Constructing Neighbor-Joining phylogenetic trees with reduced redundancy computation

Abstract Background Species of the Anopheles hyrcanus group are widely distributed in Palearctic and Oriental regions and some of them are important malaria vectors. The cryptic species of An. hyrcanus group was almost impossible to identify based only on their morphology. The phylogenetic relationship of An. hyrcanus group was also not clear. Methods Five members of An. hyrcanus group were identified by rDNA ITS2 sequencing as An. yatsushiroensis, An. belenrae, An. kleini, An. lesteri and An. sineroides. The mitochondrial genome fragments were sequenced and annotated using the mitochondrial genome of An. sinensis as reference. Based on the four segments and Joint Data sequences of these species, and other four anopheline species downloaded from GenBank, intraspecific as well as interspecific genetic distances were calculated and the phylogenetic trees were reconstructed by the methods of neighbor joining, maximum parsimony, minimum evolution and maximum likelihood. Findings Four parts of mitochondrial genomes, which were partial fragments COI + tRNA + COII (F5), ATP6 + COIII(F7 + F8), ND1(F19) and lrRNA (F21), were obtained. All fragments were connected as one sequence (referred as Joint Data), which had a total length of 3393 bp. All fragment sequences were highly conservative within species, with the maximum p distance (0.026) calculated by F19 of An. belenrae. The pairwise interspecific p distance calculated by each fragment showed minor or even no difference among An. sinensis, An. kleini and An. belenrae. However, interspecific p distances calculated by the Joint Data sequence ranged from 0.004 (An. belenrae vs An. kleini) to 0.089 (An. sineroides vs An. minimus), and the p distances of the six members of An. hyrcanus group were all less than 0.029. The phylogenetic tree showed two major clades: all subgenus Anopheles species (including six members of An. hyrcanus group, An. atroparvus and An. quadrimaculatus A) and subgenus Cellia (including An. dirus and An. minimus). The An. hyrcanus group was divided into two clusters as ((An. lesteri, An. sineroides) An. yatsushiroensis) and ((An. belenrae, An. sinensis) An. kleini)). Conclusions The An. hyrcanus group in this study could be divided into two clusters, in one of which An. belenrae, An. sinensis and An. kleini were most closely related. More molecular markers would make greater contribution to phylogenetic analysis.

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Overexpression and Phylogenetic Analysis of a Thermostable α-Glucosidase from Thermus thermophilus

Advanced Materials Research ◽

10.4028/www.scientific.net/amr.1004-1005.841 ◽

2014 ◽

Vol 1004-1005 ◽

pp. 841-848

Author(s):

Xun Li ◽

Hua Xiang Gu ◽

Hao Shi ◽

Fei Wang

Keyword(s):

Phylogenetic Trees ◽

Expression Vector ◽

Thermus Thermophilus ◽

Glycoside Hydrolases ◽

Neighbor Joining ◽

E Coli ◽

Optimal Activity ◽

Evolution Analysis ◽

Terminal Amino ◽

Ph Range

The α-glucosidase geneaglfromThermus thermophilusHB8 was cloned into expression vector pBV220. The phylogenetic trees of α-glucosidases were constructed using Neighbor-Joining (NJ) and Maximum-Parsimony (MP) methods. Evolution analysis indicated the α-glucosidase fromT. thermophileHB8 was distant from the other glycoside hydrolases 4 and 31 α-glucosidases. By weakening the mRNA secondary structure and replacing the rare codons for the N-terminal amino acids of the target protein, the expression level of theaglwas increased 30-fold. The recombinant AGL was purified by the heat treatment, and had a molecular mass of 61 kDa. The optimal activity was at pH 7.8 and 95°C over a 10 min assay. The purified enzyme was stable over a pH range of 5.4-8.6, and had a 1-h half life at 85°C. Kinetic experiments at 90°C withp-nitrophenyl-α-D-glucoside as substrate gave aKm, andVmaxof 0.072 mM and 400 U/mg. Thus, this report provides an industrial means to produce the recombinant α-glucosidase inE. coli.

