Plastid genome evolution of a monophyletic group in the subtribe Lauriineae (Laureae, Lauraceae)

Liu, Chao; Chen, Huanhuan; Tang, Lizhou; Khine, Phyo Kay; Han, Lihong; Song, Yu; Tan, Yun‐Hong

doi:10.1016/j.pld.2021.11.009

Cited by 19 publications

(25 citation statements)

References 52 publications

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“…Phylogenetic trees were reconstructed using the chloroplast genomes of L. obtusiloba from different geographic regions and 51 plastomes of the "core Laureae." Our results support the monophyletic origin of the "core Laureae" and the monophyletic status of the clade Litsea I, Lindera II, Lindera IV, Lindera V, and Lindera VI, which are consistent with some previous work (Jo et al, 2019;Liu, Chen, et al, 2021;Liu, Ma, et al, 2021;Song et al, 2020;Tian et al, 2019;Xiao et al, 2020). Phylogenetic results of the clade Litsea III, Lindera V, and Lindera VI in our studies are in agreement with a previous phylogenetic work by Zhao et al (2018), who defined the relationships among the species located in sub-clade I, and sub-clade II containing Lindera sect.…”

Section: Discussionsupporting

confidence: 93%

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Intraspecific differentiation of Lindera obtusiloba as revealed by comparative plastomic and evolutionary analyses

Tian,

Guo,

Song

et al. 2024

Ecology and Evolution

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Lindera obtusiloba Blume is the northernmost tree species in the family Lauraceae, and it is a key species in understanding the evolutionary history of this family. The species of L. obtusiloba in East Asia has diverged into the Northern and Southern populations, which are geographically separated by an arid belt. Though the morphological differences between populations have been observed and well documented, intraspecific variations at the plastomic level have not been systematically investigated to date. Here, ten chloroplast genomes of L. obtusiloba individuals were sequenced and analyzed along with three publicly available plastomes. Comparative plastomic analysis suggests that both the Northern and the Southern populations share similar overall structure, gene order, and GC content in their plastomes although the size of the plasome and the level of intraspecific variability do vary between the two populations. The Northern have relatively larger plastomes while the Southern population possesses higher intraspecific variability, which could be attributed to the complexity of the geological environments in the South. Phylogenomic analyses also support the split of the Northern and Southern clades among L. obtusiloba individuals. However, there is no obvious species boundary between var. obtusiloba and var. heterophylla in the Southern population, indicating that gene flow could still occur between these two varieties, and this could be used as a good example of reticulate evolution. It is also found that a few photosynthesis‐related genes are under positive selection, which is mainly related to the geological and environmental differences between the Northern and the Southern regions. Our results provide a reference for phylogenetic analysis within species and suggest that phylogenomic analyses with a sufficient number of nuclear and chloroplast genomic target loci from widely distributed individuals could provide a deeper understanding of the population evolution of the widespread species.

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Section: Discussionsupporting

confidence: 93%

“…Aperula, sect. Polyadenia and trinerved Lindera complex have been successfully detected and classified via whole plastomic analyses (Fijridiyanto & Murakami, 2009;Li et al, 2004Li et al, , 2007Liu, Chen, et al, 2021;Liu, Ma, et al, 2021;Tian et al, 2019;Xiao et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

Intraspecific differentiation of Lindera obtusiloba as revealed by comparative plastomic and evolutionary analyses

Tian,

Guo,

Song

et al. 2024

Ecology and Evolution

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“…ycf1 was indicated to be the most variable loci and showed better phylogenetic resolutions than standard DNA barcodes in land plants [84]. ycf2, petA-psbJ, and ndhF-rpl32-trnL UAG were not always hypervariable among different taxa [54,64,85], suggesting that the three loci were taxa-specific barcodes. Given the limited sampling in this study, more species with multiple samples of tribe Cinnamomeae should be included in future work to evaluate the discriminative power of ycf2, petA-psbJ, and ndhF-rpl32-trnL UAG .…”

Section: Candidate Dna Barcodesmentioning

confidence: 99%

Plastome structure, phylogenomics, and divergence times of tribe Cinnamomeae (Lauraceae)

