scholarly journals Complete chloroplast genome of Hordeum brevisubulatum: Genome organization, synonymous codon usage, phylogenetic relationships, and comparative structure analysis

PLoS ONE ◽  
2021 ◽  
Vol 16 (12) ◽  
pp. e0261196
Author(s):  
Guangxin Cui ◽  
Chunmei Wang ◽  
Xiaoxing Wei ◽  
Hongbo Wang ◽  
Xiaoli Wang ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Genome Engineering ◽  
De Novo ◽  
Synonymous Codon ◽  
Northern China ◽  
Synonymous Codon Usage ◽  
The Other ◽  
Coding Regions ◽  
Cp Genome ◽  
Hordeum Brevisubulatum

Background Hordeum brevisubulatum, known as fine perennial forage, is used for soil salinity improvement in northern China. Chloroplast (cp) genome is an ideal model for assessing its genome evolution and the phylogenetic relationships. We de novo sequenced and analyzed the cp genome of H. brevisubulatum, providing a fundamental reference for further studies in genetics and molecular breeding. Results The cp genome of H. brevisubulatum was 137,155 bp in length with a typical quadripartite structure. A total of 130 functional genes were annotated and the gene of accD was lost in the process of evolution. Among all the annotated genes, 16 different genes harbored introns and the genes of ycf3 and rps12 contained two introns. Parity rule 2 (PR2) plot analysis showed that majority of genes had a bias toward T over A in the coding strand in all five Hordeum species, and a slight G over C in the other four Hordeum species except for H. bogdanil. Additionally, 52 dispersed repeat sequences and 182 simple sequence repeats were identified. Moreover, some unique SSRs of each species could be used as molecular markers for further study. Compared to the other four Hordeum species, H. brevisubulatum was most closely related to H. bogdanii and its cp genome was relatively conserved. Moreover, inverted repeat regions (IRa and IRb) were less divergent than other parts and coding regions were relatively conserved compared to non-coding regions. Main divergence was presented at the SSC/IR border. Conclusions This research comprehensively describes the architecture of the H. brevisubulatum cp genome and improves our understanding of its cp biology and genetic diversity, which will facilitate biological discoveries and cp genome engineering.

scholarly journals Complete Chloroplast Genome of Calligonum Mongolicum: Genome Organization, Codon Usage Pattern, Phylogenetic Relationships, Comparative Structure and Adaptive Evolution Analysis

2020 ◽  
Author(s):  
Hui-rong Duan ◽  
Qian Zhang ◽  
Hongshan Yang ◽  
Fuping Tian ◽  
Yu Hu ◽  
...  
Keyword(s):  
Codon Usage ◽  
Adaptive Evolution ◽  
Phylogenetic Relationships ◽  
Genomic Structure ◽  
Native Plant ◽  
Coding Regions ◽  
Evolution Analysis ◽  
Optimal Codons ◽  
Related Plant ◽  
Cp Genome

Abstract BackgroundThe perennial shrub of Calligonum mongolicum is a dominant native plant in all Calligonum species, which has the largest and most widespread geographic distribution in arid deserts of northern China. Understanding the phylogenetic relationship between C. mongolicum and closely related plant species will offer guidance on the classification and identification of inter-species and their varieties. The chloroplast (cp) genome is an optimal model to decipher phylogenetic relationships and genome evolution in related plant families. In the present study, the complete cp genome of C. mongolicum was sequenced, and the characteristics were described, then the genomic structure was compared to other three Polygonaceae species.ResultsThe cp genome of C. mongolicum was 162,124 bp in length with a quadripartite structure. A total of 131 functional genes were annotated, 14 different genes of which harbored introns and exons, 50 long repeat sequences and 244 simple sequences repeats were identified. Synonymous codon usage (SCU) analysis exhibited A/T preference, and 7 codons were identified as the optimal codons. Multivariate statistical analysis of parity rule 2, ENC-plot, and neutrality plot were combined conducted to imply natural selection as the crucial constraint in SCU bias in C. mongolicum cp genome.The phylogenetic tree showed that Rumex acetosa was the most related plant to C. mongolicum. From the comparative analysis of genomic structures, the inverted repeat regions (IRa and IRb) were less divergent than other parts and coding regions was relatively conserved than non-coding regions. Compared to other species in the Polygonaceae, the borders of IRb/SSC and SSC/IRa in C. mongolicum changed greatly. Furthermore, adaptive evolution analysis of 75 orthologous protein-coding genes indicated that only the psbK gene was under positive selection, which might be crucial in the adaptive evolution of C. mongolicum.ConclusionsOur results comprehensively depicts the architecture of C. mongolicum cp genome, and will lay a vigorous foundation for further study on molecular marker selection, phylogenetic analysis, and population researches in Calligonum species.

scholarly journals Reduction of the Rate of Poliovirus Protein Synthesis through Large-Scale Codon Deoptimization Causes Attenuation of Viral Virulence by Lowering Specific Infectivity

