scholarly journals Evolutionary dynamics of the plastid inverted repeat: the effects of expansion, contraction, and loss on substitution rates

2015 ◽  
Vol 209 (4) ◽  
pp. 1747-1756 ◽  
Author(s):  
Andan Zhu ◽  
Wenhu Guo ◽  
Sakshi Gupta ◽  
Weishu Fan ◽  
Jeffrey P. Mower
Keyword(s):  
Inverted Repeat ◽  
Evolutionary Dynamics ◽  
Substitution Rates

scholarly journals The chloroplast genome evolution of Venus slipper (Paphiopedilum): IR expansion, SSC contraction, and highly rearranged SSC regions

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Yan-Yan Guo ◽  
Jia-Xing Yang ◽  
Ming-Zhu Bai ◽  
Guo-Qiang Zhang ◽  
Zhong-Jian Liu
Keyword(s):  
Gene Order ◽  
Inverted Repeat ◽  
Single Copy ◽  
Gene Content ◽  
Comparative Genomic ◽  
Substitution Rates ◽  
Plastome Evolution ◽  
Chloroplast Genomes ◽  
Ideal System ◽  
Small Single Copy

Abstract Background Paphiopedilum is the largest genus of slipper orchids. Previous studies showed that the phylogenetic relationships of this genus are not well resolved, and sparse taxon sampling documented inverted repeat (IR) expansion and small single copy (SSC) contraction of the chloroplast genomes of Paphiopedilum. Results Here, we sequenced, assembled, and annotated 77 plastomes of Paphiopedilum species (size range of 152,130 – 164,092 bp). The phylogeny based on the plastome resolved the relationships of the genus except for the phylogenetic position of two unstable species. We used phylogenetic and comparative genomic approaches to elucidate the plastome evolution of Paphiopedilum. The plastomes of Paphiopedilum have a conserved genome structure and gene content except in the SSC region. The large single copy/inverted repeat (LSC/IR) boundaries are relatively stable, while the boundaries of the inverted repeat and small single copy region (IR/SSC) varied among species. Corresponding to the IR/SSC boundary shifts, the chloroplast genomes of the genus experienced IR expansion and SSC contraction. The IR region incorporated one to six genes of the SSC region. Unexpectedly, great variation in the size, gene order, and gene content of the SSC regions was found, especially in the subg. Parvisepalum. Furthermore, Paphiopedilum provides evidence for the ongoing degradation of the ndh genes in the photoautotrophic plants. The estimated substitution rates of the protein coding genes show accelerated rates of evolution in clpP, psbH, and psbZ. Genes transferred to the IR region due to the boundary shift also have higher substitution rates. Conclusions We found IR expansion and SSC contraction in the chloroplast genomes of Paphiopedilum with dense sampling, and the genus shows variation in the size, gene order, and gene content of the SSC region. This genus provides an ideal system to investigate the dynamics of plastome evolution.

scholarly journals Consequences of Stability-Induced Epistasis for Substitution Rates

2020 ◽  
Vol 37 (11) ◽  
pp. 3131-3148 ◽  
Author(s):  
Noor Youssef ◽  
Edward Susko ◽  
Joseph P Bielawski
Keyword(s):  
Evolutionary Dynamics ◽  
Direct Method ◽  
Average Effect ◽  
Substitution Rates ◽  
Codon Substitution ◽  
Individual Site ◽  
Si Model ◽  
Selection Intensities ◽  
The Stability ◽  
Reasonable Inference

