Evolution Of Seed Plants Research Articles

Spatial transcriptomics of a lycophyte root sheds light on root evolution

Plant roots originated independently in lycophytes and euphyllophytes, whereas early vascular plants were rootless. The organization of the root apical meristem in euphyllophytes is well documented, especially in the model plant Arabidopsis. However, little is known about lycophyte roots and their molecular innovations during evolution. In this study, spatial transcriptomics was used to detect 97 root-related genes in the roots of the lycophyte Selaginella moellendorffii. A high number of genes showed expression patterns similar to what has been reported for seed plants, supporting the idea of a highly convergent evolution of mechanisms to control root development. Interaction and complementation data of SHORTROOT (SHR) and SCARECROW (SCR) homologs, furthermore, support a comparable regulation of the ground tissue (GT) between euphyllophytes and lycophytes. Root cap formation, in contrast, appears to be differently regulated. Several experiments indicated an important role of the WUSCHEL-RELATED HOMEOBOX13 gene SmWOX13a in Selaginella root cap formation. In contrast to multiple Arabidopsis WOX paralogs, SmWOX13a is able to induce root cap cells in Arabidopsis and has functionally conserved homologs in the fern Ceratopteris richardii. Lycophytes and a part of the euphyllophytes, therefore, may share a common mechanism regulating root cap formation, which was diversified or lost during seed plant evolution. In summary, we here provide a new spatial data resource for the Selaginella root, which in general advocates for conserved mechanisms to regulate root development but shows a clear divergence in the control of root cap formation, with a novel putative role of WOX genes in root cap formation in non-seed plants.

Reproductive Mechanisms in Ginkgo and Cycas: Sisters but not Twins

The study of reproductive mechanisms is of particular interest for a real understanding of seed plant evolution. Spermatophytes comprise angiosperms and four orders of gymnosperms (Cycadales, Ginkgoales, Coniferales, and Gnetales) whose main characteristic is the reproduction via seeds. Ginkgo and cycads form a sister clade to the other gymnosperms and occupy a key phylogenetic position in-between the extinct Paleozoic seed ferns and the other extant gymnosperms. This review focuses on the similarities and differences between the reproductive mechanisms of Ginkgo and Cycas, from the morphogenesis of the male and female organs to the pollination and fertilization events. Together with the morphological and cytological description, the latest available molecular data on the reproductive organ development of the two plant genera are discussed. This will, hopefully, pave the path for new studies aiming at filling the gaps in our understanding of the hormonal and genetic regulation of their reproductive mechanisms. The whole reproductive process is presented in detail, providing a comprehensive and organic picture together with complete illustrations and photographic material. Each phase of the reproductive process is dissected, pointing out the main similarities and differences found among the two genera. The comparison comprises the male and female reproductive organs development, with a focus on pollen ontogeny, shape, ultrastructure, and germination as well as ovule development and patterning, female gametophyte formation, and ovule integument differentiation. Particular attention is given to the pollination and fertilization events focusing on the role of reproductive fluids as well as zoogamy.

Dynamic genome evolution in a model fern

The large size and complexity of most fern genomes have hampered efforts to elucidate fundamental aspects of fern biology and land plant evolution through genome-enabled research. Here we present a chromosomal genome assembly and associated methylome, transcriptome and metabolome analyses for the model fern species Ceratopteris richardii. The assembly reveals a history of remarkably dynamic genome evolution including rapid changes in genome content and structure following the most recent whole-genome duplication approximately 60 million years ago. These changes include massive gene loss, rampant tandem duplications and multiple horizontal gene transfers from bacteria, contributing to the diversification of defence-related gene families. The insertion of transposable elements into introns has led to the large size of the Ceratopteris genome and to exceptionally long genes relative to other plants. Gene family analyses indicate that genes directing seed development were co-opted from those controlling the development of fern sporangia, providing insights into seed plant evolution. Our findings and annotated genome assembly extend the utility of Ceratopteris as a model for investigating and teaching plant biology.

Phylogenetic patterns suggest frequent multiple origins of secondary metabolites across the seed-plant 'tree of life'.

