Multiplexed Massively Parallel Sequencing of Plastomes Provides Insights Into the Genetic Diversity, Population Structure, and Phylogeography of Wild and Cultivated Coptis chinensis

Abstract

Root rot has been a major problem for cultivated populations of Coptis chinensis var. chinensis in recent years. C. chinensis var. brevisepala, the closest wild relative of C. chinensis var. chinensis, has a scattered distribution across southwestern China and is an important wild resource. Genetic diversity is associated with greater evolutionary potential and resilience of species or populations and is important for the breeding and conservation of species. Here, we conducted multiplexed massively parallel sequencing of the plastomes of 227 accessions of wild and cultivated C. chinensis using 111 marker pairs to study patterns of genetic diversity, population structure, and phylogeography among wild and cultivated C. chinensis populations. Wild and cultivated resources diverged approximately 2.83 Mya. The cultivated resources experienced a severe genetic bottleneck and possess highly mixed germplasm. However, high genetic diversity has been retained in the wild resources, and subpopulations in different locations differed in genotype composition. The significant divergence in the genetic diversity of wild and cultivated resources indicates that they require different conservation strategies. Wild resources require in situ conservation strategies aiming to expand population sizes while maintaining levels of genetic diversity; by contrast, germplasm resource nurseries with genotypes of cultivated resources and planned distribution measures are needed for the conservation of cultivated resources to prevent cultivated populations from undergoing severe genetic bottlenecks. The results of this study provide comprehensive insights into the genetic diversity, population structure, and phylogeography of C. chinensis and will facilitate future breeding and conservation efforts.

Genetic diversity and population divergence of Leonurus japonicus and its distribution dynamic changes from the last interglacial to the present in China

“…In this study, the genetic diversity of L. japonicus (Pi = 0.00029) was found to be similar to that of its close relative, L. cardiaca , with an average Pi of 0.00042. Interestingly, a relatively low level of genetic diversity seems common among medicinal plants with a long history of cultivation and use, such as Coptis chinensis , Ziziphus jujuba , Angelica sinensis , and Panax ginseng [ 11 , 27 – 29 ]. This may be the result of genetic bottlenecks caused by human activity, such as the cultivation of the species for personal medicinal use, which inevitably leads to the reduction of genetic diversity.…”

“…The R package “PCAtools” was used to preform PCA and make PCA plots. The STRUCTURE workflow was according to the previous study [ 11 ]: (1) The K-means clustering algorithm was ran from K = 2 to K = 10 with ten runs for each K-value to determine the optimum number of clusters [ 49 ], (2) the initial burn-in period was set to 10,000 with 100,000 MCMCs, (3) the most suitable clusters were determined using the DeltaK method on Structure Harvester ( http://taylor0.biology.ucla.edu/struct_harvest/ ) and aggregated by running the CLUMPP program [ 50 ], and (4) visualizing the structure plots by using R package “ggplot2” [ 51 ].…”

 Coptis huanjiangensis, a new species of Ranunculaceae from Guangxi, China

“…Plastoms have been extensively used in phylogeny reconstruction and species delimitation studies because of their moderate evolution rate and abundant phylogenetic information ( Dong et al 2021 ; Wang et al 2021 ; Wang et al 2022 ). The relationships of Coptis species were clearly resolved by phylogenetic studies.…”

“…Most of these species are less than 30 cm in height and grow in shady places in forest valleys at an altitude of 600–2500 meters. Due to the richness in benzylisoquinoline alkaloids, various Coptis species have been used in China ethnomedicine, and three of them, C. chinensis , C. deltoidea , and C. teeta , are used as official Huanglian ‘Weilian’, ‘Yalian’ and ‘Yunlian’ in the Chinese Pharmacopeia respectively ( Liu et al 2021 ; Wang et al 2022 ).…”

Maternal Donor and Genetic Variation of Lagerstroemia indica Cultivars

“…Plastome and nuclear ribosomal DNA (nrDNA) sequences are popular molecular markers used for plant phylogeny [ 13 , 14 , 15 , 16 , 17 ] and species identification [ 18 , 19 ] because these sequences are conserved across plant species and show variability among interspecies levels. Past studies show that the plastome and nrDNA sequences contain numerous SSRs, indels, and SNPs at the intraspecies levels, which have been used to research the genetic divergence of endangered species [ 20 , 21 ], biogeographical structure [ 22 , 23 , 24 ], gene flow among subpopulations [ 25 , 26 ], and origins and domestication of cultivars [ 27 , 28 , 29 ]. For the Lagerstroemia species, more than 17 species have sequenced the whole chloroplast genome, using these data to infer the phylogeny and divergence time of Lagerstroemia [ 30 ].…”