Leaf dorsoventrality candidate gene CpARF4 has conserved expression pattern but divergent tasiR-ARF regulation in the water fern Ceratopteris pteridoides

PREMISE

Leaves are traditionally classified into microphylls and megaphylls, and recently have been regarded as independently originating in lycophytes, ferns, and seed plants. The developmental genetics of leaf dorsoventrality, a synapomorphy in vascular plants, has been extensively studied in flowering plants. AUXIN RESPONSE FACTOR4 (ARF4) genes are key to leaf abaxial identity in flowering plants, but whether they exist in ferns is still an open question.

METHODS

ARF4 genes from Ceratopteris pteridoides, Cyrtomium guizhouense, and Parathelypteris nipponica were mined from transcriptomes and investigated in terms of evolutionary phylogeny and sequence motifs, with a focus on the tasiR-ARF binding site. In situ hybridization was used to localize expression of CpARF4 in Ceratopteris pteridoides. 5'RNA ligase-mediated-RACE was employed to verify whether CpARF4 transcripts were sliced by tasiR-ARF.

RESULTS

ARF4 genes exist in ferns, and this lineage originates from a gene duplication in the common ancestor of ferns and seed plants. ARF4 genes are of a single copy in the ferns studied here, and they contain divergent and, at most, one tasiR-ARF binding site. CpARF4 is expressed in the abaxial but not the adaxial domain of leaf primordia at various developmental stages. Transcript slicing guided by tasiR-ARF is active in C. pteridoides, but CpARF4 probably has not been affected by it.

CONCLUSIONS

Fern ARF4 genes differ in copy number and tasiR-ARF regulation relative to flowering plants, though they can be similarly expressed in the abaxial domain of leaves, revealing a key role for ARF4 genes in the evolution of leaf dorsoventrality of vascular plants.

Resolving the backbone of the Brassicaceae phylogeny for investigating trait diversity

The Brassicaceae family comprises c. 4000 species including economically important crops and the model plant Arabidopsis thaliana. Despite their importance, the relationships among major lineages in the family remain unresolved, hampering comparative research. Here, we inferred a Brassicaceae phylogeny using newly generated targeted enrichment sequence data of 1827 exons (> 940 000 bases) representing 63 species, as well as sequenced genome data of 16 species, together representing 50 of the 52 currently recognized Brassicaceae tribes. A third of the samples were derived from herbarium material, facilitating broad taxonomic coverage of the family. Six major clades formed successive sister groups to the rest of Brassicaceae. We also recovered strong support for novel relationships among tribes, and resolved the position of 16 taxa previously not assigned to a tribe. The broad utility of these phylogenetic results is illustrated through a comparative investigation of genome-wide expression signatures that distinguish simple from complex leaves in Brassicaceae. Our study provides an easily extendable dataset for further advances in Brassicaceae systematics and a timely higher-level phylogenetic framework for a wide range of comparative studies of multiple traits in an intensively investigated group of plants.

Assessing the evolutionary history of the fern family Dipteridaceae (Gleicheniales) by incorporating both extant and extinct members in a combined phylogenetic study

PREMISE OF THE STUDY

Dipteridaceae is a lineage of ferns that has existed from the early Mesozoic and is known for its extensive fossil record. By integrating information from all described extant and extinct genera into a single phylogenetic study, this paper aims to examine the taxonomy of the group on a whole and explore character evolution within the lineage across time.

METHODS

A morphological matrix of 51 characters was developed for 72 species (43 extinct and 29 extant) based on published information. Morphological characters were combined with nucleotide sequences for four chloroplast genes (rbcL, atpA, atpB, and rps4) for extant taxa, and combined parsimony analyses were conducted to infer evolutionary trends in the group.

KEY RESULTS

Dipteridaceae was found to be monophyletic and characterized by highly anastomosing minor veins forming a meshwork of areoles with free-included veinlets. Based on our analyses, we recognize six previously described genera (i.e., Goeppertella, Thaumatopteris, Clathropteris, Digitopteris, Dipteris, and Cheiropleuria) and one new genus (i.e., Sewardalea). Fossils currently described as Dictyophyllum, Kenderlykia, Hausmannia, and Protorhipis are ambiguously placed on the tree and are recognized as possibly unnatural morphogenera.

CONCLUSIONS

Overall, the evolutionary trend in Dipteridaceae has been toward increasing complexity in the venation pattern and laminal fusion. Only the Hausmannia-type frond with dichotomizing primary veins and relatively fused lamina persisted in the later part of the Mesozoic to the present. Within the crown group, we see evidence of re-radiation of frond forms in Dipteris and Cheiropleuria.

The origin and early evolution of vascular plant shoots and leaves

The morphology of plant fossils from the Rhynie chert has generated longstanding questions about vascular plant shoot and leaf evolution, for instance, which morphologies were ancestral within land plants, when did vascular plants first arise and did leaves have multiple evolutionary origins? Recent advances combining insights from molecular phylogeny, palaeobotany and evo-devo research address these questions and suggest the sequence of morphological innovation during vascular plant shoot and leaf evolution. The evidence pinpoints testable developmental and genetic hypotheses relating to the origin of branching and indeterminate shoot architectures prior to the evolution of leaves, and demonstrates underestimation of polyphyly in the evolution of leaves from branching forms in 'telome theory' hypotheses of leaf evolution. This review discusses fossil, developmental and genetic evidence relating to the evolution of vascular plant shoots and leaves in a phylogenetic framework.This article is part of a discussion meeting issue 'The Rhynie cherts: our earliest terrestrial ecosystem revisited'.

