The endemic and precious timber Pterocarpus santalinus L. f. (Red sanders) is a drought hardy tree species for conservation in peninsular India due to its high risk of illegal timber harvest. It is only found in Eastern Ghats of India, and has become threatened owing to overexploitation of its valuable timber. The development of genomic resources, particularly simple sequence repeat (SSR) markers, is essential for strict implementation of in situ conservation measures and application of DNA information based red sanders genetic resource management. However, a lack of genomic data and e cient molecular markers limit the study of its spatial and temporal population genetic structure, identi cation of diversity hotspots and tree improvement. The current study aims at comprehensive molecular characterization of red sanders and the somatic chromosome counts, ow cytometry and EST-SSR analyses. The results revealed that red sanders is diploid with 2n=20 and the 2C genome size was 0.7872 ± 0.0561pg for the rst time in this species. A total of 3128 EST-SSRs were detected based on 25,854 de novo assembled unigenes from transcriptome data and primer sets designed for 1953 SSRs. Fifty-nine EST-SSR markers were evaluated for polymorphism in the natural populations of red sanders and 13 were found to be suitable for genetic analysis. Two major transcription factor families bHLH and ERF, responsible for abiotic stress and secondary metabolite synthesis were analysed which would provide the foundation for further research on production of medicinally important biocompounds.

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 identi ed 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 identi cation. Key MessageThis is the rst report on chloroplast genome sequencing and annotation of Melia dubia. There are many confusions related to the taxonomy of the species, especially with M. azedarach, of the same genus. Phylogenetic analysis and comparative cp genomic analysis reveal species-speci c markers that could be used to delineate the species. Analysis of the whole chloroplast genome also provides opportunities for tree improvement, skimming the genetic variability in the natural populations of this species.

The endemic and precious timber Pterocarpus santalinus L. f. (Red sanders) is a drought hardy tree species for conservation in peninsular India due to its high risk of illegal timber harvest. It is only found in Eastern Ghats of India, and has become threatened owing to overexploitation of its valuable timber. The development of genomic resources, particularly simple sequence repeat (SSR) markers, is essential for strict implementation of in situ conservation measures and application of DNA information based red sanders genetic resource management. However, a lack of genomic data and efficient molecular markers limit the study of its spatial and temporal population genetic structure, identification of diversity hotspots and tree improvement. The current study aims at comprehensive molecular characterization of red sanders and the somatic chromosome counts, flow cytometry and EST-SSR analyses. The results revealed that red sanders is diploid with 2n=20 and the 2C genome size was 0.7872 ± 0.0561pg for the first time in this species. A total of 3128 EST-SSRs were detected based on 25,854 de novo assembled unigenes from transcriptome data and primer sets designed for 1953 SSRs. Fifty-nine EST-SSR markers were evaluated for polymorphism in the natural populations of red sanders and 13 were found to be suitable for genetic analysis. Two major transcription factor families bHLH and ERF, responsible for abiotic stress and secondary metabolite synthesis were analysed which would provide the foundation for further research on production of medicinally important biocompounds.

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.