Analysis of Comparative Transcriptome and Positively Selected Genes Reveal Adaptive Evolution in Leaf-Less and Root-Less Whisk Ferns

Abstract

While roots and leaves have evolved independently in lycophytes, ferns and seed plants, there is still confusion regarding the morphological evolution of ferns, especially in whisk ferns, which lack true leaves and roots and instead only exhibit leaf-like appendages and absorptive rhizoids. In this study, analyses of comparative transcriptomics on positively selected genes were performed to provide insights into the adaptive evolution of whisk fern morphologies. Significantly clustered gene families specific to whisk ferns were mainly enriched in Gene Ontology (GO) terms “binding proteins” and “transmembrane transporter activity”, and positive selection was detected in genes involved in transmembrane transporter activities and stress response (e.g., sodium/hydrogen exchanger and heat shock proteins), which could be related to the adaptive evolution of tolerance to epiphytic environments. The analysis of TF/TR gene family sizes indicated that some rapidly evolving gene families (e.g., the GRF and the MADS-MIKC families) related to the development of morphological organs were commonly reduced in whisk ferns and ophioglossoid ferns. Furthermore, the WUS homeobox-containing (WOX) gene family and the knotted1-like homeobox (KNOX) gene family, both associated with root and leaf development, were phylogenetically conserved in whisk ferns and ophioglossoid ferns. In general, our results suggested that adaptive evolution to epiphytic environments might have occurred in whisk ferns. We propose that the simplified and reduced leaf and root system in whisk ferns is the result of reduction from the common ancestor of whisk ferns and ophioglossoid ferns, rather than an independent origin.

All together now: Cellular and molecular aspects of leaf development in lycophytes, ferns, and seed plants

“…Phylogenetic analyses revealed that homologs of both TF groups cluster with their counterparts from ophioglossoid ferns. This topology suggests that the evolution of the KNOX and WOX families took place before the separation of whisk ferns and ophioglossoid ferns (Xia et al, 2022).…”

“…Homologs of C1KNOX TFs are found in Psilotum nudum (Huang et al, 2020). WOX TF homologs from the T1 clade are found in P. nudum and Tmesipteris tannensis, and members of the T3 ("modern") clade are present in P. nudum (Xia et al, 2022). The presumable T2 clade homolog reported for P. nudum (Nardmann and Werr, 2012) Organogenesis in the monoplex SAM of whisk ferns.…”

“…These data confirm the partitioning of fern SAMs into functionally different zones and the conservation of KNOX TF function in promoting indeterminacy in all plant lineages. A number of WOX homologs of leptosporangiate and ophioglossoid ferns have been mapped to the T1 and T2 clades (Nardmann and Werr, 2012;Xia et al, 2022). However, since Wu et al (2019) have shown that the WOX TFs of the T2 clade are only present in seed plants, it can be assumed that the T2 ("intermediate") clade members are probably sisters to the T2 + T3 clades (Table 1; Supplementary Figure 1; Supplementary Table 1; Wu et al, 2019).…”

“…Two CIKNOX homologs were discovered in Equisetum diffusum (Vasco and Ambrose, 2020). WOX homologs from the T1 clade were identified in Equisteum giganteum, E. arvense (Xia et al, 2022), E. diffusum (Wu et al, 2019), and E. hyemale (Supplementary Figure 1 and Supplementary Table 1). The WOX members from E. giganteum and E. arvense mapped by Xia et al (2022) to T2 clade are more likely sisters to the T2 + T3 clades (Table 1), as WOX TFs of the T2 clade are only present in seed plants (Wu et al, 2019).…”

“…The WOX members from E. giganteum and E. arvense mapped by Xia et al (2022) to T2 clade are more likely sisters to the T2 + T3 clades (Table 1), as WOX TFs of the T2 clade are only present in seed plants (Wu et al, 2019). No members of the T3 clade were found in horsetails (Xia et al, 2022).…”