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Sequence analysis of mtDNA COI gene and molecular Phylogeny of Parasitic Unionicolid Mites (Acari: Unionicolidae: Unionicola) in China

E3S Web of Conferences ◽

10.1051/e3sconf/202018504024 ◽

2020 ◽

Vol 185 ◽

pp. 04024

Author(s):

Jian Cheng ◽

Xin Huang ◽

Liangliang Huang ◽

Chungen Wen

Keyword(s):

Maximum Likelihood ◽

Sequence Analysis ◽

Nucleotide Sequence ◽

Phylogenetic Trees ◽

Coi Gene ◽

Nucleotide Sequence Analysis ◽

Gene Fragment ◽

Neighbor Joining ◽

Mtdna Coi ◽

The Relationship

A nucleotide sequence analysis of cytochrome oxidase I (COI) gene fragment from parasitic unionicolid mites is performed in this paper. The aligned nucleotide fragment is 664bp (including gaps) in length, including 374 conserved sites, 284 variable sites, 73 conversion sites, 51 transpose sites. The conversion sites are much higher than the transpose sites with a conversion transpose ratio (si/sv) of 1.4. The percentages of A+T and G+C are 64.6% and 35.4% in the nucleotide sequence which indicates a strong AT bias. From the sequence analysis of COI gene, the relationship between Unionicola chelata and Unionicola arcuate are the farthest among all the parasitic unionicolid mites while the relationship between Unionicola ischyropalpus and U.arcuata are the closest. Using U.crassipes as an outgroup, the phylogenetic trees are reconstructed with maximum likelihood(ML) and neighbor-joining(NJ) inferences (PAUP4.0b10 tool), and the results show that U.arcuata is the more evoluted speciesand Unionicola agilex might be the first separated from ancestral species.

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HAPLOTYPE DIVERSITY OF STEINERNEMA FELTIAE (NEMATODA: STEINERNEMATIDAE) IN EURASIA

Redia ◽

10.19263/redia-103.20.21 ◽

2020 ◽

Vol 103 ◽

pp. 133-136

Author(s):

MIRELLA CLAUSI ◽

DIEGO LEONE ◽

SERGEI E. SPIRIDONOV

Keyword(s):

Genetic Variability ◽

Phylogenetic Trees ◽

Entomopathogenic Nematode ◽

Haplotype Diversity ◽

Its Rdna ◽

Steinernema Feltiae ◽

Neighbor Joining ◽

Base Pairs ◽

Rdna Sequences ◽

Basal Position

Phylogenetic analysis of ITS rDNA sequences of the entomopathogenic nematode Steinernema feltiae Filipjev, 1934 (Wouts, Mráček, Gerdin and Bedding, 1982) was used to infer intraspecific genetic variability of this rhabditid nematode. Nucleotide intraspecific differences among S. feltiae isolates reached the level of 19 base pairs per ITS rDNA region, i.e. up to 2.9%. Several weakly or moderately supported intraspecific clades were detected. Sicilian and Swiss isolates of S. feltiae were found clustering together. Swiss strain ‘St. Bernard’ has been isolated on the St. Bernardino mountain pass in Switzerland in 2000. Phylogenetic relationships among S. feltiae isolates were inferred by using three different methods (maximum parsimony, neighbor joining and maximum likelihood). The topologies of the phylogenetic trees were identical and thus only ML tree is presented. ML tree revealed that S. feltiae isolates from Israel and Armenia grouped at the basal position of the tree, while in the spanning network obtained with POPART software, Iranian and Ukrainian isolates were the closest to the outgroup. In all methods of analyses, the European and Siberian strains of S. feltiae occupied terminal positions. Thus, further studies on the intraspecific genetic variability of entomopathogenic nematodes is needed.

