Transcriptional Control of Seed Life: New Insights into the Role of the NAC Family.

Transcription factors (TFs) regulate gene expression by binding to specific sequences on DNA through their DNA-binding domain (DBD), a universal process. This update conveys information about the diverse roles of TFs, focusing on the NACs (NAM-ATAF-CUC), in regulating target-gene expression and influencing various aspects of plant biology. NAC TFs appeared before the emergence of land plants. The NAC family constitutes a diverse group of plant-specific TFs found in mosses, conifers, monocots, and eudicots. This update discusses the evolutionary origins of plant NAC genes/proteins from green algae to their crucial roles in plant development and stress response across various plant species. From mosses and lycophytes to various angiosperms, the number of NAC proteins increases significantly, suggesting a gradual evolution from basal streptophytic green algae. NAC TFs play a critical role in enhancing abiotic stress tolerance, with their function conserved in angiosperms. Furthermore, the modular organization of NACs, their dimeric function, and their localization within cellular compartments contribute to their functional versatility and complexity. While most NAC TFs are nuclear-localized and active, a subset is found in other cellular compartments, indicating inactive forms until specific cues trigger their translocation to the nucleus. Additionally, it highlights their involvement in endoplasmic reticulum (ER) stress-induced programmed cell death (PCD) by activating the vacuolar processing enzyme (VPE) gene. Moreover, this update provides a comprehensive overview of the diverse roles of NAC TFs in plants, including their participation in ER stress responses, leaf senescence (LS), and growth and development. Notably, NACs exhibit correlations with various phytohormones (i.e., ABA, GAs, CK, IAA, JA, and SA), and several NAC genes are inducible by them, influencing a broad spectrum of biological processes. The study of the spatiotemporal expression patterns provides insights into when and where specific NAC genes are active, shedding light on their metabolic contributions. Likewise, this review emphasizes the significance of NAC TFs in transcriptional modules, seed reserve accumulation, and regulation of seed dormancy and germination. Overall, it effectively communicates the intricate and essential functions of NAC TFs in plant biology. Finally, from an evolutionary standpoint, a phylogenetic analysis suggests that it is highly probable that the WRKY family is evolutionarily older than the NAC family.

The complete chloroplast genome of Malva wigandii (Alef.) M.F. Ray (Malvaceae, Malvoideae).

The complete chloroplast genome sequence of wild sea mallow Malva wigandii (=Lavatera maritima) was determined and characterized in this study. The genome is 158,162 bp long, containing a pair of inverted repeats regions (IRs) of 25,166 bp, which are separated by a large single-copy region of 86,860 bp and a small single-copy region of 20,970 bp. The sea mallow chloroplast genome has 131 known genes, including 85 protein-coding genes, eight ribosomal RNA genes, and 37 tRNA genes. The phylogenomic analysis showed that M. wigandii forms a cluster with Althaea officinalis with a strong bootstrap support and is sister to sequences belonging to the tribe Gossypieae. All of them are grouped in a lineage with other members of the subfamily Malvoideae. This newly sequenced chloroplast genome sequence provides useful genetic information to explore the origin and evolution of the Mediterranean radiation that gave rise to the generic alliance of Malva.

Plant evolution in alkaline magnesium-rich soils: A phylogenetic study of the Mediterranean genus Hormathophylla (Cruciferae: Alysseae) based on nuclear and plastid sequences.

Habitats with alkaline edaphic substrates are often associated with plant speciation and diversification. The tribe Alysseae, in the family Brassicaceae, epitomizes this evolutionary trend. In this lineage, some genera, like Hormathophylla, can serve as a good case for testing the evolutionary framework. This genus is centered in the western Mediterranean. It grows on different substrates, but mostly on alkaline soils. It has been suggested that diversification in many lineages of the tribe Alysseae and in the genus Hormathophylla is linked to a tolerance for high levels of Mg+2 in xeric environments. In this study, we investigated the controversial phylogenetic placement of Hormathophylla in the tribe, the generic limits and the evolutionary relationships between the species using ribosomal and plastid DNA sequences. We also examined the putative association between the evolution of different ploidy levels, trichome morphology and the type of substrates. Our analyses demonstrated the monophyly of the genus Hormathophylla including all previously described species. Nuclear sequences revealed two lineages that differ in basic chromosome numbers (x = 7 and x = 8 or derived 11, 15) and in their trichome morphology. Contrasting results with plastid genes indicates more complex relationships between these two lineages involving recent hybridization processes. We also found an association between chloroplast haplotypes and substrate, especially in populations growing on dolomites. Finally, our dated phylogeny demonstrates that the origin of the genus took place in the mid-Miocene, during the establishment of temporal land bridges between the Tethys and Paratethys seas, with a later diversification during the upper Pliocene.

