Chloroplast Genomic Resources and Genetic Divergence of Endangered Species Bretschneidera sinensis (Bretschneideraceae)

Shang, Ce; Li, Enze; Yu, Ziyou; Lian, Mengjia; Chen, Zhuo; Liu, Kangjia; Xu, Lan; Tong, Zhaopeng; Wang, Meifang; Dong, Wenpan

doi:10.3389/fevo.2022.873100

Cited by 13 publications

(13 citation statements)

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“…For example, chloroplast genome data had resolved the systematic positions of enigmatic taxa in Saxifragales [37] and shed lights on the intergeneric relationships and spatio-temporal evolutionary history of Melocanninae (Poaceae) [36]. Moreover, the chloroplast genome sequences showed variations at the intraspecies levels, and revealed the genetic difference and diversity of endangered species [38,39] and cultivated species [40,41].…”

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confidence: 99%

Insights into the phylogeny and chloroplast genome evolution of Eriocaulon (Eriocaulaceae)

Liu

Deng

et al. 2023

BMC Plant Biol

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Background Eriocaulon is a wetland plant genus with important ecological value, and one of the famous taxonomically challenging groups among angiosperms, mainly due to the high intraspecific diversity and low interspecific variation in the morphological characters of species within this genus. In this study, 22 samples representing 15 Eriocaulon species from China, were sequenced and combined with published samples of Eriocaulon to test the phylogenetic resolution using the complete chloroplast genome. Furthermore, comparative analyses of the chloroplast genomes were performed to investigate the chloroplast genome evolution of Eriocaulon. Results The 22 Eriocaulon chloroplast genomes and the nine published samples were proved highly similar in genome size, gene content, and order. The Eriocaulon chloroplast genomes exhibited typical quadripartite structures with lengths from 150,222 bp to 151,584 bp. Comparative analyses revealed that four mutation hotspot regions (psbK-trnS, trnE-trnT, ndhF-rpl32, and ycf1) could serve as effective molecular markers for further phylogenetic analyses and species identification of Eriocaulon species. Phylogenetic results supported Eriocaulon as a monophyletic group. The identified relationships supported the taxonomic treatment of section Heterochiton and Leucantherae, and the section Heterochiton was the first divergent group. Phylogenetic tree supported Eriocaulon was divided into five clades. The divergence times indicated that all the sections diverged in the later Miocene and most of the extant Eriocaulon species diverged in the Quaternary. The phylogeny and divergence times supported rapid radiation occurred in the evolution history of Eriocaulon. Conclusion Our study mostly supported the taxonomic treatment at the section level for Eriocaulon species in China and demonstrated the power of phylogenetic resolution using whole chloroplast genome sequences. Comparative analyses of the Eriocaulon chloroplast genome developed molecular markers that can help us better identify and understand the evolutionary history of Eriocaulon species in the future.

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Insights into the phylogeny and chloroplast genome evolution of Eriocaulon (Eriocaulaceae)

Liu

Deng

et al. 2023

BMC Plant Biol

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“…In total, 460 intraspecific polymorphic sites, 104 indels and three small inversions were identified among these 39 individuals. Mutation diversity of the plastome in P. chinensis is relatively high compared to that published for other plant species, including Arnebia guttata (313 polymorphic sites, 17 individuals) (Sun et al, 2022), Bretschneidera sinensis (105 polymorphic sites, 55 indels, 12 individuals) (Shang et al, 2022), the model grass plant Brachypodium distachyon (298 polymorphic sites, 53 individuals) (Sancho et al, 2018), and Ginkgo biloba (135 polymorphic sites, 71 individuals) (Hohmann et al, 2018).…”

Section: Discussionmentioning

confidence: 82%

Variations in genetic diversity in cultivated Pistacia chinensis

Han

Zhang²,

Yang³

et al. 2022

Front. Plant Sci.