2006 ◽  
Vol 80 (19) ◽  
pp. 9687-9696 ◽  
Author(s):  
Steffen Mueller ◽  
Dimitris Papamichail ◽  
J. Robert Coleman ◽  
Steven Skiena ◽  
Eckard Wimmer
Keyword(s):  
Large Scale ◽  
De Novo ◽  
Synonymous Codon ◽  
Direct Analysis ◽  
Synonymous Codon Usage ◽  
Wild Type ◽  
Coding Region ◽  
Virus Particles ◽  
Viral Virulence ◽  
Wide Range

ABSTRACT Exploring the utility of de novo gene synthesis with the aim of designing stably attenuated polioviruses (PV), we followed two strategies to construct PV variants containing synthetic replacements of the capsid coding sequences either by deoptimizing synonymous codon usage (PV-AB) or by maximizing synonymous codon position changes of the existing wild-type (wt) poliovirus codons (PV-SD). Despite 934 nucleotide changes in the capsid coding region, PV-SD RNA produced virus with wild-type characteristics. In contrast, no viable virus was recovered from PV-AB RNA carrying 680 silent mutations, due to a reduction of genome translation and replication below a critical level. After subcloning of smaller portions of the AB capsid coding sequence into the wt background, several viable viruses were obtained with a wide range of phenotypes corresponding to their efficiency of directing genome translation. Surprisingly, when inoculated with equal infectious doses (PFU), even the most replication-deficient viruses appeared to be as pathogenic in PV-sensitive CD155tg (transgenic) mice as the PV(M) wild type. However, infection with equal amounts of virus particles revealed a neuroattenuated phenotype over 100-fold. Direct analysis indicated a striking reduction of the specific infectivity of PV-AB-type virus particles. Due to the distribution effect of many silent mutations over large genome segments, codon-deoptimized viruses should have genetically stable phenotypes, and they may prove suitable as attenuated substrates for the production of poliovirus vaccines.

scholarly journals Complete Chloroplast Genome of Calligonum Mongolicum: Genome Organization, Codon Usage Pattern, Phylogenetic Relationships, Comparative Structure and Adaptive Evolution Analysis

2020 ◽  
Author(s):  
Huirong Duan ◽  
Qian Zhang ◽  
Hongshan Yang ◽  
Fuping Tian ◽  
Yu Hu ◽  
...  
Keyword(s):  
Codon Usage ◽  
Adaptive Evolution ◽  
Phylogenetic Relationships ◽  
Genomic Structure ◽  
Native Plant ◽  
Coding Regions ◽  
Evolution Analysis ◽  
Optimal Codons ◽  
Related Plant ◽  
Cp Genome

Abstract Background The perennial shrub of Calligonum mongolicum is a dominant native plant in all Calligonum species, which has the largest and most widespread geographic distribution in arid deserts of northern China. Understanding the phylogenetic relationship between C. mongolicum and closely related plant species will offer guidance on the classification and identification of inter-species and their varieties. The chloroplast (cp) genome is an optimal model to decipher phylogenetic relationships and genome evolution in related plant families. In the present study, the complete cp genome of C. mongolicum was sequenced, and the characteristics were described, then the genomic structure was compared to other three Polygonaceae species.Results The cp genome of C. mongolicum was 162,124 bp in length with a quadripartite structure. A total of 131 functional genes were annotated, 14 different genes of which harbored introns and exons, 50 long repeat sequences and 244 simple sequences repeats were identified. Synonymous codon usage (SCU) analysis exhibited A/T preference, and 7 codons were identified as the optimal codons. Multivariate statistical analysis of parity rule 2, ENC-plot, and neutrality plot were combined conducted to imply natural selection as the crucial constraint in SCU bias in C. mongolicum cp genome.The phylogenetic tree showed that Rumex acetosa was the most related plant to C. mongolicum. From the comparative analysis of genomic structures, the inverted repeat regions (IRa and IRb) were less divergent than other parts and coding regions was relatively conserved than non-coding regions. Compared to other species in the Polygonaceae, the borders of IRb/SSC and SSC/IRa in C. mongolicum changed greatly. Furthermore, adaptive evolution analysis of 75 orthologous protein-coding genes indicated that only the psbK gene was under positive selection, which might be crucial in the adaptive evolution of C. mongolicum.Conclusions Our results comprehensively depicts the architecture of C. mongolicum cp genome, and will lay a vigorous foundation for further study on molecular marker selection, phylogenetic analysis, and population researches in Calligonum species.

Codon Usage Bias Covaries With Expression Breadth and the Rate of Synonymous Evolution in Humans, but This Is Not Evidence for Selection

Genetics ◽  
2001 ◽  
Vol 159 (3) ◽  
pp. 1191-1199
Author(s):  
Araxi O Urrutia ◽  
Laurence D Hurst
Keyword(s):  
Codon Usage ◽  
Codon Bias ◽  
Synonymous Codon ◽  
Nucleotide Composition ◽  
Synonymous Codon Usage ◽  
Synonymous Substitutions ◽  
Numerous Species ◽  
Nucleotide Content ◽  
Expression Breadth ◽  
Human Genes

