Phylogenetic analysis of perfect repeats in the genomes of unicellular cyanobacteria

We have fulfilled in silico research of number, structure, distribution and location of direct and inverted repeated sequences in eight complete genomes of unicellular cyanobacteria. Analysis of whole genome repeats has shown utility of this approach for purposes of molecular phylogeny and ecological genomics. Comparative analysis of nonrandom repeats patterns has allowed: 1) to confirm the close genetic relationship of two Prochlorococcus marinus strains (MED4 and SS120) that have reduced genomes and inhabit the econiches with different light intensities; 2) to suggest the close phylogenetic relationship of genomes Prochlorococcus marinus MIT9313 and Synechococcus WH8102 that significantly differ by sets of lightharvesting photosystem; 3) to reveal specific differences in genome organization between marine and freshwater cyanobacteria.

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Expanding diversity of Asgard archaea and the elusive ancestry of eukaryotes

10.1101/2020.10.19.343400 ◽

2020 ◽

Author(s):

Yang Liu ◽

Kira S. Makarova ◽

Wen-Cong Huang ◽

Yuri I. Wolf ◽

Anastasia Nikolskaya ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Comparative Analysis ◽

Gene Loss ◽

Protein Domain ◽

Dynamic Evolution ◽

Archaeal Diversity ◽

Metabolic Diversity ◽

Complete Genomes ◽

Conserved Core ◽

Origin Of Eukaryotes

AbstractComparative analysis of 162 (nearly) complete genomes of Asgard archaea, including 75 not reported previously, substantially expands the phylogenetic and metabolic diversity of the Asgard superphylum, with six additional phyla proposed. Phylogenetic analysis does not strongly support origin of eukaryotes from within Asgard, leaning instead towards a three-domain topology, with eukaryotes branching outside archaea. Comprehensive protein domain analysis in the 162 Asgard genomes results in a major expansion of the set of eukaryote signature proteins (ESPs). The Asgard ESPs show variable phyletic distributions and domain architectures, suggestive of dynamic evolution via horizontal gene transfer (HGT), gene loss, gene duplication and domain shuffling. The results appear best compatible with the origin of the conserved core of eukaryote genes from an unknown ancestral lineage deep within or outside the extant archaeal diversity. Such hypothetical ancestors would accumulate components of the mobile archaeal ‘eukaryome’ via extensive HGT, eventually, giving rise to eukaryote-like cells.

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Variant analysis of 1,040 SARS-CoV-2 genomes

PLoS ONE ◽

10.1371/journal.pone.0241535 ◽

2020 ◽

Vol 15 (11) ◽

pp. e0241535 ◽

Cited By ~ 2

Author(s):

Eric C. Rouchka ◽

Julia H. Chariker ◽

Donghoon Chung

Keyword(s):

Comparative Analysis ◽

Viral Genome ◽

Untranslated Region ◽

Rna Virus ◽

Population Analysis ◽

Whole Genome ◽

Coding Sequences ◽

Complete Genomes ◽

Intergenic Regions ◽

Variant Analysis

The severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) viral genome is an RNA virus consisting of approximately 30,000 bases. As part of testing efforts, whole genome sequencing of human isolates has resulted in over 1,600 complete genomes publicly available from GenBank. We have performed a comparative analysis of the sequences, in order to detect common mutations within the population. Analysis of variants occurring within the assembled genomes yields 417 variants occurring in at least 1% of the completed genomes, including 229 within the 5’ untranslated region (UTR), 152 within the 3’UTR, 2 within intergenic regions and 34 within coding sequences.

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A new frog family (Anura: Terrarana) from South America and an expanded direct-developing clade revealed by molecular phylogeny

Zootaxa ◽

10.11646/zootaxa.2211.1.1 ◽

2009 ◽

Vol 2211 (1) ◽

pp. 1-35 ◽

Cited By ~ 62

Author(s):

MATTHEW P. HEINICKE ◽

WILLIAM E. DUELLMAN ◽

LINDA TRUEB ◽

D. BRUCE MEANS ◽

ROSS D. MacCULLOCH ◽

...