To evaluate the phylogenetic patterns of the distribution and evolution of plant secondary metabolites (PSMs), we selected 8 classes of PSMs and mapped them onto an updated phylogenetic tree including 437 families of seed plants. A significant phylogenetic signal was detected in 17 of the 18 tested seed-plant clades for at least 1 of the 8 PSM classes using the D statistic. The phylogenetic signal, nevertheless, indicated weak clustering of PSMs compared to a random distribution across all seed plants. The observed signal suggests strong diversifying selection during seed-plant evolution and/or relatively weak evolutionary constraints on the evolution of PSMs. In the survey of the current phylogenetic distributions of PSMs, we found that multiple origins of PSM biosynthesis due to external selective forces for diverse genetic pathways may have played important roles. In contrast, a single origin of PSMs seems rather uncommon. The distribution patterns for PSMs observed in this study may also be useful in the search for natural compounds for medicinal purposes.

Phylogenetic Analyses and GAGA-Motif Binding Studies of BBR/BPC Proteins Lend to Clues in GAGA-Motif Recognition and a Regulatory Role in Brassinosteroid Signaling.

Plant GAGA-motif binding factors are encoded by the BARLEY B RECOMBINANT / BASIC PENTACYSTEINE (BBR/BPC) family, which fulfill indispensable functions in growth and development. BBR/BPC proteins control flower development, size of the stem cell niche and seed development through transcriptional regulation of homeotic transcription factor genes. They are responsible for the context dependent recruitment of Polycomb repressive complexes (PRC) or other repressive proteins to GAGA-motifs, which are contained in Polycomb repressive DNA-elements (PREs). Hallmark of the protein family is the highly conserved BPC domain, which is required for DNA binding. Here we study the evolution and diversification of the BBR/BPC family and its DNA-binding domain. Our analyses supports a further division of the family into four main groups (I–IV) and several subgroups, to resolve a strict monophyletic descent of the BPC domain. We prove a polyphyletic origin for group III proteins, which evolved from group I and II members through extensive loss of domains in the N-terminus. Conserved motif searches lend to the identification of a WAR/KHGTN consensus and a TIR/K motif at the very C-terminus of the BPC-domain. We could show by DPI-ELISA that this signature is required for DNA-binding in AtBPC1. Additional binding studies with AtBPC1, AtBPC6 and mutated oligonucleotides consolidated the binding to GAGA tetramers. To validate these findings, we used previously published ChIP-seq data from GFP-BPC6. We uncovered that many genes of the brassinosteroid signaling pathway are targeted by AtBPC6. Consistently, bpc6, bpc4 bpc6, and lhp1 bpc4 bpc4 mutants display brassinosteroid-dependent root growth phenotypes. Both, a function in brassinosteroid signaling and our phylogenetic data supports a link between BBR/BPC diversification in the land plant lineage and the complexity of flower and seed plant evolution.

Diversity and homologies of corystosperm seed-bearing structures from the Early Cretaceous of Mongolia

New discoveries of corystosperm seed-bearing structures from the Tevshiin Govi locality, Mongolia, which is of Early Cretaceous (Aptian–Albian) age, show that the individual seed-bearing units of Umkomasia mongolica were borne in a cone, as also documented for the very similar reproductive units of Doylea tetrahedrasperma. New material from the Tevshiin Govi locality also documents two additional species of Umkomasia – U. corniculata sp. nov. and U. trilobata sp. nov. – that most likely grew in a different environment to U. mongolica. The occurrence of three different Umkomasia species in the Early Cretaceous of Mongolia, together with other records from the Early Cretaceous of the Northern Hemisphere, indicate that previous concepts of corystosperms, based mainly on material from the Southern Hemisphere, need to be revised. The consistent reproductive architecture of the seed-bearing structures in all three corystosperm species, with a bract subtending a variously modified axis bearing ovules, is similar to the situation in Ginkgo and conifers. These underappreciated architectural commonalities among the reproductive structures of major groups of seed plants are likely significant for a deeper understanding of seed plant evolution and require further exploration.

Phylogenomics resolves the deep phylogeny of seed plants and indicates partial convergent or homoplastic evolution between Gnetales and angiosperms.

