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Comparative chloroplast genome analysis of six millet species along with related Poaceae family members

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Abstract

Millets considered as storehouse of nutrients, are C4 plants that offer a more reliable yield than other crops in low-rainfall regions. Within the millet species, comparative and reconstructed phylogenetic analysis were performed. We compared the two major millet, four minor millet and one cereal crop chloroplast genomes and obtained a complete map of the variability across the genomes. Despite variations in genome size, SSR, and the SC/IR boundary, we observed the high consistency patterns of codon bias, genome structure, and gene content. For comparison across the genome, a whole genome alignment was performed. The chloroplast genomes locally collinear blocks revealed that their gene organization and order had been well preserved. Based on the examination of the entire chloroplast genomes, phylogenetic relationships for the millet species were discovered with Oryza sativa as an outgroup using Maximum Likelihood analysis. Future breeding programmes for valuable millet and cereal crops in the Poaceae family would benefit greatly from this information.

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Abbreviations

cp:

Chloroplast

LSC:

Large single-copy

SSC:

Small single-copy

SSR:

Simple sequence repeats

IR:

Inverted repeats

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Acknowledgements

The authors would like to acknowledge Department of Plant Molecular Biology and Bioinformatics, Centre for Plant Molecular Biology and Biotechnology, Department of Millets, Tamil Nadu Agricultural University, Coimbatore for providing the necessary facilities to carry out this work.

Funding

This research was carried out in the Bioinformatics Laboratory, Dept. of Plant Molecular Biology and Bioinformatics, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University supported by the Biotechnology Information System (BTIS) program (BT/PR40235/BTIS/137/39/2022) of the Department of Biotechnology (DBT), Government of India, New Delhi.

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Author notes

  1. Dilipraj Sathyamurthy and Jayakanthan Mannu have contributed equally to this work.

Authors and Affiliations

  1. Department of Plant Molecular Biology and Bioinformatics, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, India

    Dilipraj Sathyamurthy, Jayakanthan Mannu, Senthil Natesan, Bharathi Nathan & Saranya Nallusamy

  2. Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, India

    Manikanda Boopathi Narayanan

  3. Department of Millets, Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore, India

    Kavithamani Duraisamy

Authors
  1. Dilipraj Sathyamurthy
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  2. Jayakanthan Mannu
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  3. Senthil Natesan
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  4. Bharathi Nathan
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  5. Saranya Nallusamy
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Contributions

All authors contributed to the study conception and design. Material preparation were performed by JM. Data collection and analysis were performed by DS. All authors read and approved the final manuscript.

Corresponding author

Correspondence to Jayakanthan Mannu.

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Corresponding Editor: Manoj Prasad; Reviewers: Z Suo, J Zhang.

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Sathyamurthy, D., Mannu, J., Natesan, S. et al. Comparative chloroplast genome analysis of six millet species along with related Poaceae family members. Nucleus (2024). https://doi.org/10.1007/s13237-023-00464-0

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