Pteridryaceae: A new fern family of Polypodiineae (Polypodiales) including taxonomic treatments

Zhou, Xin‐Mao; Zhang, Liang; Lu, Ngan Thi; Gao, Xin‐Fen; Zhang, Libing

doi:10.1111/jse.12305

Cited by 16 publications

(16 citation statements)

References 97 publications

(239 reference statements)

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“…Others (SCO75 AA MSC, SCO60 AA MSC, MCO NT MSC, MCO AA MSC, codon positions one and two) recovered a clade consisting of Pteridrys and Tectaria sister to a clade of Arthropteris , Oleandraceae, Davalliaceae, and Polypodiaceae. Despite the different topologies recovered in our analyses, several recent studies have recovered Tectariaceae to be monophyletic (including all three genera sampled here) ( Liu et al, 2014 ; Zhang et al, 2016 ; Zhou et al, 2018 ) although Zhou et al (2018) suggest a new family (Pteridryaceae) be recognized. While Du et al (2021) separate Tectariaceae from Pteridryaceae ( Zhou et al, 2018 ) and Arthopteridaceae (suggested by Liu et al, 2013 , but not recognized by The Pteridophyte Phylogeny Group, 2016 ), they found the three families form a clade sister to the remaining eupolypods I.…”

Section: Discussioncontrasting

confidence: 61%

Phylotranscriptomics Illuminates the Placement of Whole Genome Duplications and Gene Retention in Ferns

et al. 2022

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Ferns are the second largest clade of vascular plants with over 10,000 species, yet the generation of genomic resources for the group has lagged behind other major clades of plants. Transcriptomic data have proven to be a powerful tool to assess phylogenetic relationships, using thousands of markers that are largely conserved across the genome, and without the need to sequence entire genomes. We assembled the largest nuclear phylogenetic dataset for ferns to date, including 2884 single-copy nuclear loci from 247 transcriptomes (242 ferns, five outgroups), and investigated phylogenetic relationships across the fern tree, the placement of whole genome duplications (WGDs), and gene retention patterns following WGDs. We generated a well-supported phylogeny of ferns and identified several regions of the fern phylogeny that demonstrate high levels of gene tree–species tree conflict, which largely correspond to areas of the phylogeny that have been difficult to resolve. Using a combination of approaches, we identified 27 WGDs across the phylogeny, including 18 large-scale events (involving more than one sampled taxon) and nine small-scale events (involving only one sampled taxon). Most inferred WGDs occur within single lineages (e.g., orders, families) rather than on the backbone of the phylogeny, although two inferred events are shared by leptosporangiate ferns (excluding Osmundales) and Polypodiales (excluding Lindsaeineae and Saccolomatineae), clades which correspond to the majority of fern diversity. We further examined how retained duplicates following WGDs compared across independent events and found that functions of retained genes were largely convergent, with processes involved in binding, responses to stimuli, and certain organelles over-represented in paralogs while processes involved in transport, organelles derived from endosymbiotic events, and signaling were under-represented. To date, our study is the most comprehensive investigation of the nuclear fern phylogeny, though several avenues for future research remain unexplored.

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Section: Discussioncontrasting

confidence: 61%

Phylotranscriptomics Illuminates the Placement of Whole Genome Duplications and Gene Retention in Ferns

et al. 2022

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“…Plastomes of 208 taxa of Polypodiales, representing 109 genera and all 26 families recognized by PPG I (2016), plus Arthropteridaceae (Liu et al, 2013) and Pteridryaceae (Zhou et al, 2018), were gathered including 163 plastomes of 99 genera generated in this study plus 45 plastomes accessed via GenBank (Tables 1 and S1). Plastomes of six taxa including two newly generated plastomes from orders Cyatheales and Salviniales were employed as outgroups (Tables 1 and S1).…”

