scholarly journals Evolutionary patterns of nucleotide substitution rates in plastid genomes of Quercus

2021 ◽  
Vol 11 (19) ◽  
pp. 13401-13414
Author(s):  
Xuan Li ◽  
Yongfu Li ◽  
Steven Paul Sylvester ◽  
Mingyue Zang ◽  
Yousry A. El‐Kassaby ◽  
...  
Keyword(s):  
Nucleotide Substitution ◽  
Evolutionary Patterns ◽  
Substitution Rates ◽  
Plastid Genomes ◽  
Nucleotide Substitution Rates

scholarly journals Nucleotide substitution rates of diatom plastid encoded protein genes are correlated with genome architecture

2019 ◽  
Author(s):  
Mengjie Yu ◽  
Tracey A Ruhlman ◽  
Nahid H Hajrah ◽  
Mohammad A Khiyami ◽  
Mumdooh J Sabir ◽  
...  
Keyword(s):  
Nucleotide Substitution ◽  
Terrestrial Ecosystems ◽  
Rate Heterogeneity ◽  
Substitution Rates ◽  
Protein Coding ◽  
Plastid Genomes ◽  
Rate Acceleration ◽  
Functional Classes ◽  
Nucleotide Substitution Rates ◽  
Positive Correlations

Diatoms are the largest group of heterokont algae with more than 100,000 species. They are photosynthetic, unicellular eukaryotes that contribute ~ 45% of global primary production and inhabit marine, aquatic and terrestrial ecosystems. Despite their ubiquity and environmental significance very few diatom plastid genomes (plastomes) have been sequenced and studied. This study explored the pattern of diatom plastid nucleotide substitution rates across the entire suite of plastome protein-coding genes for 40 taxa representing the major clades. Substitution rate acceleration was lineage specific with the highest rates in the araphid 2 taxon Astrosyne radiata and radial 2 taxon Proboscia sp. Rate heterogeneity was also evident in different functional classes of genes. Similar to land plants, proteins genes involved in photosynthetic metabolism have substantially lower rates than those involved in transcription and translation. Significant positive correlations were identified between rates and measures of genomic rearrangement, but not plastome size. This work advances the current understanding of diatom plastomes and provides a foundation for future studies of their evolution.

scholarly journals Nucleotide substitution rates of diatom plastid encoded protein genes are correlated with genome architecture

2019 ◽  
Author(s):  
Mengjie Yu ◽  
Tracey A Ruhlman ◽  
Nahid H Hajrah ◽  
Mohammad A Khiyami ◽  
Mumdooh J Sabir ◽  
...  
Keyword(s):  
Nucleotide Substitution ◽  
Terrestrial Ecosystems ◽  
Rate Heterogeneity ◽  
Substitution Rates ◽  
Protein Coding ◽  
Plastid Genomes ◽  
Rate Acceleration ◽  
Functional Classes ◽  
Nucleotide Substitution Rates ◽  
Positive Correlations

Diatoms are the largest group of heterokont algae with more than 100,000 species. They are photosynthetic, unicellular eukaryotes that contribute ~ 45% of global primary production and inhabit marine, aquatic and terrestrial ecosystems. Despite their ubiquity and environmental significance very few diatom plastid genomes (plastomes) have been sequenced and studied. This study explored the pattern of diatom plastid nucleotide substitution rates across the entire suite of plastome protein-coding genes for 40 taxa representing the major clades. Substitution rate acceleration was lineage specific with the highest rates in the araphid 2 taxon Astrosyne radiata and radial 2 taxon Proboscia sp. Rate heterogeneity was also evident in different functional classes of genes. Similar to land plants, proteins genes involved in photosynthetic metabolism have substantially lower rates than those involved in transcription and translation. Significant positive correlations were identified between rates and measures of genomic rearrangement, but not plastome size. This work advances the current understanding of diatom plastomes and provides a foundation for future studies of their evolution.

scholarly journals Cell Tropism Predicts Long-term Nucleotide Substitution Rates of Mammalian RNA Viruses

2014 ◽  
Vol 10 (1) ◽  
pp. e1003838 ◽  
Author(s):  
Allison L. Hicks ◽  
Siobain Duffy
Keyword(s):  
Nucleotide Substitution ◽  
Rna Viruses ◽  
Cell Tropism ◽  
Substitution Rates ◽  
Nucleotide Substitution Rates

scholarly journals Comparing Patterns of Nucleotide Substitution Rates Among Chloroplast Loci Using the Relative Ratio Test

Genetics ◽  
1997 ◽  
Vol 146 (1) ◽  
pp. 393-399 ◽  
Author(s):  
Spencer V Muse ◽  
Brandon S Gaut
Keyword(s):  
Nucleotide Substitution ◽  
Nonsynonymous Substitution ◽  
Synonymous Substitution ◽  
Joint Analysis ◽  
Ratio Test ◽  
Substitution Rates ◽  
Chloroplast Genomes ◽  
Synonymous Substitution Rates ◽  
Nucleotide Substitution Rates ◽  
Evolutionary Lineages

Even when several genetic loci are used in molecular evolutionary studies, each locus is typically analyzed independently of the others. This type of approach makes it difficult to study mechanisms and processes that affect multiple genes. In this work we develop a statistical approach for the joint analysis of two or more loci. The tests we propose examine whether or not nucleotide substitution rates across evolutionary lineages have the same relative proportions at two loci. Theses procedures are applied to 33 genes from the chloroplast genomes of rice, tobacco, pine, and liverwort. With the exception of five clearly distinct loci, we find that synonymous substitution rates tend to change proportionally across genes. We interpret these results to be consistent with a “lineage effect” acting on the entire chloroplast genome. In contrast, nonsynonymous rates do not change proportionally across genes, suggesting that locus-specific evolutionary effects dominate patterns of nonsynonymous substitution.