Keyword(s):

New Species ◽

Molecular Phylogeny ◽

Mitochondrial Genes ◽

Direct Development ◽

Morphological Evidence ◽

New Family ◽

Close Phylogenetic Relationship ◽

Basal Clade ◽

Relationship Of ◽

A New Species

Three frogs of a new species found in cloud forests on two nearby mountains in Guyana were included in a molecular phylogeny of 17 nuclear and mitochondrial genes (10,739 aligned sites) that revealed that their closest relative is Terrarana (Brachycephalidae, Craugastoridae, Eleutherodactylidae, and Strabomantidae) and their next-closest relative is Hemiphractidae (marsupial frogs). We place these frogs in a new family, genus, and species which is strongly supported as the basal clade within Terrarana: Ceuthomantidae n. fam., Ceuthomantis smaragdinus n. gen, n. sp. Morphological evidence supports the placement of two other species from the Guiana Highlands, Pristimantis aracamuni (BarrioAmorós & Molina) and P. cavernibardus (Myers & Donnelly), in the new family and genus. This close phylogenetic relationship of terraranans and marsupial frogs, nearly all of which have direct development, supports an hypothesis that direct development evolved early in the evolution of this huge clade (~1000 species), for which we propose the unranked taxonomic epithet Orthobatrachia.

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Molecular Phylogeny of Polyporales from Bafut Forest, Cameroon and Their Importance to Rural Communities

Journal of Biology and Life Science ◽

10.5296/jbls.v10i2.14339 ◽

2019 ◽

Vol 10 (2) ◽

pp. 1

Author(s):

Tonjock Rosemary Kinge ◽

Azinue Clementine Lem ◽

Seino Richard Akwanjoh

Keyword(s):

Phylogenetic Analysis ◽

Rural Communities ◽

Molecular Phylogeny ◽

Phylogenetic Relationship ◽

Local Communities ◽

Medicinal Species ◽

Forest Reserves ◽

Phylogenetic Studies ◽

Ctab Method ◽

Relationship Of

The polyporales are a large order of pore fungi within the Basidiomycota (Kingdom Fungi). They are mostly found on decay wood with some edible and medicinal species and others causing diseases of trees. In Cameroon, the knowledge on the phylogeny of polyporales is limited, their historical uses as food, medicine, source of income and the sociological impacts are apparently threatened due to slow ethnomycology research drive. The aim of this study was to identify and determine the phylogenetic relationship of polyporales in the Bafut forest and document its uses to the local communities. DNA was extracted using CTAB method and amplified using primers ITS 1 and ITS4. Their identities were determined in GeneBank using BLAST and a phylogenetic analysis was done using MEGA version 7. For ethnomycological studies, a total of 180 semi structured questionnaires were used to collect information on traditional knowledge in four communities around the Bafut forest. Results from phylogenetic studies showed that, ten species were identified and belonged to seven genera comprising of the Microporus, Hexagonia, Ganoderma, Trametes, Favolus, Steccherinum and Cymatoderma which formed 7 independent monophyletic groups. Ethnomycological findings revealed that, polypores are used as food and medicine within these communities. Microporus xanthopus and Microporus vernicipes were used as food and medicine while all Trametes species were reported to be only medicinal. The Bafut people commonly called mushrooms “Boh” and those that grow on wood “Boh ti”. They usually differentiate the edible and nonedible mushroom using the term “yi kworu” and “yi tekworu”. Thus “Boh yi kworu” and “Boh yi tekworu” respectively. This study represents the first on the identification, phylogeny and uses of polyporales to the communities around the Bafut forest reserves and helps in their conservation.

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Molecular phylogeny and missense mutations of envelope proteins across coronaviruses

10.31219/osf.io/zkmx3 ◽

2020 ◽

Author(s):

Sk Sarif Hassan ◽

Pabitra Pal Choudhury ◽

Bidyut Roy

Keyword(s):

Amino Acids ◽

Phylogenetic Analysis ◽

Amino Acid ◽

Molecular Phylogeny ◽

Envelope Protein ◽

Envelope Proteins ◽

Parental Origin ◽

Missense Mutations ◽

E Proteins ◽

Complete Genomes

Envelope protein is one of the structural viroporins (76–109 amino acids) present in the coronavirus. Sixteen sequentially diﬀerent E proteins were observed from a total of 4917 available complete genomes as on 18th June, 2020 in the NCBI database. The missense mutations over the envelope protein across various coronaviruses of the $\beta$-genus were analyzed to know the immediate parental origin of the envelope protein of SARS-CoV2. The evolutionary origin is also endorsed by the phylogenetic analysis of the envelope proteins comparing sequence homology as well as amino acid conservations.

