Likelihood method and Tamura-Nei model in the MEGA X program.Results: We did not observe high variability in intraspecific distance within the ITSu1-4 gene region between individuals, ranged from 0.000 to 0.155 (mean = 0.033). The size of the gene region has fluctuated from 667 to 685 bp between different individuals with the percentage (G + C) contained in the ITSu1-4 gene region was ranged from 54.776% to 60.805%, mean = 60.174%. The values of Fu’s Fs, D, Fu and Li’s D* and F* were negative as well (Fs = -0.209, D = -1.824; P < 0.05, D* = -1.205; not significant, P > 0.10 and F* = -1.699; not significant, 0.10 > P > 0.05), indicating an excess of recently derived haplotypes and suggesting that either population expansion or background selection has occurred. The value Strobeck’s S the obtained between individuals in a population is high (S = 0.684). The results of evolutionary relationships of taxa obtained 3 groups with the highest value of Fst is shown in the pairs of groups II and III (Fst = 0.151), and the lowest is in groups II and I (Fst = 0.015). All of the new sequences have been deposited in GeneBank under the following accession numbers MZ636718 to MZ636756.Conclusions: This database is an important resource for researchers working on Species of pepper in Vietnam and also provides a tool to create ITSu1-4 databases for any given taxonomy.

Phylogenetic study of ribosomal DNA of cactophilicPichia species by restriction mapping

Yeast ◽  
1993 ◽  
Vol 9 (4) ◽  
pp. 315-330 ◽  
Author(s):  
Randy Shen ◽  
Marc-André Lachance
Keyword(s):  
Ribosomal Dna ◽  
Restriction Mapping ◽  
Phylogenetic Study

A phylogenetic study of the Micarea prasina group shows that Micarea micrococca includes three distinct lineages

2009 ◽  
Vol 42 (1) ◽  
pp. 7-21 ◽  
Author(s):  
Paweł CZARNOTA ◽  
Beata GUZOW-KRZEMIŃSKA
Keyword(s):  
Maximum Likelihood ◽  
Ribosomal Dna ◽  
Dna Sequences ◽  
Maximum Parsimony ◽  
Small Subunit ◽  
Sister Species ◽  
Phylogenetic Study ◽  
Rdna Sequences ◽  
Small Subunit Ribosomal Dna

AbstractThe phylogeny of the Micarea prasina group was investigated using mitochondrial small subunit ribosomal DNA sequences from 14 taxa representing this group, four other members of the genus Micarea, and Psilolechia lucida as an outgroup. A total of 31 new mtSSU rDNA sequences were generated, including 10 from the M. micrococca complex. Bayesian, maximum parsimony (MP) and maximum likelihood (ML) methods were used to analyse the data. The results show that M. micrococca is not monophyletic and forms three strongly supported lineages: 1) M. micrococca s. str., 2) M. byssacea (Th. Fr.) Czarnota, Guzow-Krzemińska & Coppins comb. nov., and 3) a putative taxon that requires further studies. Micarea viridileprosa is a sister species to M. micrococca s. str. and the recently described M. nowakii is a sister species to M. prasina s. str. The placement of M. tomentosa within the M. prasina group is confirmed. Micarea hedlundii appears to be more closely related to the M. micrococca complex than M. prasina s. str. Descriptions, illustrations, taxonomic remarks, distribution and habitat data for M. micrococca s. str. and M. byssacea are provided. A lectotype for Biatora byssacea Hampe non Zwackh and a neotype for Catillaria prasina β [var.] byssacea are selected.

Identification of Closely Related Hydrobaenus Species (Diptera: Chironomidae) Using the Second Internal Transcribed Spacer (ITS2) Region of Ribosomal DNA

2004 ◽  
Vol 26 (3-4) ◽  
pp. 207-213 ◽  
Author(s):  
Hidetake Asari ◽  
Shiro Kasuya ◽  
Tadashi Kobayashi ◽  
Shigeo Kondo ◽  
Isao Nagano ◽  
...  
Keyword(s):  
Ribosomal Dna ◽  
Internal Transcribed Spacer ◽  
Its2 Region ◽  
Second Internal Transcribed Spacer

Systematics of the subfamily Haplorchiinae (Trematoda: Heterphyidae), based on nuclear ribosomal DNA genes and ITS2 region

2010 ◽  
Vol 59 (3) ◽  
pp. 460-465 ◽  
Author(s):  
Urusa Thaenkham ◽  
Paron Dekumyoy ◽  
Chalit Komalamisra ◽  
Megumi Sato ◽  
Do Trung Dung ◽  
...  
Keyword(s):  
Ribosomal Dna ◽  
Nuclear Ribosomal Dna ◽  
Its2 Region

scholarly journals Genetic Diversity and Molecular Characterization of Mosquitoes (Diptera: Culicidae) In North-Central Nigeria Using Ribosomal DNA ITS2 and Mitochondrial 16S-DNA Sequences

2020 ◽  
Vol 44 (2) ◽  
pp. 78-91
Author(s):  
Oluyinka A. Iyiola
Keyword(s):  
16S Rdna ◽  
Dna Sequences ◽  
Mosquito Species ◽  
Evolutionary Relationship ◽  
Malaria Vector Control ◽  
Phylogenetic Study ◽  
Its2 Region ◽  
Morphological Identification ◽  
North Central ◽  
Mitochondrial 16S Rdna

Mosquitoes are vectors of various life-threatening diseases like malaria, yellow fever, dengue fever etc. Their close proximity to human habitations allows ease for disease transmission. They have been identified by key morphological tools like their wings, legs, bristles etc. but closely related species are difficult to identify based on morphology. Molecular tools have, therefore, been employed to help with the more accurate identification. This study was aimed at identifying and characterizing different mosquito species in five different states in North-Central Nigeria using internal transcribed spacer 2 (ITS2) and mitochondrial 16S rDNA regions. Mosquito larvae were collected from stagnant water in breeding places at each collection site in North-central Nigeria. Morphological identification was carried out using standard keys. DNA extraction was performed using EZNA extraction kit. PCR amplification of ribosomal ITS2 and mitochondrial 16S-rDNA gene regions were carried out. The PCR amplicons were sequenced using primers initially used for the PCR. Sequence data were aligned in MEGA 6.0 using ClustalW multiple alignment feature and then compared with GenBank databases for similarity.  Phylogenetic analysis of DNA sequences from the ITS2 region was able to distinguish two mosquito subfamilies; Anophelinae and Culicinae as well as differentiate between and amongst Culex and Aedes species. However, it was unable to effectively distinguish between the two different species of Anopheles sequenced. Mitochondrial 16S rRNA marker was also able to distinguish the two mosquito subfamilies. It efficiently identified and differentiated Culex, Aedes and Anopheles mosquito species sequenced in this study. This study concludes that heterogeneity among Nigerian populations of Anopheles mosquitoes of may likely impact malaria vector control programs. We recommend the combination of nuclear and mitochondrial markers for effective and reliable phylogenetic study and determination of evolutionary relationship among mosquito species.

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