Detecting the Signatures of Adaptive Evolution in Protein-Coding Genes

2013 ◽  
Vol 101 (1) ◽  
pp. 19.1.1-19.1.21 ◽  
Author(s):  
Joseph P. Bielawski
Keyword(s):  
Adaptive Evolution ◽  
Protein Coding ◽  
Protein Coding Genes

scholarly journals Comparative analysis of chloroplast genomes for five Dicliptera species (Acanthaceae): molecular structure, phylogenetic relationships, and adaptive evolution

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8450 ◽  
Author(s):  
Sunan Huang ◽  
Xuejun Ge ◽  
Asunción Cano ◽  
Betty Gaby Millán Salazar ◽  
Yunfei Deng
Keyword(s):  
Adaptive Evolution ◽  
Phylogenetic Relationships ◽  
Single Copy ◽  
Rrna Genes ◽  
Trna Genes ◽  
Evolutionary Analysis ◽  
Protein Coding ◽  
Variable Regions ◽  
Protein Coding Genes ◽  
Chloroplast Genomes

The genus Dicliptera (Justicieae, Acanthaceae) consists of approximately 150 species distributed throughout the tropical and subtropical regions of the world. Newly obtained chloroplast genomes (cp genomes) are reported for five species of Dilciptera (D. acuminata, D. peruviana, D. montana, D. ruiziana and D. mucronata) in this study. These cp genomes have circular structures of 150,689–150,811 bp and exhibit quadripartite organizations made up of a large single copy region (LSC, 82,796–82,919 bp), a small single copy region (SSC, 17,084–17,092 bp), and a pair of inverted repeat regions (IRs, 25,401–25,408 bp). Guanine-Cytosine (GC) content makes up 37.9%–38.0% of the total content. The complete cp genomes contain 114 unique genes, including 80 protein-coding genes, 30 transfer RNA (tRNA) genes, and four ribosomal RNA (rRNA) genes. Comparative analyses of nucleotide variability (Pi) reveal the five most variable regions (trnY-GUA-trnE-UUC, trnG-GCC, psbZ-trnG-GCC, petN-psbM, and rps4-trnL-UUA), which may be used as molecular markers in future taxonomic identification and phylogenetic analyses of Dicliptera. A total of 55-58 simple sequence repeats (SSRs) and 229 long repeats were identified in the cp genomes of the five Dicliptera species. Phylogenetic analysis identified a close relationship between D. ruiziana and D. montana, followed by D. acuminata, D. peruviana, and D. mucronata. Evolutionary analysis of orthologous protein-coding genes within the family Acanthaceae revealed only one gene, ycf15, to be under positive selection, which may contribute to future studies of its adaptive evolution. The completed genomes are useful for future research on species identification, phylogenetic relationships, and the adaptive evolution of the Dicliptera species.

scholarly journals A Bayesian Mutation–Selection Framework for Detecting Site-Specific Adaptive Evolution in Protein-Coding Genes

2020 ◽  
Author(s):  
Nicolas Rodrigue ◽  
Thibault Latrille ◽  
Nicolas Lartillot
Keyword(s):  
Adaptive Evolution ◽  
Real Data ◽  
Data Sets ◽  
Protein Coding ◽  
Site Specific ◽  
Protein Coding Genes ◽  
Codon Substitution ◽  
Selection Framework ◽  
Dna Alignment ◽  
The Impact

Abstract In recent years, codon substitution models based on the mutation–selection principle have been extended for the purpose of detecting signatures of adaptive evolution in protein-coding genes. However, the approaches used to date have either focused on detecting global signals of adaptive regimes—across the entire gene—or on contexts where experimentally derived, site-specific amino acid fitness profiles are available. Here, we present a Bayesian site-heterogeneous mutation–selection framework for site-specific detection of adaptive substitution regimes given a protein-coding DNA alignment. We offer implementations, briefly present simulation results, and apply the approach on a few real data sets. Our analyses suggest that the new approach shows greater sensitivity than traditional methods. However, more study is required to assess the impact of potential model violations on the method, and gain a greater empirical sense its behavior on a broader range of real data sets. We propose an outline of such a research program.

scholarly journals Preliminary assessment of adaptive evolution of mitochondrial protein coding genes in darters (Percidae: Etheostomatinae)