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Tetranucleotide usage highlights genomic heterogeneity among mycobacteriophages

F1000Research ◽

10.12688/f1000research.6077.1 ◽

2015 ◽

Vol 4 ◽

pp. 36

Author(s):

Benjamin Siranosian ◽

Sudheesha Perera ◽

Edward Williams ◽

Chen Ye ◽

Christopher de Graffenried ◽

...

Keyword(s):

Sequence Alignment ◽

Phylogenetic Trees ◽

Null Model ◽

Gene Content ◽

Neighbor Joining ◽

Monophyletic Clade ◽

Genome Sequences ◽

Genomic Architecture ◽

A Genome ◽

Computationally Expensive

BackgroundThe genomic sequences of mycobacteriophages, phages infecting mycobacterial hosts, are diverse and mosaic. Mycobacteriophages often share little nucleotide similarity, but most of them have been grouped into lettered clusters and further into subclusters. Traditionally, mycobacteriophage genomes are analyzed based on sequence alignment or knowledge of gene content. However, these approaches are computationally expensive and can be ineffective for significantly diverged sequences. As an alternative to alignment-based genome analysis, we evaluated tetranucleotide usage in mycobacteriophage genomes. These methods make it easier to characterize features of the mycobacteriophage population at many scales.DescriptionWe computed tetranucleotide usage deviation (TUD), the ratio of observed counts of 4-mers in a genome to the expected count under a null model. TUD values are comparable between members of a phage subcluster and distinct between subclusters. With few exceptions, neighbor joining phylogenetic trees and hierarchical clustering dendrograms constructed using TUD values place phages in a monophyletic clade with members of the same subcluster. Regions in a genome with exceptional TUD values can point to interesting features of genomic architecture. Finally, we found that subcluster B3 mycobacteriophages contain significantly overrepresented 4-mers and 6-mers that are atypical of phage genomes.ConclusionsStatistics based on tetranucleotide usage support established clustering of mycobacteriophages and can uncover interesting relationships within and between sequenced phage genomes. These methods are efficient to compute and do not require sequence alignment or knowledge of gene content. The code to download mycobacteriophage genome sequences and reproduce our analysis is freely available athttps://github.com/bsiranosian/tango_final.

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Modulation of Toxin-Antitoxin System Rnl AB Type II in Phage-Resistant Gammaproteobacteria Surviving Photodynamic Treatment

Journal of lasers in medical sciences ◽

10.15171/jlms.2019.03 ◽

2018 ◽

Vol 10 (1) ◽

pp. 21-28

Author(s):

Nava Hosseini ◽

Maryam Pourhajibagher ◽

Nasim Chiniforush ◽

Nazanin Hosseinkhan ◽

Parizad Rezaie ◽

...

Keyword(s):

Phylogenetic Trees ◽

Bacterial Population ◽

Defense Mechanism ◽

Type Ii ◽

Neighbor Joining ◽

Photodynamic Treatment ◽

Diverse Range ◽

T4 Bacteriophage ◽

K 12

Type II toxin-antitoxin (TA) systems are the particular type of TA modules which take part in different kinds of cellular actions, such as biofilm formation, persistence, stress endurance, defense of the bacterial cell against multiple phage attacks, plasmid maintenance, and programmed cell death in favor of bacterial population. Although several bioinformatics and Pet lab studies have already been conducted to understand the functionality of already discovered TA systems, still, more work in this area is required. Rnl AB type II TA module, which is composed of RnlA toxin and RnlB antitoxin, is a newly discovered type II TA module which takes part in the defense mechanism against T4 bacteriophage attack in Escherichia coli K-12 strain MH1 that has not been widely studied in other bacteria. Because of the significant role of class Gammaproteobacteriacea in a diverse range of health problems, we chose here to focus on this class to survey the presence of the Rnl AB TA module. For better categorization and description of the distribution of this module in this class of bacteria, the corresponding phylogenetic trees are illustrated here. Neighbor-joining and the maximum parsimony methods were used in this study to take a look at the distribution of domains present in RnlA and RnlB proteins, among members of Gammaproteobacteria. Also, the possible roles of photodynamic therapy (PDT) in providing a substrate for better phage therapy are herein discussed.