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Identification of the evolution history and genetic diversity of a species is important in the utilization of novel genetic variation in this species, as well as for its conservation. Pistacia chinensis is an important biodiesel tree crop in China, due to the high oil content of its fruit. The aim of this study was to uncover the genetic structure of P. chinensis and to investigate the influence of intraspecific gene flow on the process of domestication and the diversification of varieties. We investigated the genetic structure of P. chinensis, as well as evolution and introgression in the subpopulations, through analysis of the plastid and nuclear genomes of 39 P. chinensis individuals from across China. High levels of variation were detected in the P. chinensis plastome, and 460 intraspecific polymorphic sites, 104 indels and three small inversions were identified. Phylogenetic analysis and population structure using the plastome dataset supported five clades of P. chinensis. Population structure analysis based on the nuclear SNPs showed two groups, clearly clustered together, and more than a third of the total individuals were classified as hybrids. Discordance between the plastid and nuclear genomes suggested that hybridization events may have occurred between highly divergent samples in the P. chinensis subclades. Most of the species in the P. chinensis subclade diverged between the late Miocene and the mid-Pliocene. The processes of domestication and cultivation have decreased the genetic diversity of P. chinensis. The extensive variability and structuring of the P. chinensis plastid together with the nuclear genomic variation detected in this study suggests that much unexploited genetic diversity is available for improvement in this recently domesticated species.

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“…The phylogeny of the species in Lagerstroemia was well resolved based on the whole plastome sequences from this paper and from previous studies [ 30 , 32 , 46 ], revealing the maternal donor of crape myrtle cultivars. Only a few studies have assessed the intraspecific variation of the whole plastomes and nrDNA sequences [ 18 , 20 , 21 , 47 , 48 ]. The plastid genome markers have less use in analyzing the genetic diversity of cultivars, owing to their limited polymorphic sites.…”

Section: Discussionmentioning

confidence: 99%

“…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 ].…”

Section: Introductionmentioning

confidence: 99%

Maternal Donor and Genetic Variation of Lagerstroemia indica Cultivars

Guo

Liu

et al. 2023

IJMS

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Lagerstroemia indica L. is a well-known ornamental plant with large pyramidal racemes, long flower duration, and diverse colors and cultivars. It has been cultivated for nearly 1600 years and is essential for investigating the germplasm and assessing genetic variation to support international cultivar identification and breeding programs. In this study, 20 common Lagerstroemia indica cultivars from different varietal groups and flower morphologies, as well as multiple wild relative species, were analyzed to investigate the maternal donor of Lagerstroemia indica cultivars and to discover the genetic variation and relationships among cultivars based on plastome and nuclear ribosomal DNA (nrDNA) sequences. A total of 47 single nucleotide polymorphisms (SNPs) and 24 insertion/deletions (indels) were identified in the 20 L. indica cultivars’ plastome and 25 SNPs were identified in the nrDNA. Phylogenetic analysis based on the plastome sequences showed that all the cultivars formed a clade with the species of L. indica, indicating that L. indica was the maternal donor of the cultivars. Population structure and PCA analyses supported two clades of cultivars, which exhibited significant genetic differences according to the plastome dataset. The results of the nrDNA supported that all 20 cultivars were divided into three clades and most of the cultivars had at least two genetic backgrounds and higher gene flow. Our results suggest that the plastome and nrDNA sequences can be used as molecular markers for assessing the genetic variation and relationships of L. indica cultivars.

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Chloroplast Genomic Resources and Genetic Divergence of Endangered Species Bretschneidera sinensis (Bretschneideraceae)

Cited by 13 publications

References 53 publications

Insights into the phylogeny and chloroplast genome evolution of Eriocaulon (Eriocaulaceae)

Insights into the phylogeny and chloroplast genome evolution of Eriocaulon (Eriocaulaceae)

Variations in genetic diversity in cultivated Pistacia chinensis

Maternal Donor and Genetic Variation of Lagerstroemia indica Cultivars

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