Taxonomic identity of the Iranian diploid Triticum as evidenced by nrDNA ITS analysis

Phytotaxa ◽  
2013 ◽  
Vol 143 (1) ◽  
pp. 43 ◽  
Author(s):  
Fatemeh Nasernakhaei ◽  
Mohammad Reza Rahiminejad ◽  
Hojjatolah Saeidi ◽  
Manoochehr Tavasoli
Keyword(s):  
Gene Pool ◽  
Sscp Analysis ◽  
Nrdna Its ◽  
Neighbor Joining ◽  
Its Analysis ◽  
Anther Length ◽  
Its Nrdna ◽  
Diploid Level ◽  
Phylogenetic Neighbor

This study concerns the taxonomic investigation of the Iranian diploid Triticum gene pool using morphology and PCR-SSCP analysis of ITS nrDNA. A co-occurrence of two character states of leaf indumentum and anther length was found to be diagnostically significant among these taxa. Three SSCP profiles were detected among our specimens. Sequencing the representatives of different SSCP patterns detected three new nrITS haplotypes. Based on the results of this study we concluded that the genus Triticum at diploid level is represented by two taxa in Iran : T. monococcum subsp. aegilopoides and T. urartu, which is a new taxonomic interpretation of the former taxon. The phylogenetic neighbor-joining tree based on nrITS confirms this interpretation.

Hidden in plain sight—a new Strigula species segregated from Strigula novae-zelandiae (Lichenized Ascomycota: Strigulaceae)

Phytotaxa ◽  
2019 ◽  
Vol 424 (5) ◽  
pp. 267-281 ◽  
Author(s):  
MARLEY FORD ◽  
DAN J. BLANCHON ◽  
ANDREW VEALE ◽  
ERIN J. DOYLE ◽  
JEREMY R. ROLFE ◽  
...  
Keyword(s):  
New Species ◽  
New Zealand ◽  
Conservation Status ◽  
Morphological Characters ◽  
Its Sequence ◽  
Nrdna Its ◽  
Its Nrdna ◽  
A New Species

A new species, Strigula oleistrata, segregated from S. novae-zelandiae is described. The new species is widely sympatric with Strigula novae-zelandiae from which it is separated by a range of morphological characters and also by its nrDNA ITS sequence. As a result of this segregation, a new circumscription of S. novae-zelandiae is also provided. Comments on the ecology and conservation status of both species, and a revised key to the foliicolous Strigula species of New Zealand are provided.

Phylogenetic relationship of some Onobrychis taxa naturally grown in Turkey based on morphology and nuclear ribosomal DNA ITS Sequences

2016 ◽  
Author(s):  
Süleyman AVCI ◽  
Nilgün Tekin ◽  
Cengiz SANCAK ◽  
Sebahattin ÖZCAN ◽  
Amir Orojpour Marangi
Keyword(s):  
Ribosomal Dna ◽  
Clustering Analysis ◽  
Molecular Data ◽  
Its Sequences ◽  
Nuclear Ribosomal Dna ◽  
Morphological Data ◽  
Nrdna Its ◽  
Neighbor Joining ◽  
Quantitative Characters ◽  
Relationship Of

Phylogenetic relationships were studied based on morphology and nuclear ribosomal DNA internal transcript spacer (nrDNA ITS) sequences in 49 populations of 36 Onobrychis taxa belonging to 5 sections (Dendobrychis, Lophobrychis, Onobrychis, Heliobrychis and Hymenobrychis) naturally grown in Turkey. The morphological data (46 quantitative characters) were standardized and submitted for PCA analysis before the performance of hierarchical clustering analysis. In addition, a 577-bp region of the nrDNA ITS sequences was compared to generate a dendrogram using the neighbor-joining method. According to the obtained results, the Onobrychis genus is clearly divided into the Onobrychis and Sisyrosema subgenera both molecularly and morphologically; however, in terms of molecular data, while the Onobrychis subgenus showed polyphyletic features, the Sisyrosema subgenus had monophyletic features. Additionally, long-wing taxa belonging to Dendobrychis and Onobrychis and O. crista-galli belonging to Lophobrychis located in the same clade in Onobrychis showed polyphyletic features. This finding was confirmed in terms of long-wing taxa as well as morphology and indicated that these three sections were entangled with each other under the Onobrychis subgenus.