Evolution and Expression Patterns of CYC/TB1 Genes in Anacyclus: Phylogenetic Insights for Floral Symmetry Genes in Asteraceae.

Homologs of the CYC/TB1 gene family have been independently recruited many times across the eudicots to control aspects of floral symmetry The family Asteraceae exhibits the largest known diversification in this gene paralog family accompanied by a parallel morphological floral richness in its specialized head-like inflorescence. In Asteraceae, whether or not CYC/TB1 gene floral symmetry function is preserved along organismic and gene lineages is unknown. In this study, we used phylogenetic, structural and expression analyses focused on the highly derived genus Anacyclus (tribe Anthemidae) to address this question. Phylogenetic reconstruction recovered eight main gene lineages present in Asteraceae: two from CYC1, four from CYC2 and two from CYC3-like genes. The species phylogeny was recovered in most of the gene lineages, allowing the delimitation of orthologous sets of CYC/TB1 genes in Asteraceae. Quantitative real-time PCR analysis indicated that in Anacyclus three of the four isolated CYC2 genes are more highly expressed in ray flowers. The expression of the four AcCYC2 genes overlaps in several organs including the ligule of ray flowers, as well as in anthers and ovules throughout development.

Ornithophily for the nonspecialist: Differential pollination efficiency of the Macaronesian island paleoendemic Navaea phoenicea (Malvaceae) by generalist passerines.

PREMISE OF THE STUDY: A bird pollination syndrome exists in the Canary Islands archipelago across independent plant lineages despite the absence of specialist birds. The pollination efficiency of current floral visitors remains unknown for many plant species despite this being a fundamental factor in testing hypotheses about the origin of the syndrome. Here, we studied the components of pollination efficiency in the paleoendemic Navaea phoenicea, a species exhibiting conspicuous anatomical modifications associated with bird pollination. METHODS: We measured the components of the pollination efficiency (PE) of species foraging on flowers. The measured quantitative components were visitation frequency patterns to plants and individual flowers. The qualitative components were the contributions to the fitness of male and female functions (pollen removal and deposition and fruit set). KEY RESULTS: Pollination by warbler species was highly efficient, but visit frequency was low; conversely, Canarian chiffchaffs had high visit frequency and low efficiency. Overall PE was almost 0 for blue tits due to disruptive behavior. We also found insects acting as nectar robbers. CONCLUSIONS: Pollination efficiency of three of the four bird species visiting flowers of Navaea phoenicea may be high enough to maintain selective pressure on floral traits of a relict pollination syndrome. The behavior of these birds plays a crucial role in their pollination efficiency. Perching, by generalist passerines when visiting N. phoenicea flowers, is the most efficient habit. The frequency and PE of insect visits calls into question their role as legitimate visitors.

Pollinator shifts drive petal epidermal evolution on the Macaronesian Islands bird-flowered species.

Pollinator shifts are considered to drive floral trait evolution, yet little is still known about the modifications of petal epidermal surface at a biogeographic region scale. Here we investigated how independent shifts from insects to passerine birds in the Macaronesian Islands consistently modified this floral trait (i.e. absence of papillate cells). Using current phylogenies and extensive evidence from field observations, we selected a total of 81 plant species and subspecies for petal microscopy and comparative analysis, including 19 of the 23 insular species pollinated by opportunistic passerine birds (Macaronesian bird-flowered element). Species relying on passerine birds as the most effective pollinators (bird-pollinated) independently evolved at least five times and in all instances associated with a loss of papillate cells, whereas species with a mixed pollination system (birds plus insects and/or other vertebrates) evolved at least five times in Macaronesia and papillate cells were lost in only 25% of these transitions. Our findings suggest that petal micromorphology is a labile trait during pollinator shifts and that papillate cells tend to be absent on those species where pollinators have limited mechanical interaction with flowers, including opportunistic passerine birds that forage by hovering or from the ground.

Foliar secretory structures in Crotoneae (Euphorbiaceae): Diversity, anatomy, and evolutionary significance.