F1000Research ◽  
2019 ◽  
Vol 8 ◽  
pp. 464 ◽  
Author(s):  
Leos G. Kral ◽  
Sara Watson
Keyword(s):  
Positive Selection ◽  
Adaptive Evolution ◽  
Gene Evolution ◽  
Mitochondrial Gene ◽  
Mitochondrial Protein ◽  
Preliminary Assessment ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Show Evidence ◽  
Selection Of

Background: Mitochondrial DNA of vertebrates contains genes for 13 proteins involved in oxidative phosphorylation. Some of these genes have been shown to undergo adaptive evolution in a variety of species. This study examines all mitochondrial protein coding genes in 11 darter species to determine if any of these genes show evidence of positive selection. Methods: The mitogenome from four darter was sequenced and annotated. Mitogenome sequences for another seven species were obtained from GenBank. Alignments of each of the protein coding genes were subject to codon-based identification of positive selection by Selecton, MEME and FEL. Results: Evidence of positive selection was obtained for six of the genes by at least one of the methods. CYTB was identified as having evolved under positive selection by all three methods at the same codon location. Conclusions: Given the evidence for positive selection of mitochondrial protein coding genes in darters, a more extensive analysis of mitochondrial gene evolution in all the extant darter species is warranted.

scholarly journals The complete mitochondrial genome of Calyptogena marissinica (Heterodonta: Veneroida: Vesicomyidae): insight into the deep-sea adaptive evolution of vesicomyids

2019 ◽  
Author(s):  
Mei Yang ◽  
Lin Gong ◽  
Jixing Sui ◽  
Xinzheng Li
Keyword(s):  
Energy Metabolism ◽  
Mitochondrial Genome ◽  
Adaptive Evolution ◽  
Deep Sea ◽  
Phylogenetic Analyses ◽  
Gene Arrangement ◽  
Protein Coding ◽  
Mitochondrial Energy Metabolism ◽  
Protein Coding Genes ◽  
Rna Genes

AbstractThe deep sea is one of the most extreme environments on earth, with low oxygen, high hydrostatic pressure and high levels of toxins. Species of the family Vesicomyidae are among the dominant chemosymbiotic bivalves found in this harsh habitat. Mitochondria play a vital role in oxygen usage and energy metabolism; thus, they may be under selection during the adaptive evolution of deep-sea vesicomyids. In this study, the mitochondrial genome (mitogenome) of the vesicomyid bivalve Calyptogena marissinica was sequenced with Illumina sequencing. The mitogenome of C. marissinica is 17,374 bp in length and contains 13 protein-coding genes, 2 ribosomal RNA genes (rrnS and rrnL) and 22 transfer RNA genes. All of these genes are encoded on the heavy strand. Some special elements, such as tandem repeat sequences, “G(A)nT” motifs and AT-rich sequences, were observed in the control region of the C. marissinica mitogenome, which is involved in the regulation of replication and transcription of the mitogenome and may be helpful in adjusting the mitochondrial energy metabolism of organisms to adapt to the deep-sea environment. The gene arrangement of protein-coding genes was identical to that of other sequenced vesicomyids. Phylogenetic analyses clustered C. marissinica with previously reported vesicomyid bivalves with high support values. Positive selection analysis revealed evidence of adaptive change in the mitogenome of Vesicomyidae. Ten potentially important adaptive residues were identified, which were located in cox1, cox3, cob, nad2, nad4 and nad5. Overall, this study sheds light on the mitogenomic adaptation of vesicomyid bivalves that inhabit the deep-sea environment.

scholarly journals Understanding the adaptive evolution of mitochondrial genomes in intertidal chitons

2020 ◽  
Author(s):  
Dipanjana Dhar ◽  
Debayan Dey ◽  
Soumalee Basu ◽  
Helena Fortunato
Keyword(s):  
Adaptive Evolution ◽  
Intertidal Zone ◽  
Molecular Mechanisms ◽  
Proton Translocation ◽  
Protein Structures ◽  
Dynamic Environment ◽  
Extreme Environment ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Genetic Components