Active suppression of a leaf meristem orchestrates determinate leaf growth

Leaves are flat determinate organs derived from indeterminate shoot apical meristems. The presence of a specific leaf meristem is debated, as anatomical features typical of meristems are not present in leaves. Here we demonstrate that multiple NGATHA (NGA) and CINCINNATA-class-TCP (CIN-TCP) transcription factors act redundantly, shortly after leaf initiation, to gradually restrict the activity of a leaf meristem in Arabidopsis thaliana to marginal and basal domains, and that their absence confers persistent marginal growth to leaves, cotyledons and floral organs. Following primordia initiation, the restriction of the broadly acting leaf meristem to the margins is mediated by the juxtaposition of adaxial and abaxial domains and maintained by WOX homeobox transcription factors, whereas other marginal elaboration genes are dispensable for its maintenance. This genetic framework parallels the morphogenetic program of shoot apical meristems and may represent a relic of an ancestral shoot system from which seed plant leaves evolved.

DOI:http://dx.doi.org/10.7554/eLife.15023.001

Leaf evolution in early-diverging ferns: insights from a new fern-like plant from the Late Devonian of China

BACKGROUND AND AIMS

With the exception of angiosperms, the main euphyllophyte lineages (i.e. ferns sensu lato, progymnosperms and gymnosperms) had evolved laminate leaves by the Late Devonian. The evolution of laminate leaves, however, remains unclear for early-diverging ferns, largely represented by fern-like plants. This study presents a novel fern-like taxon with pinnules, which provides new insights into the early evolution of laminate leaves in early-diverging ferns.

METHODS

Macrofossil specimens were collected from the Upper Devonian (Famennian) Wutong Formation of Anhui and Jiangsu Provinces, South China. A standard degagement technique was employed to uncover compressed plant portions within the rock matrix.

KEY RESULTS

A new fern-like taxon, SHOUGANGIA BELLA GEN ET SP NOV: , is described and represents an early-diverging fern with highly derived features. It has a partially creeping stem with adventitious roots only on one side, upright primary and secondary branches arranged in helices, tertiary branches borne alternately or (sub)oppositely, laminate and usually lobed leaves with divergent veins, and complex fertile organs terminating tertiary branches and possessing multiple divisions and numerous terminal sporangia.

CONCLUSIONS

Shougangia bella provides unequivocal fossil evidence for laminate leaves in early-diverging ferns. It suggests that fern-like plants, along with other euphyllophyte lineages, had independently evolved megaphylls by the Late Devonian, possibly in response to a significant decline in atmospheric CO2 concentration. Among fern-like plants, planate ultimate appendages are homologous with laminate pinnules, and in the evolution of megaphylls, fertile organs tend to become complex.

The evolution, morphology, and development of fern leaves

Leaves are lateral determinate structures formed in a predictable sequence (phyllotaxy) on the flanks of an indeterminate shoot apical meristem. The origin and evolution of leaves in vascular plants has been widely debated. Being the main conspicuous organ of nearly all vascular plants and often easy to recognize as such, it seems surprising that leaves have had multiple origins. For decades, morphologists, anatomists, paleobotanists, and systematists have contributed data to this debate. More recently, molecular genetic studies have provided insight into leaf evolution and development mainly within angiosperms and, to a lesser extent, lycophytes. There has been recent interest in extending leaf evolutionary developmental studies to other species and lineages, particularly in lycophytes and ferns. Therefore, a review of fern leaf morphology, evolution and development is timely. Here we discuss the theories of leaf evolution in ferns, morphology, and diversity of fern leaves, and experimental results of fern leaf development. We summarize what is known about the molecular genetics of fern leaf development and what future studies might tell us about the evolution of fern leaf development.

A role for PHANTASTICA in medio-lateral regulation of adaxial domain development in tomato and tobacco leaves

BACKGROUND AND AIMS

Diverse leaf forms in nature can be categorized into two groups: simple and compound. A simple leaf has a single blade unit, whilst a compound leaf is dissected into leaflets. For both simple and compound leaves, a MYB domain transcription factor PHANTASTICA (PHAN) plays an important role in establishing the adaxial domain in the leaf. Absence of PHAN in arabidopsis and antirrhinum leaves supresses blade development, and in tomato suppresses leaflet development. However, in the rachis and petiole regions of tomato leaves where PHAN and the adaxial domain coexist, it has been unclear why leaf blade and leaflets are not formed. We hypothesized that PHAN regulates the medio-lateral extent of the adaxial domain, thereby determining compound leaf architecture.

METHODS

To test this hypothesis, we generated and analysed transgenic tomato plants expressing tomato PHAN (SlPHAN) under the Cauliflower mosaic virus (CaMV) 35S promoter in both sense and antisense orientations, and tobacco plants that over-express tomato SlPHAN.

KEY RESULTS

Modulations in SlPHAN resulted in a variety of leaf morphologies such as simple, ternate and compound in either a peltate or non-peltate arrangement. Measurements of the extent of the adaxial domain along the wild-type tomato leaf axis showed that the adaxial domain is narrowed in the rachis and petiole in comparison with regions where laminar tissue arises. In antiSlPHAN transgenic leaves, no blade or leaflet was formed where the adaxial domain was medio-laterally narrowed, and KNOX gene expression was correlatively upregulated. CaMV35S::SlPHAN expression led to widening of the adaxial domain and ectopic blade outgrowth in the rachis of tomato and in the petiole of tobacco. Taken together, these results suggest that SlPHAN plays a role in medio-lateral extension of the adaxial domain and contributes to final leaf morphology in tomato.

CONCLUSIONS

This study provides a novel insight into leaf architecture in tomato and highlights how changes in the expression domain of a master regulator gene such as SlPHAN can be translated into diverse final leaf morphologies.