PREMISE OF THE STUDY: Phylogenetic and morphological studies have helped clarify the systematics of large and complex groups such as the tribe Crotoneae (Euphorbiaceae). However, very little is known about the diversity, structure, and function of anatomical features in this tribe. Crotoneae comprises the species-rich pantropical genus Croton and six small neotropical genera. Here we characterized the anatomy of leaf secretory structures in members of this tribe and explored their function and evolutionary significance. METHODS: Young and mature leaves of 26 species were studied using standard anatomical light microscopy techniques. Three sections of Croton and one representative of Brasiliocroton and Astraea were sampled. KEY RESULTS: We identified five types of secretory structures: laticifers, colleters, extrafloral nectaries, idioblasts, and secretory trichomes. Laticifers were present in all species studied except Croton alabamensis, which instead presented secretory parenchyma cells. Articulated laticifers are reported in Crotoneae for the first time. Colleters of the standard type were observed in the majority of the sampled taxa. Extrafloral nectaries were present in section Cleodora and in B. mamoninha, but absent in section Lamprocroton and Astraea lobata. Idioblasts were spread throughout the palisade and/or spongy parenchyma in most of the studied species. Secretory trichomes were restricted to Lamprocroton except for C. imbricatus. CONCLUSIONS: This study revealed a high diversity of secretory structures, including novel ones, in one of the largest clades of Euphorbiaceae. Our results are promising for investigations on the anatomical and ecophysiological bases of species diversification within Euphorbiaceae.

Floral development and evolution of capitulum structure in Anacyclus (Anthemideae, Asteraceae).

BACKGROUND AND AIMS: Most of the diversity in the pseudanthia of Asteraceae is based on the differential symmetry and sexuality of its flowers. In Anacyclus, where there are (1) homogamous capitula, with bisexual, mainly actinomorphic and pentamerous flowers; and (2) heterogamous capitula, with peripheral zygomorphic, trimerous and long-/short-rayed female flowers, the floral ontogeny was investigated to infer their origin. METHODS: Floral morphology and ontogeny were studied using scanning electron microscope and light microscope techniques. KEY RESULTS: Disc flowers, subtended by paleae, initiate acropetally. Perianth and androecium initiation is unidirectional/simultaneous. Late zygomorphy occurs by enlargement of the adaxial perianth lobes. In contrast, ray flowers, subtended by involucral bracts, initiate after the proximal disc buds, breaking the inflorescence acropetal pattern. Early zygomorphy is manifested through the fusion of the lateral and abaxial perianth lobes and the arrest of the adaxials. We report atypical phenotypes with peripheral 'trumpet' flowers from natural populations. The peripheral 'trumpet' buds initiate after disc flowers, but maintain an actinomorphic perianth. All phenotypes are compared and interpreted in the context of alternative scenarios for the origin of the capitulum and the perianth identity. CONCLUSIONS: Homogamous inflorescences display a uniform floral morphology and development, whereas the peripheral buds in heterogamous capitula display remarkable plasticity. Disc and ray flowers follow different floral developmental pathways. Peripheral zygomorphic flowers initiate after the proximal actinomorphic disc flowers, behaving as lateral independent units of the pseudanthial disc from inception. The perianth and the androecium are the most variable whorls across the different types of flowers, but their changes are not correlated. Lack of homology between hypanthial appendages and a calyx, and the perianth double-sided structure are discussed for Anacyclus together with potential causes of its ray flower plasticity.

Genome size and base composition variation in natural and experimental Narcissus (Amaryllidaceae) hybrids.

BACKGROUND AND AIMS: Although there is evidence that both allopolyploid and homoploid hybridization lead to rapid genomic changes, much less is known about hybrids from parents with different basic numbers without further chromosome doubling. Two natural hybrids, Narcissus × alentejanus (2n = 19) and N. × perezlarae (2n = 29), originated by one progenitor (N. cavanillesii, 2n = 28) and two others (N. serotinus, 2n = 10 and N. miniatus, 2n = 30, respectively) allow us to study how DNA content and composition varies in such hybrids. METHODS: Flow cytometry measurements with two staining techniques, PI and DAPI, were used to estimate 2C values and base composition (AT/GC ratio) in 390 samples from 54 wild populations of the two natural hybrids and their parental species. In addition, 20 synthetic F(1) hybrid individuals were also studied for comparison. KEY RESULTS: Natural hybrids presented 2C values intermediate between those found in their parental species, although intra-population variance was very high in both hybrids, particularly for PI. Genome size estimated from DAPI was higher in synthetic hybrids than in hybrids from natural populations. In addition, differences for PI 2C values were detected between synthetic reciprocal crosses, attributable to maternal effects, as well as between natural hybrids and those synthetic F(1) hybrids in which N. cavanillesii acted as a mother. CONCLUSIONS: Our results suggest that natural hybrid populations are composed of a mixture of markedly different hybrid genotypes produced either by structural chromosome changes, consistent with classic cytogenetic studies in Narcissus, or by transposon-mediated events.

