scholarly journals Comparative analysis of codon usage patterns in chloroplast genomes of five Miscanthus species and related species

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12173
Author(s):  
Jiajing Sheng ◽  
Xuan She ◽  
Xiaoyu Liu ◽  
Jia Wang ◽  
Zhongli Hu
Keyword(s):  
Comparative Analysis ◽  
Codon Usage ◽  
Related Species ◽  
Influencing Factor ◽  
Model Organisms ◽  
Evolutionary Analysis ◽  
Optimal Codons ◽  
Chloroplast Genomes ◽  
Representative Species ◽  
Usage Patterns

Miscanthus is not only a perennial fiber biomass crop, but also valuable breeding resource for its low-nutrient requirements, photosynthetic efficiency and strong adaptability to environment. In the present study, the codon usage patterns of five different Miscanthus plants and other two related species were systematically analyzed. The results indicated that the cp genomes of the seven representative species were preference to A/T bases and A/T-ending codons. In addition, 21 common high-frequency codons and 4–11 optimal codons were detected in the seven chloroplast genomes. The results of ENc-plot, PR2-plot and neutrality analysis revealed the codon usage patterns of the seven chloroplast genomes are influenced by multiple factors, in which nature selection is the main influencing factor. Comparative analysis of the codon usage frequencies between the seven representative species and four model organisms suggested that Arabidopsis thaliana, Populus trichocarpa and Saccharomyces cerevisiae could be considered as preferential appropriate exogenous expression receptors. These results might not only provide important reference information for evolutionary analysis, but also shed light on the way to improve the expression efficiency of exogenous gene in transgenic research based on codon optimization.

scholarly journals Comparative analysis of codon usage patterns in chloroplast genomes of six Euphorbiaceae species

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8251 ◽  
Author(s):  
Zhanjun Wang ◽  
Beibei Xu ◽  
Bao Li ◽  
Qingqing Zhou ◽  
Guiyi Wang ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Comparative Analysis ◽  
Codon Usage ◽  
Plant Species ◽  
Populus Trichocarpa ◽  
Model Organisms ◽  
Mutation Pressure ◽  
Chloroplast Genomes ◽  
Usage Patterns ◽  
Exogenous Expression

Euphorbiaceae plants are important as suppliers of biodiesel. In the current study, the codon usage patterns and sources of variance in chloroplast genome sequences of six different Euphorbiaceae plant species have been systematically analyzed. Our results revealed that the chloroplast genomes of six Euphorbiaceae plant species were biased towards A/T bases and A/T-ending codons, followed by detection of 17 identical high-frequency codons including GCT, TGT, GAT, GAA, TTT, GGA, CAT, AAA, TTA, AAT, CCT, CAA, AGA, TCT, ACT, TAT and TAA. It was found that mutation pressure was a minor factor affecting the variation of codon usage, however, natural selection played a significant role. Comparative analysis of codon usage frequencies of six Euphorbiaceae plant species with four model organisms reflected that Arabidopsis thaliana, Populus trichocarpa, and Saccharomyces cerevisiae should be considered as suitable exogenous expression receptor systems for chloroplast genes of six Euphorbiaceae plant species. Furthermore, it is optimal to choose Saccharomyces cerevisiae as the exogenous expression receptor. The outcome of the present study might provide important reference information for further understanding the codon usage patterns of chloroplast genomes in other plant species.

Analysis of codon usage patterns of the chloroplast genomes in the Poaceae family

2012 ◽  
Vol 60 (5) ◽  
pp. 461 ◽  
Author(s):  
Yuerong Zhang ◽  
Xiaojun Nie ◽  
Xiaoou Jia ◽  
Cunzhen Zhao ◽  
Siddanagouda S. Biradar ◽  
...  
Keyword(s):  
Codon Usage ◽  
Synonymous Codon ◽  
Synonymous Codon Usage ◽  
Mutational Bias ◽  
Plot Analysis ◽  
Optimal Codons ◽  
Chloroplast Genomes ◽  
Usage Patterns ◽  
Poaceae Family ◽  
High Representation

