Search

Red algae (Rhodophyta) belong to the superphylum Archaeplastida, and are a species-rich group exhibiting diverse morphologies. Theory has it that the unicellular red algal ancestor went through a phase of genome contraction caused by adaptation to extreme environments. More recently, the classes Porphyridiophyceae, Bangiophyceae, and Florideophyceae experienced genome expansions, coinciding with an increase in morphological complexity. Transcription-associated proteins (TAPs) regulate transcription, show lineage-specific patterns, and are related to organismal complexity. To better understand red algal TAP complexity and evolution, we investigated the TAP family complement of uni- and multi-cellular red algae. We found that the TAP family complement correlates with gain of morphological complexity in the multicellular Bangiophyceae and Florideophyceae, and that abundance of the C2H2 zinc finger transcription factor family may be associated with the acquisition of morphological complexity. An expansion of heat shock transcription factors (HSF) occurred within the unicellular Cyanidiales, potentially as an adaption to extreme environmental conditions.

The developmental transition from a fertilized ovule to a dispersed diaspore (seed or fruit) involves complex differentiation processes of the ovule's integuments leading to the diversity in mature seed coat structures in angiosperms. In this study, comparative imaging and transcriptome analysis were combined to investigate the morph-specific developmental differences during outer seed coat differentiation and mucilage production in Aethionema arabicum, the Brassicaceae model for diaspore dimorphism. One of the intriguing adaptations of this species is the production and dispersal of morphologically distinct, mucilaginous and non-mucilaginous diaspores from the same plant (dimorphism). The dehiscent fruit morph programme producing multiple mucilaginous seed diaspores was used as the default trait combination, similar to Arabidopsis thaliana, and was compared with the indehiscent fruit morph programme leading to non-mucilaginous diaspores. Synchrotron-based radiation X-ray tomographic microscopy revealed a co-ordinated framework of morph-specific early changes in internal anatomy of developing A. arabicum gynoecia including seed abortion in the indehiscent programme and mucilage production by the mucilaginous seed coat. The associated comparative analysis of the gene expression patterns revealed that the unique seed coat dimorphism of Ae. arabicum provides an excellent model system for comparative study of the control of epidermal cell differentiation and mucilage biosynthesis by the mucilage transcription factor cascade and their downstream cell wall and mucilage remodelling genes. Elucidating the underlying molecular framework of the dimorphic diaspore syndrome is key to understanding differential regulation of bet-hedging survival strategies in challenging environments, timely in the face of global climatic change., (© 2021 The Authors. The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd.)

Plant genomes encode many lineage-specific, unique transcription factors. Expansion of such gene families has been previously found to coincide with the evolution of morphological complexity, although comparative analyses have been hampered by severe sampling bias. Here, we make use of the recently increased availability of plant genomes. We have updated and expanded previous rule sets for domain-based classification of transcription associated proteins (TAPs), comprising transcription factors and transcriptional regulators. The genome-wide annotation of these protein families has been analyzed and made available via the novel TAPscan web interface. We find that many TAP families previously thought to be specific for land plants actually evolved in streptophyte (charophyte) algae; 26 out of 36 TAP family gains are inferred to have occurred in the common ancestor of the Streptophyta (uniting the land plants-Embryophyta-with their closest algal relatives). In contrast, expansions of TAP families were found to occur throughout streptophyte evolution. 17 out of 76 expansion events were found to be common to all land plants and thus probably evolved concomitant with the water-to-land-transition., (© The Author(s) 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.)

Across the plant kingdom, phytochrome (PHY) photoreceptors play an important role during adaptive and developmental responses to light. In Arabidopsis thaliana , light-activated PHYs accumulate in the nucleus, where they regulate downstream signaling components, such as phytochrome interacting factors (PIFs). PIFs are transcription factors that act as repressors of photomorphogenesis; their inhibition by PHYs leads to substantial changes in gene expression. The nuclear function of PHYs, however, has so far been investigated in only a few non-seed plants. Here, we identified putative target genes of PHY signaling in the moss Physcomitrella patens and found light-regulated genes that are putative orthologs of PIF-controlled genes in Arabidopsis. Phylogenetic analyses revealed that an ancestral PIF-like gene was already present in streptophyte algae, i.e., before the water-to-land transition of plants. The PIF homologs in the genome of P. patens resemble Arabidopsis PIFs in their protein domain structure, molecular properties, and physiological effects, albeit with notable differences in the motif-dependent PHY interaction. Our results suggest that P. patens PIFs are involved in PHY signaling. The PHY-PIF signaling node that relays light signals to target genes has been largely conserved during land plant evolution, with evidence of lineage-specific diversification., (© 2017 American Society of Plant Biologists. All rights reserved.)