Section: Sampling Sequencing and Genome Assemblymentioning

confidence: 99%

Simultaneous diversification of Polypodiales and angiosperms in the Mesozoic

Zhang

et al. 2021

Cladistics

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Comprising about 82% of the extant fern species diversity, Polypodiales are generally believed to have diversified in the Late Cretaceous. We estimated the divergence times of Polypodiales using both penalized likelihood and Bayesian methods, based on a dataset consisting of 208 plastomes representing all 28 families and 14 fossil constraints reflecting current interpretations of fossil record. Our plastome phylogeny recovered the same six major lineages as a recent nuclear phylogeny, but the position of Dennstaedtiineae was different. The present phylogeny showed high resolution of relationships among the families of Polypodiales, especially among those forming the Aspleniineae. The divergence time estimates supported the most recent common ancestor of Polypodiales and its closest relative dating back to the Triassic, establishment of the major lineages in the Jurassic, and a likely accelerated radiation during the late Jurassic and the Early Cretaceous. The estimated divergence patterns of Polypodiales and angiosperms converge to a scenario in which their main lineages were established simultaneously shortly before the onset of the Cretaceous Terrestrial Revolution, and further suggest a pre-Cretaceous hidden history for both lineages. The pattern of simultaneous diversifications shown here elucidate an important gap in our understanding of the Terrestrial Revolution that shaped today's ecosystems.

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“…Plastome sequences of 124 taxa, representing all 50 recognized families and 11 orders of ferns (following Liu et al, 2013 ; PPG I, 2016 ; Zhou et al, 2018 ), were gathered in this study, which includes 42 novel plastomes from 15 families with a focus on Hymenophyllales and Gleicheniales ( Table 1 ; Supplementary Table 1 ), plus 82 plastomes accessed via GenBank ( Table 1 ). Plastomes of two seed plants and one lycophyte were employed as outgroups ( Table 1 ).…”

Section: Methodsmentioning

confidence: 99%

Structural Variation of Plastomes Provides Key Insight Into the Deep Phylogeny of Ferns

Kuo

Zuo

et al. 2022

Front. Plant Sci.

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Structural variation of plastid genomes (plastomes), particularly large inversions and gene losses, can provide key evidence for the deep phylogeny of plants. In this study, we investigated the structural variation of fern plastomes in a phylogenetic context. A total of 127 plastomes representing all 50 recognized families and 11 orders of ferns were sampled, making it the most comprehensive plastomic analysis of fern lineages to date. The samples included 42 novel plastomes of 15 families with a focus on Hymenophyllales and Gleicheniales. We reconstructed a well-supported phylogeny of all extant fern families, detected significant structural synapomorphies, including 9 large inversions, 7 invert repeat region (IR) boundary shifts, 10 protein-coding gene losses, 7 tRNA gene losses or anticodon changes, and 19 codon indels (insertions or deletions) across the deep phylogeny of ferns, particularly on the backbone nodes. The newly identified inversion V5, together with the newly inferred expansion of the IR boundary R5, can be identified as a synapomorphy of a clade composed of Dipteridaceae, Matoniaceae, Schizaeales, and the core leptosporangiates, while a unique inversion V4, together with an expansion of the IR boundary R4, was verified as a synapomorphy of Gleicheniaceae. This structural evidence is in support of our phylogenetic inference, thus providing key insight into the paraphyly of Gleicheniales. The inversions of V5 and V7 together filled the crucial gap regarding how the “reversed” gene orientation in the IR region characterized by most extant ferns (Schizaeales and the core leptosporangiates) evolved from the inferred ancestral type as retained in Equisetales and Osmundales. The tRNA genes trnR-ACG and trnM-CAU were assumed to be relicts of the early-divergent fern lineages but intact in most Polypodiales, particularly in eupolypods; and the loss of the tRNA genes trnR-CCG, trnV-UAC, and trnR-UCU in fern plastomes was much more prevalent than previously thought. We also identified several codon indels in protein-coding genes within the core leptosporangiates, which may be identified as synapomorphies of specific families or higher ranks. This study provides an empirical case of integrating structural and sequence information of plastomes to resolve deep phylogeny of plants.

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Pteridryaceae: A new fern family of Polypodiineae (Polypodiales) including taxonomic treatments

Cited by 16 publications

References 97 publications

Phylotranscriptomics Illuminates the Placement of Whole Genome Duplications and Gene Retention in Ferns

Phylotranscriptomics Illuminates the Placement of Whole Genome Duplications and Gene Retention in Ferns

Simultaneous diversification of Polypodiales and angiosperms in the Mesozoic

Structural Variation of Plastomes Provides Key Insight Into the Deep Phylogeny of Ferns

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