Lineage‐specific plastid degradation in subtribe Gentianinae (Gentianaceae)

Fu, Ping; Sun, Shan‐Shan; Twyford, Alex D.; Li, Bei‐Bei; Zhou, Rui‐Qi; Chen, Shi‐Long; Gao, Qingbo; Favre, Adrien

doi:10.1002/ece3.7281

Cited by 25 publications

(49 citation statements)

References 84 publications

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“…Divergence time estimates were usually similar for comparable nodes of the plastid and rDNA dated trees (Fig. 1), and in the range of earlier studies although we recovered broader 95% HPD intervals than some (compare with Fu et al 2021a), and slightly older ages than others (e.g., Favre et al 2016). We found that the crown age of Gentiana was ca.…”

Section: Phylogenetic Relationships and Molecular Datingsupporting

confidence: 85%

“…Phyllocalyx (Kusn.) T.N.Ho and G. sect Chondrophyllae because of their particularly derived sequences (Fu et al 2021a). Accession numbers are provided in Appendix I [accessions to be provided upon acceptance].…”

Section: Samples Dna Extraction and Sequencingmentioning

confidence: 99%

“…We imported raw data in Geneious Prime ® 2019.0.4 (Kearse et al 2012) (Biomatters Ltd, Auckland, New Zealand), where raw reads were trimmed with BBDuk and mapped (Geneious mapper) against the entire plastid and rDNA-cistron (incl. ETS, 18S, ITS 1, 5.8S, ITS2, and 26S) sequences available for closely related species in earlier studies (plastids from Fu et al 2021a; rDNA-cistron from Favre et al 2020).…”

Section: Samples Dna Extraction and Sequencingmentioning

confidence: 99%

“…To perform molecular dating, we ran the analyses separately for the plastid and rDNA datasets, using the HKY substitution model, the Yule model and the relaxed clock model. We used a calibration strategy identical to Fu et al (2021a): The split between G. sect. Cruciata and G. sect.…”

Section: Phylogenetic Analyses and Molecular Datingmentioning

confidence: 99%

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Incongruences between nuclear and plastid phylogenies challenge the identification of correlates of diversification in Gentiana in the European Alpine System

2021

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Mountains are reservoirs for a tremendous biodiversity which was fostered by a suite of factors acting in concert throughout evolutionary times. These factors can be climatic, geological, or biotic, but the way they combine through time to generate diversity remains unknown. Here, we investigate these factors as correlates of diversification of three closely related sections of Gentiana in the European Alpine System. Based upon phylogenetic approaches coupled with divergence dating and ancestral state reconstructions, we attempted to identify the role of bedrock preferences, chromosome numbers coupled with relative genome sizes estimates, as well as morphological features through time. We also investigated extant climatic preferences using a heavily curated set of occurrence records individually selected for superior precision, and quantified rates of climatic niche evolution in each section. We found that a number of phylogenetic incongruences derail the identification of correlates of diversification, yet a number of patterns persist regardless of the topology considered. All the studied correlates are likely to have contributed to the diversification of Gentiana in Europe, however, their respective importance varied through time and across clades. Chromosomal variation and divergence of climatic preferences appear to correlate with diversification throughout the evolution of European Gentiana (Oligocene to present), whereas shifts in bedrock preferences appear to have been more defining during recent diversification (Pliocene). Overall, a complex interaction among climatic, geological and biotic attributes appear to have supported the diversification of Gentiana across the mountains of Europe, which based upon phylogenetic as well as other evidence, was probably also bolstered by hybridization.

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Section: Phylogenetic Relationships and Molecular Datingsupporting

confidence: 85%

Section: Samples Dna Extraction and Sequencingmentioning

confidence: 99%

Section: Samples Dna Extraction and Sequencingmentioning

confidence: 99%

Section: Phylogenetic Analyses and Molecular Datingmentioning

confidence: 99%

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Incongruences between nuclear and plastid phylogenies challenge the identification of correlates of diversification in Gentiana in the European Alpine System

2021

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“…Gentiana leucomelaena Maxim., belonging to section Chondrophyllae series Humiles Marquand, has distribution range in Qinghai-Tibetan Plateau and adjacent areas. As the most species-rich section, there is very limited available plastome data in section Chondrophyllae at present (Fu et al 2021 ).…”

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confidence: 99%

Complete plastid genome of Gentiana leucomelaena Maxim. (Gentianaceae) and phylogenetic analysis

Miao²

2021

Mitochondrial DNA Part B

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The complete plastid genome of Gentiana leucomelaena Maxim., belonging to the most species-rich section Chondrophyllae in Gentiana , was determined and analyzed in this study. It has a circular-mapping molecular with the length of 131,856 bp, the shortest one among all available Gentiana plastomes. Gentiana leucomelaena has gene mutation, for example ndh and rpl 2 intron, and reversed SSC region comparing with the available species in sections Cruciata , Frigida , Kudoa , Isomeria and Microsperma . Phylogenetic analysis showed that G. leucomelaena clustered together with section Cruciata with a long branch. The plastome provides in this work will contribute to elucidate the phylogenetics and evolution in Gentiana .

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Rampant intraspecific variation of plastid genomes in Gentiana section Chondrophyllae

Sun,

Pan,

et al. 2024

Ecology and Evolution

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Exploring the level of intraspecific diversity in taxa experienced radiation is helpful to understanding speciation and biodiversity assembly. Gentiana section Chondrophyllae sensu lato encompasses more than 180 species and occupies more a half of species in the genus. In this study, we collected samples across the range of three species (Gentiana aristata, G. crassuloides and G. haynaldii) in section Chondrophyllae s.l., and recovered the intra‐species variation by comparing with closely related taxon. Using 25 newly sequenced plastid genomes together with previously published data, we compared structural differences, quantified the variations in plastome size, and measured nucleotide diversity in various regions. Our results showed that the plastome size variation in the three Chondrophyllae species ranged from 285 to 628 bp, and the size variation in LSC, IR and SSC ranged from 236 to 898 bp, 52 to 393 bp and 135 to 356 bp, respectively. Nucleotide diversity of plastome or any of the four regions was much higher than the control species. The average nucleotide diversity in plastomes of the three species ranged from 0.0010 to 0.0023 in protein coding genes, and from 0.0023 to 0.0061 in intergenic regions. More repeat sequence variations were detected within the three Chondrophyllae species than the control species. Various plastid sequence matrixes resulted in different backbone topology in two target species, showed uncertainty in phylogenetic relationship based inference. In conclusion, our results recovered that species of G. section Chondrophyllae s.l. has high intraspecific plastome variation, and provided insights into the radiation in this speciose lineage.

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Lineage‐specific plastid degradation in subtribe Gentianinae (Gentianaceae)

Cited by 25 publications

References 84 publications

Incongruences between nuclear and plastid phylogenies challenge the identification of correlates of diversification in Gentiana in the European Alpine System

Incongruences between nuclear and plastid phylogenies challenge the identification of correlates of diversification in Gentiana in the European Alpine System

Complete plastid genome of Gentiana leucomelaena Maxim. (Gentianaceae) and phylogenetic analysis

Rampant intraspecific variation of plastid genomes in Gentiana section Chondrophyllae

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