Summary: Whole genome duplication leads to autopolyploidy and brings about an increase in cell size, concentration of secondary metabolites and enhanced cytosine methylation. The increased cell size offers a positive advantage to polyploids for cell‐surface‐related activities, but there is a differential response to change in body size across species and taxonomic groups. Although polyploidy has been very extensively studied, having genetic, ecological and evolutionary implications, there is no report that underscores the significance of native secondary metabolitesvis‐à‐visbody size with ploidy change. To address this problem we targeted unique diploid–autotetraploid paired sets of eight diverse clones of six species ofCymbopogon– a species complex of aromatic grasses that accumulate qualitatively different monoterpene essential oils (secondary metabolite) in their vegetative biomass. Based on the qualitative composition of essential oils and the plant body size relationship between the diploid versus autotetraploid paired sets, we show that polyploidy brings about enhanced accumulation of secondary metabolites in all cases, but exerts differential effects on body size in various species. It is observed that the accumulation of alcohol‐type metabolites (e.g. geraniol) does not inhibit increase in body size with ploidy change from 2× to 4× (r = 0.854,P < 0.01), but aldehyde‐type metabolites (e.g. citral) appear to drastically impede body development (r = −0.895). Such a differential response may be correlated to the metabolic steps involved in the synthesis of essential oil components. When changed to tetraploidy, the progenitor diploids requiring longer metabolic steps in production of their secondary metabolites are stressed, and those having shorter metabolite routes better utilize their resources for growth and vigour.In situimmunodetection of 5‐methylcytosine sites reveals enhanced DNA methylation in autopolyploids. It is underpinned that the qualitative composition of secondary metabolites found in the vegetative biomass of the progenitor diploid has a decisive bearing on the body size of the derived autotetraploids and brings about an enhancement in genome‐wide cytosine methylation.

Ocimum L. of family Lamiaceae is a well known genus for its ethnobotanical, medicinal and aromatic properties, which are attributed to innumerable phenylpropanoid and terpenoid compounds produced by the plant. To enrich genomic resources for understanding various pathways, de novo transcriptome sequencing of two important species, O. sanctum and O. basilicum, was carried out by Illumina paired-end sequencing. The sequence assembly resulted in 69117 and 130043 transcripts with an average length of 1646 ± 1210.1 bp and 1363 ± 1139.3 bp for O. sanctum and O. basilicum, respectively. Out of the total transcripts, 59648 (86.30%) and 105470 (81.10%) from O. sanctum and O. basilicum, and respectively were annotated by uniprot blastx against Arabidopsis, rice and lamiaceae. KEGG analysis identified 501 and 952 transcripts from O. sanctum and O. basilicum, respectively, related to secondary metabolism with higher percentage of transcripts for biosynthesis of terpenoids in O. sanctum and phenylpropanoids in O. basilicum. Higher digital gene expression in O. basilicum was validated through qPCR and correlated to higher essential oil content and chromosome number (O. sanctum, 2n = 16; and O. basilicum, 2n = 48). Several CYP450 (26) and TF (40) families were identified having probable roles in primary and secondary metabolism. Also SSR and SNP markers were identified in the transcriptomes of both species with many SSRs linked to phenylpropanoid and terpenoid pathway genes. This is the first report of a comparative transcriptome analysis of Ocimum species and can be utilized to characterize genes related to secondary metabolism, their regulation, and breeding special chemotypes with unique essential oil composition in Ocimum.

Habitat divergence plays a driving role in speciation. Severe environmental fluactuations and/or stress may bring about unreduced gamete formation in germline or mitotic errors in somatic tissues, enabling the establishment of new genomic states. However, fixation of any such variation should involve merchanisms that produce reproductively isolated lineages. This could be realized either through polyploidy enabling alteration in genomic constitution involving chromosome duplication and/or numerical/structural chromome alterations or by hybridization/homoploidy. Whereas polyploidy may lead to stable genomic states owing to their tolerance to post-polyploid genetic modification; the interspecies hybridization is often maladaptive but can also promote speciation through generation of homoploid hybrids (i.e. hybridization without polyploidy) enabling reproductive isolation of evolving hybrids. However, homoploidy as a speciation mechanism is considered only as a minor contributor in evolution, but polyploidy, more particularly autopolyploidy stands apart as a major evolutionary force owing to its wide occurrence and short generation time, and shall continue to be as an effective speciation mechanism to sustain habitat disturbance emanating from rigors of climate change.