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Chloroplast genome skimming of a potential agroforestry species Melia dubia. Cav and its comparative phylogenetic analysis with major Meliaceae members

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Abstract

Melia dubia Cav. is a fast-growing plywood species gaining popularity due to high economic returns. This study aimed to assemble and annotate the chloroplast (cp) genome of M. dubia and compare it with previously published cp genomes within the Meliaceae family. The chloroplast genome was constructed by the de novo and reference-based assembly of paired-end reads generated by long-read sequencing of genomic DNA. The cp genome, sized 171,956 bp, comprised a typical angiosperm quadripartite structure. The large single-copy (LSC) region of 76,055 bp and a small single-copy (SSC) region of 18,693 bp cover 55% of the genome. The pair of inverted repeats (IRA and IRB) were 38,604 bp each (covering 45% of the genome). We identified unique genes (112), including protein-coding genes (79), tRNA (29) and 4 rRNA genes. Phylogenetic analysis using complete cp genomes of 11 species from Meliaceae revealed that M. dubia and M. azedarach shared a sister clade. Comparative analysis using cp genome of M. dubia, M. azedarach and Azadirachta indica revealed a high sequence similarity (> 70%). Five intergenic regions were highly conserved among the three cp genomes. The gene trnG-UCC at LSC region was found to be more divergent in M. dubia and M. azedarach, while it shows complete conservation within M. dubia and A. indica. This is the first report of the chloroplast genome in M. dubia. The available levels of taxonomic expertise and clarity in species delineation within the Melia genus are low. The information generated provides scope for identifying new barcodes which increases the discriminatory power of the species within the genus beyond morphological identification.

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Data availability

All data generated or analyzed during this study are included in this published article (and its supplementary information files). The complete Chloroplast genome sequence of Melia dubia was submitted to the third party annotation section of the GenBank databases at the National Centre for Biotechnology Information (NCBI) under the accession number TPA: BK059531.

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Funding

The study was funded by Indian Council of Forestry Research and Education.

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Authors and Affiliations

  1. Division of Plant Biotechnology and Cytogenetics, Institute of Forest Genetics and Tree Breeding, PB No. 1061, Forest Campus, Coimbatore, 641 002, India

    Aghila Samji, Komal Eashwarlal, Senthil Shanmugavel, Santhosh Kumar & Rekha Ravindranath Warrier

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  1. Aghila Samji
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  5. Rekha Ravindranath Warrier
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Contributions

All authors contributed to the study conception and design. AS and KE contributed equally to material preparation, data collection and analysis. SS and KSK provided technical support during the initial phases of analysis. RRW involved in conceptualisation, resources, supervision, funding acquisition, writing original draft and editing. All authors read and approved the final manuscript.

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Correspondence to Rekha Ravindranath Warrier.

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On behalf of all authors, the corresponding author states that there is no conflict of interest.

Additional information

The complete Chloroplast genome sequence of Melia dubia was submitted to the third party annotation section of the GenBank databases at the National Centre for Biotechnology Information (NCBI) under the accession number TPA: BK059531.

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Samji, A., Eashwarlal, K., Shanmugavel, S. et al. Chloroplast genome skimming of a potential agroforestry species Melia dubia. Cav and its comparative phylogenetic analysis with major Meliaceae members. 3 Biotech 13, 30 (2023). https://doi.org/10.1007/s13205-022-03447-1

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