Five molecular markers reveal extensive morphological homoplasy and reticulate evolution in the Malva alliance (Malvaceae).

The Malva alliance is a well-defined group with extensive morphological homoplasy. As a result, the relationships among the taxa as well as the evolution of morphological traits have remained elusive and the traditional classifications are highly artificial. Using five molecular markers (nuclear ITS, plastid matK plus trnK, ndhF, trnL-trnF, psbA-trnH), we arrived at a phylogenetic hypothesis of this group, the genera Alcea, Althaea and Malvalthaea being studied here for the first time with molecular data. Althaea and, in particular, Lavatera and Malva are highly polyphyletic as currently circumscribed, because their diagnostic characters, the number and degree of fusion of the epicalyx bracts, evolve in a highly homoplasious manner. In contrast, fruit morphology largely agrees with the molecularly delimited groups. Hybrid origins confirmed for the genus Malvalthaea and for Lavatera mauritanica and hybridization in the group of ruderal small-flowered mallows underline the importance of reticulate evolution in shaping the history of this group and complicating the interpretation of morphological evolution.

Ecology matters: Atlantic-Mediterranean disjunction in the sand-dune shrub Armeria pungens (Plumbaginaceae).

Inferring the evolutionary history of Mediterranean plant lineages from current genetic, distributional and taxonomic patterns is complex because of a number of palaeoclimatic and geological interconnected factors together with landscape heterogeneity and human influence. Therefore, choosing spatially simplified systems as study groups is a suitable approach. An amplified fragment length polymorphism (AFLP) study using two restriction enzyme combinations (EcoRI/MseI and KpnI/MseI) was carried out to estimate the structure of genetic variation throughout the range of Armeria pungens. This species has a West Iberian-Corso/Sardinian disjunct distribution on coastal sand-dune ecosystems. Bayesian, amova and genetic distance analyses of the AFLP data revealed the same distinguishable genetic groups, which do not match the main geographical disjunction. Corso-Sardinian populations were found to be genetically closer to southwest Portuguese than to those from the Gulf of Cadiz (the closest geographically). Eastwards long-distance dispersal is therefore invoked to explain this geographical disjunction. A GIS analysis based on bioclimatic envelope modelling aiming to characterize the current locations of A. pungens found strong similarities between the Portugal and Corsica-Sardinia sites and less so between these areas and the Gulf of Cadiz. This coincident pattern between AFLP and climatic data suggests that the geographical disjunction is better explained by climatic factors than by the likeliness of a stochastic dispersal event. Such a combined phylogeographical-GIS modelling approach proves to be enlightening in reconstructing the evolutionary history of plant species.

Phylogenetic relationships within the tribe Malveae (Malvaceae, subfamily Malvoideae) as inferred from ITS sequence data.

Phylogenetic relationships among genera of tribe Malveae (Malvaceae, subfamily Malvoideae) were reconstructed using sequences of the internal transcribed spacer (ITS) region of the 18S-26S nuclear ribosomal repeat. Newly generated sequences were combined with those available from previous generic level studies to assess the current circumscription of the tribe, monophyly of some of the larger genera, and character evolution within the tribe. The ITS data do not support monophyly of most generic alliances as presently defined, nor do the data support monophyly of several Malveae genera. Two main well-supported clades were recovered, which correspond primarily to taxa that either possess or lack involucral bracts, respectively. Chromosomal evolution has been dynamic in the tribe with haploid numbers varying from n = 5 to 36. Aneuploid reduction, hybridization, and/or polyploidization have been important evolutionary processes in this group.

Fine-scale geographical structure, intra-individual polymorphism and recombination in nuclear ribosomal internal transcribed spacers in Armeria (Plumbaginaceae).