After decades of molecular phylogenetic studies, the deep phylogeny of gymnosperms has not been resolved, and the phylogenetic placement of Gnetales remains one of the most controversial issues in seed plant evolution. To resolve the deep phylogeny of seed plants and to address the sources of phylogenetic conflict, we conducted a phylotranscriptomic study with a sampling of all 13 families of gymnosperms and main lineages of angiosperms. Multiple datasets containing up to 1 296 042 sites across 1308 loci were analysed, using concatenation and coalescence approaches. Our study generated a consistent and well-resolved phylogeny of seed plants, which places Gnetales as sister to Pinaceae and thus supports the Gnepine hypothesis. Cycads plus Ginkgo is sister to the remaining gymnosperms. We also found that Gnetales and angiosperms have similar molecular evolutionary rates, which are much higher than those of other gymnosperms. This implies that Gnetales and angiosperms might have experienced similar selective pressures in evolutionary histories. Convergent molecular evolution or homoplasy is partially responsible for the phylogenetic conflicts in seed plants. Our study provides a robustly reconstructed backbone phylogeny that is important for future molecular and morphological studies of seed plants, in particular gymnosperms, in the light of evolution.

Phylogenetic analysis of F-bZIP transcription factors indicates conservation of the zinc deficiency response across land plants

Basic leucine zipper (bZIP) transcription factors control important developmental and physiological processes in plants. In Arabidopsis thaliana, the three gene F-bZIP subfamily has been associated with zinc deficiency and salt stress response. Benefiting from the present abundance of plant genomic data, we performed an evolutionary and structural characterization of plant F-bZIPs. We observed divergence during seed plant evolution, into two groups and inferred different selective pressures for each. Group 1 contains AtbZIP19 and AtbZIP23 and appears more conserved, whereas Group 2, containing AtbZIP24, is more prone to gene loss and expansion events. Transcriptomic and experimental data reinforced AtbZIP19/23 as pivotal regulators of the zinc deficiency response, mostly via the activation of genes from the ZIP metal transporter family, and revealed that they are the main regulatory switch of AtZIP4. A survey of AtZIP4 orthologs promoters across different plant taxa revealed an enrichment of the Zinc Deficiency Response Element (ZDRE) to which both AtbZIP19/23 bind. Overall, our results indicate that while the AtbZIP24 function in the regulation of the salt stress response may be the result of neo-functionalization, the AtbZIP19/23 function in the regulation of the zinc deficiency response may be conserved in land plants (Embryophytes).

Sequenced genomes and rapidly emerging technologies pave the way for conifer evolutionary developmental biology.

Conifers, Ginkgo, cycads and gnetophytes comprise the four groups of extant gymnosperms holding a unique position of sharing common ancestry with the angiosperms. Comparative studies of gymnosperms and angiosperms are the key to a better understanding of ancient seed plant morphologies, how they have shifted over evolution to shape modern day species, and how the genes governing these morphologies have evolved. However, conifers and other gymnosperms have been notoriously difficult to study due to their long generation times, inaccessibility to genetic experimentation and unavailable genome sequences. Now, with three draft genomes from spruces and pines, rapid advances in next generation sequencing methods for genome wide expression analyses, and enhanced methods for genetic transformation, we are much better equipped to address a number of key evolutionary questions relating to seed plant evolution. In this mini-review we highlight recent progress in conifer developmental biology relevant to evo-devo questions. We discuss how genome sequence data and novel techniques might allow us to explore genetic variation and naturally occurring conifer mutants, approaches to reduce long generation times to allow for genetic studies in conifers, and other potential upcoming research avenues utilizing current and emergent techniques. Results from developmental studies of conifers and other gymnosperms in comparison to those in angiosperms will provide information to trace core molecular developmental control tool kits of ancestral seed plants, but foremost they will greatly improve our understanding of the biology of conifers and other gymnosperms in their own right.

A transcriptomics investigation into pine reproductive organ development.

