The Impact of Selection at the Amino Acid Level on the Usage of Synonymous Codons

Mitochondrial genomes of vertebrates are generally thought to evolve under strong selection for size reduction and gene order conservation. Therefore, a growing number of mitogenomes with duplicated regions changes our view on the genome evolution. Among Aves, order Psittaciformes (parrots) is especially noteworthy because of its large morphological, ecological, and taxonomical diversity, which offers an opportunity to study genome evolution in various aspects. Former analyses showed that tandem duplications comprising the control region with adjacent genes are restricted to several lineages in which the duplication occurred independently. However, using an appropriate polymerase chain reaction strategy, we demonstrate that early diverged parrot groups contain mitogenomes with the duplicated region. These findings together with mapping duplication data from other mitogenomes onto parrot phylogeny indicate that the duplication was an ancestral state for Psittaciformes. The state was inherited by main parrot groups and was lost several times in some lineages. The duplicated regions were subjected to concerted evolution with a frequency higher than the rate of speciation. The duplicated control regions may provide a selective advantage due to a more efficient initiation of replication or transcription and a larger number of replicating genomes per organelle, which may lead to a more effective energy production by mitochondria. The mitogenomic duplications were associated with phenotypic features and parrots with the duplicated region can live longer, show larger body mass as well as predispositions to a more active flight. The results have wider implications on the presence of duplications and their evolution in mitogenomes of other avian groups.

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“…2009 ; Lin et al. 2012 ; Brule and Grayhack 2017 ) and selection acting at the amino acid level ( Morton 2001 ; Błażej et al. 2017 ).…”

Section: Resultsmentioning

confidence: 99%

New insight into parrots’ mitogenomes indicates that their ancestor contained a duplicated region

Urantówka

Kroczak

Silva³

et al. 2018

Molecular Biology and Evolution

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112

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“…The different frequencies among synonymous codons are called the codon usage bias (CUB). The CUB is widespread in organisms, and the degree of CUB is affected by nucleotide composition [ 9 ], DNA replication [ 10 , 11 ], translation process [ 12 , 13 ], tRNA abundance [ 14 , 15 ], gene function [ 16 ], gene length [ 17 , 18 ], protein structure [ 19 , 20 , 21 ], environmental temperature [ 22 ], selection at the amino acid level [ 23 ], and mutational and selective pressure [ 24 , 25 ]. CUB is also determined by the balance between gene mutation and natural selection [ 26 ].…”

Section: Introductionmentioning

confidence: 99%

Differences in Codon Usage Bias between Photosynthesis-Related Genes and Genetic System-Related Genes of Chloroplast Genomes in Cultivated and Wild Solanum Species

Zhang

Wang

et al. 2018

IJMS

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Solanum is one of the largest genera, including two important crops—potato (Solanum tuberosum) and tomato (Solanum lycopersicum). In this study we compared the chloroplast codon usage bias (CUB) among 12 Solanum species, between photosynthesis-related genes (Photo-genes) and genetic system-related genes (Genet-genes), and between cultivated species and wild relatives. The Photo-genes encode proteins for photosystems, the photosynthetic electron transport chain, and RuBisCO, while the Genet-genes encode proteins for ribosomal subunits, RNA polymerases, and maturases. The following findings about the Solanum chloroplast genome CUB were obtained: (1) the nucleotide composition, gene expression, and selective pressure are identified as the main factors affecting chloroplast CUB; (2) all these 12 chloroplast genomes prefer A/U over G/C and pyrimidines over purines at the third-base of codons; (3) Photo-genes have higher codon adaptation indexes than Genet-genes, indicative of a higher gene expression level and a stronger adaptation of Photo-genes; (4) gene function is the primary factor affecting CUB of Photo-genes but not Genet-genes; (5) Photo-genes prefer pyrimidine over purine, whereas Genet-genes favor purine over pyrimidine, at the third position of codons; (6) Photo-genes are mainly affected by the selective pressure, whereas Genet-genes are under the underlying mutational bias; (7) S. tuberosum is more similar with Solanum commersonii than with Solanum bulbocastanum; (8) S. lycopersicum is greatly different from the analyzed seven wild relatives; (9) the CUB in codons for valine, aspartic acid, and threonine are the same between the two crop species, S. tuberosum and S. lycopersicum. These findings suggest that the chloroplast CUB contributed to the differential requirement of gene expression activity and function between Photo-genes and Genet-genes and to the performance of cultivated potato and tomato.

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“…Moreover, the preference for certain codons may be related to either directional mutation or specific selection [104]. In the case of directional mutation, it is hypothesized that some codons are more prone to mutation, resulting in lower S values [87].…”

Section: Discussionmentioning

confidence: 99%

“…These help M. tuberculosis prevent host-immune system interactions [105]. As for specific selection, it is thought to lead to efficient translation processes and accurate protein synthesis due to the use of more frequent codons by highly expressed genes [104]. This can be a reflection of an organism’s adaptation to an environment, and it is likely that the “Common BE genomes” share “synchronized regulation mechanisms of translational optimization” [106].…”

Section: Discussionmentioning

confidence: 99%

Comparative genomics of Bacteria commonly identified in the built environment

et al. 2019

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BackgroundThe microbial community of the built environment (BE) can impact the lives of people and has been studied for a variety of indoor, outdoor, underground, and extreme locations. Thus far, these microorganisms have mainly been investigated by culture-based methods or amplicon sequencing. However, both methods have limitations, complicating multi-study comparisons and limiting the knowledge gained regarding in-situ microbial lifestyles. A greater understanding of BE microorganisms can be achieved through basic information derived from the complete genome. Here, we investigate the level of diversity and genomic features (genome size, GC content, replication strand skew, and codon usage bias) from complete genomes of bacteria commonly identified in the BE, providing a first step towards understanding these bacterial lifestyles.ResultsHere, we selected bacterial genera commonly identified in the BE (or “Common BE genomes”) and compared them against other prokaryotic genera (“Other genomes”). The “Common BE genomes” were identified in various climates and in indoor, outdoor, underground, or extreme built environments. The diversity level of the 16S rRNA varied greatly between genera. The genome size, GC content and GC skew strength of the “Common BE genomes” were statistically larger than those of the “Other genomes” but were not practically significant. In contrast, the strength of selected codon usage bias (S value) was statistically higher with a large effect size in the “Common BE genomes” compared to the “Other genomes.”ConclusionOf the four genomic features tested, the S value could play a more important role in understanding the lifestyles of bacteria living in the BE. This parameter could be indicative of bacterial growth rates, gene expression, and other factors, potentially affected by BE growth conditions (e.g., temperature, humidity, and nutrients). However, further experimental evidence, species-level BE studies, and classification by BE location is needed to define the relationship between genomic features and the lifestyles of BE bacteria more robustly.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-5389-z) contains supplementary material, which is available to authorized users.

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The Impact of Selection at the Amino Acid Level on the Usage of Synonymous Codons

Cited by 21 publications

References 97 publications

New insight into parrots’ mitogenomes indicates that their ancestor contained a duplicated region

New insight into parrots’ mitogenomes indicates that their ancestor contained a duplicated region

Differences in Codon Usage Bias between Photosynthesis-Related Genes and Genetic System-Related Genes of Chloroplast Genomes in Cultivated and Wild Solanum Species

Comparative genomics of Bacteria commonly identified in the built environment

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