Plastome-Wide Nucleotide Substitution Rates Reveal Accelerated Rates in Papilionoideae and Correlations with Genome Features Across Legume Subfamilies

2017 ◽  
Vol 84 (4) ◽  
pp. 187-203 ◽  
Author(s):  
Erika N. Schwarz ◽  
Tracey A. Ruhlman ◽  
Mao-Lun Weng ◽  
Mohammad A. Khiyami ◽  
Jamal S. M. Sabir ◽  
...  
Keyword(s):  
Nucleotide Substitution ◽  
Substitution Rates ◽  
Genome Features ◽  
Nucleotide Substitution Rates

scholarly journals Evolutionary Dynamics and Global Diversity of Influenza A Virus

2015 ◽  
Vol 89 (21) ◽  
pp. 10993-11001 ◽  
Author(s):  
Daniel Rejmanek ◽  
Parviez R. Hosseini ◽  
Jonna A. K. Mazet ◽  
Peter Daszak ◽  
Tracey Goldstein
Keyword(s):  
East Asia ◽  
Influenza A Virus ◽  
Influenza A ◽  
Evolutionary Dynamics ◽  
Nucleotide Substitution ◽  
Health Care Spending ◽  
Asian Countries ◽  
Substitution Rates ◽  
Country Level ◽  
Nucleotide Substitution Rates

ABSTRACTThe increasing number of zoonotic infections caused by influenza A virus (IAV) subtypes of avian origin (e.g., H5N1 and H7N9) in recent years underscores the need to better understand the factors driving IAV evolution and diversity. To evaluate the current feasibility of global analyses to contribute to this aim, we evaluated information in the public domain to explore IAV evolutionary dynamics, including nucleotide substitution rates and selection pressures, using 14 IAV subtypes in 32 different countries over a 12-year period (2000 to 2011). Using geospatial information from 39,785 IAV strains, we examined associations between subtype diversity and socioeconomic, biodiversity, and agricultural indices. Our analyses showed that nucleotide substitution rates for 11 of the 14 evaluated subtypes tended to be higher in Asian countries, particularly in East Asia, than in Canada and the United States. Similarly, at a regional level, subtypes H5N1, H5N2, and H6N2 exhibited significantly higher substitution rates in East Asia than in North America. In contrast, the selection pressures (measured as ratios of nonsynonymous to synonymous evolutionary changes [dN/dSratios]) acting on individual subtypes showed little geographic variation. We found that the strongest predictors for the detected subtype diversity at the country level were reporting effort (i.e., total number of strains reported) and health care spending (an indicator of economic development). Our analyses also identified major global gaps in IAV reporting (including a lack of sequences submitted from large portions of Africa and South America and a lack of geolocation information) and in broad subtype testing which, until addressed, will continue to hinder efforts to track the evolution and diversity of IAV around the world.IMPORTANCEIn recent years, an increasing number of influenza A virus (IAV) subtypes, including H5N1, H7N9, and H10N8, have been detected in humans. High fatality rates have led to an increased urgency to better understand where and how novel pathogenic influenza virus strains emerge. Our findings showed that mutational rates of 11 commonly encountered subtypes were higher in East Asian countries than in North America, suggesting that there may be a greater risk for the emergence of novel pathogenic strains in East Asia. In assessing the potential drivers of IAV subtype diversity, our analyses confirmed that reporting effort and health care spending were the best predictors of the observed subtype diversity at the country level. These findings underscore the need to increase sampling and reporting efforts for all subtypes in many undersampled countries throughout the world.

Nucleotide substitution rates for the full set of mitochondrial protein-coding genes in Coleoptera

2010 ◽  
Vol 56 (2) ◽  
pp. 796-807 ◽  
Author(s):  
Joan Pons ◽  
Ignacio Ribera ◽  
Jaume Bertranpetit ◽  
Michael Balke
Keyword(s):  
Nucleotide Substitution ◽  
Mitochondrial Protein ◽  
Substitution Rates ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Nucleotide Substitution Rates

scholarly journals Reconstruction of the Ancestral Plastid Genome in Geraniaceae Reveals a Correlation between Genome Rearrangements, Repeats, and Nucleotide Substitution Rates

2013 ◽  
Vol 31 (3) ◽  
pp. 645-659 ◽  
Author(s):  
Mao-Lun Weng ◽  
John C. Blazier ◽  
Madhumita Govindu ◽  
Robert K. Jansen
Keyword(s):  
Plastid Genome ◽  
Nucleotide Substitution ◽  
Genome Rearrangements ◽  
Substitution Rates ◽  
Nucleotide Substitution Rates

scholarly journals Effect of the assignment of ancestral CpG state on the estimation of nucleotide substitution rates in mammals

2008 ◽  
Vol 8 (1) ◽  
pp. 265 ◽  
Author(s):  
Daniel J Gaffney ◽  
Peter D Keightley
Keyword(s):  
Nucleotide Substitution ◽  
Substitution Rates ◽  
Nucleotide Substitution Rates

scholarly journals Estimation of AT and GC content distributions of nucleotide substitution rates in bacterial core genomes

2019 ◽  
Vol 4 (1) ◽  
Author(s):  
Jon Bohlin ◽  
Brittany Rose ◽  
John H.-O. Pettersson
Keyword(s):  
Nucleotide Substitution ◽  
Gc Content ◽  
Substitution Rates ◽  
Nucleotide Substitution Rates
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