scholarly journals A phylogenomic data-driven exploration of viral origins and evolution

2015 ◽  
Vol 1 (8) ◽  
pp. e1500527 ◽  
Author(s):  
Arshan Nasir ◽  
Gustavo Caetano-Anollés
Keyword(s):  
Full Advantage ◽  
Functional Data ◽  
Horizontal Transfer ◽  
Genetic Information ◽  
Viral Evolution ◽  
Data Driven ◽  
Phylogenomic Analysis ◽  
Structural Domains ◽  
Origin And Evolution ◽  
Evolution Of Viruses

The origin of viruses remains mysterious because of their diverse and patchy molecular and functional makeup. Although numerous hypotheses have attempted to explain viral origins, none is backed by substantive data. We take full advantage of the wealth of available protein structural and functional data to explore the evolution of the proteomic makeup of thousands of cells and viruses. Despite the extremely reduced nature of viral proteomes, we established an ancient origin of the “viral supergroup” and the existence of widespread episodes of horizontal transfer of genetic information. Viruses harboring different replicon types and infecting distantly related hosts shared many metabolic and informational protein structural domains of ancient origin that were also widespread in cellular proteomes. Phylogenomic analysis uncovered a universal tree of life and revealed that modern viruses reduced from multiple ancient cells that harbored segmented RNA genomes and coexisted with the ancestors of modern cells. The model for the origin and evolution of viruses and cells is backed by strong genomic and structural evidence and can be reconciled with existing models of viral evolution if one considers viruses to have originated from ancient cells and not from modern counterparts.

Measuring Pharmacogene Variant Function at Scale Using Multiplexed Assays

2021 ◽  
Vol 62 (1) ◽  
Author(s):  
Renee C. Geck ◽  
Gabriel Boyle ◽  
Clara J. Amorosi ◽  
Douglas M. Fowler ◽  
Maitreya J. Dunham
Keyword(s):  
Next Generation Sequencing ◽  
Functional Data ◽  
Genetic Variants ◽  
Genetic Information ◽  
Annual Review ◽  
Publication Date ◽  
Drug Selection ◽  
Functional Consequences ◽  
Pharmacology And Toxicology ◽  
Generation Sequencing

As costs of next-generation sequencing decrease, identification of genetic variants has far outpaced our ability to understand their functional consequences. This lack of understanding is a central challenge to a key promise of pharmacogenomics: using genetic information to guide drug selection and dosing. Recently developed multiplexed assays of variant effect enable experimental measurement of the function of thousands of variants simultaneously. Here, we describe multiplexed assays that have been performed on nearly 25,000 variants in eight key pharmacogenes ( ADRB2, CYP2C9, CYP2C19, NUDT15, SLCO1B1, TMPT, VKORC1, and the LDLR promoter), discuss advances in experimental design, and explore key challenges that must be overcome to maximize the utility of multiplexed functional data. Expected final online publication date for the Annual Review of Pharmacology and Toxicology, Volume 62 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

scholarly journals The origin and evolution of viruses inferred from fold family structure

2020 ◽  
Vol 165 (10) ◽  
pp. 2177-2191 ◽  
Author(s):  
Fizza Mughal ◽  
Arshan Nasir ◽  
Gustavo Caetano-Anollés
Keyword(s):  
Family Structure ◽  
Origin And Evolution ◽  
Fold Family ◽  
Evolution Of Viruses

scholarly journals Expanding magnetic organelle biogenesis in the domain Bacteria

Microbiome ◽  
2020 ◽  
Vol 8 (1) ◽  
Author(s):  
Wei Lin ◽  
Wensi Zhang ◽  
Greig A. Paterson ◽  
Qiyun Zhu ◽  
Xiang Zhao ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Biological Significance ◽  
Gene Clusters ◽  
Magnetic Sensors ◽  
Evolutionary Origin ◽  
Phylogenomic Analysis ◽  
Organelle Biogenesis ◽  
Taxonomic Distribution ◽  
Origin And Evolution ◽  
Bacterial Phyla