Xiao

2022

BMC Genomics

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Background Tribe Cinnamomeae is a species-rich and ecologically important group in tropical and subtropical forests. Previous studies explored its phylogenetic relationships and historical biogeography using limited loci, which might result in biased molecular dating due to insufficient parsimony-informative sites. Thus, 15 plastomes were newly sequenced and combined with published plastomes to study plastome structural variations, gene evolution, phylogenetic relationships, and divergence times of this tribe. Results Among the 15 newly generated plastomes, 14 ranged from 152,551 bp to 152,847 bp, and the remaining one (Cinnamomum chartophyllum XTBGLQM0164) was 158,657 bp. The inverted repeat (IR) regions of XTBGLQM0164 contained complete ycf2, trnICAU, rpl32, and rpl2. Four hypervariable plastid loci (ycf1, ycf2, ndhF-rpl32-trnLUAG, and petA-psbJ) were identified as candidate DNA barcodes. Divergence times based on a few loci were primarily determined by prior age constraints rather than by DNA data. In contrast, molecular dating using complete plastid protein-coding genes (PCGs) was determined by DNA data rather than by prior age constraints. Dating analyses using PCGs showed that Cinnamomum sect. Camphora diverged from C. sect. Cinnamomum in the late Oligocene (27.47 Ma). Conclusions This study reports the first case of drastic IR expansion in tribe Cinnamomeae, and indicates that plastomes have sufficient parsimony-informative sites for molecular dating. Besides, the dating analyses provide preliminary insights into the divergence time within tribe Cinnamomeae and can facilitate future studies on its historical biogeography.

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“…Recently, plastome sequences were used to construct robust trees in which the Cryptocaryeae form a well-supported monophyletic clade (Song & al., 2017. By developing a well-resolved backbone phylogeny for the Lauraceae, confirmed that the tribes Cassytheae, Caryodaphnopsideae, Cryptocaryeae, Hypodaphnideae, Laureae, and Neocinnamomeae are highly supported (ML-BS 100% and BI-PP 1.0), as expected from morphology (Tian & al., 2019;Liu & al., 2022). Also using plastome sequences, another recent phylogenetic study showed a well-supported Beilschmiedia group comprising 35 species, suggesting the Beilschmiedia clade diverged in the Upper Paleogene and that migration of Beilschmiedia between Asia and the Americas occurred many times .…”

Section: ■ Introductionmentioning

confidence: 99%

Phylogeny and biogeography of the Cryptocaryeae (Lauraceae)

Song,

Xia,

Tan

et al. 2023

TAXON

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The biogeographical history of many lineages within the Lauraceae remains poorly known because of the difficulty of assigning macrofossils to living genera, poor pollen preservation, and the absence of sufficiently resolved or well‐supported phylogenies. Here, we utilize plastid genome sequencing to reinvestigate the phylogenetic and biogeographic history of trees in the tribe Cryptocaryeae, an important component of broad‐leaved forests worldwide, with around 800 species that rely on vertebrate frugivores to disperse their seeds. A new time‐calibrated phylogeny with high support for 176 species was used to infer the biogeographic history and speciation rates based on inferences of BAMM analyses. A monophyletic Cryptocaryeae with Aspidostemon, Beilschmiedia, Cryptocarya, Dahlgrenodendron, and Eusideroxylon clades was confirmed. The five clades of Cryptocaryeae were estimated to share a common ancestor in tropical Africa or Asia in the Early Cretaceous around 123 Ma. The Beilschmiedia and Cryptocarya clades were estimated to have originated in South America around 66 Ma. Extant subclades of the Beilschmiedia clade could colonize Australia by 35 Ma and extant subclades of the Cryptocarya clade could colonize Australia by 42 Ma. Diversification rates of the Beilschmiedia clade accelerated 14 and 12 Ma after its origin and diversification rates of the Cryptocarya clade accelerated 18 Ma after its origin. Over 45% extant Cryptocaryeae species originated in the three periods of accelerated differentiation in the Miocene of Asia and Australia. Long‐distance dispersal has had a major influence on biogeography, with dispersal to Asia likely occurring seven times, Zealandia six times, America three times, Australia three times, Africa twice, and Oceania at least once. Over 70% extant Cryptocaryeae species which diverged before the Quaternary grow in the Southern Hemisphere, while 90% extant Cryptocaryeae species which diverged in the Quaternary grow in the Northern Hemisphere. The Cryptocaryeae originated in and diversified with the first angiosperm‐dominated broad‐leaved evergreen forests, from the Cretaceous to the Paleogene. Long‐distance seed dispersal, probably by birds, although possibly also by flotation, has allowed the tribe to track these forests in space and time, despite a failure to adapt to cold, dry, or highly seasonal environments.

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Plastid genome evolution of a monophyletic group in the subtribe Lauriineae (Laureae, Lauraceae)

Cited by 19 publications

References 52 publications

Intraspecific differentiation of Lindera obtusiloba as revealed by comparative plastomic and evolutionary analyses

Intraspecific differentiation of Lindera obtusiloba as revealed by comparative plastomic and evolutionary analyses

Plastome structure, phylogenomics, and divergence times of tribe Cinnamomeae (Lauraceae)

Phylogeny and biogeography of the Cryptocaryeae (Lauraceae)

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