Introduction: The Indeterminate Domain (IDD) proteins are a plant-specific subclass of C2H2 Zinc Finger transcription factors. Some of these transcription factors play roles in diverse aspects of plant metabolism and development, but the function of most of IDD genes is unknown and the molecular evolution of the subfamily has not been explored in detail.Methods: In this study, we mined available genome sequences of green plants (Viridiplantae) to reconstruct the phylogeny and then described the motifs/expression patterns of IDD genes.Key Results: We identified the complete set of IDD genes of 16 Streptophyta genomes. We found that IDD and its sister clade STOP arose by a duplication at the base of Streptophyta. Once on land, the IDD genes duplicated extensively, giving rise to at least ten lineages. Some of these lineages were lost in extant non-vascular plants and gymnosperms, but all of them were retained in angiosperms, duplicating profoundly in dicots and monocots and acquiring, at the same time, surprising heterogeneity in their C-terminal regions and expression patterns.Conclusions: IDDs were present in the last common ancestor of Streptophyta. On land, IDDs duplicated extensively, leading to ten lineages. Later, IDDs were recruited by angiosperms where they diversified greatly in number, C-terminal and expression patterns. Interestingly, such diversification occurred during the evolution of novel traits of the plant body. This study provides a solid framework of the orthology relationships of green land plant IDD transcription factors, thus increasing the accuracy of orthologue identification in model and non-model species and facilitating the identification of agronomically important genes related to plant metabolism and development.

Background: C₄ photosynthesis is a mechanism that plants have evolved to reduce the rate of photorespiration during the carbon fixation process. The C₄ pathway allows plants to adapt to high temperatures and light while more efficiently using resources, such as water and nitrogen. Despite decades of studies, the evolution of the C₄ pathway from a C₃ ancestor remains a biological enigma. Interestingly, species with C₃-C₄ intermediates photosynthesis are usually found closely related to the C₄ lineages. Indeed, current models indicate that the assembly of C₄ photosynthesis was a gradual process that included the relocalization of photorespiratory enzymes, and the establishment of intermediate photosynthesis subtypes. More than a third of the C₄ origins occurred within the grass family (Poaceae). In particular, the Otachyriinae subtribe (Paspaleae tribe) includes 35 American species from C₃, C₄, and intermediates taxa making it an interesting lineage to answer questions about the evolution of photosynthesis. Results: To explore the molecular mechanisms that underpin the evolution of C₄ photosynthesis, the transcriptomic dynamics along four different leaf segments, that capture different stages of development, were compared among Otachyriinae non-model species. For this, leaf transcriptomes were sequenced, de novo assembled, and annotated. Gene expression patterns of key pathways along the leaf segments showed distinct differences between photosynthetic subtypes. In addition, genes associated with photorespiration and the C₄ cycle were differentially expressed between C₄ and C₃ species, but their expression patterns were well preserved throughout leaf development. Conclusions: New, high-confidence, protein-coding leaf transcriptomes were generated using high-throughput short-read sequencing. These transcriptomes expand what is currently known about gene expression in leaves of non-model grass species. We found conserved expression patterns of C₄ cycle and photorespiratory genes among C₃, intermediate, and C₄ species, suggesting a prerequisite for the evolution of C₄ photosynthesis. This dataset represents a valuable contribution to the existing genomic resources and provides new tools for future investigation of photosynthesis evolution.

Inflorescence forms of panicoid grasses (Panicoideae s.s.) are remarkably diverse and they look very labile to human eyes; however, when performing a close inspection one can identify just a small subset of inflorescence types among a huge morphospace of possibilities. Consequently, some evolutionary constraints have restricted, to some extent, the diversification of their inflorescence. Developmental and genetic mechanisms, the photosynthetic type and plant longevity have been postulated as candidate constraints for angiosperms and panicoids in particular; however, it is not clear how these factors operate and which of these have played a key role during the grass inflorescence evolution. To gain insight into this matter the macroevolutionary aspects of panicoid inflorescences are investigated. The inflorescence aspect (lax versus condensed), homogenization, truncation of the terminal spikelet, plant longevity and photosynthetic type were the traits selected for this study. Maximum likelihood and Bayesian Markov chain Monte Carlo methods were used to test different models of evolution and to evaluate the existence of evolutionary correlation among the traits. Both, models and evolutionary correlation were tested and analysed in a phylogenetic context by plotting the characters on a series of trees. For those cases in which the correlation was confirmed, test of contingency and order of trait acquisition were preformed to explore further the patterns of such co-evolution. The data reject the independent model of inflorescence trait evolution and confirmed the existence of evolutionary contingency. The results support the general trend of homogenization being a prerequisite for the loss of the terminal spikelet of the main axis. There was no evidence for temporal order in the gain of homogenization and condensation; consequently, the homogenization and condensation could occur simultaneously. The correlation between inflorescence traits with plant longevity and photosynthetic type is not confirmed. The findings indicate that the lability of the panicoid inflorescence is apparent, not real. The results indicate that the history of the panicoids inflorescence is a combination of inflorescence trait contingency and order of character acquisition. These indicate that developmental and genetic mechanisms may be important constraints that have limited the diversification of the inflorescence form in panicoid grasses.

