Transcriptome sequencing data provide a solid base to understand the phylogenetic relationships, biogeography and reticulated evolution of the genus Zamia L. (Cycadales: Zamiaceae).

Background And Aims: Cycads are a key lineage to understand the early evolution of seed plants and their response to past environmental changes. However, tracing the evolutionary trajectory of cycad species is challenging when the robust relationships at inter- or infrageneric level are not well resolved.

Methods: Here, using 2901 single-copy nuclear genes, we explored the species relationships and gene flow within the second largest genus of cycads, i.

The evolution and development of sporangia-The fundamental reproductive organ of land plant sporophytes.

A key innovation of land plants is the origin and evolution of the sporangium, the fundamental reproductive structure of the diploid sporophyte. In vascular plants, whether the structure is a cone, fertile leaf, or flower-all are clusters of sporangia. The evolution of morphologically distinct sporangia (heterospory) and retention of the gametophyte evolved three times independently as a prerequisite for the evolution of seeds.

Evolutionary trends of reproductive phenotype in Cycadales: an analysis of morphological evolution in Ceratozamia.

Background And Aims: The size and shape of reproductive structures is especially relevant in evolution because these characters are directly related to the capacity for pollination and seed dispersal, a process that plays a basic role in evolutionary patterns. The evolutionary trajectories of reproductive phenotypes in gymnosperms have received special attention in terms of pollination and innovations related to the emergence of the spermatophytes. However, variability of reproductive structures, evolutionary trends and the role of environment in the evolution of cycad species have not been well documented and explored.

The genome of the Wollemi pine, a critically endangered "living fossil" unchanged since the Cretaceous, reveals extensive ancient transposon activity.

We present the genome of the living fossil, , a southern hemisphere conifer morphologically unchanged since the Cretaceous. Presumed extinct until rediscovery in 1994, the Wollemi pine is critically endangered with less than 60 wild adults threatened by intensifying bushfires in the Blue Mountains of Australia. The 12 Gb genome is among the most contiguous large plant genomes assembled, with extremely low heterozygosity and unusual abundance of DNA transposons.

Phylotranscriptomics Shed Light on Intrageneric Relationships and Historical Biogeography of (Cycadales).

Brongn. is one of the species-rich genera of Cycadales comprising 38 species that are mainly distributed in Mexico, with a few species reported from neighboring regions. Phylogenetic relationships within the genus need detailed investigation based on extensive datasets and reliable systematic approaches.

Monograph of (Zamiaceae, Cycadales): an endangered genus.

(Zamiaceae, Cycadales), is a member one of the most endangered seed plant groups. Species of grow from near sea level up to 2,100 meters in Mexico and Mesoamerica. We present a modern taxonomic treatment of , based on fieldwork combined with detailed study of herbarium specimens in and from Mexico and Central America.

Phylotranscriptomic Analyses of Mycoheterotrophic Monocots Show a Continuum of Convergent Evolutionary Changes in Expressed Nuclear Genes From Three Independent Nonphotosynthetic Lineages.

Mycoheterotrophy is an alternative nutritional strategy whereby plants obtain sugars and other nutrients from soil fungi. Mycoheterotrophy and associated loss of photosynthesis have evolved repeatedly in plants, particularly in monocots. Although reductive evolution of plastomes in mycoheterotrophs is well documented, the dynamics of nuclear genome evolution remains largely unknown.

Phylogenomic resolution of order- and family-level monocot relationships using 602 single-copy nuclear genes and 1375 BUSCO genes.

We assess relationships among 192 species in all 12 monocot orders and 72 of 77 families, using 602 conserved single-copy (CSC) genes and 1375 benchmarking single-copy ortholog (BUSCO) genes extracted from genomic and transcriptomic datasets. Phylogenomic inferences based on these data, using both coalescent-based and supermatrix analyses, are largely congruent with the most comprehensive plastome-based analysis, and nuclear-gene phylogenomic analyses with less comprehensive taxon sampling. The strongest discordance between the plastome and nuclear gene analyses is the monophyly of a clade comprising Asparagales and Liliales in our nuclear gene analyses, versus the placement of Asparagales and Liliales as successive sister clades to the commelinids in the plastome tree.

Developmental Morphology and Anatomy Shed Light on Both Parallel and Convergent Evolution of the Umbellate Inflorescence in Monocots, Underlain by a New Variant of Metatopy.

Inflorescence structure is very diverse and homoplasious, yet the developmental basis of their homoplasy is poorly understood. To gain an understanding of the degree of homology that these diverse structures share, we characterize the developmental morphology and anatomy of various umbellate inflorescences across the monocots and analyzed them in an evolutionary context. To characterize branching order, we characterized the developmental morphology of multiple inflorescences with epi-illumination, and vascular anatomy with Laser Ablation Tomography, a novel high-throughput method to reconstruct three-dimensional vasculature.

Flower and Spikelet Construction in Rapateaceae (Poales).

The family Rapateaceae represents an early-divergent lineage of Poales with biotically pollinated showy flowers. We investigate developmental morphology and anatomy in all three subfamilies and five tribes of Rapateaceae to distinguish between contrasting hypotheses on spikelet morphology and to address questions on the presence of nectaries and gynoecium structure. We support an interpretation of the partial inflorescence (commonly termed spikelet), as a uniaxial system composed of a terminal flower and numerous empty phyllomes.

Expression analyses in Ginkgo biloba provide new insights into the evolution and development of the seed.