Abstract Background The discovery of membrane-enclosed, metabolically functional organelles in Bacteria has transformed our understanding of the subcellular complexity of prokaryotic cells. Biomineralization of magnetic nanoparticles within magnetosomes by magnetotactic bacteria (MTB) is a fascinating example of prokaryotic organelles. Magnetosomes, as nano-sized magnetic sensors in MTB, facilitate cell navigation along the local geomagnetic field, a behaviour referred to as magnetotaxis or microbial magnetoreception. Recent discovery of novel MTB outside the traditionally recognized taxonomic lineages suggests that MTB diversity across the domain Bacteria are considerably underestimated, which limits understanding of the taxonomic distribution and evolutionary origin of magnetosome organelle biogenesis. Results Here, we perform the most comprehensive metagenomic analysis available of MTB communities and reconstruct metagenome-assembled MTB genomes from diverse ecosystems. Discovery of MTB in acidic peatland soils suggests widespread MTB occurrence in waterlogged soils in addition to subaqueous sediments and water bodies. A total of 168 MTB draft genomes have been reconstructed, which represent nearly a 3-fold increase over the number currently available and more than double the known MTB species at the genome level. Phylogenomic analysis reveals that these genomes belong to 13 Bacterial phyla, six of which were previously not known to include MTB. These findings indicate a much wider taxonomic distribution of magnetosome organelle biogenesis across the domain Bacteria than previously thought. Comparative genome analysis reveals a vast diversity of magnetosome gene clusters involved in magnetosomal biogenesis in terms of gene content and synteny residing in distinct taxonomic lineages. Phylogenetic analyses of core magnetosome proteins in this largest available and taxonomically diverse dataset support an unexpectedly early evolutionary origin of magnetosome biomineralization, likely ancestral to the origin of the domain Bacteria. Conclusions These findings expand the taxonomic and phylogenetic diversity of MTB across the domain Bacteria and shed new light on the origin and evolution of microbial magnetoreception. Potential biogenesis of the magnetosome organelle in the close descendants of the last bacterial common ancestor has important implications for our understanding of the evolutionary history of bacterial cellular complexity and emphasizes the biological significance of the magnetosome organelle.

scholarly journals Padlock and Proximity Probes forIn Situand Array-Based Analyses: Tools for the Post-Genomic Era

2003 ◽  
Vol 4 (5) ◽  
pp. 525-530 ◽  
Author(s):  
Ulf Landegren ◽  
Fredrik Dahl ◽  
Mats Nilsson ◽  
Simon Fredriksson ◽  
Johan Banér ◽  
...  
Keyword(s):  
Full Advantage ◽  
High Throughput ◽  
General Problem ◽  
Genetic Information ◽  
Biological Systems ◽  
Biological Information ◽  
Dna Ligation ◽  
Health And Disease ◽  
Macromolecular Composition ◽  
Detection Specificity

Highly specific high-throughput assays will be required to take full advantage of the accumulating information about the macromolecular composition of cells and tissues, in order to characterize biological systems in health and disease. We discuss the general problem of detection specificity and present the approach our group has taken, involving the reformatting of analogue biological information to digital reporter segments of genetic information via a series of DNA ligation assays. The assays enable extensive, coordinated analyses of the numbers and locations of genes, transcripts and protein.

scholarly journals Data-driven kNN estimation in nonparametric functional data analysis

2017 ◽  
Vol 153 ◽  
pp. 176-188 ◽  
Author(s):  
Lydia-Zaitri Kara ◽  
Ali Laksaci ◽  
Mustapha Rachdi ◽  
Philippe Vieu
Keyword(s):  
Data Analysis ◽  
Functional Data Analysis ◽  
Functional Data ◽  
Data Driven

scholarly journals nrDNA-ITS Variation, Structure, and Molecular Phylogeny of Abies beshanzuensis (Pinaceae), a Critically Endangered Species