Abstract In numerous species, from bacteria to Drosophila, evidence suggests that selection acts even on synonymous codon usage: codon bias is greater in more abundantly expressed genes, the rate of synonymous evolution is lower in genes with greater codon bias, and there is consistency between genes in the same species in which codons are preferred. In contrast, in mammals, while nonequal use of alternative codons is observed, the bias is attributed to the background variance in nucleotide concentrations, reflected in the similar nucleotide composition of flanking noncoding and exonic third sites. However, a systematic examination of the covariants of codon usage controlling for background nucleotide content has yet to be performed. Here we present a new method to measure codon bias that corrects for background nucleotide content and apply this to 2396 human genes. Nearly all (99%) exhibit a higher amount of codon bias than expected by chance. The patterns associated with selectively driven codon bias are weakly recovered: Broadly expressed genes have a higher level of bias than do tissue-specific genes, the bias is higher for genes with lower rates of synonymous substitutions, and certain codons are repeatedly preferred. However, while these patterns are suggestive, the first two patterns appear to be methodological artifacts. The last pattern reflects in part biases in usage of nucleotide pairs. We conclude that we find no evidence for selection on codon usage in humans.

scholarly journals Effect of genome composition and codon bias on infectious bronchitis virus evolution and adaptation to target tissues

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Giovanni Franzo ◽  
Claudia Maria Tucciarone ◽  
Matteo Legnardi ◽  
Mattia Cecchinato
Keyword(s):  
Codon Usage ◽  
Codon Bias ◽  
Synonymous Codon ◽  
Synonymous Codon Usage ◽  
Accessory Proteins ◽  
Effective Number ◽  
Genome Composition ◽  
Infectious Bronchitis ◽  
Selective Forces ◽  
Effective Number Of Codons

Abstract Background Infectious bronchitis virus (IBV) is one of the most relevant viruses affecting the poultry industry, and several studies have investigated the factors involved in its biological cycle and evolution. However, very few of those studies focused on the effect of genome composition and the codon bias of different IBV proteins, despite the remarkable increase in available complete genomes. In the present study, all IBV complete genomes were downloaded (n = 383), and several statistics representative of genome composition and codon bias were calculated for each protein-coding sequence, including but not limited to, the nucleotide odds ratio, relative synonymous codon usage and effective number of codons. Additionally, viral codon usage was compared to host codon usage based on a collection of highly expressed genes in IBV target and nontarget tissues. Results The results obtained demonstrated a significant difference among structural, non-structural and accessory proteins, especially regarding dinucleotide composition, which appears under strong selective forces. In particular, some dinucleotide pairs, such as CpG, a probable target of the host innate immune response, are underrepresented in genes coding for pp1a, pp1ab, S and N. Although genome composition and dinucleotide bias appear to affect codon usage, additional selective forces may act directly on codon bias. Variability in relative synonymous codon usage and effective number of codons was found for different proteins, with structural proteins and polyproteins being more adapted to the codon bias of host target tissues. In contrast, accessory proteins had a more biased codon usage (i.e., lower number of preferred codons), which might contribute to the regulation of their expression level and timing throughout the cell cycle. Conclusions The present study confirms the existence of selective forces acting directly on the genome and not only indirectly through phenotype selection. This evidence might help understanding IBV biology and in developing attenuated strains without affecting the protein phenotype and therefore immunogenicity.

scholarly journals Comparative analysis and phylogenetic investigation of Hong Kong Ilex chloroplast genomes

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Bobby Lim-Ho Kong ◽  
Hyun-Seung Park ◽  
Tai-Wai David Lau ◽  
Zhixiu Lin ◽  
Tae-Jin Yang ◽  
...  
Keyword(s):  
Hong Kong ◽  
Comparative Analysis ◽  
Phylogenetic Relationships ◽  
Species Level ◽  
The Other ◽  
Trna Genes ◽  
Protein Coding ◽  
Chloroplast Genomes ◽  
Plant Group ◽  
Ilex Rotunda

AbstractIlex is a monogeneric plant group (containing approximately 600 species) in the Aquifoliaceae family and one of the most commonly used medicinal herbs. However, its taxonomy and phylogenetic relationships at the species level are debatable. Herein, we obtained the complete chloroplast genomes of all 19 Ilex types that are native to Hong Kong. The genomes are conserved in structure, gene content and arrangement. The chloroplast genomes range in size from 157,119 bp in Ilex graciliflora to 158,020 bp in Ilex kwangtungensis. All these genomes contain 125 genes, of which 88 are protein-coding and 37 are tRNA genes. Four highly varied sequences (rps16-trnQ, rpl32-trnL, ndhD-psaC and ycf1) were found. The number of repeats in the Ilex genomes is mostly conserved, but the number of repeating motifs varies. The phylogenetic relationship among the 19 Ilex genomes, together with eight other available genomes in other studies, was investigated. Most of the species could be correctly assigned to the section or even series level, consistent with previous taxonomy, except Ilex rotunda var. microcarpa, Ilex asprella var. tapuensis and Ilex chapaensis. These species were reclassified; I. rotunda was placed in the section Micrococca, while the other two were grouped with the section Pseudoaquifolium. These studies provide a better understanding of Ilex phylogeny and refine its classification.

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