Plastome sequences of an ancient fern lineage reveal remarkable changes in gene content and architecture

Abstract

The plastomes of are the smallest reported for a fern so far. The loss of the gene suite is associated with the reduction of the small single copy, instead of the inverted repeat as noted for other groups of plants. Putative C-to-U and U-to-C transitions were observed in several instances in the three plastomes, suggesting that posttranscriptional modification of RNA is likely a common phenomenon in this clade as well.

The complete plastid genome sequence of Trichomanes trollii (Hymenophyllaceae)

“…Recently, the placement of Marattiales seems to be converging as sister group to leptosporangiate ferns (Gao et al , Zhong et al , Knie et al 2015, Lu et al 2015, Rothfels et al 2015, Labiak and Karol , Kuo et al 2018, Qi et al 2018) and this position is further supported here. Likewise, several recent studies (Karol et al 2010, Grewe et al , Ruhfel et al , Zhong et al , Lu et al 2015, Gitzendanner et al 2018) place Equisetum as sister of Ophioglossidae in agreement with the present results and this position appears better supported than the alternative arrangement of Equisetum as sister to all other ferns (Kuo et al , Kim et al , Knie et al 2015, Rothfels et al 2015, Labiak and Karol ). However, the recent large‐scale analyses using massive transcriptome data unequivocally support Equisetum as the sister of all other ferns (Qi et al 2018, Shen et al 2018).…”

“…Actinostachys pennula (Sw.) Hook. KU764518 (Labiak and Karol ), Adiantum capillus‐veneris L. NC_004766 (Wolf et al 2003), Alsophila spinulosa (Wall. ex Hook.)…”

“…KM052729 (Marchant et al unpublished), Cycas taitungensis C.F.Shen et al NC_009618 (Wu et al ), Cyrtomium devexiscapulae (Koidz.) Ching KT599100 (Lu et al 2015), Cystopteris chinensis (Ching) X.C.Zhang & R.Wei KY427337 (Wei et al ), Diplopterygium glaucum (Thunb. ex Houtt.)…”

“…Filmy ferns (Hymenophyllales) represent another deep fern lineage with unclear relationships. They clearly belong to the early diverging leptosporangiate ferns, but some studies have resolved them as sister to Gleicheniales (Pryer et al 2004, Lehtonen et al ) while most studies seem to resolve them as sister to all other nonosmundalean leptosporangiate ferns (Pryer et al 2001, Schuettpelz and Pryer , Lehtonen , Knie et al 2015, Rothfels et al 2015, Wolf et al 2018). Yet, some analyses have found Gleicheniales diverging before Hymenophyllales (Kuo et al , Knie et al 2015), or Gleicheniales as a paraphyletic grade in respect to Hymenophyllales (Qi et al 2018, Shen et al 2018).…”

“…A typical feature giving the common name ‘filmy fern’ is the membranaceous lamina which lack stomata and has only one cell‐layer between the veins (Kramer and Green ). These characteristics make the fossil record of filmy ferns very poor, with Hymenophyllum iwatsukii Herrera et al from the Early Cretaceous and Hopetedia praetermissa Axsmith et al from the Late Triassic being exceptionally well preserved examples (Axsmith et al 2001, Herrera et al ). Based on fossil‐calibrated molecular dating the origin of filmy fern lineage has been dated at Permian or Carboniferous (Schuettpelz and Pryer , 2009, Testo and Sundue , Lehtonen et al ).…”