Variations in the 16S–23S rRNA internal transcribed spacer of fibrolytic Butyrivibrio isolates from the reindeer rumen

2011 ◽  
Vol 57 (7) ◽  
pp. 617-622 ◽  
Author(s):  
Kirsti E. Præsteng ◽  
Roderick I. Mackie ◽  
Isaac K.O. Cann ◽  
Svein D. Mathiesen ◽  
Monica A. Sundset
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Rangifer Tarandus ◽  
Its Region ◽  
16S Rrna Gene Sequencing ◽  
23S Rrna ◽  
Rrna Gene ◽  
Its Sequence ◽  
Neighbor Joining ◽  
Phylogenetic Neighbor

Strains of Butyrivibrio are principal cellulytic bacteria in the rumen of the High Arctic Svalbard reindeer ( Rangifer tarandus platyrhynchus ). According to phylogenetic analysis based on 16S rRNA gene sequencing, Butyrivibrio can be divided into three subgroups within the Clostridia class of the phylum Firmicutes, but the current phenotypic and genotypic differentiation within the family Lachnospiraceae is insufficient. This current study describes the sequence diversity of the 16S–23S rRNA intergenic transcribed spacer (ITS) region of Butyrivibrio isolates from reindeer. A total of 17 different ITS sequences with sizes between 449 and 784 nt were obtained. Genes encoding tRNAIle and tRNAAla were identified in four of the sequences. Phylogenetic neighbor-joining trees were constructed based on the ITS sequence and compared with a phylogenetic neighbor-joining tree based on 16S rRNA gene sequences previously obtained for the same isolates. These comparisons indicated a better differentiation between strains in the ITS sequence than the 16S rRNA gene based tree. Through this study, a better means for identifying and tracking fibrolytic and potentially probiotic Butyrivibrio strains in reindeer and other ruminants has been provided.

nrDNA ITS analysis of Paecilomyces farinosus isolates

2003 ◽  
Vol 11 (6) ◽  
pp. 480-485
Author(s):  
HUANG Bo ◽  
WANG Bin ◽  
FAN Mei-Zhen ◽  
LI Zeng-Zhi ◽  
WANG Cheng-Shu ◽  
...  
Keyword(s):  
Nrdna Its ◽  
Paecilomyces Farinosus ◽  
Its Analysis

scholarly journals Variant analysis of SARS-CoV-2 strains with phylogenetic analysis and the Coronavirus Antiviral and Resistance Database

2022 ◽  
Author(s):  
Murat Sayan ◽  
Ayse Arikan ◽  
Murat Isbilen
Keyword(s):  
Phylogenetic Analysis ◽  
Next Generation Sequencing ◽  
Missense Mutations ◽  
Stanford University ◽  
Neighbor Joining ◽  
Library Preparation ◽  
Analysis Method ◽  
Variant Analysis ◽  
Generation Sequencing ◽  
Phylogenetic Neighbor

Aims: This study determined SARS-CoV-2 variations by phylogenetic and virtual phenotyping analyses. Materials & methods: Strains isolated from 143 COVID-19 cases in Turkey in April 2021 were assessed. Illumina NexteraXT library preparation kits were processed for next-generation ]sequencing. Phylogenetic (neighbor-joining method) and virtual phenotyping analyses (Coronavirus Antiviral and Resistance Database [CoV-RDB] by Stanford University) were used for variant analysis. Results: B.1.1.7–1/2 (n = 103, 72%), B.1.351 (n = 5, 3%) and B.1.525 (n = 1, 1%) were identified among 109 SARS-CoV-2 variations by phylogenetic analysis and B.1.1.7 (n = 95, 66%), B.1.351 (n = 5, 4%), B.1.617 (n = 4, 3%), B.1.525 (n = 2, 1.4%), B.1.526-1 (n = 1, 0.6%) and missense mutations (n = 15, 10%) were reported by CoV-RDB. The two methods were 85% compatible and B.1.1.7 (alpha) was the most frequent SARS-CoV-2 variation in Turkey in April 2021. Conclusion: The Stanford CoV-RDB analysis method appears useful for SARS-CoV-2 lineage surveillance.

scholarly journals Molecular characterization and genetic diversity of Jatropha curcas L. in Costa Rica

2016 ◽  
Author(s):  
Marcela Vásquez-Mayorga ◽  
Eric J Fuchs ◽  
Eduardo J Hernández ◽  
Franklin Herrera ◽  
Jesús Hernández ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Costa Rica ◽  
Jatropha Curcas ◽  
Geographical Origin ◽  
Wide Distribution ◽  
Costa Rican ◽  
Nrdna Its ◽  
Neighbor Joining ◽  
Germplasm Bank ◽  
Nj Tree

We estimated the genetic diversity of 50 Jatropha curcas Costa Rican samples using 18 EST-SSR, one G-SSR and nrDNA-ITS markers. We also evaluated the phylogenetic relationships among samples using nuclear ribosomal ITS markers. Non-toxicity was also evaluated using G-SSRs and SCARs markers. A Neighbor-Joining (NJ) tree and a Maximum Likelihood (ML) tree were constructed using SSR markers and ITS sequences, respectively. Heterozygosity was moderate (He = 0.346), but considerable when compared to worldwide values for J. curcas. The PIC (PIC = 0.276) and inbreeding coefficient (f = -0.102) were both low. Clustering was not related to the geographical origin of accessions but Costa Rican J. curcas consistently clustered as a separate group. International accessions clustered independently of collection sites suggesting a lack of genetic structure, probably due to a wide distribution of this crop and ample gene flow. Molecular markers identified only one non-toxic accession (JCCR-24) from Mexico. This work is part of a countrywide effort to characterize the genetic diversity of Jatropha curcas germplasm bank in Costa Rica.