The development of reproductive structures in gymnosperms is still poorly studied because of a lack of genomic information and useful genetic tools. The hermaphroditic reproductive structure derived from unisexual gymnosperms is an even less studied aspect of seed plant evolution. To extend our understanding of the molecular mechanism of hermaphroditism and the determination of sexual identity of conifer reproductive structures in general, unisexual and bisexual cones from Pinus tabuliformis were profiled for gene expression using 60K microarrays. Expression patterns of genes during progression of sexual cone development were analysed using RNA-seq. The results showed that, overall, the transcriptomes of male structures in bisexual cones were more similar to those of female cones. However, the expression of several MADS-box genes in the bisexual cones was similar to that of male cones at the more juvenile developmental stage, while despite these expression shifts, male structures of bisexual cones and normal male cones were histologically indistinguishable and cone development was continuous. This study represents a starting point for in-depth analysis of the molecular regulation of cone development and also the origin of hermaphroditism in pine.

Root contraction in Cycas and Zamia (Cycadales) determined by gelatinous fibers.

• Reaction wood (RW) in seed plants can induce late and usually secondary changes in organ orientation. Conifers produce compression wood (CW), generated by compression tracheids, which generate a push force. Angiosperms produce tension wood (TW), generated by tension wood fibers (TWF) often described as "gelatinous fibers," which exert a pull force. Usually RW is produced eccentrically, but it can occur concentrically, as in aerial roots of Ficus. However, gymnosperms can produce gelatinous fibers (tension fibers, TF), as in cortical and secondary phloem tissues (Gnetum). TFs are therefore limited neither to wood, xylem, nor angiosperms. Here we demonstrate that TFs in secondary phloem are involved in contraction of roots of cycads and compare them with TFs of Ficus.• We sectioned root material of cycads at various stages of seedling development using simple staining and histochemical procedures to follow the course of secondary phloem development. Aerial roots of Ficus were compared with the cycad root material.• Tension fibers (gelatinous fibers) occur extensively and continuously in the secondary phloem in roots that undergo contraction. Older tissues, but notably the xylem, become distorted by contraction. TFs in cycads correspond in cell wall features to TFs that occur in Ficus, but do not occur in secondary xylem. The individual fibers visibly contract.• Tissue contraction in Cycas and Zamia corresponds to that found in angiosperms and Gnetum and further broadens the scope of the activity of tension tissues. This finding possibly indicates that gelatinous fibers originated at a very early period of seed plant evolution.

The ABC model of flower development: then and now

In 1991, we published a paper in Development that proposed the ABC model of flower development, an early contribution to the genetic analysis of development in plants. In this, we used a series of homeotic mutants, and double and triple mutants, to establish a predictive model of organ specification in developing flowers. This model has served as the basis for much subsequent work, especially towards understanding seed plant evolution. Here, we discuss several aspects of this story, that could be a much longer one. One surprising conclusion is that materials and methods that might have led to similar work, and to the same model, were available 100 years before our experiments, belying the belief that progress in biology necessarily comes from improvements in methods, rather than in concepts.

Celebrating Giant Steps toward a Synthetic History of Angiosperm Evolution

Celebrating Giant Steps toward a Synthetic History of Angiosperm Evolution

The evolution of reproductive structures in seed plants: a re‐examination based on insights from developmental genetics

The study of developmental genetics is providing insights into how plant morphology can and does evolve, and into the fundamental nature of specific organs. This new understanding has the potential to revise significantly the way we think about seed plant evolution, especially with regard to reproductive structures. Here, we have sought to take a step in bridging the divide between genetic data and critical fields such as paleobotany and systematics. We discuss the evidence for several evolutionarily important interpretations, including the possibility that ovules represent meristematic axes with their own type of lateral determinate organs (integuments) and a model that considers carpels as analogs of complex leaves. In addition, we highlight the aspects of reproductive development that are likely to be highly labile and homoplastic, factors that have major implications for the understanding of seed plant relationships. Although these hypotheses may suggest that some long-standing interpretations are misleading, they also open up whole new avenues for comparative study and suggest concrete best practices for evolutionary analyses of development.

