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

Aghila Samji; Komal Eashwarlal; Senthil Shanmugavel; Santhosh Kumar; Rekha Ravindranath Warrier

doi:10.1007/s13205-022-03447-1

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

3 Biotech. 2023 Jan;13(1):30. doi: 10.1007/s13205-022-03447-1. Epub 2022 Dec 31.

Authors

Aghila Samji¹, Komal Eashwarlal¹, Senthil Shanmugavel¹, Santhosh Kumar¹, Rekha Ravindranath Warrier¹

Affiliation

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

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.

Supplementary information: The online version contains supplementary material available at 10.1007/s13205-022-03447-1.

Keywords: Conservation; Cp genome; Meliaceae; Phylogeny; Species delineation.

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