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

Abstract

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.

An Open and Continuously Updated Fern Tree of Life

“…We recover (P, (D, e)) with moderate support (BS 92%); this topology agrees with other phylogenomic studies based on whole plastomes (Lu et al, 2015; Lehtonen and Cárdenas, 2019) and nuclear data (Rothfels et al, 2015; Qi et al, 2018; Shen et al, 2018), as well as a plastid supermatrix (Lehtonen, 2011). The whole plastome study of Du et al (2021) recovered a novel topology comprising ((D, P), e) under some analysis settings but (P, (D, e)) under others; a similar study with expanded sampling generally supported ((D, P), e) (Du et al, 2022).…”

“…While manual inclusion lists are not an ideal long-term solution because they cannot grow with GenBank, this case demonstrates that such lists are a reasonable option for taxonomically difficult groups, and more importantly, the improvement that can result from input from taxonomic experts. Another example of the advantage of a continuously updated tree is the publication of 42 additional fern plastome samples while this paper was in revision (Du et al, 2022). While we were unable to integrate these data into the current version of FTOL, they will be automatically added when the next version of GenBank data is released, and we expected the next version of FTOL will reflect this new knowledge.…”

Systematics and Plastome Evolution in Schizaeaceae

“…In other words, there might be a concerted loss of ndh -related genes in both genomic compartments ( Figure 4 ), a feature that has been suggested to be the initial (but irreversible) step toward mycoheterotrophy in flowering plants ( Graham et al, 2017 ; Lin et al, 2017 ). Interestingly, a separate fern lineage Stromatopteris (Gleicheniaceae), which also produces mycoheterotrophic gametophytes ( Bierhorst, 1971b ), has likewise experienced ndh gene losses in the plastome ( Du et al, 2022 ).…”

“…However, these genes do not seem to be associated with the specialization of gametophytic lifestyle in Schizaeaceae, and are mostly considered to have minor functions in the plastid. For instance, rps16 has been lost several times in ferns ( Zhang et al, 2014 ; Kuo et al, 2018a ; Du et al, 2022 ). Ycf94 , which was recently identified in plastomes of seed-free plants and whose function is still unknown ( Song et al, 2018 ), seems to be absent only in Schizaeaceae ( Du et al, 2022 ).…”

“…For instance, rps16 has been lost several times in ferns ( Zhang et al, 2014 ; Kuo et al, 2018a ; Du et al, 2022 ). Ycf94 , which was recently identified in plastomes of seed-free plants and whose function is still unknown ( Song et al, 2018 ), seems to be absent only in Schizaeaceae ( Du et al, 2022 ).…”