Leucangium carthusianum var. purpureum, a new purple truffle from China

Phytotaxa ◽  
2018 ◽  
Vol 347 (2) ◽  
pp. 165
Author(s):  
MENG CHEN ◽  
LI FAN
Keyword(s):  
New Taxon ◽  
Nrdna Its ◽  
New Variety ◽  
Molecular Analyses ◽  
Its Nrdna ◽  
The Status

Leucangium carthusianum var. purpureum var. nov. is described and illustrated in this paper. The new variety is distinguished from L. carthusianum var. carthusianum by its small, purple and smooth ascomata. Molecular analyses based on nrDNA-ITS, nrDNA-LSU and EF1-α are provided to confirm the status of the new taxon.

scholarly journals Molecular characterization and genetic diversity ofJatropha curcasL. in Costa Rica

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e2931 ◽  
Author(s):  
Marcela Vásquez-Mayorga ◽  
Eric J. Fuchs ◽  
Eduardo J. Hernández ◽  
Franklin Herrera ◽  
Jesús Hernández ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Costa Rica ◽  
Jatropha Curcas ◽  
Geographical Origin ◽  
Wide Distribution ◽  
Costa Rican ◽  
Nrdna Its ◽  
Neighbor Joining ◽  
Germplasm Bank ◽  
Nj Tree

We estimated the genetic diversity of 50Jatropha curcassamples from the Costa Rican germplasm bank using 18 EST-SSR, one G-SSR and nrDNA-ITS markers. We also evaluated the phylogenetic relationships among samples using nuclear ribosomal ITS markers. Non-toxicity was evaluated using G-SSRs and SCARs markers. A Neighbor-Joining (NJ) tree and a Maximum Likelihood (ML) tree were constructed using SSR markers and ITS sequences, respectively. Heterozygosity was moderate (He = 0.346), but considerable compared to worldwide values forJ. curcas. The PIC (PIC = 0.274) and inbreeding coefficient (f =  − 0.102) were both low. Clustering was not related to the geographical origin of accessions. International accessions clustered independently of collection sites, suggesting a lack of genetic structure, probably due to the wide distribution of this crop and ample gene flow. Molecular markers identified only one non-toxic accession (JCCR-24) from Mexico. This work is part of a countrywide effort to characterize the genetic diversity of theJatropha curcasgermplasm bank in Costa Rica.

scholarly journals Molecular characterization and genetic diversity of Jatropha curcas L. in Costa Rica

2017 ◽  
Author(s):  
Marcela Vásquez-Mayorga ◽  
Eric J Fuchs ◽  
Eduardo J Hernández ◽  
Franklin Herrera ◽  
Jesús Hernández ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Costa Rica ◽  
Jatropha Curcas ◽  
Geographical Origin ◽  
Wide Distribution ◽  
Costa Rican ◽  
Nrdna Its ◽  
Neighbor Joining ◽  
Germplasm Bank ◽  
Nj Tree

We estimated the genetic diversity of 50 Jatropha curcas Costa Rican samples using 18 EST-SSR, one G-SSR and nrDNA-ITS markers. We also evaluated the phylogenetic relationships among samples using nuclear ribosomal ITS markers. Non-toxicity was also evaluated using G-SSRs and SCARs markers. A Neighbor-Joining (NJ) tree and a Maximum Likelihood (ML) tree were constructed using SSR markers and ITS sequences, respectively. Heterozygosity was moderate (He = 0.346), but considerable when compared to worldwide values for J. curcas. The PIC (PIC = 0.276) and inbreeding coefficient (f = -0.102) were both low. Clustering was not related to the geographical origin of accessions but Costa Rican J. curcas consistently clustered as a separate group. International accessions clustered independently of collection sites suggesting a lack of genetic structure, probably due to a wide distribution of this crop and ample gene flow. Molecular markers identified only one non-toxic accession (JCCR-24) from Mexico. This work is part of a countrywide effort to characterize the genetic diversity of Jatropha curcas germplasm bank in Costa Rica.

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