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Tetranucleotide usage highlights genomic heterogeneity among mycobacteriophages

F1000Research ◽

10.12688/f1000research.6077.2 ◽

2015 ◽

Vol 4 ◽

pp. 36 ◽

Cited By ~ 2

Author(s):

Benjamin Siranosian ◽

Sudheesha Perera ◽

Edward Williams ◽

Chen Ye ◽

Christopher de Graffenried ◽

...

Keyword(s):

Sequence Alignment ◽

Phylogenetic Trees ◽

Null Model ◽

Gene Content ◽

Neighbor Joining ◽

Monophyletic Clade ◽

Genome Sequences ◽

Genomic Architecture ◽

A Genome ◽

Computationally Expensive

BackgroundThe genomic sequences of mycobacteriophages, phages infecting mycobacterial hosts, are diverse and mosaic. Mycobacteriophages often share little nucleotide similarity, but most of them have been grouped into lettered clusters and further into subclusters. Traditionally, mycobacteriophage genomes are analyzed based on sequence alignment or knowledge of gene content. However, these approaches are computationally expensive and can be ineffective for significantly diverged sequences. As an alternative to alignment-based genome analysis, we evaluated tetranucleotide usage in mycobacteriophage genomes. These methods make it easier to characterize features of the mycobacteriophage population at many scales.DescriptionWe computed tetranucleotide usage deviation (TUD), the ratio of observed counts of 4-mers in a genome to the expected count under a null model. TUD values are comparable between members of a phage subcluster and distinct between subclusters. With few exceptions, neighbor joining phylogenetic trees and hierarchical clustering dendrograms constructed using TUD values place phages in a monophyletic clade with members of the same subcluster. Regions in a genome with exceptional TUD values can point to interesting features of genomic architecture. Finally, we found that subcluster B3 mycobacteriophages contain significantly overrepresented 4-mers and 6-mers that are atypical of phage genomes.ConclusionsStatistics based on tetranucleotide usage support established clustering of mycobacteriophages and can uncover interesting relationships within and between sequenced phage genomes. These methods are efficient to compute and do not require sequence alignment or knowledge of gene content. The code to download mycobacteriophage genome sequences and reproduce our analysis is freely available athttps://github.com/bsiranosian/tango_final.

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Molecular identification of common hard ticks (Acari: Ixodidae) in Xinjiang, China

Zootaxa ◽

10.11646/zootaxa.4950.1.2 ◽

2021 ◽

Vol 4950 (1) ◽

pp. 46-60

Author(s):

QIGUO WANG ◽

YUJIANG ZHANG ◽

SURONG SUN ◽

TAO LUO ◽

WENTING MOU ◽

...

Keyword(s):

16S Rdna ◽

Phylogenetic Trees ◽

Rhipicephalus Sanguineus ◽

Genetic Distances ◽

Neighbor Joining ◽

Minimum Evolution ◽

Rdna Genes ◽

Hard Ticks ◽

Distance Model ◽

Two Parameter

We provide data on the cytochrome c oxidase subunit I (COI) and 16S rDNA genes for eight species of common hard ticks in Xinjiang: Dermacentor montanus, D. niveus, Haemaphysalis sulcate, Hyalomma asiaticum asiaticum, Hya. detritum, Hya. scupense, Rhipicephalus sanguineus and R. pumilio. Genetic distances, calculated based on the Kimura two-parameter (K2P) distance model, found the same trend of intraspecies level≤interspecies level<intragenus level. Phylogenetic trees, constructed with the neighbor-joining (NJ) and minimum-evolution (ME) methods, demonstrated that each species clustered into separate clades, thus confirming the usefulness of CO1 and 16S rDNA genes for tick species identification. The genera Dermacentor, Haemaphysalis and Rhipicephalus were all recovered in the phylogenetic analysis, as was the subfamily Rhipicephalinae, but a monophyletic Hyalomma was not.