The highly conserved spermatophyte cell wall DUF642 protein family: Phylogeny and first evidence of interaction with cell wall polysaccharides in vitro

The evolution of spermatophyte plants involved fundamental changes in cell wall structure and function which resulted from diversification of carbohydrates and proteins. Cell wall proteomic analyses identified a novel family of proteins of yet unknown function, the DUF642 (Domain of Unknown Function 642) proteins. To investigate the evolution of the DUF642 gene family, 154 gene sequences from 24 plant species were analyzed, and phylogenetic inferences were conducted using the Maximum Likelihood and Bayesian Inference methods. Orthologous genes were detected in spermatophyte species and absent in non-seed known plant genomes. Protein sequences shared conserved motifs that defined the signature of the family. Distribution of conserved motifs indicated an ancestral intragenic duplication event. Gene phylogeny documented paleoduplication events originating three or four clades, depending on root position. When based on mid-point rooting, it retrieved four monophyletic clades: A, B, C, and D. A glycosylphosphatidylinositol (GPI)-anchor site and one or two galactose-binding domains-like (GBDLs) could be predicted for some DUF642 proteins. The B, C, and D clades grouped the predicted GPI-anchored proteins. First evidence of in vitro interaction of a DUF642 protein with a cell wall polysaccharide fraction is provided. A competition assay with cellulose prevented this interaction. The degree of diversification and the conservation of the family suggested that DUF642 proteins are key components in seed plant evolution.

Evolution of the PEBP Gene Family in Plants: Functional Diversification in Seed Plant Evolution

The phosphatidyl ethanolamine-binding protein (PEBP) gene family is present in all eukaryote kingdoms, with three subfamilies identified in angiosperms (FLOWERING LOCUS T [FT], MOTHER OF FT AND TFL1 [MFT], and TERMINAL FLOWER1 [TFL1] like). In angiosperms, PEBP genes have been shown to function both as promoters and suppressors of flowering and to control plant architecture. In this study, we focus on previously uncharacterized PEBP genes from gymnosperms. Extensive database searches suggest that gymnosperms possess only two types of PEBP genes, MFT-like and a group that occupies an intermediate phylogenetic position between the FT-like and TFL1-like (FT/TFL1-like). Overexpression of Picea abies PEBP genes in Arabidopsis (Arabidopsis thaliana) suggests that the FT/TFL1-like genes (PaFTL1 and PaFTL2) code for proteins with a TFL1-like function. However, PaFTL1 and PaFTL2 also show highly divergent expression patterns. While the expression of PaFTL2 is correlated with annual growth rhythm and mainly confined to needles and vegetative and reproductive buds, the expression of PaFTL1 is largely restricted to microsporophylls of male cones. The P. abies MFT-like genes (PaMFT1 and PaMFT2) show a predominant expression during embryo development, a pattern that is also found for many MFT-like genes from angiosperms. P. abies PEBP gene expression is primarily detected in tissues undergoing physiological changes related to growth arrest and dormancy. A first duplication event resulting in two families of plant PEBP genes (MFT-like and FT/TFL1-like) seems to coincide with the evolution of seed plants, in which independent control of bud and seed dormancy was required, and the second duplication resulting in the FT-like and TFL1-like clades probably coincided with the evolution of angiosperms.

Resolving the systematic and phylogenetic position of isolated ovules: a case study on a new genus from the Permian of China

