Dynamic evolution of MADS-box genes in extant ferns via large-scale phylogenomic analysis.

Introduction: Several studies of MADS-box transcription factors in flowering plants have been conducted, and these studies have indicated that they have conserved functions in floral organ development; MIKC-type MADS-box genes has been proved to be expanded in ferns, however, few systematic studies of these transcription factors have been conducted in non-seed plants. Although ferns and seed plants are sister groups, they exhibit substantial morphological differences.

Methods: Here, we clarified the evolution of MADS-box genes across 71 extant fern species using available transcriptome, genome, and gene expression data.

 (Marattiaceae), a new fern species from Yunnan, China.

Ting Wang tris, H.F.Chen & Y.

Whole Genome Duplication Events Likely Contributed to the Aquatic Adaptive Evolution of Parkerioideae.

As the only aquatic lineage of Pteridaceae, Parkerioideae is distinct from many xeric-adapted species of the family and consists of the freshwater species and the only mangrove ferns from the genus . Previous studies have shown that whole genome duplication (WGD) has occurred in Parkerioideae at least once and may have played a role in their adaptive evolution; however, more in-depth research regarding this is still required. In this study, comparative and evolutionary transcriptomics analyses were carried out to identify WGDs and explore their roles in the environmental adaptation of Parkerioideae.

Insights into cryptic speciation of quillworts in China.

Cryptic species are commonly misidentified because of high morphological similarities to other species. One group of plants that may harbor large numbers of cryptic species is the quillworts ( spp.), an ancient aquatic plant lineage.

Simplified Genomic Data Revealing the Decline of Population Accompanied by the Uplift of Dry-Hot Valley in Yunnan, China.

Understanding the evolutionary history of endangered species is crucial for identifying the main reasons for species endangerment in the past and predicting the changing trends and evolutionary directions of their future distribution. In order to study the impact of environmental changes caused by deep valley incision after the uplift of the Qinghai-Tibet Plateau on endangered species, we collected 23 samples belonging to four populations of , an endangered fern endemic to the dry-hot valleys (DHV) of Yunnan. Single-nucleotide variation sites (SNPs) were obtained by the genotyping-by-sequencing (GBS) method, and approximately 8085 SNP loci were identified.

Untying the Gordian knot of plastid phylogenomic conflict: A case from ferns.

Phylogenomic studies based on plastid genome have resolved recalcitrant relationships among various plants, yet the phylogeny of Dennstaedtiaceae at the level of family and genera remains unresolved due to conflicting plastid genes, limited molecular data and incomplete taxon sampling of previous studies. The present study generated 30 new plastid genomes of Dennstaedtiaceae (9 genera, 29 species), which were combined with 42 publicly available plastid genomes (including 24 families, 27 genera, 42 species) to explore the evolution of Dennstaedtiaceae. In order to minimize the impact of systematic errors on the resolution of phylogenetic inference, we applied six strategies to generate 30 datasets based on CDS, intergenic spacers, and whole plastome, and two tree inference methods (maximum-likelihood, ML; and multispecies coalescent, MSC) to comprehensively analyze the plastome-scale data.

Population Diversity Analysis Provide Insights into Provenance Identification of .

() is a valuable genuine herb. The source of this species is difficult to be identified by traditional methods including morphology, spectroscopy, and chromatography. We used the restriction site-associated DNA sequencing (RAD-seq) approach to perform the high-throughput sequencing of 24 provenances.

Lycophyte transcriptomes reveal two whole-genome duplications in Lycopodiaceae: Insights into the polyploidization of .

Lycophytes are an ancient clade of the non-flowering vascular plants with chromosome numbers that vary from tens to hundreds. They are an excellent study system for examining whole-genome duplications (WGDs), or polyploidization, in spore-dispersed vascular plants. However, a lack of genome sequence data limits the reliable detection of very ancient WGDs, small-scale duplications (SSDs), and recent WGDs.

and (Pteridaceae), two new diploid species from China, based on morphological, cytological, and molecular data.

