scholarly journals ITS secondary structure reconstruction to resolve taxonomy and phylogeny of the Betula L. genus

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10889
Author(s):  
Andrii S. Tarieiev ◽  
Oliver Gailing ◽  
Konstantin V. Krutovsky
Keyword(s):  
Secondary Structure ◽  
Phylogenetic Trees ◽  
Phylogenetic Analyses ◽  
Resolving Power ◽  
Nucleotide Variation ◽  
Neighbor Joining ◽  
Closely Related Species ◽  
Modern Genomic ◽  
Inference Methods ◽  
Its1 And Its2

The taxonomy and phylogeny of the Betula L. genus remain unresolved and are very difficult to assess due to several factors, especially because of frequent hybridization among different species. In the current study, we used nucleotide sequences of two internal transcribed spacer regions (ITS1 and ITS2), which are commonly used as phylogenetic markers. In addition to their nucleotide variation we reconstructed their secondary structure and used it to resolve phylogenetic relationships of some birch species. We explored whether consideration of secondary structure in phylogenetic analyses based on neighbor-joining, maximum parsimony, maximum likelihood, and Bayesian inference methods would help us obtain more solid support of the reconstructed phylogenetic trees. The results were not unambiguous. There were only a few clades with higher support when secondary structure was included into analysis. The phylogenetic trees generated using different methods were mostly in agreement with each other. However, the resolving power of these markers is still insufficient to reliably discriminate some closely related species. To achieve this aim more reliably there is a need for application of modern genomic approaches in combination with traditional ones.

scholarly journals Characterization of the complete mitochondrial genome of Myrmus lateralis (Heteroptera, Rhopalidae) and its implication for phylogenetic analyses

ZooKeys ◽  
2021 ◽  
Vol 1070 ◽  
pp. 13-30
Author(s):  
Wanqing Zhao ◽  
Dajun Liu ◽  
Qian Jia ◽  
Xin Wu ◽  
Hufang Zhang
Keyword(s):  
Phylogenetic Trees ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Purifying Selection ◽  
Sister Group ◽  
Start Codon ◽  
Rrna Genes ◽  
Trna Genes ◽  
Protein Coding ◽  
Inference Methods

Mitochondrial genomes (mitogenomes) are widely used in research studies on phylogenetic relationships and evolutionary history. Here, we sequenced and analyzed the mitogenome of the scentless plant bug Myrmus lateralis Hsiao, 1964 (Heteroptera, Rhopalidae). The complete 17,309 bp genome encoded 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and a control region. The mitogenome revealed a high A+T content (75.8%), a positive AT-skew (0.092), and a negative GC-skew (–0.165). All 13 PCGs were found to start with ATN codons, except for cox1, in which TTG was the start codon. The Ka/Ks ratios of 13 PCGs were all lower than 1, indicating that purifying selection evolved in these genes. All tRNAs could be folded into the typical cloverleaf secondary structure, except for trnS1 and trnV, which lack dihydrouridine arms. Phylogenetic trees were constructed and analyzed based on the PCG+rRNA from 38 mitogenomes, using maximum likelihood and Bayesian inference methods, showed that M. lateralis and Chorosoma macilentum Stål, 1858 grouped together in the tribe Chorosomatini. In addition, Coreoidea and Pyrrhocoroidea were sister groups among the superfamilies of Trichophora, and Rhopalidae was a sister group to Alydidae + Coreidae.

scholarly journals Bali Bananas (Musa spp. L.) Genetic Relationship Based on Internal Transcribed Spacer 2 (ITS-2)

2020 ◽  
Vol 43 (4) ◽  
Author(s):  
Fenny Martha Dwivany ◽  
Muhammad Rifki Ramadhan ◽  
Carolin Lim ◽  
Agus Sutanto ◽  
Husna Nugrahapraja ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Genetic Relationship ◽  
Internal Transcribed Spacer ◽  
Phylogenetic Trees ◽  
Resolving Power ◽  
Structure Information ◽  
Musa Spp ◽  
Internal Transcribed Spacer 2 ◽  
B Genome ◽  
A Genome