Transcription factors (TFs) often trigger developmental decisions, yet, their transcripts are often only moderately regulated and thus not easily detected by conventional statistics on expression data. Here we present a method that allows to determine such genes based on trajectory analysis of time-resolved transcriptome data. As a proof of principle, we have analysed apical stem cells of filamentous moss (P. patens) protonemata that develop from leaflets upon their detachment from the plant. By our novel correlation analysis of the post detachment transcriptome kinetics we predict five out of 1,058 TFs to be involved in the signaling leading to the establishment of pluripotency. Among the predicted regulators is the basic helix loop helix TF PpRSL1, which we show to be involved in the establishment of apical stem cells in P. patens. Our methodology is expected to aid analysis of key players of developmental decisions in complex plant and animal systems.

The Plant Transcription Factor Database (PlnTFDB; http://plntfdb.bio.uni-potsdam.de/v3.0/) is an integrative database that provides putatively complete sets of transcription factors (TFs) and other transcriptional regulators (TRs) in plant species (sensu lato) whose genomes have been completely sequenced and annotated. The complete sets of 84 families of TFs and TRs from 19 species ranging from unicellular red and green algae to angiosperms are included in PlnTFDB, representing >1.6 billion years of evolution of gene regulatory networks. For each gene family, a basic description is provided that is complemented by literature references, and multiple sequence alignments of protein domains. TF or TR gene entries include information of expressed sequence tags, 3D protein structures of homologous proteins, domain architecture and cross-links to other computational resources online. Moreover, the different species in PlnTFDB are linked to each other by means of orthologous genes facilitating cross-species comparisons.

Diversification of transcription-associated protein (TAP) families during land plant evolution is a key process yielding increased complexity of plant life. Understanding the evolutionary relationships between these genes is crucial to gain insight into plant evolution. We have determined a substantial set of TAPs that are focused on, but not limited to, land plants using PSI-BLAST searches and subsequent filtering and clustering steps. Phylogenies were created in an automated way using a combination of distance and maximum likelihood methods. Comparison of the data to previously published work confirmed their accuracy and usefulness for the majority of gene families. Evidence is presented that the flowering plant apical stem cell regulator WUSCHEL evolved from an ancestral homeobox gene that was already present after the water-to-land transition. The presence of distinct expanded gene families, such as COP1 and HIT in moss, is discussed within the evolutionary backdrop. Comparative analyses revealed that almost all angiosperm transcription factor families were already present in the earliest land plants, whereas many are missing among unicellular algae. A global analysis not only of transcription factors but also of transcriptional regulators and novel putative families is presented. A wealth of data about plant TAP families and all data accrued throughout their automated detection and analysis are made available via the PlanTAPDB Web interface. Evolutionary relationships of these genes are readily accessible to the nonexpert at a mouse-click. Initial analyses of selected gene families revealed that PlanTAPDB can easily be exerted for knowledge discovery.

Bryophytes are useful models for the study of plant evolution, development, plant–fungal symbiosis, stress responses, and gametogenesis. Additionally, their dominant haploid gametophytic phase makes them great models for functional genomics research, allowing straightforward genome editing and gene knockout via CRISPR or homologous recombination. Until 2016, however, the only bryophyte genome sequence published was that of Physcomitrium patens. Throughout recent years, several other bryophyte genomes and transcriptome datasets became available, enabling better comparative genomics in evolutionary studies. The increase in the number of bryophyte genome and transcriptome resources available has yielded a plethora of annotations, databases, and bioinformatics tools to access the new data, which covers the large diversity of this clade and whose biology comprises features such as association with arbuscular mycorrhiza fungi, sex chromosomes, low gene redundancy, or loss of RNA editing genes for organellar transcripts. Here we provide a guide to resources available for bryophytes with regards to genome and transcriptome databases and bioinformatics tools. [ABSTRACT FROM AUTHOR]