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Comparative Analysis of Emerging B.1.1.7+E484K SARS-CoV-2 isolates from Pennsylvania

10.1101/2021.04.21.440801 ◽

2021 ◽

Author(s):

Ahmed M. Moustafa ◽

Colleen Bianco ◽

Lidiya Denu ◽

Azad Ahmed ◽

Brandy Neide ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Comparative Analysis ◽

Comparative Genomics ◽

Neutralizing Antibodies ◽

Whole Genome ◽

High Coverage ◽

The Us ◽

The Uk ◽

Induced Immunity

AbstractRapid whole genome sequencing of SARS-CoV-2 has presented the ability to detect new emerging variants of concern in near real time. Here we report the genome of a virus isolated in Pennsylvania in March 2021 that was identified as lineage B.1.1.7 (VOC-202012/01) that also harbors the E484K spike mutation, which has been shown to promote “escape” from neutralizing antibodies in vitro. We compare this sequence to the only 5 other B.1.1.7+E484K genomes from Pennsylvania, all of which were isolated in mid March. Beginning in February 2021, only a small number (n=60) of isolates with this profile have been detected in the US, and only a total of 253 have been reported globally (first in the UK in December 2020). Comparative genomics of all currently available high coverage B.1.1.7+E484K genomes (n=235) available on GISAID suggested the existence of 7 distinct groups or clonal complexes (CC; as defined by GNUVID) bearing the E484K mutation raising the possibility of 7 independent acquisitions of the E484K spike mutation in each background. Phylogenetic analysis suggested the presence of at least 3 distinct clades of B.1.1.7+E484K circulating in the US, with the Pennsylvanian isolates belonging to two distinct clades. Increased genomic surveillance will be crucial for detection of emerging variants of concern that can escape natural and vaccine induced immunity.

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Phylogenetic Relatedness and Genome Structure of Yersinia ruckeri Revealed by Whole Genome Sequencing and a Comparative Analysis

Frontiers in Microbiology ◽

10.3389/fmicb.2021.782415 ◽

2021 ◽

Vol 12 ◽

Author(s):

Mostafa Y. Abdel-Glil ◽

Uwe Fischer ◽

Dieter Steinhagen ◽

Una McCarthy ◽

Heinrich Neubauer ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Comparative Analysis ◽

Genetic Relatedness ◽

Critical Role ◽

Genome Structure ◽

The United States ◽

Genomic Islands ◽

Stable Set ◽

Whole Genome ◽

Yersinia Ruckeri

Yersinia ruckeri is the causative agent of enteric redmouth disease (ERM), a serious infection that affects global aquaculture with high economic impact. The present study used whole genome sequences to perform a comparative analysis on 10 Y. ruckeri strains and to explore their genetic relatedness to other members of the genus. Y. ruckeri, Yersinia entomophaga, and Yersinia nurmii formed a species complex that constitutes the most basal lineage of the genus. The results showed that the taxonomy of Y. ruckeri strains is better defined by using a core genome alignment and phylogenetic analysis. The distribution of accessory genes in all Yersinia species revealed the presence of 303 distinctive genes in Y. ruckeri. Of these, 169 genes were distributed in 17 genomic islands potentially involved in the pathogenesis of ERM via (1) encoding virulence factors such as Afp18, Yrp1, phage proteins and (2) improving the metabolic capabilities by enhancing utilization and metabolism of iron, amino acids (specifically, arginine and histidine), and carbohydrates. The genome of Y. ruckeri is highly conserved regarding gene structure, gene layout and functional categorization of genes. It contains various components of mobile genetic elements but lacks the CRISPR-Cas system and possesses a stable set of virulence genes possibly playing a critical role in pathogenicity. Distinct virulence plasmids were exclusively restricted to a specific clonal group of Y. ruckeri (CG4), possibly indicating a selective advantage. Phylogenetic analysis of Y. ruckeri genomes revealed the co-presence of multiple genetically distant lineages of Y. ruckeri strains circulating in Germany. Our results also suggest a possible dissemination of a specific group of strains in the United States, Peru, Germany, and Denmark. In conclusion, this study provides new insights into the taxonomy and evolution of Y. ruckeri and contributes to a better understanding of the pathogenicity of ERM in aquaculture. The genomic analysis presented here offers a framework for the development of more efficient control strategies for this pathogen.

