evolSOM: An R package for analyzing conservation and displacement of biological variables with self-organizing maps.

Motivation: Unraveling the connection between genes and traits is crucial for solving many biological puzzles. Ribonucleic acid molecules and proteins, derived from these genetic instructions, play crucial roles in shaping cell structures, influencing reactions, and guiding behavior. This fundamental biological principle links genetic makeup to observable traits, but integrating and extracting meaningful relationships from this complex, multimodal data present a significant challenge.

Molecular Evolution of RAMOSA1 (RA1) in Land Plants.

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.

De novo transcriptome assemblies of C and C non-model grass species reveal key differences in leaf development.

Background: C photosynthesis is a mechanism that plants have evolved to reduce the rate of photorespiration during the carbon fixation process. The C 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 C pathway from a C ancestor remains a biological enigma.

Step by step evolution of Indeterminate Domain (IDD) transcriptional regulators: from algae to angiosperms.

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.

Evolutionary history of HOMEODOMAIN LEUCINE ZIPPER transcription factors during plant transition to land.

Plant transition to land required several regulatory adaptations. The mechanisms behind these changes remain unknown. Since the evolution of transcription factors (TFs) families accompanied this transition, we studied the HOMEODOMAIN LEUCINE ZIPPER (HDZ) TF family known to control key developmental and environmental responses.

Macro-Climatic Distribution Limits Show Both Niche Expansion and Niche Specialization among C4 Panicoids.

Grasses are ancestrally tropical understory species whose current dominance in warm open habitats is linked to the evolution of C4 photosynthesis. C4 grasses maintain high rates of photosynthesis in warm and water stressed environments, and the syndrome is considered to induce niche shifts into these habitats while adaptation to cold ones may be compromised. Global biogeographic analyses of C4 grasses have, however, concentrated on diversity patterns, while paying little attention to distributional limits.

TCP transcription factor, BRANCH ANGLE DEFECTIVE 1 (BAD1), is required for normal tassel branch angle formation in maize.

In grass inflorescences, a structure called the "pulvinus" is found between the inflorescence main stem and lateral branches. The size of the pulvinus affects the angle of the lateral branches that emerge from the main axis and therefore has a large impact on inflorescence architecture. Through EMS mutagenesis we have identified three complementation groups of recessive mutants in maize having defects in pulvinus formation.

Determinants of the DNA binding specificity of class I and class II TCP transcription factors.

TCP proteins constitute a family of plant transcription factors with more than 20 members in angiosperms. They can be divided in two classes based on sequence homology and the presence of an insertion within the basic region of the TCP DNA binding and dimerization domain. Here, we describe binding site selection studies with the class I protein TCP16, showing that its DNA binding preferences are similar to those of class II proteins.

Evolution of AGL6-like MADS box genes in grasses (Poaceae): ovule expression is ancient and palea expression is new.

AGAMOUS-like6 (AGL6) genes encode MIKC-type MADS box transcription factors and are closely related to SEPALLATA and AP1/FUL-like genes. Here, we focus on the molecular evolution and expression of the AGL6-like genes in grasses. We have found that AGL6-like genes are expressed in ovules, lodicules (second whorl floral organs), paleas (putative first whorl floral organs), and floral meristems.

Diversification of inflorescence development in the PCK clade (Poaceae: Panicoideae: Paniceae).

In grasses, inflorescence diversification and its correlation with species evolution are intriguing and not well understood. Part of this problem lies in our lack of comprehension about the inflorescence morphological complexity of grasses. We focused our study on the PCK clade (named for phosphoenol pyruvate carboxykinase), a well-supported monophyletic group for which the relationships among its taxa are not well resolved.

Evidence for distinct roles of the SEPALLATA gene LEAFY HULL STERILE1 in Eleusine indica and Megathyrsus maximus (Poaceae).

LEAFY HULL STERILE1 (LHS1) is an MIKC-type MADS-box gene in the SEPALLATA class. Expression patterns of LHS1 homologs vary among species of grasses, and may be involved in determining palea and lemma morphology, specifying the terminal floret of the spikelet, and sex determination. Here we present LHS1 expression data from Eleusine indica (subfamily Chloridoideae) and Megathyrsus maximus (subfamily Panicoideae) to provide further insights into the hypothesized roles of the gene.

Inflorescence, spikelet, and floral development in Panicum maximum and Urochloa plantaginea (Poaceae).

Inflorescence development in Panicum maximum and Urochloa plantaginea was comparatively studied with scanning electron and light microscopy to test the transfer of P. maximum to Urochloa and to look for developmental features applicable to future cladistic studies of the phosphoenol pyruvate carboxykinase (PCK) subtype of C(4) photosynthesis clade (P. maximum and some species of Brachiaria, Chaetium, Eriochloa, Melinis, and Urochloa).