Abstract
BackgroundChrysanthemum indicum L., an important ancestral species of the flowering plant chrysanthemum, can be used as medicine and for functional food development. Due to the lack of hereditary information for this species and the difficulty of germplasm identification, we herein provide new genetic insight from the perspective of intraspecific transcriptome comparison and present single sequence repeat (SSR) molecular marker recognition technology.ResultsThrough the study of a diploid germplasm (DIWNT) and a tetraploid germplasm (DIWT), the following outcome were obtained. (1) A significant difference in Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations for specific homologous genes was observed using the OrthoMCL method for the identification of homologous gene families between the two cytotypes. Ka/Ks analysis of common, single-copy homologous family members also revealed a greater difference among genes that experienced positive selection than among those experiencing positive selection. (2) Of more practical value, 2575 SSR markers were predicted and partly verified. We used TaxonGap as a visual tool to inspect genotype uniqueness and screen for high-performance molecular loci; we recommend four primers of 65 randomly selected primers with a combined identification success rate of 88.6% as priorities for further development of DNA fingerprinting of C. indicum germplasm.ConclusionsThe SSR technology based on next-generation sequencing was proved to be successful in the identification of C. indicum germplasms. And the information on the intraspecfic genetic divergence generated by transcriptome comparison deepened the understanding of this complex species’ nature.
Highlights
Chrysanthemum indicum L., an important ancestral species of the flowering plant chrysanthemum, can be used as medicine and for functional food development
We used TaxonGap as a visual tool to inspect genotype uniqueness and screen for high-performance molecular loci; we recommend four primers of 65 randomly selected primers with a combined identification success rate of 88.6% as priorities for further development of DNA fingerprinting of C. indicum germplasm
Comparison of specific expressed homologous genes between the two germplasms Among the 18,056 homologous gene families identified by the OrthoMCL method, 17,406 (96.40%) were common to both germplasms, whereas 208 (1.15%) and 442 (2.45%) families were specific to DIWNT and DIWT, respectively
Summary
Chrysanthemum indicum L., an important ancestral species of the flowering plant chrysanthemum, can be used as medicine and for functional food development. Han et al BMC Genomics (2018) 19:291 is still in a “complex” state [1, 3, 4]; it has diverse morphological features without distinct boundaries, and genetic variation exists both within and among populations [1, 5,6,7,8,9], making germplasm identification difficult This obstacle must be overcome to identify wild medicinal herbs and determine the authenticity and purity of cultivated varieties. A previous study reported that based on both low overall genetic variation and high individual phenotypic diversity, C. indicum has experienced rapid adaptive radiation [6] These reports suggest the potential challenge in characterizing the intraspecific genetic divergence of this species. Comparison of the types and intensities of natural selection for common homologous genes shared by different OTUs might lead to a better understanding of the inherited variation from an evolutionary point of view
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