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Comparative mitogenomes and phylogenetic analysis reveal taxonomic relationship of genera Teredorus and Systolederus (Orthoptera, Tetrigoidea)

Zootaxa ◽

10.11646/zootaxa.5027.1.7 ◽

2021 ◽

Vol 5027 (1) ◽

pp. 127-135

Author(s):

XUEJUAN LI ◽

YUXIN LIU ◽

LILIANG LIN

Keyword(s):

Phylogenetic Analysis ◽

Comparative Analysis ◽

Phylogenetic Relationship ◽

Morphological Characteristics ◽

Mitochondrial Genomes ◽

Taxonomic Relationship ◽

Mitochondrial Sequences ◽

Relationship Of

The genera Teredorus and Systolederus belong to Tetriginae and Metrodorinae respectively. However, species within these two genera have strikingly similar features, made it difficult to identify clearly by morphological characteristics. In this study, we sequenced the mitochondrial genomes (mitogenomes) of two Teredorus species, and compared them with Systolederus mitochondrial sequences. The sequenced mitogenomes of T. hainanensis and T. bashanensis are 14,946 bp and 14,775 bp in size, respectively. The A+T content of mitogenomes is 76.2% (T. hainanensis) and 74.0% (T. bashanensis). Comparative analysis showed that mitochondrial sequences and structure were similar within these two genera. The results of K2P distances and phylogenetic analysis revealed that Systolederus and Teredorus might be likely considered as one genus of Teredorus. It will provide important resources for further understanding of the taxonomy and phylogenetic relationship of Systolederus and Teredorus.

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Full-Genome Sequences and Phylogenetic Analysis of Archived Danish European Bat Lyssavirus 1 (EBLV-1) Emphasize a Higher Genetic Resolution and Spatial Segregation for Sublineage 1a

Viruses ◽

10.3390/v13040634 ◽

2021 ◽

Vol 13 (4) ◽

pp. 634

Author(s):

Sten Calvelage ◽

Conrad M. Freuling ◽

Anthony R. Fooks ◽

Dirk Höper ◽

Denise A. Marston ◽

...

Keyword(s):

Phylogenetic Analysis ◽

High Throughput Sequencing ◽

Phylogenetic Analyses ◽

Spatial Segregation ◽

Full Genome ◽

Genome Sequences ◽

Genetic Characteristics ◽

Close Phylogenetic Relationship ◽

Almost All ◽

Relationship Of

European bat lyssavirus type 1 (EBLV-1) is the causative agent for almost all reported rabies cases found in European bats. In recent years, increasing numbers of available EBLV-1 full genomes and their phylogenetic analyses helped to further elucidate the distribution and genetic characteristics of EBLV-1 and its two subtypes, namely EBLV-1a and EBLV-1b. Nonetheless, the absence of full-genome sequences from regions with known detections of EBLV-1 still limit the understanding of the phylogeographic relations between viruses from different European regions. In this study, a set of 21 archived Danish EBLV-1 samples from the years 1985 to 2009 was processed for the acquisition of full-genome sequences using a high-throughput sequencing approach. Subsequent phylogenetic analysis encompassing all available EBLV-1 full genomes from databases revealed the Danish sequences belong to the EBLV-1a subtype and further highlighted the distinct, close phylogenetic relationship of Danish, Dutch and German isolates in this region. In addition, the formation of five putative groups nearly exclusively formed by Danish isolates and the overall increased resolution of the EBLV-1a branch indicate a higher genetic diversity and spatial segregation for this sublineage than was previously known. These results emphasize the importance of phylogenetic analyses of full-genome sequences of lyssaviruses for genetic geography.

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Phylogenetic Analysis of T-Box Genes Demonstrates the Importance of Amphioxus for Understanding Evolution of the Vertebrate Genome

Genetics ◽

10.1093/genetics/156.3.1249 ◽

2000 ◽

Vol 156 (3) ◽

pp. 1249-1257

Author(s):

Ilya Ruvinsky ◽

Lee M Silver ◽

Jeremy J Gibson-Brown

Keyword(s):

Phylogenetic Analysis ◽

Whole Genome Duplication ◽

Genome Duplication ◽

Gene Families ◽

Vertebrate Evolution ◽

Whole Genome ◽

Vertebrate Genome ◽

T Box ◽

Genetic Complexity ◽

History Of

Abstract The duplication of preexisting genes has played a major role in evolution. To understand the evolution of genetic complexity it is important to reconstruct the phylogenetic history of the genome. A widely held view suggests that the vertebrate genome evolved via two successive rounds of whole-genome duplication. To test this model we have isolated seven new T-box genes from the primitive chordate amphioxus. We find that each amphioxus gene generally corresponds to two or three vertebrate counterparts. A phylogenetic analysis of these genes supports the idea that a single whole-genome duplication took place early in vertebrate evolution, but cannot exclude the possibility that a second duplication later took place. The origin of additional paralogs evident in this and other gene families could be the result of subsequent, smaller-scale chromosomal duplications. Our findings highlight the importance of amphioxus as a key organism for understanding evolution of the vertebrate genome.

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