Banana is one of the most essential commodities in Bali island. It is not only for nutrition sources but also for cultural and religious aspects. However, Bali banana genetic diversity has not been explored; therefore, in this study, we focused on its genetic relationship using a molecular approach. This research aimed to determine the genetic relationship of Bali banana cultivars using the internal transcribed spacer 2 (ITS-2) region as a molecular marker. A total of 39 banana samples (Musa spp. L.) were collected from Bali island. The ITS-2 DNA regions were then amplified and sequenced from both ends. ITS-2 sequences were predicted using the ITS2 Database (http://its2.bioapps.biozentrum.uni-wuerzburg.de/). The multiple sequences alignment was performed using ClustalX for nucleotide-based tree and LocARNA to provide the secondary structure information. Phylogenetic trees were constructed using neighbor-joining (Kimura-2-parameter model, 1,000 bootstrap). The result showed that two clades were formed, one clade was abundant in A genome (AA and AAA), and the other rich in the B genome (BB and ABB). This result suggested that cultivars that had similar genomic compositions tended to be grouped within the same clade and separated with different genomic compositions. This study gives perspectives that ITS-2 sequences in bananas are quite similar and differ much compared to other families. Secondary structure has been described to provide more robust resolving power in phylogenetic analysis.

scholarly journals A short guide to phylogeny reconstruction

2008 ◽  
Vol 53 (No. 10) ◽  
pp. 442-446 ◽  
Author(s):  
E. Michu
Keyword(s):  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Dna Sequences ◽  
Phylogenetic Trees ◽  
Phylogenetic Analyses ◽  
Amino Acid Sequences ◽  
Short Introduction ◽  
Closely Related Species ◽  
Origin And Evolution ◽  
Anatomical Characters

This review is a short introduction to phylogenetic analysis. Phylogenetic analysis allows comprehensive understanding of the origin and evolution of species. Generally, it is possible to construct the phylogenetic trees according to different features and characters (e.g. morphological and anatomical characters, RAPD patterns, FISH patterns, sequences of DNA/RNA and amino acid sequences). The DNA sequences are preferable for phylogenetic analyses of closely related species. On the other hand, the amino acid sequences are used for phylogenetic analyses of more distant relationships. The sequences can be analysed using many computer programs. The methods most often used for phylogenetic analyses are neighbor-joining (NJ), maximum parsimony (MP), maximum likelihood (ML) and Bayesian inference.

scholarly journals Phylogenetic Relationships of Macaques (Cercopithecidae: Macaca) Inferred from Partial Mitochondrial DNA (mtDNA) Cytochrome Oxidase II (COII) gene

1970 ◽  
Vol 4 (1) ◽  
pp. 42-51
Author(s):  
Noor Aisyah Rahim ◽  
Millawati Gani ◽  
Mohd Tajuddin Abdullah
Keyword(s):  
Mitochondrial Dna ◽  
Cytochrome Oxidase ◽  
Phylogenetic Relationships ◽  
Phylogenetic Trees ◽  
Phylogenetic Analyses ◽  
Neighbor Joining ◽  
Sister Clade ◽  
Molecular Phylogenetic ◽  
Coii Gene ◽  
Cytochrome Oxidase Ii

The molecular phylogenetic relationships among ten species of macaques were assessed using mitochondrialDNA (mtDNA) cytochrome oxidase II (COII) gene. The 27 individuals comprising of ten species within genusMacaca, namely, M. sylvanus, M. mulatta, M. cyclopis, M. arctoides, M. fascicularis, M. assamensis, M.thibetana, M. nemestrina, M. leonina and M. silenus were used in this study. The phylogenetic trees werereconstructed using neighbor-joining (NJ), maximum parsimony (MP) and maximum likelihood (ML) methods.Based on our constructed tree, it is suggested that the results from phylogenetic analyses demonstrated fourgroups of macaques. In addition, the trees showed topology of M. sylvanus as a sister clade to all Asianmacaques. The silenus group, which diverged first after M. sylvanus formed their own clade, consisted ofmacaque species M. silenus, M. nemestrina and M. leonina. Meanwhile, the sinica group consisted of M.assamensis and M. thibetana, and the fascicularis group comprised of M. fascicularis, M. arctoides, M. mulattaand M. cyclopis. Our ML tree also showed that M. arctoides is a member of fascicularis group. Our study, alsoindicated that our results neglect the classification based on outer appearances and supports the proposedmolecular work view.

