Phylogenomic analysis of Ranunculales resolves branching events across the order

Lane, A. Kelly; Augustin, Megan M.; Ayyampalayam, Saravanaraj; Plant, Alastair Robert; Gleissberg, Stefan; Stilio, Verónica S. Di; dePamphilis, Claude W.; Wong, Gane Ka‐Shu; Kutchan, Toni M.; Leebens‐Mack, James H.

doi:10.1093/botlinnean/boy015

Cited by 21 publications

(14 citation statements)

References 45 publications

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“…Using Bayesian analysis, the complete plastome dataset obtained a fully resolved phylogeny for Ranunculaceae (Fig. 4), which was better resolved than all the previous molecular and phylogenomic studies 15,33–35,39–45 .…”

Section: Discussionmentioning

confidence: 95%

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Structural variation of the complete chloroplast genome and plastid phylogenomics of the genus Asteropyrum (Ranunculaceae)

Yao

Lyu

et al. 2019

Sci Rep

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Two complete chloroplast genome sequences of Asteropyrum, as well as those of 25 other species from Ranunculaceae, were assembled using both Illumina and Sanger sequencing methods to address the structural variation of the cp genome and the controversial systematic position of the genus. Synteny and plastome structure were compared across the family. The cp genomes of the only two subspecies of Asteropyrum were found to be differentiated with marked sequence variation and different inverted repeat-single copy (IR-SC) borders. The plastomes of both subspecies contains 112 genes. However, the IR region of subspecies peltatum carries 27 genes, whereas that of subspecies cavaleriei has only 25 genes. Gene inversions, transpositions, and IR expansion-contraction were very commonly detected in Ranunculaceae. The plastome of Asteropyrum has the longest IR regions in the family, but has no gene inversions or transpositions. Non-coding regions of the cp genome were not ideal markers for inferring the generic relationships of the family, but they may be applied to interpret species relationship within the genus. Plastid phylogenomic analysis using complete cp genome with Bayesian method and partitioned modeling obtained a fully resolved phylogenetic framework for Ranunculaceae. Asteropyrum was detected to be sister to Caltha, and diverged early from subfamily Ranunculoideae.

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Section: Discussionmentioning

confidence: 95%

“…A large number of molecular phylogenetic as well as several phylogenomic analyses have been conducted for Ranunculaceae 33–35,39–45 . However, these studies have suffered from poor resolution largely due to an insufficient phylogenetic signal or insufficient sampling.…”

Section: Discussionmentioning

confidence: 99%

Structural variation of the complete chloroplast genome and plastid phylogenomics of the genus Asteropyrum (Ranunculaceae)

Yao

Lyu

et al. 2019

Sci Rep

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“…order (Ranunculales, cf. Lane et al, 2018;or Zingiberales, cf. Carlsen et al, 2018), family (Goodeniaceae, cf.…”

Section: Introductionmentioning

confidence: 99%

Nuclear and plastid DNA phylogeny of tribe Cardueae (Compositae) with Hyb-Seq data: A new subtribal classification and a temporal diversification framework

Herrando‐Moraira

Calleja

Galbany‐Casals

et al. 2019

Molecular Phylogenetics and Evolution

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Classification of the tribe Cardueae in natural subtribes has always been a challenge due to the lack of support of some critical branches in previous phylogenies based on traditional Sanger markers. With the aim to propose a new subtribal delimitation, we applied a Hyb-Seq approach to a set of 76 Cardueae species representing all the subtribes and informal groups defined in the tribe, targeting 1061 nuclear conserved orthology loci (COS) designed for Compositae and obtaining chloroplast coding regions as byproduct of off-target reads. For the extraction of target nuclear data, we used two strategies, PHYLUCE and HybPiper, and 776 and 1055 COS loci were recovered with each of them, respectively. Additionally, 87 chloroplast genes were assembled and annotated. With the three datasets, phylogenetic relationships within the tribe were reconstructed under approaches of concatenation (using supermatrices as input for maximum likelihood analysis with RAxML) and coalescence (species tree estimated with ASTRAL based on the individual gene trees of each COS locus). The phylogenetic analyses of the nuclear datasets fully resolved virtually all nodes with very high support. Although nuclear and plastid tree topologies are highly congruent, they still present some incongruences, which are shortly discussed. On the basis of the phylogenies obtained, we propose a new taxonomic scheme of 12 monophyletic and morphologically consistent subtribes: Carlininae, Cardopatiinae, Echinopsinae, Dipterocominae (new), Xerantheminae (new), Berardiinae (new), Staehelininae (new), Onopordinae (new), Carduinae (redelimited), Arctiinae (new), Saussureinae (new), and Centaureinae. Another main key result of the study was the high resolution recovered at the backbone of the Cardueae tree, which led to obtain better inter-subtribal relationships. Using as tree base the nuclear HybPiper phylogeny, we updated the temporal framework for the origin and diversification of the tribe and subtribes. Overall, the power of Hyb-Seq is demonstrated to solve relationships traditionally suggested by morphology but never recovered with support using Sanger sequencing of a few DNA markers.

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“…Transcriptomic and genomic resources are a valuable tool for studying development within an evolutionary context, as they enable the search for candidate loci and their regulatory regions, contributing to the upgrading of study systems into model lineages. Thalictrum L. is an emerging model lineage within the Ranunculales (Damerval and Becker, 2017), the sister group to all other eudicots (Lane et al, 2018). The genus is therefore an extant representative of a privileged phylogenetic node, before a major evolutionary radiation within the flowering plants (Zeng et al, 2017).…”

Section: Figurementioning

confidence: 99%

Genomic and transcriptomic resources for candidate gene discovery in the Ranunculids

2021

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Transcriptomic and genomic resources are a valuable tool for studying development within an evolutionary context, as they enable the search for candidate loci and their regulatory regions, contributing to the upgrading of study systems into model lineages. Thalictrum L. is an emerging model lineage within the Ranunculales (Damerval and Becker, 2017), the sister group to all other eudicots (Lane et al., 2018). The genus is therefore an extant representative of a privileged phylogenetic node, before a major evolutionary radiation within the flowering plants (Zeng et al., 2017). Thalictrum is a temperate genus of approximately 200 species with floral diversity that encompasses unisexual and windpollinated flowers, in association with polyploidy (Soza et al., 2012, 2013). Certain species, mainly T. thalictroides (L.) A. J. Eames & B. Boivin, are amenable to virus-induced gene silencing (Di Stilio et al., 2010), which has enabled functional studies of ABC model floral MADS-box genes (

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Phylogenomic analysis of Ranunculales resolves branching events across the order

Cited by 21 publications

References 45 publications

Structural variation of the complete chloroplast genome and plastid phylogenomics of the genus Asteropyrum (Ranunculaceae)

Structural variation of the complete chloroplast genome and plastid phylogenomics of the genus Asteropyrum (Ranunculaceae)

Nuclear and plastid DNA phylogeny of tribe Cardueae (Compositae) with Hyb-Seq data: A new subtribal classification and a temporal diversification framework

Genomic and transcriptomic resources for candidate gene discovery in the Ranunculids

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