SUMMARY: Aethionema arabicum is an important model plant for Brassicaceae trait evolution, particularly of seed (development, regulation, germination, dormancy) and fruit (development, dehiscence mechanisms) characters. Its genome assembly was recently improved but the gene annotation was not updated. Here, we improved the Ae. arabicum gene annotation using 294 RNA‐seq libraries and 136 307 full‐length PacBio Iso‐seq transcripts, increasing BUSCO completeness by 11.6% and featuring 5606 additional genes. Analysis of orthologs showed a lower number of genes in Ae. arabicum than in other Brassicaceae, which could be partially explained by loss of homeologs derived from the At‐α polyploidization event and by a lower occurrence of tandem duplications after divergence of Aethionema from the other Brassicaceae. Benchmarking of MADS‐box genes identified orthologs of FUL and AGL79 not found in previous versions. Analysis of full‐length transcripts related to ABA‐mediated seed dormancy discovered a conserved isoform of PIF6‐β and antisense transcripts in ABI3, ABI4 and DOG1, among other cases found of different alternative splicing between Turkey and Cyprus ecotypes. The presented data allow alternative splicing mining and proposition of numerous hypotheses to research evolution and functional genomics. Annotation data and sequences are available at the Ae. arabicum DB (https://plantcode.online.uni‐marburg.de/aetar_db). Significance Statement: Improved gene annotation of Aethionema arabicum using long‐read transcript sequencing provides a plethora of full‐length isoforms and an important resource for Brassicaceae evolution studies. [ABSTRACT FROM AUTHOR]

Summary: The Arabidopsis COP1/SPA complex is a key repressor of photomorphogenesis that suppresses light signaling in the dark. Both COP1 and SPA proteins are essential components of this complex. Although COP1 also exists in humans, SPA genes are specific to the green lineage.To elucidate the evolution of SPA genes we analyzed SPA functions in the moss Physcomitrella patens by characterizing knockout mutants in the two Physcomitrella SPA genes PpSPAa and PpSPAb.Light‐grown PpspaAB double mutants exhibit smaller gametophores than the wild‐type. In the dark, PpspaAB mutant gametophores show enhanced continuation of growth but etiolate normally. Gravitropism in the dark is reduced in PpspaAB mutant protonemata. The expression of light‐regulated genes is mostly not constitutive in PpspaAB mutants. PpSPA and PpCOP1 interact; PpCOP1 also interacts with the transcription factor PpHY5 and, indeed, PpHY5 is destabilized in dark‐grown Physcomitrella. Degradation of PpHY5 in darkness, however, does not require PpSPAa and PpSPAb.The data suggest that COP1/SPA‐mediated light signaling is only partially conserved between Arabidopsis and Physcomitrella. Whereas COP1/SPA interaction and HY5 degradation in darkness is conserved, the role of SPA proteins appears to have diverged. PpSPA genes, unlike their Arabidopsis counterparts, are only required to suppress a subset of light responses in darkness. See also the Commentary on this article by Hiltbrunner, 224: 1412–1414. [ABSTRACT FROM AUTHOR]

Arbuscular mycorrhiza is one of the most common plant symbiotic interactions observed today. Due to their nearly ubiquitous occurrence and their beneficial impact on both partners it was suggested that this mutualistic interaction was crucial for plants to colonize the terrestrial habitat approximately 500 Ma ago. On the plant side the association is established via the common symbiotic pathway (CSP). This pathway allows the recognition of the fungal symbiotic partner, subsequent signaling to the nucleus, and initiation of the symbiotic program with respect to specific gene expression and cellular re-organization. The downstream part of the CSP is a regulatory network that coordinates the transcription of genes necessary to establish the symbiosis, comprising multiple GRAS transcription factors (TFs). These regulate their own expression as an intricate transcriptional network. Deduced from non-host genome data the loss of genes encoding CSP components coincides with the loss of the interaction itself. Here, we analyzed bryophyte species with special emphasis on the moss Physcomitrella patens , supposed to be a non-host, for the composition of the GRAS regulatory network components. We show lineage specific losses and expansions of several of these factors in bryophytes, potentially coinciding with the proposed host/non-host status of the lineages. We evaluate losses and expansions and infer clade-specific evolution of GRAS TFs. [ABSTRACT FROM AUTHOR]