Codon usage patterns of 23 Poaceae chloroplast genomes were analysed in this study. Neutrality analysis indicated that the codon usage patterns have significant correlations with GC12 and GC3 and also showed strong bias towards a high representation of NNA and NNT codons. The Nc-plot showed that although a large proportion of points follow the parabolic line of trajectory, several genes with low ENc values lie below the expected curve, suggesting that mutational bias played a major role in the codon biology of the Poaceae chloroplast genome. Parity Rule 2 plot analysis showed that T was used more frequently than A in all the genomes. Correspondence analysis of relative synonymous codon usage indicated that the first axis explained only a partial amount of variation of codon usage. Furthermore, the gene length and expression level were also found to drive codon usage variation. These findings revealed that besides natural selection, other factors might also exert some influences in shaping the codon usage bias in Poaceae chloroplast genomes. The optimal codons of these 23 genomes were also identified in this study.

Comparative analysis of codon usage patterns in chloroplast genomes of the Asteraceae family

2013 ◽  
Vol 32 (4) ◽  
pp. 828-840 ◽  
Author(s):  
Xiaojun Nie ◽  
Pingchuan Deng ◽  
Kewei Feng ◽  
Peixun Liu ◽  
Xianghong Du ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Codon Usage ◽  
Chloroplast Genomes ◽  
Usage Patterns ◽  
Asteraceae Family

scholarly journals Analysis of Codon Usage Patterns in Giardia duodenalis Based on Transcriptome Data from GiardiaDB

Genes ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 1169
Author(s):  
Xin Li ◽  
Xiaocen Wang ◽  
Pengtao Gong ◽  
Nan Zhang ◽  
Xichen Zhang ◽  
...  
Keyword(s):  
Codon Usage ◽  
Genetic Manipulation ◽  
Molecular Genetic ◽  
Gc Content ◽  
Giardia Duodenalis ◽  
Codon Usage Pattern ◽  
Protein Size ◽  
New Genes ◽  
Optimal Codons ◽  
Usage Patterns

Giardia duodenalis, a flagellated parasitic protozoan, the most common cause of parasite-induced diarrheal diseases worldwide. Codon usage bias (CUB) is an important evolutionary character in most species. However, G. duodenalis CUB remains unclear. Thus, this study analyzes codon usage patterns to assess the restriction factors and obtain useful information in shaping G. duodenalis CUB. The neutrality analysis result indicates that G. duodenalis has a wide GC3 distribution, which significantly correlates with GC12. ENC-plot result—suggesting that most genes were close to the expected curve with only a few strayed away points. This indicates that mutational pressure and natural selection played an important role in the development of CUB. The Parity Rule 2 plot (PR2) result demonstrates that the usage of GC and AT was out of proportion. Interestingly, we identified 26 optimal codons in the G. duodenalis genome, ending with G or C. In addition, GC content, gene expression, and protein size also influence G. duodenalis CUB formation. This study systematically analyzes G. duodenalis codon usage pattern and clarifies the mechanisms of G. duodenalis CUB. These results will be very useful to identify new genes, molecular genetic manipulation, and study of G. duodenalis evolution.

scholarly journals Analysis of codon usage patterns of the chloroplast genome in Delphinium grandiflorum L. reveals a preference for AT-ending codons as a result of major selection constraints

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10787
Author(s):  
Huirong Duan ◽  
Qian Zhang ◽  
Chunmei Wang ◽  
Fang Li ◽  
Fuping Tian ◽  
...  
Keyword(s):  
Codon Usage ◽  
Driving Forces ◽  
Gc Content ◽  
Pressure Effects ◽  
Perennial Herb ◽  
Evolutionary Analysis ◽  
Plot Analysis ◽  
Optimal Codons ◽  
Mapping Analysis ◽  
Cp Genome