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A phylogenetic approach to the Philippines endemic centipedes of the genus Scolopendra Linnaeus, 1758 (Scolopendromorpha, Scolopendridae), with the description of a new species

Zootaxa ◽

10.11646/zootaxa.4483.3.1 ◽

2018 ◽

Vol 4483 (3) ◽

pp. 401

Author(s):

CARLES DOMÉNECH ◽

VICTOR M. BARBERA ◽

EDUARDO LARRIBA

Keyword(s):

Dna Sequences ◽

Endemic Species ◽

Phylogenetic Trees ◽

Morphological Characters ◽

Genetic Distances ◽

The Philippines ◽

Neighbor Joining ◽

Separate Species ◽

Additional Species ◽

A New Species

The genus Scolopendra Linnaeus, 1758 is represented in the Philippines’ fauna by five species, two of which are endemic. Mitochondrial DNA sequences of gene cytochrome c oxidase subunit I (COI) were obtained from six Scolopendra specimens belonging to two endemic species and a new one, described here as Scolopendra paradoxa Doménech sp. nov. These sequences were analyzed together with another forty-one sequences from GenBank, including additional species of Scolopendra and a few representatives of other Scolopendridae genera. Phylogenetic trees inferred from the COI analysis using maximum likelihood and neighbor joining showed the three Philippines Scolopendra endemic species as a polyphyletic group coherent with their respective morphologies, although the position of S. spinosissima Kraepelin, 1903 varied within the obtained trees. Species delimitation based on standard external morphological characters was also concordant with the observed genetic distances, monophyly and node support, confirming S. subcrustalis Kronmüller, 2009 and S. paradoxa sp. nov. as separate species also at the molecular level, while only the position of S. spinosissima could not be properly established with any of the statistical methods used. In addition, the male genitalia of the three studied species were found to lack gonopods and a penis. Remarks on the ultimate legs prefemoral spinous formula of S. spinosissima plus a key to the species of the genus Scolopendra in the Philippines are provided.

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Origins of an Anasazi Scarlet Macaw Feather Artifact

American Antiquity ◽

10.2307/2694780 ◽

1998 ◽

Vol 63 (1) ◽

pp. 131-142 ◽

Cited By ~ 7

Author(s):

Nancy Borson ◽

Frances Berdan ◽

Edward Stark ◽

Jack States ◽

Peter J. Wettstein

Keyword(s):

Molecular Biology ◽

Ancient Dna ◽

Phylogenetic Trees ◽

American Southwest ◽

The Other ◽

Neighbor Joining ◽

Nucleotide Substitutions ◽

Construction Technique ◽

Scarlet Macaw ◽

Prior Hypothesis

An artifact ascribed to the Anasazi culture (dated here to 920 ± 35 B.P.) is unique in its integrity, construction technique, style, and materials, including multiple yucca ropes with attached adult scarlet macaw feathers joined to a Sciurus aberti (tassel-eared squirrel) pelt and hide straps. We applied methods from anthropology and molecular biology to ascertain the origins of materials and manufacturing technique. The cytochrome b gene from the ancient DNA of the pelt was sequenced in its entirety. This gene was unique as defined by new nucleotide substitutions that distinguished it from the other S. aberti alleles. Phylogenetic trees constructed by both neighbor-joining and maximum parsimony methods are consistent with this unique allele being most closely related to genes from two extant American Southwest S. aberti subspecies and more distantly related to Mexican S. aberti genes. Our observations support the conclusion that the entire artifact was constructed in the American Southwest using native materials, including the squirrel pelt and scarlet macaw feathers. This contradicts a prior hypothesis that the feather rope component was assembled before being traded north from Mexico.

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