Order‐level fern plastome phylogenomics: new insights from Hymenophyllales

Abstract

Although our analyses could not confidently resolve the phylogenetic position of Hymenophyalles, the results here highlight the danger of drawing conclusions from "all-in" phylogenomic data set without exploring potential inconsistencies in the data. Finally, our first order-level reconstruction of fern plastome structural evolution provides a useful framework for future plastome research.

The complete plastid genome sequence of Trichomanes trollii (Hymenophyllaceae)

“…In taxonomically better sampled analyses of much larger number of nuclear loci Hymenophyllales and Gleicheniales formed a clade, but Gleicheniales was paraphyletic with respect to Hymenophyllales (Qi et al 2018, Shen et al 2018. In contrast, the plastome analysis by Kuo et al (2018) supported, under most analyses, the monophyly of Gleicheniales, but the relationship between Hymenophyllales and Gleicheniales remained ambiguous. It seems clear that the monophyly of Gleicheniales and its relationship with Hymenophyllales needs to be investigated further also by taking into account morphological data and fossil evidence.…”

“…Three of these sites were C-to-U edits and 35 U-to-C edits. The plastome organization is basically the same as in closely related Callistopteris, with inverted repeat including ndhB, rps7, rps12, and part of the ycf2 (Kuo et al 2018).…”

“…Recently, Kuo et al (2018) published plastomes of two Hymenophyllales genera, Hymenophyllum and Callistopteris. In this paper the first complete plastome of genus Trichomanes is presented with its structure and gene content described within a phylogenetic context.…”

Exploring the plastid genome disparity of liverworts

“…Ferns show a declining trend in the taxon coverage from order to family to species (Table ). With the recent publication of the first plastome sequence of a filmy fern (Kuo et al, ), ferns have remarkably good coverage, with all orders having at least one complete plastid genome available. The relatively good coverage of angiosperms in all three criteria is notable given the number of species required to be covered.…”

“…Ferns show a declining trend in the taxon coverage from order to family to species (Table 1). With the recent publication of the first plastome sequence of a filmy fern (Kuo et al, 2018), ferns have remarkably good coverage, with all orders having at least one complete Fig. 3.…”