Genomic and cytogenetic analysis of Calendula officinalis L.: Insights into metabolite pathways and ploidy

• Morphological differences in the NOR regions and chromosome number confirmed the tetraploid karyotype (2n=4x=32) of C. officinalis L. • Out of 47,644 contigs (N50), 5,091 were functional items linked to molecular function. • Sequencing six genes (F3H, CHI, CHS, 4CL, C4H, PAL) provided insights into the molecular processes of rutin synthesis. • C. officinalis L. chloroplast genome spanned 150,465 bp, revealing 21 microsatellites and 132 genes (86 protein-coding, 38 tRNA, 8 rRNA). Calendula officinalis L, containing a variety of secondary metabolites such as flavonoids, polyphenols, and host of other important therapeutic phytoconstituents is a medicinal plant with diverse pharmaceutical applications. Despite such reporting, there are only certain unclear reports on its genetic makeup, mutations, and evolutionary patterns of the chloroplast and the entire genome of this plant. In order to deepen the understanding of production pathways of these metabolites, it is necessary that the genetic and molecular mechanisms are probed with the identification of genes and regulatory elements. It is in this context, this study is designed to explore the significance of the chromosomal complement and ploidy level through cytogenetic analysis. Interestingly it is for the very first time, efforts were taken to study the sequence the chloroplast genome of the C. officinalis , with special reference to (accession TN-82-766), six plastome genes involved in the synthesis of rutin. The results of this study pursued with Illumina Novaseq 6000 platform helped the detection of four chromosomes with NOR (nuclear organization region) sites suggesting that the studied cultivar is tetraploid with a total of 32 chromosomes. With a total of 768,031,486 raw sequencing reads trimmed and assembled using the CLC Genomic Workbench version 20 (CLC Bio, Qiagen), the present investigation showed approximately 47,466 N50 contigs with lengths greater than 6,613 bp. In hiring Smallanthus sonchifolius (ASM2352597v1) genome as a reference, we predicted an engagement of 199 rRNAs, 206 ncRNAs, 4138 tRNAs, 4886 mRNAs, 8061 genes, 2828 exons, and 2084 CDSs. The fully annotated nuclear and chloroplast genome sequences (150465 bp) were submitted to the NCBI database with accession numbers JARQZI000000000 and OQ515449, respectively. It is with great sincerity and humility we trust that results of this study will serve as a foundation for further research on complete genome of C. officinalis.