AbstractMitochondria are the centre of energy metabolism in eukaryotic cells and its genes are thus key to the evolution of molecular mechanisms that metabolize cellular energy. Intertidal zone is one of the most stressful environments with extreme shifts in temperature, salinity, pH and oxygen concentrations. Marine molluscs, particularly chitons belong to the ecologically dominant organisms in this extreme environment, symbolizing an ideal model to understand mitochondrial stress adaptation. Here, we used concatenated mitochondrial genetic components separately from seven chitons of the intertidal zone to reconstruct phylogenetic relationships among these species. We performed selection analyses considering sites and branches of individual protein-coding genes to identify potentially adaptive residues and localize them in the protein structures of mt subunits. Our results exhibited significant amino acid changes in sites under diversifying selection of all the protein-coding genes, indicative of the adaptive evolution of mitochondrial genome in chitons. Furthermore, we obtained sites in the transmembrane helices lining the proton translocation channel as well as in surrounding loop regions, providing implication towards functional modification of the OXPHOS proteins essential for survival in dynamic environment of the intertidal zone.

scholarly journals Intermolecular interactions drive protein adaptive and co-adaptive evolution at both species and population levels

2021 ◽  
Author(s):  
Junhui Peng ◽  
Li Zhao
Keyword(s):  
Intermolecular Interactions ◽  
Adaptive Evolution ◽  
Large Scale ◽  
Genomic Analysis ◽  
Building Blocks ◽  
Protein Coding ◽  
Functional Annotations ◽  
Protein Coding Genes ◽  
Almost All ◽  
Evolution Of Proteins

AbstractProteins are the building blocks for almost all the functions in cells. Understanding the molecular evolution of proteins and the forces that shape protein evolution is an essential step in understanding the basis of function and evolution. Previous studies have shown that adaptation occurs frequently at the protein surface, such as in genes involved in host-pathogen interactions. However, it remains unclear whether adaptive sites are distributed randomly or at regions that are associated with particular structural or functional characteristics across the genome, since many of the proteins lack structural or functional annotations. Here, we seek to tackle this question by combining large-scale bioinformatic prediction, structural analysis, phylogenetic inference, and population genomic analysis of Drosophila protein-coding genes. By estimating and comparing the rate of adaptive substitutions at protein and residue level, we showed that adaptation is more relevant to function-related rather than structure-related properties. Among the function-related properties, we found that molecular interactions in proteins contribute to adaptive evolution, and putative binding residues exhibit higher rates of adaptation. We observed that physical interactions might play a role in the co-adaptation of fast-adaptive proteins. We found that strongly differentiated amino acids in protein coding genes are mostly adaptive, which may contribute to the long-term adaptive evolution. Our results suggest important roles of intermolecular interactions and co-adaptation in the adaptive evolution of proteins both at the species and population levels.

scholarly journals DGINN, an automated and highly-flexible pipeline for the Detection of Genetic INNovations on protein-coding genes

2020 ◽  
Author(s):  
Lea Picard ◽  
Quentin Ganivet ◽  
Omran Allatif ◽  
Andrea Cimarelli ◽  
Laurent Guéguen ◽  
...  
Keyword(s):  
Adaptive Evolution ◽  
Gene List ◽  
Biological Processes ◽  
Efficient Tool ◽  
Arms Races ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Large Gene ◽  
Large Panel ◽  
Search For Homologues

AbstractAdaptive evolution has shaped major biological processes. Finding the protein-coding genes and the sites that have been subjected to adaptation during evolutionary time is a major endeavor. However, very few methods fully automate the identification of positively selected genes, and widespread sources of genetic innovations as gene duplication and recombination are absent from most pipelines. Here, we developed DGINN, a highly-flexible and public pipeline to Detect Genetic INNovations and adaptive evolution in protein-coding genes. DGINN automates, from a gene’s sequence, all steps of the evolutionary analyses necessary to detect the aforementioned innovations, including the search for homologues in databases, assignation of orthology groups, identification of duplication and recombination events, as well as detection of positive selection using five different methods to increase precision and ranking of genes when a large panel is analyzed. DGINN was validated on nineteen genes with previously-characterized evolutionary histories in primates, including some engaged in host-pathogen arms-races. The results obtained with DGINN confirm and also expand results from the literature, establishing DGINN as an efficient tool to automatically detect genetic innovations and adaptive evolution in diverse datasets, from the user’s gene of interest to a large gene list in any species range.

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