Caelestium genus novum (Polygonaceae, Polygoneae): evidence bаsed on the results of molecular phylogenetic analyses of tribe Polygoneae, established with consideration of the secondary structure of the ITS rDNA regions

2019 ◽  
pp. 47-79 ◽  
Author(s):  
O. V. Yurtseva ◽  
E. V. Mavrodiev
Keyword(s):  
Secondary Structure ◽  
Close Relationships ◽  
Plastid Genome ◽  
New Genus ◽  
Phylogenetic Analyses ◽  
Tien Shan ◽  
Hybrid Origin ◽  
Bayesian Analyses ◽  
Molecular Phylogenetic ◽  
Its1 And Its2

The genus Bactria, recently described to house Atraphaxis ovczinnikovii from the Pamirs and Bactria lazkovii from the Central Tien Shan, may also include Polygonum tianschanicum from the Eastern Tien Shan. In order to re-circumscribe Bactria and to clarify the place of Polygonum tianschanicum in tribe Polygoneae, we performed Maximum Likelihood (ML) and Bayesian analyses of combined regions of the plastid genome and ITS1–2 regions of nrDNA for 58 species of tribe Polygoneae, with special attention to the secondary structure of pre-rRNA of the ITS1 and ITS2 loci. In all our analyses, Bactria lazkovii and Polygonum tianschanicum formed a highly supported clade, sister to Bactria ovczinnikovii in the plastid trees, but separate from the latter, as well as from the remaining genera in the ITS-based trees. Details of the secondary structure of pre-rRNA of the ITS1 and ITS2 loci also confirmed the close relationships of Bactria lazkovii and Polygonum tianschanicum, quite different from Bactria ovczinnikovii. Based on the molecular analyses, details of the secondary structure of pre-rRNA of the ITS1 and ITS2 loci, fine morphological distinctions, and distributional data, we propose the new genus Caelestium Yurtseva et Mavrodiev, presumably of hybrid origin, to include C. lazkovii and C. tianschanicum.

scholarly journals E6 and E7 gene polymorphisms in human papillomavirus Type-6 identified in Southwest China

2019 ◽  
Vol 16 (1) ◽  
Author(s):  
Zuyi Chen ◽  
Qiongyao Li ◽  
Jian Huang ◽  
Jin Li ◽  
Feng Yang ◽  
...  
Keyword(s):  
Human Papillomavirus ◽  
Maximum Likelihood ◽  
Secondary Structure ◽  
Phylogenetic Trees ◽  
Southwest China ◽  
Selective Pressure ◽  
Phylogenetic Analyses ◽  
Evolutionary Genetics ◽  
Low Risk ◽  
Reference Sequence

Abstract Background Human papillomavirus type-6 (HPV6) is the major etiological agent of anogenital warts both men and women. The present study aimed to characterize the genetic diversity among HPV6 in Southwest China, and to investigate the origin of, selective pressure experienced by, and impact of the resultantly identified genetic variants on the HPV6 secondary structure. Methods Phylogenetic trees were constructed by Maximum-likelihood and the Kimura 2-parameters methods by Molecular Evolutionary Genetics Analysis version 6.0. The diversity of secondary structure was analyzed by PSIPred software. The selection pressures acting on the E6/E7 genes were estimated by Phylogenetic Analyses by Maximum Likelihood version 4.8 software. Results HPV6 was the most prevalent low risk HPV type in southwest China. In total, 143 E6 and E7 gene sequences of HPV6 isolated from patients were sequenced and compared to GenBank HPV6 reference sequence X00203. The results of these analyses revealed that both the HPV6 E6 and E7 were highly conserved within the analyzed patient samples, and comprised only 3 types of variant sequence, respectively. Furthermore, the analysis of HPV6 E6 and E7 sequences revealed seven/five single-nucleotide mutations, two/four and five/one of which were non-synonymous and synonymous, respectively. The phylogenetic analyses of the E6 and E7 sequences indicated that they belonged to sub-lineage A1 and sub-lineage B1, whereas the selective pressure analyses showed that only the E7 mutation sites 4R, 34E, and 52F were positive selection. Conclusions HPV6 (detection rate = 13.10%) was very prevalent in southwest China, both the HPV6 E6 and E7 sequences were highly conserved within the analyzed patient samples in southwest China, indicating that the low risk HPV6 can adapt to the environment well without much evolution.

