There is phylogenetic ambiguity in the genus Lithocarpus and subfamily Quercoideae (Family: Fagaceae). Lithocarpus dealbatus, an ecologically important tree, is the dominant species among the Quercoideae in India. Although several studies have been conducted on the species’ regeneration and ecological and economic significance, limited information is available on its phylo-genomics. To resolve the phylogeny in Quercoideae, we sequenced and assembled the 161,476 bp chloroplast genome of L. dealbatus, which has a large single-copy section of 90,732 bp and a small single-copy region of 18,987 bp, separated by a pair of inverted repeat regions of 25,879 bp. The chloroplast genome contained 133 genes, of which 86 were protein-coding genes, 39 were transfer RNAs, and eight were ribosomal RNAs. Analysis of repeat elements and RNA editing sites revealed interspecific similarities within the Lithocarpus genus. DNA diversity analysis identified five highly diverged coding and noncoding hotspot regions in the four genera, which can be used as polymorphic markers for species/taxon delimitation across the four genera of Quercoideae viz., Lithocarpus, Quercus, Castanea, and Castanopsis. The chloroplast-based phylogenetic analysis among the Quercoideae established a monophyletic origin of Lithocarpus, and a closer evolutionary lineage with a few Quercus species. Besides providing insights into the chloroplast genome architecture of L. dealbatus, the study identified five mutational hotspots having high taxon-delimitation potential across four genera of Quercoideae.

Genome sequence and identification of specific genes involved in the targeted secondary metabolite biosynthesis are two essential requirements for the improvement of any medicinal plant. Commiphora wightii (Arnott) Bhandari (family: Burseraceae), a medicinal plant native to Western India, produces a phytosterol guggulsterone, which is useful for treating atherosclerosis, arthritis, high cholesterol, acne, and obesity. For enhanced guggulsterone yield, key genes involved in its biosynthesis pathway need to be predicted, for which the genome sequence of the species is a pre-requisite. Therefore, we assembled the first-ever hybrid draft genome of C. wightii with a genome size of 1.03 Gb and 107,221 contigs using Illumina and PacBio platforms. The N50 and L50 values in this assembled genome were ~74 Kb and 3486 bp, respectively with a guanine–cytosine (GC) content of 35.6% and 98.7%. The Benchmarking Universal Single Copy Ortholog (BUSCO) value indicated good integrity of assembly. Analysis predicted the presence of 31,187 genes and 342.35 Mb repeat elements in the genome. The comparative genome analysis of C. wightii with relevant orthogroups predicted a few key genes associated with phytosterol biosynthesis and secondary metabolism pathways. The assembled draft genome and the predicted genes should help the future variety development program with improved guggulsterone contents in C. wightii.

Genome characterization is an essential aspect for understanding the origin and physiological adaptation of any species. The size of the genome, its constitution, and ploidy level provide the valuable information on the taxonomic relationship, which is further utilized in genetic crop improvement program concentrating on traits of interest. Musa sp., also known as the banana/plantain, is a fruit and vegetable that is grown all over the world. Because of the inter- and intra-specific hybridization with their wild diploids, the majority of banana cultivars are triploid and seedless in nature. Today's banana cultivars have different genome sizes and ploidies as a consequence, which contributes to their unique shape and climate adaptation. However, limited information is available on the genomic resources of wild and cultivated bananas commonly found in the northeastern region of India. In this study, we performed the morphological characterization, genome size estimation, and ploidy analysis of 16 Musa germplasm collected from northeast India. Morphological characterization and flow cytometry-based (FCM) 2C DNA content revealed significant variation in the ploidy level among the collected Musa germplasms. Further, the present result revealed that the morphological scoring based on ploidy and genome composition was not always consistent with the flowcytometry DNA content data. The neighbor-joining (NJ) tree based on morphology scoring of Musa sp. var. fushrey jhapari (NBRI-0020) clustered into the diploid group (Group II), however, it was not a diploid, which confirmed in flow cytometry data-based NJ tree (Group I). It is further revealed that the Musa sp. var. fishery jhapari (NBRI-0020) had a total morphological score of 54, which did not fall under any genome composition category, however, it showed relatively closer to diploid group in the morphology-based NJ Tree. In the contrary, Musa balbisiana var. jungli kol (NBRI-0027) and Musa sp. var. jungli kol (NBRI-0028) were found to be diploid in flow cytometry data, while those on morphology scoring were categorized as triploid, thereby flow cytometric data must be supplemented with morphology-based data for an accurate genome composition categorization. Our findings in this present study provides valuable insight into the composition of wild and cultivated Musa genome. In most of the cases (~ 68.75%; 11 out of 16) of Northeast India Musa genotypes, the morphology scoring-based genome composition did not match with FCM-based genome composition, indicating the morphology-based genome composition of Musa genotypes from North-East India is not straightforward and accurate. This present data on Musa genotypes of Northeast India will supplement the morphological traits-driven breeding program for banana genetic improvement. Furthermore, our findings shed light on the genome evolution of bananas in north-east India which is still remained unexplored because of its complex evolutionary processes.