Plastome-based phylogenomics resolves the placement of the sanguinolenta group in the spikemoss of lycophyte (Selaginellaceae)

Zhang, Hongrui; Wei, Ran; Xiang, Qiao‐Ping; Zhang, Xian‐Chun

doi:10.1016/j.ympev.2020.106788

Cited by 24 publications

(55 citation statements)

References 46 publications

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“…The results of three analyses based on plastome data sets (CDS, codon 1-2, and AA) in the present analyses ( Fig. 1 a–c) were mostly consistent with the results of Zhang et al. (2020) .…”

Section: Resultssupporting

confidence: 87%

“…1 f, Table 1 ). The studies of Zhang et al., 2019 , Zhang et al, 2020 suggested that species in clade E have lower substitution rates and simpler plastome structures, whereas species in clades A–D have higher substitution rates and more complex plastome structures. Our analyses indicate that the frequency of RNA editing in Selaginella plastomes may be positively correlated with the variation in plastome structure and the substitution rate.…”

Section: Discussionmentioning

confidence: 99%

“…Compared with species in clade D, species in clades A had a relatively lower number of RNA editing sites ( Fig. 1 f, Table 1 ), but more complex plastome structures and an accelerated substitution rate ( Zhang et al., 2019 , Zhang et al, 2020 ). More comprehensive taxon sampling and transcriptomic evidence are needed to illuminate the evolutionary patterns of RNA editing in Selaginella .…”

Section: Discussionmentioning

confidence: 99%

“…38% in Isoëtales, and ca . 51–57% in Selaginellales ( Mower et al., 2019 ; Zhang et al., 2019 , Zhang et al, 2020 ). The present study showed that even for the corrected data set consisting of the most frequently edited first and second codon positions (codon1r-2r), the average GC content of the sampled Selaginella species (49.1%) was still relatively higher than those of club mosses (41.6–42.7%) and quillworts (44.5%) ( Table 1 , Table 2 ).…”

Section: Discussionmentioning

confidence: 99%

“…Selaginella , the single genus in Selaginellaceae (Selaginellales or spike moss), is distributed worldwide and contains about 700–800 species ( PPG, 2016 ; Weststrand and Korall, 2016 ). All sequenced Selaginella plastomes have a remarkably high GC content (50.7–56.5%) ( Zhang et al, 2020 ), and because high GC content is thought to be correlated with organellar RNA editing, Selaginella species are supposed to have high levels of RNA editing ( Malek et al., 1996 ; Tsuji et al., 2007 ; Smith, 2009 ; Hecht et al., 2011 ; Oldenkott et al., 2014 ).…”

Section: Introductionmentioning

confidence: 99%

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Extreme plastid RNA editing may confound phylogenetic reconstruction: A case study of Selaginella (lycophytes)

2020

Plant Diversity

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Cytidine-to-uridine (C-to-U) RNA editing is common in coding regions of organellar genomes throughout land plants. In most cases RNA editing alters translated amino acids or creates new start codons, potentially confounds phylogenetic reconstructions. In this study, we used the spike moss genus Selaginella (lycophytes), which has the highest frequency of RNA editing, as a model to test the effects of extreme RNA editing on phylogenetic reconstruction. We predicted the C-to-U RNA editing sites in coding regions of 18 Selaginella plastomes, and reconstructed the phylogenetic relationships within Selaginella based on three data set pairs consisted of plastome or RNA-edited coding sequences, first and second codon positions, and translated amino acid sequences, respectively. We predicted between 400 and 3100 RNA editing sites of 18 Selaginella plastomes. The numbers of RNA editing sites in plastomes were highly correlated with the GC content of first and second codon positions, but not correlated with the GC content of plastomes as a whole. Contrast phylogenetic analyses showed that there were substantial differences (e.g., the placement of clade B in Selaginella ) between the phylogenies generated by the plastome and RNA-edited data sets. This empirical study provides evidence that extreme C-to-U RNA editing in the coding regions of organellar genomes alters the sequences used for phylogenetic reconstruction, and might even confound phylogenetic reconstruction. Therefore, RNA editing sites should be corrected when plastid or mitochondrial genes are used for phylogenetic studies, particularly in those lineages with abundant organellar RNA editing sites, such as hornworts, quillworts, spike mosses, and some seed plants.

