A report on the chloroplast genome of Melia dubia Cav. (Sapindales: Meliaceae), a potential agroforestry species

Abstract

Background: 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. Methods and Results: 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, covers 55% of the genome. The pair of inverted repeats (IRA and IRB) of 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 hared 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. Conclusions: The available levels of taxonomic expertise and clarity in species delineation within the Melia genus is low. The information generated provides scope for identifying new barcodes which increases the discriminatory power of the species within the genus beyond morphological identification.