BACKGROUND AND AIMS: Isolation and drift are the main causes for geographic structure of molecular variation. In contrast, the one found in a previous survey in Armeria (Plumbaginaceae) for nuclear ribosomal ITS multicopy regions was species-independent and has been hypothesized to be due to extensive gene-flow and biased concerted evolution. Since this was inferred from a genus-level phylogenetic analysis, the aim of this study was to check for the occurrence of such structure and the validity of the proposed model at a local scale, in a southern Spanish massif (Sierra Nevada), as well as to examine the evolutionary implications at the organism level. METHODS: In addition to 117 sequences of direct PCR products from genomic DNA, 50 sequences of PCR products from cloned DNA were obtained to analyse cases of intragenomic polymorphisms for the ITS regions. KEY RESULTS: Sequence data confirm the occurrence of a species-independent structure at a local scale and reveal insights through the analysis of contact areas between different ITS copies (ribotypes). A comparison between cloned and direct sequences (a) confirms that, within these contact areas, ITS copies co-occur both in different individuals and within single genomes; and (b) reveals recombination between different copies. CONCLUSIONS: This study supports the utility of direct sequences for detecting intra-individual polymorphism and for partially inferring the ITS copies involved, given previous knowledge of the variability. The main evolutionary implication at the organism level is that gene-flow and concerted evolution shape the geographic structure of ITS variation.

Origin of the disjunct tetraploid Cardamine amporitana (Brassicaceae) assessed with nuclear and chloroplast DNA sequence data.

Seventy-four nucleotide sequences from the ITS regions of nuclear ribosomal DNA and 76 from the trnL-trnF spacer of chloroplast DNA were used to address the origin of tetraploid Cardamine amporitana, the conspecifity of central Italian and northeastern Spanish populations, and the possible cause for such geographic disjunction. Because of the complex lineage relationships in Cardamine, the sampling included 22 taxa. In the results, both data sets are highly congruent in supporting a close relationship of C. amporitana to the widespread Eurasian C. amara. Low genetic variability in northeastern Spanish populations of C. amporitana suggests long-distance dispersal from central Italy. The interior position of the single northeastern Spanish haplotype in a statistical parsimony network of trnL-trnF haplotypes however does not support this scenario and invokes other plausible phylogeographic explanations. The disappearance of geographically intermediate populations and genetic impoverishment by migration and isolation, both probably associated with Quaternary climatic oscillations, appears as an alternative hypothesis to explain the phylogeographic pattern. A recent hybridization event is reported between C. amporitana and a diploid from the C. pratensis group in central Italy on the basis of additive polymorphisms in ITS for all the 22 distinguishing nucleotides.

Additive polymorphisms and reticulation in an ITS phylogeny of thrifts (Armeria, Plumbaginaceae).

A parsimony analysis of 133 sequences of the nuclear ribosomal DNA ITS1+5.8S+ITS2 region from 71 taxa in Armeria was carried out. The presence of additive polymorphic sites (APS; occurring in 14 accessions) fits the reticulate scenario proposed in previous work for explaining the ITS pattern of variation on a much smaller scale and is based mainly on the geographical structure of the data, irrespective of taxonomic boundaries. Despite the relatively low bootstrap values and large polytomies, part of which are likely due to disruptive effects of reticulation and concerted evolution in these multicopy sequences, the ITS analysis has phylogenetic and biogeographic implications. APS detected in this study are consistent with hypothesized hybridization events, although biased concerted evolution, previously documented in the genus, needs to be invoked for specific cases and may be responsible for a possible "sink" effect in terminals from a large clade. The causes for sequences of the same species appearing in different clades (here termed transclade) are discussed.

Phylogeny of the Macaronesian endemic Crambe section Dendrocrambe (Brassicaceae) based on internal transcribed spacer sequences of nuclear ribosomal DNA.

The 14 species of Crambe L. sect. Dendrocrambe DC. (Brassicaceae) form a monophyletic group endemic to the Canary and Madeira archipelagos. Both parsimony and maximum likelihood analyses of sequence data from the two internal transcribed spacer regions of nuclear ribosomal DNA were used to estimate phylogenetic relationships within this section. These analyses support the monophyly of three major clades. No clade is restricted to a single island, and therefore it appears that inter-island colonization has been the main avenue for speciation in these two archipelagos. The two species endemic to Fuerteventura (C. sventenii) and Madeira (C. fruticosa) comprise a clade, providing the first evidence for a floristic link between the Eastern Canary Islands and the archipelago of Madeira. Both maximum likelihood and weighted parsimony analyses show that this clade is sister to the two other clades, although bootstrap support for this relationship is weak. Parsimony optimizations of ecological zones and island distribution suggest a colonization route from the low-altitude areas of the lowland scrub toward the high-elevation areas of the laurel and pine forests. In addition, Tenerife is likely the ancestral island for species endemic to the five westernmost islands of Gran Canaria, La Gomera, El Hierro, La Palma, and Tenerife.