Molecular phylogenetic analyses based on the complete plastid genomes and nuclear sequences reveal Daphne (Thymelaeaceae) to be non-monophyletic as current circumscription

Lee, Shiou Yih; Xu, Ke‐Wang; Huang, Cui‐Ying; Lee, Jung-Hyun; Liao, Wenbo; Zhang, Yonghong; Fan, Qingxia

doi:10.1016/j.pld.2021.11.001

Cited by 12 publications

(12 citation statements)

References 50 publications

(60 reference statements)

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“… 2022 ), NC_060562 (Lee et al. 2022 ), NC_060829 (unpublished), NC_062858 (unpublished), ON244034 (this study). The phylogenetic tree was drawn based on the ML tree.…”

Section: Methodssupporting

confidence: 51%

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Complete chloroplast genome of Daphne pseudomezereum var. koreana (Thymelaeaceae)

YOO

Park

2023

Mitochondrial DNA Part B

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Daphne pseudomezereum A. Gray var. koreana (Nakai) Hamaya is a shrub distributed in high mountains in Japan and Korea and is used as a medicinal plant. The complete chloroplast genome of D. pseudomezereum var. koreana is 171,152 bp long with four subregions consisting of a large single-copy region (84,963 bp), a small single-copy region (41,725 bp), and a pair of inverted repeats (2739 bp). The genome includes 139 genes (93 protein-coding genes, eight rRNAs, and 38 tRNAs). Phylogenetic analyses show that D. pseudomezereum var. koreana is nested within the Daphne clade in the narrow sense and that it forms a distinct lineage.

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“… 2022 ), NC_060562 (Lee et al. 2022 ), NC_060829 (unpublished), NC_062858 (unpublished), ON244034 (this study). The phylogenetic tree was drawn based on the ML tree.…”

Section: Methodssupporting

confidence: 51%

“… 2021 ), NC_060495 (Lee et al. 2022 ), NC_060562 (Lee et al. 2022 ), NC_060829 (unpublished), NC_062858 (unpublished), ON244034 (this study).…”

Section: Methodsmentioning

confidence: 49%

Complete chloroplast genome of Daphne pseudomezereum var. koreana (Thymelaeaceae)

YOO

Park

2023

Mitochondrial DNA Part B

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“…It is well known that the chloroplast genome could provide much richer genetic information and a better solution than DNA regions for revealing the phylogeny of complicated genera and discriminating closely related species [ 53 , 54 ]. In our previous study, the plastid genome was confirmed to be a DNA super barcode that could efficiently discriminate most species in Fritillaria in China, but the results from ITS and other universal DNA barcodes analyses were disappointing [ 25 , 53 ].…”

Section: Discussionmentioning

confidence: 99%

Comparison of plastid genomes and ITS of two sister species in Gentiana and a discussion on potential threats for the endangered species from hybridization

et al. 2023

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Background Gentiana rigescens Franchet is an endangered medicinal herb from the family Gentianaceae with medicinal values. Gentiana cephalantha Franchet is a sister species to G. rigescens possessing similar morphology and wider distribution. To explore the phylogeny of the two species and reveal potential hybridization, we adopted next-generation sequencing technology to acquire their complete chloroplast genomes from sympatric and allopatric distributions, as along with Sanger sequencing to produce the nrDNA ITS sequences. Results The plastid genomes were highly similar between G. rigescens and G. cephalantha. The lengths of the genomes ranged from 146,795 to 147,001 bp in G. rigescens and from 146,856 to 147,016 bp in G. cephalantha. All genomes consisted of 116 genes, including 78 protein-coding genes, 30 tRNA genes, four rRNA genes and four pseudogenes. The total length of the ITS sequence was 626 bp, including six informative sites. Heterozygotes occurred intensively in individuals from sympatric distribution. Phylogenetic analysis was performed based on chloroplast genomes, coding sequences (CDS), hypervariable sequences (HVR), and nrDNA ITS. Analysis based on all the datasets showed that G. rigescens and G. cephalantha formed a monophyly. The two species were well separated in phylogenetic trees using ITS, except for potential hybrids, but were mixed based on plastid genomes. This study supports that G. rigescens and G. cephalantha are closely related, but independent species. However, hybridization was confirmed to occur frequently between G. rigescens and G. cephalantha in sympatric distribution owing to the lack of stable reproductive barriers. Asymmetric introgression, along with hybridization and backcrossing, may probably lead to genetic swamping and even extinction of G. rigescens. Conclusion G. rigescens and G. cephalantha are recently diverged species which might not have undergone stable post-zygotic isolation. Though plastid genome shows obvious advantage in exploring phylogenetic relationships of some complicated genera, the intrinsic phylogeny was not revealed because of matrilineal inheritance here; nuclear genomes or regions are hence crucial for uncovering the truth. As an endangered species, G. rigescens faces serious threats from both natural hybridization and human activities; therefore, a balance between conservation and utilization of the species is extremely critical in formulating conservation strategies.