Abstract Do interactions between residues in a protein (i.e., epistasis) significantly alter evolutionary dynamics? If so, what consequences might they have on inference from traditional codon substitution models which assume site-independence for the sake of computational tractability? To investigate the effects of epistasis on substitution rates, we employed a mechanistic mutation-selection model in conjunction with a fitness framework derived from protein stability. We refer to this as the stability-informed site-dependent (S-SD) model and developed a new stability-informed site-independent (S-SI) model that captures the average effect of stability constraints on individual sites of a protein. Comparison of S-SI and S-SD offers a novel and direct method for investigating the consequences of stability-induced epistasis on protein evolution. We developed S-SI and S-SD models for three natural proteins and showed that they generate sequences consistent with real alignments. Our analyses revealed that epistasis tends to increase substitution rates compared with the rates under site-independent evolution. We then assessed the epistatic sensitivity of individual site and discovered a counterintuitive effect: Highly connected sites were less influenced by epistasis relative to exposed sites. Lastly, we show that, despite the unrealistic assumptions, traditional models perform comparably well in the presence and absence of epistasis and provide reasonable summaries of average selection intensities. We conclude that epistatic models are critical to understanding protein evolutionary dynamics, but epistasis might not be required for reasonable inference of selection pressure when averaging over time and sites.

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.

Distribution and evolutionary dynamics of Stowaway Miniature Inverted repeat Transposable Elements (MITEs) in grasses

2013 ◽  
Vol 68 (1) ◽  
pp. 106-118 ◽  
Author(s):  
Miguel Minaya ◽  
Manuel Pimentel ◽  
Roberta Mason-Gamer ◽  
Pilar Catalan
Keyword(s):  
Transposable Elements ◽  
Inverted Repeat ◽  
Evolutionary Dynamics

scholarly journals Two Korean Endemic Clematis Chloroplast Genomes: Inversion, Reposition, Expansion of the Inverted Repeat Region, Phylogenetic Analysis, and Nucleotide Substitution Rates

Plants ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 397
Author(s):  
Kyoung Su Choi ◽  
Young-Ho Ha ◽  
Hee-Young Gil ◽  
Kyung Choi ◽  
Dong-Kap Kim ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Inverted Repeat ◽  
Nonsynonymous Substitution ◽  
Single Copy ◽  
Inverted Repeat Region ◽  
Substitution Rates ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Chloroplast Genomes ◽  
Fundamental Information

Previous studies on the chloroplast genome in Clematis focused on the chloroplast structure within Anemoneae. The chloroplast genomes of Cleamtis were sequenced to provide information for studies on phylogeny and evolution. Two Korean endemic Clematis chloroplast genomes (Clematis brachyura and C. trichotoma) range from 159,170 to 159,532 bp, containing 134 identical genes. Comparing the coding and non-coding regions among 12 Clematis species revealed divergent sites, with carination occurring in the petD-rpoA region. Comparing other Clematis chloroplast genomes suggested that Clematis has two inversions (trnH-rps16 and rps4), reposition (trnL-ndhC), and inverted repeat (IR) region expansion. For phylogenetic analysis, 71 protein-coding genes were aligned from 36 Ranunculaceae chloroplast genomes. Anemoneae (Anemoclema, Pulsatilla, Anemone, and Clematis) clades were monophyletic and well-supported by the bootstrap value (100%). Based on 70 chloroplast protein-coding genes, we compared nonsynonymous (dN) and synonymous (dS) substitution rates among Clematis, Anemoneae (excluding Clematis), and other Ranunculaceae species. The average synonymoussubstitution rates (dS)of large single copy (LSC), small single copy (SSC), and IR genes in Anemoneae and Clematis were significantly higher than those of other Ranunculaceae species, but not the nonsynonymous substitution rates (dN). This study provides fundamental information on plastid genome evolution in the Ranunculaceae.

scholarly journals Genes Translocated into the Plastid Inverted Repeat Show Decelerated Substitution Rates and Elevated GC Content

2016 ◽  
Vol 8 (8) ◽  
pp. 2452-2458 ◽  
Author(s):  
Fay-Wei Li ◽  
Li-Yaung Kuo ◽  
Kathleen M. Pryer ◽  
Carl J. Rothfels
Keyword(s):  
Inverted Repeat ◽  
Gc Content ◽  
Substitution Rates

scholarly journals Expansion of inverted repeat does not decrease substitution rates inPelargoniumplastid genomes

2016 ◽  
Vol 214 (2) ◽  
pp. 842-851 ◽  
Author(s):  
Mao-Lun Weng ◽  
Tracey A. Ruhlman ◽  
Robert K. Jansen
Keyword(s):  
Inverted Repeat ◽  
Substitution Rates
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