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Repetitive Sequences, Codon Usage Bias and Phylogenetic Analysis of the Plastome of Miliusa glochidioides

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Abstract

Annonaceae is the largest family in Magnoliales, exhibiting the greatest diversity among and within genera. In this study, we conducted an analysis of repetitive sequences and codon usage bias in the previously acquired plastome of Miliusa glochidioides. Using a concatenated dataset of shared genes, we constructed the phylogenetic relationships among 27 Annonaceae species. The results showed that the size of the plastomes in the Annonaceae ranged from 159 to 202 kb, with the size of the inverted repeat region ranging from 40 to 65 kb. Within the plastome of M. glochidioides, we identified 42 SSRs, 36 tandem repeats, and 9 dispersed repeats. These SSRs consist of three nucleotide types and eight motif types, with a preference for A/T bases, primarily located in the large single-copy regions and intergenic spacers. Tandem and dispersed repeat sequences were predominantly detected in the IR region. Through codon usage bias analysis, we identified 30 high-frequency codons and 11 optimal codons. The plastome of M. glochidioides demonstrated relatively weak codon usage bias, favoring codons with A/T endings, primarily influenced by natural selection. Phylogenetic analysis revealed that all four subfamilies formed monophyletic groups, with Cananga odorata (Ambavioideae) and Anaxagorea javanica (Anaxagoreoideae) successively nested outside Annonoideae + Malmeoideae. These findings improve our understanding of the plastome of M. glochidioides and provide additional insights for studying plastome evolution in Annonaceae.

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Data Availability

The data source is the NCBI database: https://www.ncbi.nlm.nih.gov/nuccore/MN241494,MN241495,KU563738,MT742547,MN241491,MK087989,MT742546,MN241496,MN253545,MN241488,MN241489,MH992130,MN241490,MW136266,MW829282,MZ936420,OK216144,MN253543,MN253544,OL979152,OM047203,OM914484,OM937139,MW018366,MK035708,MN016933,MK087990,NC_037005,NC_030504, (accessed on 1 June 2023). Data is provided within the manuscript or supplementary information files.

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Acknowledgements

The authors thank Dr. **ao Chunfen for her assistance with material collection.

Funding

This work was funded by the National Natural Science Foundation of China (31800184).

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Authors and Affiliations

  1. Key Laboratory of Urban Agriculture in South China, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Economics and Information, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China

    Yangying Gan & **ao**g Liu

  2. College of Life Sciences, Sun Yet-sen University, Guangzhou, 510275, China

    **gyao **

  3. Horticulture Center, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China

    Caixia Peng

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  1. Yangying Gan
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Contributions

Y.G. designed the study and wrote the manuscript. J.P. analyzed the data and revised the manuscript. X.L. and C.P. analyzed some of the data and revised the manuscript. All authors read and contributed to the final version of the manuscript.

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Correspondence to Yangying Gan.

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Gan, Y., **, J., Liu, X. et al. Repetitive Sequences, Codon Usage Bias and Phylogenetic Analysis of the Plastome of Miliusa glochidioides. Biochem Genet (2024). https://doi.org/10.1007/s10528-024-10874-7

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