Out of a hundred sequenced and published land plant genomes, four are not of flowering plants. This severely skewed taxonomic sampling hinders our comprehension of land plant evolution at large. Moreover, most genetically accessible model species are flowering plants as well. If we are to gain a deeper understanding of how plants evolved and still evolve, and which of their developmental patterns are ancestral or derived, we need to study a more diverse set of plants. Here, I thus argue that we need to sequence genomes of so far neglected lineages, and that we need to develop more non-seed plant model species. [ABSTRACT FROM AUTHOR]

Background Plants have evolved light sensing mechanisms to optimally adapt their growth and development to the ambient light environment. The COP1/SPA complex is a key negative regulator of light signaling in the well-studied dicot Arabidopsis thaliana. COP1 and members of the four SPA proteins are part of an E3 ubiquitin ligase that acts in darkness to ubiquitinate several transcription factors involved in light responses, thereby targeting them for degradation by the proteasome. While COP1 is also found in humans, SPA proteins appear specific to plants. Here, we have functionally addressed evolutionary conservation of COP1 and SPA orthologs from the moss Physcomitrella, the monocot rice and the dicot Arabidopsis. Results To this end, we analyzed the activities of COP1- and SPA-like proteins from Physcomitrella patens and rice when expressed in Arabidopsis. Expression of rice COP1 and Physcomitrella COP1 protein sequences predominantly complemented all phenotypic aspects of the viable, hypomorphic cop1-4 mutant and the null, seedling-lethal cop1-5 mutant of Arabidopsis: rice COP1 fully rescued the constitutive-photomorphogenesis phenotype in darkness and the leaf expansion defect of cop1 mutants, while it partially restored normal photoperiodic flowering in cop1. Physcomitrella COP1 partially restored normal seedling growth and flowering time, while it fully restored normal leaf expansion in the cop1 mutants. In contrast, expression of a SPA ortholog from Physcomitrella (PpSPAb) in Arabidopsis spa mutants did not rescue any facet of the spa mutant phenotype, suggesting that the PpSPAb protein is not functionally conserved or that the Arabidopsis function evolved after the split of mosses and seed plants. The SPA1 ortholog from rice (OsSPA1) rescued the spa mutant phenotype in dark-grown seedlings, but did not complement any spa mutant phenotype in light-grown seedlings or in adult plants. Conclusion Our results show that COP1 protein sequences from Physcomitrella, rice and Arabidopsis have been functionally conserved during evolution, while the SPA proteins showed considerable functional divergence. This may - at least in part - reflect the fact that COP1 is a single copy gene in seed plants, while SPA proteins are encoded by a small gene family of two to four members with possibly sub- or neofunctionalized tasks. [ABSTRACT FROM AUTHOR]

The maize smut fungus Ustilago maydis is a model organism for elucidating host colonization strategies of biotrophic fungi. Here, we performed an in depth transcriptional profiling of the entire plant-associated development of U. maydis wild-type strains. In our analysis, we focused on fungal metabolism, nutritional strategies, secreted effectors, and regulatory networks. Secreted proteins were enriched in three distinct expression modules corresponding to stages on the plant surface, establishment of biotrophy, and induction of tumors. These modules are likely the key determinants for U. maydis virulence. With respect to nutrient utilization, we observed that expression of several nutrient transporters was tied to these virulence modules rather than being controlled by nutrient availability. We show that oligopeptide transporters likely involved in nitrogen assimilation are important virulence factors. By measuring the intramodular connectivity of transcription factors, we identified the potential drivers for the virulence modules. While known components of the b- mating type cascade emerged as inducers for the plant surface and biotrophy module, we identified a set of yet uncharacterized transcription factors as likely responsible for expression of the tumor module. We demonstrate a crucial role for leaf tumor formation and effector gene expression for one of these transcription factors. [ABSTRACT FROM AUTHOR]