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“…The results of three analyses based on plastome data sets (CDS, codon 1-2, and AA) in the present analyses ( Fig. 1 a–c) were mostly consistent with the results of Zhang et al. (2020) .…”

Section: Resultssupporting

confidence: 87%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Extreme plastid RNA editing may confound phylogenetic reconstruction: A case study of Selaginella (lycophytes)

2020

Plant Diversity

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No phylogenomic support for a Cenozoic origin of the “living fossil” Isoetes

Wikström

Larsén

Khodabandeh

et al. 2023

American J of Botany

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Premise:The isoetalean lineage has a rich fossil record that extends to the Devonian, but the age of the living clade is unclear. Recent results indicate that it is young, from the Cenozoic, whereas earlier work based on less data from a denser taxon sampling yielded Mesozoic median ages. Methods: We analyzed node ages in Isoetes using two genomic data sets (plastome and nuclear ribosomal cistron), three clock models implemented in MrBayes (ILN, WN, and TK02 models), and a conservative approach to calibration. Results: While topological results were consistently resolved in Isoetes estimated crown group ages range from the latest Paleozoic (mid-Permian) to the Mesozoic depending on data type and clock model. The oldest estimates were retrieved using the autocorrelated TK02 clock model. An (early) Cenozoic age was only obtained under one specific condition (plastome data analyzed with the uncorrelated ILN clock model). That same plastome data set also yielded the oldest (mid-Permian) age estimate when analyzed with the autocorrelated TK02 clock model. Adding the highly divergent, recently established sister species Isoetes wormaldii to the data set approximately doubled the average median node depth to the Isoetes crown group. Conclusions: There is no consistent support for a Cenozoic origin of the living clade Isoetes. We obtained seemingly well-founded, yet strongly deviating results depending on data type and clock model. The single most important future improvement is probably to add calibration points, which requires an improved understanding of the isoetalean fossil record or alternative bases for calibration.

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Integrative taxonomy of the Selaginella helvetica group based on morphological, molecular and ecological data

Zhang

Wei

Xiang

et al. 2021

TAXON

Self Cite

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The Eurasian and Mediterranean Selaginella helvetica group is one of the taxonomically challenging groups in the cosmopolitan lycophyte genus Selaginella. Species of the S. helvetica group are all small plants with lax strobili composed of more or less isomorphic sporophylls (isosporophylls) that are basically non-resupinate. Owing to the similar and minute morphological characteristics, the inapplicability of chloroplast DNA markers for species delimitation and the lack of range-wide sampling, no comprehensive study has been conducted on these species so far. In this study, we performed phylogenetic analyses based on populationscale sampling of 126 individuals, covering the entire geographical distribution and morphological variation of this group. Five chloroplast (rbcL, psbA, atpI, atpF, atpF-H) and two nuclear DNA regions (26S rDNA, pgiC) were used to explore species diversity of this group. The phylogeny inferred from nuclear DNA datasets revealed nine well-supported monophyletic groups, which provided important evidence for species delimitation and called for taxonomic revision of some taxa. However, in the chloroplast phylogeny, individuals of only three species (S. denticulata, S. helvetica, S. tamamontana) formed monophyletic groups, respectively. We further investigated genome size for each species by flow cytometry and evaluated 21 morphological characteristics of 79 herbarium specimens. MaxEnt analysis was performed to predict the potential suitable distribution of each species. As a result of total evidence, 10 taxa were recognized in the S. helvetica group. The delimitation of S. denticulata, S. laxistrobila, S. nipponica, S. pallidissima, S. prostrata, and S. tamamontana was congruent with previous taxonomical treatments. We reinstated S. shensiensis as an independent species and treated S. longistrobilina as its synonym. Selaginella helvetica (s.str.) is confined to Europe and North Asia, former records of it from the Himalaya-Hengduan mountains represent an independent species (S. jiulongensis comb. nov.). The nuclear pgiC phylogeny and flow cytometry evidence indicated that S. pseudonipponica is an allotetraploid with S. shensiensis and S. nipponica as its parents. Our results highlight that nuclear DNA markers rather than chloroplast DNA markers are more informative in delimitation of closely related species in Selaginella.

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Plastome-based phylogenomics resolves the placement of the sanguinolenta group in the spikemoss of lycophyte (Selaginellaceae)

Cited by 24 publications

References 46 publications

Extreme plastid RNA editing may confound phylogenetic reconstruction: A case study of Selaginella (lycophytes)

Extreme plastid RNA editing may confound phylogenetic reconstruction: A case study of Selaginella (lycophytes)

No phylogenomic support for a Cenozoic origin of the “living fossil” Isoetes

Integrative taxonomy of the Selaginella helvetica group based on morphological, molecular and ecological data

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