Phylogeny and historical biogeography of Lithospermeae (Boraginaceae): Disentangling the possible causes of Miocene diversifications

Chacón, Juliana; Luebert, Federico; Selvi, Federico; Weigend, Maximilian

doi:10.1016/j.ympev.2019.106626

Cited by 16 publications

(15 citation statements)

References 92 publications

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“…The chloroplast gene data were used to estimate the divergence times among Arnebia species. Two priors from the findings of ( Chacón et al, 2019 ) were used for these analyses. The crown age of Lithospermeae was constrained to 42.5 Mya [95% highest posterior density (HPD): 35.3–51.5 Mya].…”

Section: Methodsmentioning

confidence: 99%

Phylogenomics and Genetic Diversity of Arnebiae Radix and Its Allies (Arnebia, Boraginaceae) in China

Sun

Wang

et al. 2022

Front. Plant Sci.

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Arnebiae Radix is a traditional medicine with pleiotropic properties that has been used for several 100 years. There are five species of Arnebia in China, and the two species Arnebia euchroma and Arnebia guttata are the source plants of Arnebiae Radix according to the Chinese Pharmacopoeia. Molecular markers that permit species identification and facilitate studies of the genetic diversity and divergence of the wild populations of these two source plants have not yet been developed. Here, we sequenced the chloroplast genomes of 56 samples of five Arnebia species using genome skimming methods. The Arnebia chloroplast genomes exhibited quadripartite structures with lengths from 149,539 and 152,040 bp. Three variable markers (rps16-trnQ, ndhF-rpl32, and ycf1b) were identified, and these markers exhibited more variable sites than universal chloroplast markers. The phylogenetic relationships among the five Arnebia species were completely resolved using the whole chloroplast genome sequences. Arnebia arose during the Oligocene and diversified in the middle Miocene; this coincided with two geological events during the late Oligocene and early Miocene: warming and the progressive uplift of Tianshan and the Himalayas. Our analyses revealed that A. euchroma and A. guttata have high levels of genetic diversity and comprise two and three subclades, respectively. The two clades of A. euchroma exhibited significant genetic differences and diverged at 10.18 Ma in the middle Miocene. Three clades of A. guttata diverged in the Pleistocene. The results provided new insight into evolutionary history of Arnebia species and promoted the conservation and exploitation of A. euchroma and A. guttata.

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Section: Methodsmentioning

confidence: 99%

Phylogenomics and Genetic Diversity of Arnebiae Radix and Its Allies (Arnebia, Boraginaceae) in China

Sun

Wang

et al. 2022

Front. Plant Sci.

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“…Time estimates were done based on a global molecular clock and fossil data. That was, we used the nal aligned sequences with 14 species, which were converted to MEGA format by using MEGAX software [62], and the phylogenetic tree of 14 species with .nwk format.…”

Section: Divergence Time Estimatesmentioning

confidence: 99%

Chloroplast genome and historical biogeography of the three Magnolias

Min

Guo

Yin

et al. 2021

Preprint

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Magnolia officinalis, M. officinalis subsp.biloba and M. hypoleuca are all typical medicinal plants, belonging to genus Magnolia and Family Magnoliaceae. Their molecular information, particularly genetic difference, were known less. In this study, the platform Illumina HiSeq was used to sequence and assemble a novel cp (chloroplast) genome of M. hypoleuca followed by cp purification. Combined with two published cp rawdata, gene cycles and function annotations were comparably performed for the three plant species. The results indicated that 19 791 019 clean reads was assembled for M. hypoleuca cp, Q30 being 91.33%, and genome 160 051 bp. Its GC content is 39.2%, including 37 tRNAs and 8 rRNAs. The M. hypoleuca had smaller chloroplast genome and more introns (or exons) than M. officinalis and M. officinalis subsp.biloba. And there were respectively 11 and 8 more functional genes in M. hypoleuca cp than that in the other two. Based on cp complete genomes sequences, we constructed the phylogenetic relationship and estimated the divergence time of the three species by ML (Maximum likelihood) method, with other 10 published Magnoliaceae species. The results showed that M. officinalis subsp.biloba and M. officinalis might diverge from M. hypoleuca around 18.98 Ma, then they diverged from each other around 15.00 Ma. Additionally, the middle Miocene warming period might play an important role in the demographic and evolutionary histories of the three Magnolias, which provided a novel insight of the origin and dispersal routes of M. hypoleuca.

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“…In the current study, we used a ploidy-aware likelihoodbased genotyping to quantify genetic diversity and to investigate the population structure of the polyploid plant Alkanna tinctoria Tausch (Boraginaceae) across most of its distribution area in mainland Greece. In addition, as a potential outgroup species, we included the closely related A. sieberi A.DC (Chacón et al, 2019), a rare endemic species on Crete Island. A. tinctoria is a tetraploid perennial herb mainly distributed in Greece and other Mediterranean countries (Dimopoulos et al, 2013;Strid, 2016).…”

Section: Introductionmentioning

confidence: 99%

Spatial and Ecological Drivers of Genetic Structure in Greek Populations of Alkanna tinctoria (Boraginaceae), a Polyploid Medicinal Herb

Ahmad

Leroy

Krigas³

et al. 2021

Front. Plant Sci.

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Background and Aims: Quantifying genetic variation is fundamental to understand a species’ demographic trajectory and its ability to adapt to future changes. In comparison with diploids, however, genetic variation and factors fostering genetic divergence remain poorly studied in polyploids due to analytical challenges. Here, by employing a ploidy-aware framework, we investigated the genetic structure and its determinants in polyploid Alkanna tinctoria (Boraginaceae), an ancient medicinal herb that is the source of bioactive compounds known as alkannin and shikonin (A/S). From a practical perspective, such investigation can inform biodiversity management strategies.Methods: We collected 14 populations of A. tinctoria within its main distribution range in Greece and genotyped them using restriction site-associated DNA sequencing. In addition, we included two populations of A. sieberi. By using a ploidy-aware genotype calling based on likelihoods, we generated a dataset of 16,107 high-quality SNPs. Classical and model-based analysis was done to characterize the genetic structure within and between the sampled populations, complemented by genome size measurements and chromosomal counts. Finally, to reveal the drivers of genetic structure, we searched for associations between allele frequencies and spatial and climatic variables.Key Results: We found support for a marked regional structure in A. tinctoria along a latitudinal gradient in line with phytogeographic divisions. Several analyses identified interspecific admixture affecting both mainland and island populations. Modeling of spatial and climatic variables further demonstrated a larger contribution of neutral processes and a lesser albeit significant role of selection in shaping the observed genetic structure in A. tinctoria.Conclusion: Current findings provide evidence of strong genetic structure in A. tinctoria mainly driven by neutral processes. The revealed natural genomic variation in Greek Alkanna can be used to further predict variation in A/S production, whereas our bioinformatics approach should prove useful for the study of other non-model polyploid species.

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Phylogeny and historical biogeography of Lithospermeae (Boraginaceae): Disentangling the possible causes of Miocene diversifications

Cited by 16 publications

References 92 publications

Phylogenomics and Genetic Diversity of Arnebiae Radix and Its Allies (Arnebia, Boraginaceae) in China

Phylogenomics and Genetic Diversity of Arnebiae Radix and Its Allies (Arnebia, Boraginaceae) in China

Chloroplast genome and historical biogeography of the three Magnolias

Spatial and Ecological Drivers of Genetic Structure in Greek Populations of Alkanna tinctoria (Boraginaceae), a Polyploid Medicinal Herb

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