Codon usage pattern analysis of <i>Gnetum luofuense</i> (Gnetales) based on transcriptome data

Deng, Nan; Liu, Caixia; Song, Qingjun; Yao, Min; Yang, Rui; Ma, Fengfeng; Tian, Yuxin

doi:10.1002/agj2.20383

Agronomy Journal

2020

DOI: 10.1002/agj2.20383

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Codon usage pattern analysis of Gnetum luofuense (Gnetales) based on transcriptome data

Nan Deng¹,

Caixia Liu²,

Qingjun Song³

et al.

Abstract: The Gnetum genus is an important medical, grain, and oil crop with ambiguous phylogenetic placement in seed plants. In the current study, full-length transcripts from G. luofuense L. leaves were utilized for codon usage pattern analysis.For this, a total of 30,666 full-length transcripts were used for analysis after data filtering. The GC content of all transcripts was 44.75%, with GC1 being the highest at 50.98%. Eighteen codons were identified as optimal codons, and 16 codons ending with A/U, indicating a hi… Show more

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Cited by 3 publications

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Agriculture, biology, and environment: Twenty first century challenges and opportunities

et al. 2021

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The 6th International Conference on Agricultural and Biological Sciences (ABS 2020), was planned to be held in the People's Republic of China. Due to the COVID-19 pandemic, ABS 2020, "Agricultural and Biological Sciences: Plant, Soil, Animal, and Environment", was the first online conference in Agricultural and Biological Sciences history. Each paper addressed a slightly different topic and provided identifiable challenges and research key questions in agriculture, agronomy, food production and security, and environmental hazards. The role of Agricultural and Biological Sciences of China is the generation of research knowledge that influence everyday activities. There were 41 manuscripts submitted, of which 25 were accepted for publication. The research domains varied and included the role of specific plant on soil C-cycling, haploid induction, and natural doubling of Zea mays L.; plant species and soil rhizosphere microflora; forest tree biomass succession and dynamics relevant to C-sequestration; making sandy land agriculture friendly; plantation age on C, N, and P stoichiometry; codon uses pattern of Gnetum luofuoense C.Y. Cheng using transcriptome data; suitability of plant landscape unit and natural parks; regeneration protocol of Jatropha curcas L., etc. The purpose of this special section is to generate an improved communication among international scientists that we hope will lead to enhanced food security.

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Agriculture, biology, and environment: Twenty first century challenges and opportunities

et al. 2021

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Codon usage bias and genetic diversity in chloroplast genomes of Elaeagnus species (Myrtiflorae: Elaeagnaceae)

Zhou

Nie

et al. 2023

Physiol Mol Biol Plants

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Comparative Analysis of the Codon Usage Pattern in the Chloroplast Genomes of Gnetales Species

Yang,

Wang,

Gong

et al. 2024

IJMS

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Codon usage bias refers to the preferential use of synonymous codons, a widespread phenomenon found in bacteria, plants, and animals. Codon bias varies among species, families, and groups within kingdoms and between genes within an organism. Codon usage bias (CUB) analysis sheds light on the evolutionary dynamics of various species and optimizes targeted gene expression in heterologous host plants. As a significant order of gymnosperms, species within Gnetales possess extremely high ecological and pharmaceutical values. However, comprehensive analyses of CUB within the chloroplast genomes of Gnetales species remain unexplored. A systematic analysis was conducted to elucidate the codon usage patterns in 13 diverse Gnetales species based on the chloroplast genomes. Our results revealed that chloroplast coding sequences (cp CDSs) in 13 Gnetales species display a marked preference for AT bases and A/T-ending codons. A total of 20 predominantly high-frequency codons and between 2 and 7 optimal codons were identified across these species. The findings from the ENC-plot, PR2-plot, and neutrality analyses suggested that both mutation pressure and natural selection exert influence on the codon bias in these 13 Gnetales species, with natural selection emerging as the predominant influence. Correspondence analysis (COA) demonstrated variation in the codon usage patterns among the Gnetales species and indicated mutation pressure is another factor that could impact CUB. Additionally, our research identified a positive correlation between the measure of idiosyncratic codon usage level of conservatism (MILC) and synonymous codon usage order (SCUO) values, indicative of CUB’s potential influence on gene expression. The comparative analysis concerning codon usage frequencies among the 13 Gnetales species and 4 model organisms revealed that Saccharomyces cerevisiae and Nicotiana tabacum were the optimal exogenous expression hosts. Furthermore, the cluster and phylogenetic analyses illustrated distinct patterns of differentiation, implying that codons, even with weak or neutral preferences, could affect the evolutionary trajectories of these species. Our results reveal the characteristics of codon usage patterns and contribute to an enhanced comprehension of evolutionary mechanisms in Gnetales species.

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Codon usage pattern analysis of Gnetum luofuense (Gnetales) based on transcriptome data

Cited by 3 publications

References 48 publications

Agriculture, biology, and environment: Twenty first century challenges and opportunities

Agriculture, biology, and environment: Twenty first century challenges and opportunities

Codon usage bias and genetic diversity in chloroplast genomes of Elaeagnus species (Myrtiflorae: Elaeagnaceae)

Comparative Analysis of the Codon Usage Pattern in the Chloroplast Genomes of Gnetales Species

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