Isolated ovules occur in many fossil plant assemblages, where they provide important insights into seed-plant diversity and evolution. However, in many cases, the ovules cannot be attributed to individual groups of seed plants, restricting systematic and evolutionary assessments that can be made from otherwise well-characterized fossil taxa. In the present paper, we describe a new kind of ovule discovered in tuffaceous sediments from the Permian-aged Xuanwei Formation in Guizhou Province, China. This ovule has 180° rotational symmetry and an integument comprising a variably thick sarcotesta, a uniformly thick sclerotesta and a uniformly thin endotesta. The nucellus is attached to the integument at least basally and contains a collapsed seed megaspore; a nucellar apex is absent. Both the integument and nucellus are vascularized by paired bundles in the major plane of the ovule; the integumentary bundles are considerably larger than the nucellar bundles and the nucellar bundles emerge from a conical vascular pad. Generation of a three-dimensional reconstruction based on serial peels revealed the gross morphology and organization of the ovule and highlighted the presence of features consistent with cardiocarpalean-type ovules (ovule shape, histological features of the integument) and also features more typical of lagenostomalean- and trigonocarpalean-type ovules (large integumentary bundles, presence of nucellar bundles). To assess the affinity and evolutionary significance of the ovule, it has been included in a cladistic matrix of cardiocarpalean-, lagenostomalean- and trigonocarpalean-type ovules. Results place the ovule within the cardiocarpalean group of ovules known to have been produced by several plant groups, including cordaitean coniferophytes, pteridosperms and Palaeozoic conifers. The cladistic topology supports generic level distinction of the present species, requiring the establishment of Muricosperma guizhouensis Seyfullah & J.Hilton gen. & sp. nov. Lagenostomalean ovules produced by hydrasperman pteridosperms form a basal paraphyletic grade, whereas trigonocarpalean ovules produced by medullosan pteridosperms form a monophyletic group in which Stephanospermum is paraphyletic with respect to Rhynchosperma and Pachytesta. The results also place the Mississippian ovule Mitrospermum bulbosum apart from all of the Pennsylvanian species of Mitrospermum that form a strongly supported clade. Consequently, M. bulbosum is transferred to the new genus Whitaddera Seyfullah & J.Hilton as W. bulbosa (Long) Seyfullah & J.Hilton. © 2010 The Linnean Society of London, Botanical Journal of the Linnean Society, 2010, 164, 84–108.

Early seed plant radiation: an ecological hypothesis

Abstract The earliest steps of seed plant evolution have been extensively studied during the past 25 years. There is a growing body of evidence indicating that the first major spermatophyte radiation occurred during the Late Devonian. At least fourteen Late Devonian species are now recognized, and our knowledge of the diversity of those early seed plants has dramatically increased. Five morphotypes of seeds have been defined, mostly based on cupule morphology and on the number and degree of fusion of the integumentary lobes. In this paper, we critically discuss the abundant environmental information in order to characterize the environment in which this radiation occurred. Sedimentological information indicates that seed plants evolved in disturbed environments. It is suggested that early seed plants thrived in the shade of the dominating Archaeopteris , and that their evolution was canalized by this strong biotic pressure. We also confirm the previous suggestion that the variability of seed morphotypes can be explained by the weak abiotic selective pressure that existed in the Archaeopteris understory.

Nystroemiaceae, a new family of Permian gymnosperms from China with an unusual combination of features

Nystroemiaceae is proposed as a new family of gymnosperms from the Permian of Cathaysia that adds to the diversity of gymnosperms known from this critical time in seed plant evolution. This family is characterized by bifurcating and highly branched pinnate ovuliferous organs bearing bicornute ovules (seeds) and entire leaves with anastomozing veins that are born on complex and modern-looking branching systems with clear axillary branching. The reconstruction is based on numerous large specimens from two localities in North China, in which the different plant parts are attached to each other. The ovulate structures show some apparently plesiomorphic (primitive) character states more typical of early seed plants, whereas the leaves and branches show the clearly apomorphic (derived) character states of broad-leaved gymnosperms.

Interpreting the Function of Saccate Pollen in Ancient Conifers and Other Seed Plants

Saccate pollen is present in many ancient seed plants and in two families of extant conifers. In living conifers, saccate pollen occurs in taxa that combine erect ovulate cones at the time of pollination, inverted ovules, and pollination drops. Sacci function primarily to float pollen grains through a liquid pollination drop and concentrate them near the nucellus of the ovule. The morphology and anatomy of sacci are crucial to the proper operation of this pollination mechanism, and similar size proportions in fossil and modern saccate grains suggest that ancient pollen may have functioned in the same way as modern forms. Multivariate analysis of discrete pollen characters performed on data from in situ grains of several groups of fossil seed plants indicates that modern saccus morphology and structure appear as early as the Upper Carboniferous in some nonconiferous seed plants but later in the evolutionary history of the conifer lineage. Combined evidence from pollen morphology suggests that sacci may have functioned in their modern capacity by the Upper Carboniferous in at least some groups of seed plants, which is consistent with the occurrence of potentially inverted ovules in many extinct groups producing saccate pollen. This study also suggests that modern saccus morphology has evolved independently several times over the course of seed plant evolution.