Comparative analysis of organellar genomes between diploid and tetraploid Chrysanthemum indicum with its relatives

Huihui Liu; Zhuangwei Hou; Lei Xu; Qing Ma; Min Wei; Luke R Tembrock; Shuo Zhang; Zhiqiang Wu

doi:10.3389/fpls.2023.1228551

Comparative analysis of organellar genomes between diploid and tetraploid Chrysanthemum indicum with its relatives

Front Plant Sci. 2023 Aug 18:14:1228551. doi: 10.3389/fpls.2023.1228551. eCollection 2023.

Authors

Huihui Liu¹, Zhuangwei Hou², Lei Xu¹, Qing Ma¹, Min Wei¹, Luke R Tembrock³, Shuo Zhang^{2

4}, Zhiqiang Wu^{2

5}

Affiliations

¹ China Resources Sanjiu Medical & Pharmaceutical Co., Ltd, Shenzhen, China.
² Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China.
³ Department of Agricultural Biology, Colorado State University, Fort Collins, CO, United States.
⁴ National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China.
⁵ Kunpeng Institute of Modern Agriculture at Foshan, Foshan, China.

Abstract

Chrysanthemum indicum, a species native to Eastern Asia is well known as one of the progenitor species of the cultivated Chrysanthemum which is grown for its ornamental and medicinal value. Previous genomic studies on Chrysanthemum have largely ignored the dynamics of plastid genome (plastome) and mitochondria genome (mitogenome) evolution when analyzing this plant lineage. In this study, we sequenced and assembled the plastomes and mitogenomes of diploid and tetraploid C. indicum as well as the morphologically divergent variety C. indicum var. aromaticum. We used published data from 27 species with both plastome and mitogenome complete sequences to explore differences in sequence evolution between the organellar genomes. The size and structure of organellar genome between diploid and tetraploid C. indicum were generally similar but the tetraploid C. indicum and C. indicum var. aromaticum were found to contain unique sequences in the mitogenomes which also contained previously undescribed open reading frames (ORFs). Across Chrysanthemum mitogenome structure varied greatly but sequences transferred from plastomes in to the mitogenomes were conserved. Finally, differences observed between mitogenome and plastome gene trees may be the result of the difference in the rate of sequence evolution between genes in these two genomes. In total the findings presented here greatly expand the resources for studying Chrysanthemum organellar genome evolution with possible applications to conservation, breeding, and gene banking in the future.

Keywords: Asteraceae; Chrysanthemum indicum; intragenomic gene transfers; organelle genome; phylogenetic analysis; tetraploid; variants.

Grants and funding

This project was funded by the Science, Technology, and Innovation Commission of Shenzhen Municipality (RCYX20200714114538196), and it was also supported by the National Natural Science Foundation of China (31970244 and 32170238), and the Funding through the Elite Young Scientists Program of the Chinese Academy of Agricultural Sciences was also given to Zhiqiang Wu. In addition, this project was supported by Science Technology and Innovation Commission of Shenzhen Municipality of China (ZDSYS 20200811142605017), Innovation Team and Talents Cultivation Program of the National Administration of Traditional Chinese Medicine (ZYYCXTD-D-202005) and molecular marker-assisted selection of new varieties of Chrysanthemum indicum (R21017).