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“…The ITS region was used for phylogenetic reconstruction of Wikstroemia . Despite insufficiency in delimiting plants at the species level, the ITS regions of most Wikstroemia species are publicly available and partly provide an insight into phylogenetic relationships between closely related species ( He et al 2021 ; Lee et al 2022 ). We downloaded all species of Daphneae ( Thymelaeaceae ) with ITS gene sequences available in NCBI GenBank for analysis.…”

Section: Materials and Methodsmentioning

confidence: 99%

“…The quality and quantity of the DNA extract were determined using Nanodrop spectrophotometer (Thermo Fisher, USA). Polymerase chain reaction was carried out based on the program setting as proposed by Lee et al (2022) using the universal primers, ITS1 and ITS4 ( White et al 1990 ). The amplicon was verified under UV and the PCR product was Sanger sequenced both forward and reverse directions.…”

Section: Materials and Methodsmentioning

confidence: 99%

Wikstroemia fragrans (Thymelaeaceae, Daphneae), a new species from Mount Danxia, China based on morphological and molecular evidence

Chen

Lee

Guo³

et al. 2022

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A new species, Wikstroemia fragrans (Thymelaeaceae, Daphneae), from Danxiashan National Park, Shaoguan, Guangdong of China is described and illustrated. It is similar to the sympatric W. trichotoma, but can be differentiated easily from the latter by its shorter racemose inflorescences, yellowish green calyx tube, and smaller leaves. It also resembles the allopatric W. fargesii, but differs from it by its strigose-pubescent ovary and disk scale that is 2- or 3-dentate apically. Phylogenetic analysis using the nuclear DNA internal transcribed spacer (ITS) region revealed that W. fragrans falls within the Wikstroemia clade; based on current sampling, W. fragrans is closely-related to W. capitata. It is also the first species of Wikstroemia known to be endemic to the Danxia landform and is classified provisionally as Critically Endangered according to the IUCN Red List Categories and Criteria.

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Molecular phylogenetic analyses based on the complete plastid genomes and nuclear sequences reveal Daphne (Thymelaeaceae) to be non-monophyletic as current circumscription

Cited by 12 publications

References 50 publications

Complete chloroplast genome of Daphne pseudomezereum var. koreana (Thymelaeaceae)

Complete chloroplast genome of Daphne pseudomezereum var. koreana (Thymelaeaceae)

Comparison of plastid genomes and ITS of two sister species in Gentiana and a discussion on potential threats for the endangered species from hybridization

Wikstroemia fragrans (Thymelaeaceae, Daphneae), a new species from Mount Danxia, China based on morphological and molecular evidence

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Molecular phylogenetic analyses based on the complete plastid genomes and nuclear sequences reveal Daphne (Thymelaeaceae) to be non-monophyletic as current circumscription

Cited by 12 publications

References 50 publications

Complete chloroplast genome of Daphne pseudomezereum var. koreana (Thymelaeaceae)

Complete chloroplast genome of Daphne pseudomezereum var. koreana (Thymelaeaceae)

Comparison of plastid genomes and ITS of two sister species in Gentiana and a discussion on potential threats for the endangered species from hybridization

﻿Wikstroemia fragrans (Thymelaeaceae, Daphneae), a new species from Mount Danxia, China based on morphological and molecular evidence

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Wikstroemia fragrans (Thymelaeaceae, Daphneae), a new species from Mount Danxia, China based on morphological and molecular evidence