scholarly journals Abundant Mitochondrial Genome Diversity, Population Differentiation and Convergent Evolution in Pines

Genetics ◽  
1998 ◽  
Vol 150 (4) ◽  
pp. 1605-1614
Author(s):  
Junyuan Wu ◽  
Konstantin V Krutovskii ◽  
Steven H Strauss
Keyword(s):  
Mitochondrial Dna ◽  
Population Differentiation ◽  
Mitochondrial Gene ◽  
Dna Polymorphisms ◽  
Neighbor Joining ◽  
Closely Related Species ◽  
Breeding Programs ◽  
Length Polymorphisms ◽  
Polymerase Chain ◽  
Mitochondrial Genome Diversity

Abstract We examined mitochondrial DNA polymorphisms via the analysis of restriction fragment length polymorphisms in three closely related species of pines from western North America: knobcone (Pinus attenuata Lemm.), Monterey (P. radiata D. Don), and bishop (P. muricata D. Don). A total of 343 trees derived from 13 populations were analyzed using 13 homologous mitochondrial gene probes amplified from three species by polymerase chain reaction. Twenty-eight distinct mitochondrial DNA haplotypes were detected and no common haplotypes were found among the species. All three species showed limited variability within populations, but strong differentiation among populations. Based on haplotype frequencies, genetic diversity within populations (HS) averaged 0.22, and population differentiation (GST and θ) exceeded 0.78. Analysis of molecular variance also revealed that >90% of the variation resided among populations. For the purposes of genetic conservation and breeding programs, species and populations could be readily distinguished by unique haplotypes, often using the combination of only a few probes. Neighbor-joining phenograms, however, strongly disagreed with those based on allozymes, chloroplast DNA, and morphological traits. Thus, despite its diagnostic haplotypes, the genome appears to evolve via the rearrangement of multiple, convergent subgenomic domains.

scholarly journals Molecular record for the first authentication of Isaria cicadae from Vietnam

2021 ◽  
Vol 16 (1) ◽  
pp. 711-718
Author(s):  
Thuan Duc Lao ◽  
Hanh Van Trinh ◽  
Loi Vuong ◽  
Luyen Tien Vu ◽  
Thuy Ai Huyen Le ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Genomic Dna ◽  
Morphological Analysis ◽  
Phylogenetic Analyses ◽  
Neighbor Joining ◽  
Pcr Assay ◽  
Parsimony Method ◽  
Maximum Parsimony Method ◽  
Cordyceps Cicadae ◽  
High Bootstrap

Abstract The entomopathogenic fungus T011, parasitizing on nymph of Cicada, collected in the coffee garden in Dak Lak Province, Vietnam, was preliminarily morphologically identified as Isaria cicadae, belonged to order Hypocreales and family Clavicipitaceae. To ensure the authenticity of T011, phylogenetic analysis of the concatenated set of multiple genes including ITS, nrLSU, nrSSU, Rpb1, and Tef1 was applied to support the identification. Genomic DNA was isolated from dried sample T011. The PCR assay sequencing was applied to amplify ITS, nrLSU, nrSSU, Rpb1, and Tef1 gene. For phylogenetic analysis, the concatenated data of both target gens were constructed with MEGAX with a 1,000 replicate bootstrap based on the neighbor-joining, maximum likelihood, maximum parsimony method. As the result, the concatenated data containing 62 sequences belonged to order Hypocreales, families Clavicipitaceae, and 2 outgroup sequences belonged to order Hypocreales, genus Verticillium. The phylogenetic analysis results indicated that T011 was accepted at subclade Cordyceps and significantly formed the monophyletic group with referent Cordyceps cicadae (Telemorph of Isaria cicadae) with high bootstrap value. The phylogenetically analyzed result was strongly supported by our morphological analysis described as the Isaria cicadae. In summary, phylogenetic analyses based on the concatenated dataset were successfully applied to strengthen the identification of T011 as Isaria cicadae.