Otachyriinae Butzin, one of the three subtribes within the Paspaleae tribe of grasses, includes seven genera and approximately 35 species. Interestingly, this subtribe comprises species with C₃, C₃-C₄ intermediate, and C₄ photosynthesis. The circumscription of Otachyriinae has changed through time, and still varies among treatments in current use. The monophyly of this subtribe has been recovered in previous studies based on plastid markers. A phylogenetic study taking into account polyploidy and a low-copy nuclear gene (LCNG) is still lacking in Paspaleae. A phylogeny including data from a LCNG is paramount to uncover reticulated evolution within the group. The purpose of the present study was to reconstruct the evolutionary history of Otachyriinae, based on both chloroplast and LCNG DNA with a focus on polyploidization. Several incongruences between gene trees allowed us to explore relationships between diploid and polyploid taxa. Our study identified several promising topics for future studies: genetic allopolyploidy and autopolyploidy was here documented using the characteristic pattern of double-labelled gene trees. The molecular evidence indicates that at least 40% of species of Otachyriinae show phylogenetic signature of polyploidy (16 taxa appear double-labelled in the nuclear gene trees); furthermore, the results support an allopolyploid origin of at least nine taxa in the subtribe: Rugoloa polygonata, a species with unknown photosynthetic pathway, the proto-kranz species Steinchisma laxum and Rugoloa hylaeica, and the C₃ species Hymenachne felliana, H. grumosa, H. hemitomon, H. donacifolia, H. pernambucense, and P. grande. Also, our results confirm that the C₄ genus Anthaenantia is unambiguously monophyletic and show that Anthaenantia lanata is an autopolyploid. We recognized six genera within subtribe Otachyriinae: Anthaenantia, Hymenachne, Otachyrium, Plagiantha, Rugoloa, and Steinchisma. Finally, Panicum species with historically ambiguous placements, i.e. P. condensatum, P. grande, P. harleyi, P. leptachne, P. longum, and P. stagnatile were transferred to the genus Hymenachne.

Inflorescence forms in grasses lead to a general assumption that their evolution is random. We reconstructed the ancestral inflorescence for Poaceae subtribe Eleusininae and outlined possible evolutionary pathways to test the hypotheses of (1) non-directionality in grass inflorescence evolution and (2) an evolutionary direction from complex to simpler inflorescence architectures in this lineage. By studying early stages of inflorescence and spikelet development, we investigated ontogenetic changes that may correlate with evolutionary pathways identified. The approach presented here indicates that the current diversity of inflorescences found in Eleusininae is probably a result of two distinct evolutionary pathways. The main path involves a multi-staged course with shortening of main axis internodes first, followed by a decrease in number of primary branches and florets per spikelet. We postulate that reduced elongation of the internodes may affect the apical and axillary meristems performance, which in turn promotes a decrease in the number of primary branches and floret per spikelet. Current diversity in inflorescences of Eleusininae may be a consequence of a reductive evolution. We found that the evolutionary directionality of inflorescences in Eleusininae may be associated with developmental events that affected inflorescence morphology at early stages.

RAMOSA1 (RA1) is a Cys2-His2-type (C2H2) zinc finger transcription factor that controls plant meristem fate and identity and has played an important role in maize domestication. Despite its importance, the origin of RA1 is unknown, and the evolution in plants is only partially understood. In this paper, we present a well-resolved phylogeny based on 73 amino acid sequences from 48 embryophyte species. The recovered tree topology indicates that, during grass evolution, RA1 arose from two consecutive SUPERMAN duplications, resulting in three distinct grass sequence lineages: RA1-like A, RA1-like B, and RA1; however, most of these copies have unknown functions. Our findings indicate that RA1 and RA1-like play roles in the nucleus despite lacking a traditional nuclear localization signal. Here, we report that copies diversified their coding region and, with it, their protein structure, suggesting different patterns of DNA binding and protein–protein interaction. In addition, each of the retained copies diversified regulatory elements along their promoter regions, indicating differences in their upstream regulation. Taken together, the evidence indicates that the RA1 and RA1-like gene families in grasses underwent subfunctionalization and neofunctionalization enabled by gene duplication.