Background Codon usage bias analysis is a suitable strategy for identifying the principal evolutionary driving forces in different organisms. Delphinium grandiflorum L. is a perennial herb with high economic value and typical biological characteristics. Evolutionary analysis of D. grandiflorum can provide a rich resource of genetic information for developing hybridization resources of the genus Delphinium. Methods Synonymous codon usage (SCU) and related indices of 51 coding sequences from the D. grandiflorum chloroplast (cp) genome were calculated using Codon W, Cups of EMBOSS, SPSS and Microsoft Excel. Multivariate statistical analysis combined by principal component analysis (PCA), correspondence analysis (COA), PR2-plot mapping analysis and ENC plot analysis was then conducted to explore the factors affecting the usage of synonymous codons. Results The SCU bias of D. grandiflorum was weak and codons preferred A/T ending. A SCU imbalance between A/T and G/C at the third base position was revealed by PR2-plot mapping analysis. A total of eight codons were identified as the optimal codons. The PCA and COA results indicated that base composition (GC content, GC3 content) and gene expression were important for SCU bias. A majority of genes were distributed below the expected curve from the ENC plot analysis and up the standard curve by neutrality plot analysis. Our results showed that with the exception of notable mutation pressure effects, the majority of genetic evolution in the D. grandiflorum cp genome might be driven by natural selection. Discussions Our results provide a theoretical foundation for elucidating the genetic architecture and mechanisms of D. grandiflorum, and contribute to enriching D. grandiflorum genetic resources.

A detailed comparative analysis on the overall codon usage patterns in West Nile virus

2013 ◽  
Vol 14 ◽  
pp. 396-400 ◽  
Author(s):  
Gonzalo Moratorio ◽  
Andrés Iriarte ◽  
Pilar Moreno ◽  
Héctor Musto ◽  
Juan Cristina
Keyword(s):  
Comparative Analysis ◽  
West Nile Virus ◽  
Codon Usage ◽  
West Nile ◽  
Usage Patterns

scholarly journals Chloroplast Genome Sequences and Comparative Analyses of Combretaceae Mangroves with Related Species

2020 ◽  
Vol 2020 ◽  
pp. 1-12
Author(s):  
Ying Zhang ◽  
Hai-Li Li ◽  
Jun-Di Zhong ◽  
Yun Wang ◽  
Chang-Chun Yuan
Keyword(s):  
Comparative Analysis ◽  
Chloroplast Genome ◽  
Related Species ◽  
Mangrove Species ◽  
Mangrove Plant ◽  
Significant Information ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Chloroplast Genomes ◽  
Conserved Gene

In the Combretaceae family, only two species of Lumnitzera and one species of Laguncularia belong to mangroves. Among them, Lumnitzera littorea (Jack) Voigt. is an endangered mangrove plant in China for the limited occurrence and seed abortion. In contrast, Lumnitzera racemosa Willd. is known as the most widespread mangrove plant in China. Laguncularia racemosa C. F. Gaertn., an exotic mangrove in China, has the fast growth and high adaptation ability. To better understand the phylogenetic positions of these mangroves in Combretaceae and in Myrtales and to provide information for studies on evolutionary adaptation for intertidal habitat, the complete chloroplast (cp) genomes of Lu. racemosa and La. racemosa were sequenced. Furthermore, we present here the results from the assembly and annotation of the two cp genomes, which were further subjected to the comparative analysis with Lu. littorea cp genomes we published before and other eleven closely related species within Myrtales. The chloroplast genomes of the three Combretaceae mangrove species: Lu. littorea, Lu. racemosa, and La. racemosa are 159,687 bp, 159,473 bp, and 158,311 bp in size. All three cp genomes host 130 genes including 85 protein-coding genes, 37 tRNAs, and 4 rRNAs. A comparative analysis of those three genomes revealed the high similarity of genes in coding-regions and conserved gene order in the IR and LSC/SSC regions. The differences between Lumnitzera and Laguncularia cp genomes are the locations of rps19 and rpl2 genes in the IR/SC boundary regions. Investigating the effects of selection events on shared protein-coding genes showed a relaxed selection had acted on the ycf2, ycf1, and matK genes of Combretaceae mangroves compared to the nonmangrove species Eucalyptus aromaphloia. The phylogenetic analysis based on the whole chloroplast genome sequence with one outgroup species strongly supported three Combretaceae mangroves together with other two Combretaceae species formed a cluster in Combretaceae. This study is the first report on the comparative analysis of three Combretaceae mangrove chloroplast genomes, which will provide the significant information for understanding photosynthesis and evolution in Combretaceae mangrove plants.

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