2018 ◽  
Author(s):  
Zengling Ma ◽  
Yuping Sun ◽  
Deliang Chen ◽  
Changfeng Zhao ◽  
Qimeng Jiang ◽  
...  
Keyword(s):  
Endangered Species ◽  
Molecular Phylogeny ◽  
Genetic Information ◽  
Its Region ◽  
Original Data ◽  
Nrdna Its ◽  
Sequence Structure ◽  
Origin And Evolution ◽  
Critically Endangered Species ◽  
Deep Exploration

Abies beshanzuensis, an extremely endangered species, attracts serious concerns on genetic diversity recovery and population protection. However, little genetic information was known about it till now. In this study, intra-/intergenomic ITS variation, secondary structure, and molecular phylogeny of A.beshanzuensis were determined by nrDNA-ITS marker, and results indicated that, ITS region featured rich polymorphism in ITS1 and highly conservative in 5.8S/ITS2 among intra-/inter-genome, implying rich genetic diversities and the occurrence of non-concerted evolution in ITS region. Predicated 5.8S structure possessed Helices-Loops with 3 motifs (M1/M2/M3) and 5 helices B4-B8, and ITS2 could form conservative Clover-like structure with 5 ribotypes, manifesting genetically structural generalities and individualities. Thirteen ITS pseudogenes were also identified from 76 samples (or clones). Molecular phylogeny revealed that, A.beshanzuensis shared genetically closer relationships with A.fanjingshanensis, A.chensiensis, A.yuanbaoshanensis among genus Abies. The available original data provided rich genetic information on ITS sequence, structure and molecular phylogeny of A.beshanzuensis, which not only updated the databases of ITS sequences as well as secondary structures essential for phylogenetic reference and DNA barcoding analyses, but also contributed to deep exploration of population diversities, origin and evolution as well theoretical direction for population recovery and protection of A.beshanzuensis.

scholarly journals Origin and Evolution Analysis and Genetic Characteristics of Echovirus 9 in China

2021 ◽  
Author(s):  
Fenfen SI ◽  
Tianjiao JI ◽  
Dongyan WANG ◽  
Yong ZHANG ◽  
Shuangli ZHU ◽  
...  
Keyword(s):  
Amino Acid ◽  
Clinical Symptoms ◽  
Viral Evolution ◽  
Amino Acid Identity ◽  
Whole Genome Sequence ◽  
Temperature Sensitive ◽  
Time Resolved ◽  
Genetic Characteristics ◽  
Geographic Population ◽  
Origin And Evolution

Abstract BackgroundEchovirus 9 (E9) is associated with a wide variety of diseases and medical conditions, and the clinical symptoms of sporadic cases caused by E9 often are severe. With a high global prevalence, E9 has caused multiple outbreaks worldwide. However, little is known about the genetic and geographic population dynamics of E9.MethodA total of 131 VP1 gene sequences, including15 generated in this study and 116 obtained from GenBank, were used to coestimate time-resolved phylogenies to infer viral evolution and transmission in worldwide. Overlapping fragments representing whole genomes were amplified by reverse transcription polymerase chain reaction (RT-PCR) using specific primers. Then, we reported the genetic characteristics of fifteen E9 strains in the Chinese Mainland. Similarity plots and bootscanning analysis were used to determine recombination patterns of E9.ResultsThe estimated mean evolutionary rate of global E9 VP1 gene was 4.278 × 10−3 substitutions per site per year (95% confidence interval [CI], 3.822× 10−3/site/year to 4.710× 10−3/site/year), and the common ancestor of E9 likely emerged around 1868 (95% CI, 1840 to 1892). The full-length genomic sequences of the fifteen E9 strains showed 76.9-79.6% nucleotide identity and 95.3–95.9% amino acid identity with E9 Barty strain. 11 of 15 E9 whole genome sequence present four recombination patterns, and E9 recombinants have extensive genetic exchanges in the 2C and P3 regions with other Enterovirus B (EV-B) circulated in China. Four of six E9 strains were temperature sensitive, and two were temperature resistant, and a comparative genomics analysis suggested that 411, 865 and 867 amino acid substitution in the P1 region was related to temperature sensitivity.ConclusionThis study highlights a persistent transmission network of E9 in worldwide, provides valuable information regarding the molecular epidemiology of E9.

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