scholarly journals Two new species of Undifilum, fungal endophytes of Astragalus (locoweeds) in the United States

Botany ◽  
2012 ◽  
Vol 90 (9) ◽  
pp. 866-875 ◽  
Author(s):  
Deana L. Baucom ◽  
Marie Romero ◽  
Robert Belfon ◽  
Rebecca Creamer
Keyword(s):  
New Species ◽  
New Mexico ◽  
Random Amplified Polymorphic Dna ◽  
Phylogenetic Analyses ◽  
Fungal Endophytes ◽  
Morphological Characteristics ◽  
Its Region ◽  
The United States ◽  
Neighbor Joining

New species of Undifilum , from locoweeds Astragalus lentiginosus Vitman and Astragalus mollissimus Torr., are described using morphological characteristics and molecular phylogenetic analyses as Undifilum fulvum Baucom & Creamer sp. nov. and Undifilum cinereum Baucom & Creamer sp. nov. Fungi were isolated from dried plants of A. lentiginosus var. araneosus , diphysus , lentiginosus , and wahweapensis collected from Arizona, Oregon, and Utah, USA, and A. mollissimus var. biglovii , earleii , and mollissimus collected from New Mexico, Oklahoma, and Texas, USA. Endophytic fungi from Astragalus locoweeds were compared to Undifilum oxytropis isolates obtained from dried plant material of Oxytropis lamberteii from New Mexico and Oxytropis sericea from Arizona, Colorado, New Mexico, Utah, and Wyoming. Extremely slow growth in vitro was observed for all, and conidia, if present, were ellipsoid with transverse septa. However, in vitro color, growth on four different media, and conidium size differed between fungi from Astragalus spp. and U. oxytropis. Neighbor-joining analyses of internal transcribed spacer (ITS) region and glyceraldehyde-3-phosphate dehydrogenase (GPD) gene sequences revealed that U. fulvum and U. cinereum formed a clade distinct from U. oxytropis. This was supported by neighbor-joining analyses of results generated from random amplified polymorphic DNA (RAPD) fragments using two different primers.

Mitogenome of Alaudala cheleensis (Passeriformes: Alaudidae) and comparative analyses of Sylvioidea mitogenomes

Zootaxa ◽  
2021 ◽  
Vol 4952 (2) ◽  
pp. 331-353
Author(s):  
CHAO YANG ◽  
LE ZHAO ◽  
QINGXIONG WANG ◽  
HAO YUAN ◽  
XUEJUAN LI ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Gene Order ◽  
Phylogenetic Relationships ◽  
Gene Rearrangement ◽  
Phylogenetic Analyses ◽  
Protein Coding ◽  
Comparative Analyses ◽  
Protein Coding Genes ◽  
Basal Position

To gain a better understanding of mitogenome features and phylogenetic relationships in Sylvioidea, a superfamily of Passerida, suborder Passeri, Passeriformes, the whole mitogenome of Alaudala cheleensis Swinhoe (Alaudidae) was sequenced, a comparative mitogenomic analysis of 18 Sylvioidea species was carried out, and finally, a phylogeny was reconstructed based on the mitochondrial dataset. Gene order of the A. cheleensis mitogenome was similar to that of other Sylvioidea species, including the gene rearrangement of cytb-trnT-CR1-trnP-nad6-trnE-remnant CR2-trnF-rrnS. There was slightly higher A+T content than that of G+C in the mitogenome, with an obvious C skew. The ATG codon initiated all protein-coding genes, while six terminating codons were used. The secondary structure of rrnS contained three domains and 47 helices, whereas rrnL included six domains and 60 helices. All tRNAs could be folded into a classic clover-leaf secondary structure except for trnS (AGY). The CR1 could be divided into three domains, including several conserved boxes (C-string, F, E, D, C and B-box, Bird similarity box, CSB1). Comparative analyses within Sylvioidea mitogenomes showed that most mitochondrial features were consistent with that of the A. cheleensis mitogenome. The basal position of the Alaudidae within the Sylvioidea in our phylogenetic analyses is consistent with other recent studies. 

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