Although the seed is a key morphological innovation, its origin remains unknown and molecular data outside angiosperms is still limited. Ginkgo biloba, with a unique place in plant evolution, being one of the first extant gymnosperms where seeds evolved, can testify to the evolution and development of the seed. Initially, to better understand the development of the ovules in Ginkgo biloba ovules, we performed spatio-temporal expression analyses in seeds at early developing stages, of six candidate gene homologues known in angiosperms: WUSCHEL, AINTEGUMENTA, BELL1, KANADI, UNICORN, and C3HDZip.

Plant ecological genomics at the limits of life in the Atacama Desert.

The Atacama Desert in Chile-hyperarid and with high-ultraviolet irradiance levels-is one of the harshest environments on Earth. Yet, dozens of species grow there, including Atacama-endemic plants. Herein, we establish the Talabre-Lejía transect (TLT) in the Atacama as an unparalleled natural laboratory to study plant adaptation to extreme environmental conditions.

Cycad-Weevil Pollination Symbiosis Is Characterized by Rapidly Evolving and Highly Specific Plant-Insect Chemical Communication.

Coevolution between plants and insects is thought to be responsible for generating biodiversity. Extensive research has focused largely on antagonistic herbivorous relationships, but mutualistic pollination systems also likely contribute to diversification. Here we describe an example of chemically-mediated mutualistic species interactions affecting trait evolution and lineage diversification.

Contrasting physiological traits of shade tolerance in Pinus and Podocarpaceae native to a tropical Vietnamese forest: insight from an aberrant flat-leaved pine.

The absence of pines from tropical forests is a puzzling biogeographical oddity potentially explained by traits of shade intolerance. Pinus krempfii (Lecomte), a flat-leaved pine endemic to the Central Highlands of Vietnam, provides a notable exception as it seems to compete successfully with shade-tolerant tropical species. Here, we test the hypothesis that successful conifer performance at the juvenile stage depends on physiological traits of shade tolerance by comparing the physiological characteristics of P.

A novelty in (Zamiaceae, Cycadales) from the Sierra Madre del Sur, Mexico: biogeographic and morphological patterns, DNA barcoding and phenology.

is a genus of cycads occurring in eastern Mexico and Central America. In this study, we describe a new species from the Pacific region of Mexico in Guerrero state. This locality represents the most northwestern Mexico distribution for the genus.

The Plant Ontology Facilitates Comparisons of Plant Development Stages Across Species.

The Plant Ontology (PO) is a community resource consisting of standardized terms, definitions, and logical relations describing plant structures and development stages, augmented by a large database of annotations from genomic and phenomic studies. This paper describes the structure of the ontology and the design principles we used in constructing PO terms for plant development stages. It also provides details of the methodology and rationale behind our revision and expansion of the PO to cover development stages for all plants, particularly the land plants (bryophytes through angiosperms).

Complex reproductive secretions occur in all extant gymnosperm lineages: a proteomic survey of gymnosperm pollination drops.

Complex protein-containing reproductive secretions are a conserved trait amongst all extant gymnosperms; the pollination drops of most groups include carbohydrate-modifying enzymes and defence proteins. Pollination drops are aqueous secretions that receive pollen and transport it to the ovule interior in gymnosperms (Coniferales, Cycadales, Ginkgoales, Gnetales). Proteins are well established as components of pollination drops in conifers (Coniferales) and Ephedra spp.

Monocot plastid phylogenomics, timeline, net rates of species diversification, the power of multi-gene analyses, and a functional model for the origin of monocots.

Premise Of The Study: We present the first plastome phylogeny encompassing all 77 monocot families, estimate branch support, and infer monocot-wide divergence times and rates of species diversification.

Methods: We conducted maximum likelihood analyses of phylogeny and BAMM studies of diversification rates based on 77 plastid genes across 545 monocots and 22 outgroups. We quantified how branch support and ascertainment vary with gene number, branch length, and branch depth.

Taxonomic review of (Zamiaceae) in the Sierra Madre Oriental, Mexico.

The genus is revised for the Sierra Madre Oriental in Mexico. This region is one of the biogeographic areas with the greatest diversity of species in this genus. These species are highly variable morphologically and this variability has led to a complex taxonomic history with many synonyms, particularly with reference to .

Gymnosperms on the EDGE.

Driven by limited resources and a sense of urgency, the prioritization of species for conservation has been a persistent concern in conservation science. Gymnosperms (comprising ginkgo, conifers, cycads, and gnetophytes) are one of the most threatened groups of living organisms, with 40% of the species at high risk of extinction, about twice as many as the most recent estimates for all plants (i.e.

Crowds Replicate Performance of Scientific Experts Scoring Phylogenetic Matrices of Phenotypes.

Scientists building the Tree of Life face an overwhelming challenge to categorize phenotypes (e.g., anatomy, physiology) from millions of living and fossil species.

The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution.

The draft genome of the moss model, Physcomitrella patens, comprised approximately 2000 unordered scaffolds. In order to enable analyses of genome structure and evolution we generated a chromosome-scale genome assembly using genetic linkage as well as (end) sequencing of long DNA fragments. We find that 57% of the genome comprises transposable elements (TEs), some of which may be actively transposing during the life cycle.

The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics.

The Planteome project (http://www.planteome.org) provides a suite of reference and species-specific ontologies for plants and annotations to genes and phenotypes.