Codon usage by chloroplast gene is bias in Hemiptelea davidii

Liu, Huabo; Lu, Yizeng; Lan, Baoliang

doi:10.1007/s12041-019-1167-1

Cited by 48 publications

(47 citation statements)

References 27 publications

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“…Chloroplast is a kind of special organelle for photosynthesis in plant cells, which has a complete gene expression system independent of nuclear genome, therefore, chloroplast genome plays an important role in plant phylogeny and taxonomic research. The GC content of the genomes in most species is conserved, and the GC content of the nuclear genome protein-coding genes usually higher than 40%, but the GC content in the chloroplast genome usually less than 40% (Liu et al, 2020). In this study, 53 protein-coding sequences of the chloroplast genomes in Platycarya were studied, and the characteristics of the codon usage of the chloroplast genomes were analyzed.…”

Section: Discussionmentioning

confidence: 99%

Analysis of Codon Usage Bias in the <i>Platycarya</i> Chloroplast Genome

Wang¹,

Wang²,

Li³

et al. 2021

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To detect the codon usage characteristics of chloroplast genomes in Platycarya genus, the CodonW、CUSP and SPSSAU software were employed to analyze the codon usage patterns of the chloroplast genomes protein-coding sequence in Platycarya longipes and Platycarya strobilacea in this research. Results show that the GC content of chloroplast genomes was 37.75% and 37.80%, the average GC content in the 3rd position was 27.16% and 27.25%. the range of effective codon number from 35.19 to 56.98, and there were more than 2/3 genes when ENC value greater than 45, which indicated a weak preference. According to the results of neutrality plot analysis, ENC-plot analysis and PR2-plot analysis, codon bias in most Platycarya chloroplast genes were affected by natural selection, while a few were affected by mutations or other factors. And based on the ENC value, five groups of high-expressed and low-expressed genes were identified, 16 codons were ended with A/U among the 18 optimal codons. The research has implications on codon optimization, enhancing the expression efficiency of exogenous gene and phylogenetic analysis.

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Section: Discussionmentioning

confidence: 99%

Analysis of Codon Usage Bias in the <i>Platycarya</i> Chloroplast Genome

Wang¹,

Wang²,

Li³

et al. 2021

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“…Compared to the mitochondrial genome and nuclear genome, the complete cp genome, which possesses many characteristics, including a small size, simple and highly conserved structure, single parental inheritance, and haploid nature, is widely applied in species identification, phylogenetic analysis, and adaptive evolutionary analysis ( Raubeson et al, 2007 ). Codon usage in many plant species, such as Hemiptelea davidii, Haberlea rhodopensis, Medicago sativa , and so forth, has been investigated extensively based on the cp genome database ( Liu et al, 2020 ; Ivanova et al, 2017 ; Tao et al, 2017 ). The cp genome of D. grandiflorum has been assembled and characterized using Illumina sequencing platform, it was 157,339 bp in length, which contained a pair of inverted repeated regions (52,304 bp), a large single copy region (88,098 bp) and a small single copy region (16,937 bp) ( Duan et al, 2020 ).…”

Section: Introductionmentioning

confidence: 99%

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

Duan

Zhang

Wang

et al. 2021

PeerJ

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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.

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Section: Resultsmentioning

confidence: 99%

“…This value is equal to the ratio of the actual observed value of synonymous codons to the expected value of the average use of synonymous codons. If there is no bias for codon usage, then the RSCU value will be 1; if the codon is used more frequently than other synonymous codons, then its RSCU value will be greater than 1; otherwise, the RSCU value will be less than 1 (Nie et al, 2012;Liu et al, 2020). The results of the RSCU value analysis (Supplementary Table S5) of various amino acids showed that there were 31 codons with RSCU ≥ 1, of which 12 codons, such as UUA, AGA, CAA, and GGA, end in A; 16 codons, such as UCU, GCU, ACU, and UAU, end in U; and the only ones ending with G are UUG, UGG, and AUG.…”

Section: Statistics Of Codon Usage Biasmentioning

confidence: 99%

Complete Chloroplast Genome Sequence of Erigeron breviscapus and Characterization of Chloroplast Regulatory Elements

Ouyang

Guo

et al. 2021

Front. Plant Sci.

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Erigeron breviscapus is a famous medicinal plant. However, the limited chloroplast genome information of E. breviscapus, especially for the chloroplast DNA sequence resources, has hindered the study of E. breviscapus chloroplast genome transformation. Here, the complete chloroplast (cp) genome of E. breviscapus was reported. This genome was 152,164bp in length, included 37.2% GC content and was structurally arranged into two 24,699bp inverted repeats (IRs) and two single-copy areas. The sizes of the large single-copy region and the small single-copy region were 84,657 and 18,109bp, respectively. The E. breviscapus cp genome consisted of 127 coding genes, including 83 protein coding genes, 36 transfer RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes. For those genes, 95 genes were single copy genes and 16 genes were duplicated in two inverted regions with seven tRNAs, four rRNAs, and five protein coding genes. Then, genomic DNA of E. breviscapus was used as a template, and the endogenous 5' and 3' flanking sequences of the trnI gene and trnA gene were selected as homologous recombinant fragments in vector construction and cloned through PCR. The endogenous 5' flanking sequences of the psbA gene and rrn16S gene, the endogenous 3' flanking sequences of the psbA gene, rbcL gene, and rps16 gene and one sequence element from the psbN-psbH chloroplast operon were cloned, and certain chloroplast regulatory elements were identified. Two homologous recombination fragments and all of these elements were constructed into the cloning vector pBluescript SK (+) to yield a series of chloroplast expression vectors, which harbored the reporter gene EGFP and the selectable marker aadA gene. After identification, the chloroplast expression vectors were transformed into Escherichia coli and the function of predicted regulatory elements was confirmed by a spectinomycin resistance test and fluorescence intensity measurement. The results indicated that aadA gene and EGFP gene were efficiently expressed under the regulation of predicted regulatory elements and the chloroplast expression vector had been successfully constructed, thereby providing a solid foundation for establishing subsequent E. breviscapus chloroplast transformation system and genetic improvement of E. breviscapus.

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Codon usage by chloroplast gene is bias in Hemiptelea davidii

Cited by 48 publications

References 27 publications

Analysis of Codon Usage Bias in the <i>Platycarya</i> Chloroplast Genome

Analysis of Codon Usage Bias in the <i>Platycarya</i> Chloroplast Genome

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

Complete Chloroplast Genome Sequence of Erigeron breviscapus and Characterization of Chloroplast Regulatory Elements

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