Understanding how natural hybridization and polyploidizations originate in plants requires identifying potential diploid ancestors. However, cryptic plant species are widespread, particularly in (Pteridaceae). Identifying cryptic species with different polyploidy levels is a challenge because spp.

Phylogenomic Analysis Reconstructed the Order Matoniales from Paleopolyploidy Veil.

Phylogenetic conflicts limit our understanding of the evolution of terrestrial life under multiple whole genome duplication events, and the phylogeny of early terrestrial plants remains full of controversy. Although much incongruence has been solved with so-called robust topology based on single or lower copy genes, the evolutionary mechanisms behind phylogenetic conflicts such as polyploidization remain poorly understood. Here, through decreasing the effects of polyploidization and increasing the samples of species, which represent all four orders and eight families that comprise early leptosporangiate ferns, we have reconstructed a robust phylogenetic tree and network with 1125 1-to-1 orthologs based on both coalescent and concatenation methods.

Convergent molecular evolution of phosphoenolpyruvate carboxylase gene family in C and crassulacean acid metabolism plants.

Phosphoenolpyruvate carboxylase (PEPC), as the key enzyme in initial carbon fixation of Cand crassulacean acid mechanism (CAM) pathways, was thought to undergo convergent adaptive changes resulting in the convergent evolution of C and CAM photosynthesis in vascular plants. However, the integral evolutionary history and convergence of PEPC in plants remain poorly understood. In the present study, we identified the members of PEPC gene family across green plants with seventeen genomic datasets, found ten conserved motifs and modeled three-dimensional protein structures of 90 plant-type PEPC genes.

, a new endangered species of Dipteridaceae from Shenzhen, southern China.

, a new species of ferns from Shenzhen, Guangdong, southern China, is identified and described. It closely resembles but possesses several unique traits, such as long rhizome scales, castaneous stipe, and abaxially pale fronds with two fan-shaped fronds connected by a broad wing. Molecular evidence showed that is allied to , whereas it has morphologically significant differences ( < 0.

(Dryopteridaceae), a new species from Hunan, China.

, a new species growing on limestone in the Wulingshan Mountains, Hunan, China, is described and illustrated. This species is most similar to and on general morphological traits, such as the form of scales, rhizome and sori, but differs by the number of vascular bundles at the base of the petiole, length to width ratio of lamina, stalk length of basal pinnae, division of the lamina, apex form of the pinnule and habitat. Moreover, molecular phylogenetic analysis using the chloroplast L gene suggested that , as the sister group of , is a monophyletic clade.

Finding missing diversity from synonyms of (Pteridaceae).

Although taxonomists target the remote wild regions to discover new species, taxa lacking a comprehensive and modern systematic treatment may be the new hotspot for biodiversity discovery. The development of molecular systematics integrated with microscopic observation techniques has greatly improved the ability of taxonomists to identify species correctly. Ching ex J.

Rediscovery of (Marattiaceae) after 100 years, and its revision.

The border area between south-eastern Yunnan, China and northern Vietnam is one of the regions with richest biological diversity including that of the fern genus (Marattiaceae). Based on the analysis of morphology and DNA sequences of multiple chloroplast regions (, , spacer and spacer), we revised (Hayata) J.M.

Transcriptomic Evidence of Adaptive Evolution of the Epiphytic Fern .

Epiphytic ferns have been found to flourish after angiosperms dominated forest communities, and they play important roles in rainforest canopies. How do epiphytic ferns adapt to tropical rainforest canopy habitats? At present, we know little about the molecular mechanism underlying this adaptation. is a well-known epiphytic fern that is closely related to the terrestrial species .

Gold nanoparticles anchored onto three-dimensional graphene: simultaneous voltammetric determination of dopamine and uric acid.

An electrochemical sensor is described for simultaneous voltammetric determination of dopamine (DA) and uric acid (UA). It is based on the use of a nanomaterial composed of gold nanoparticles and 3-dimensional graphene (Au NP@3D GR). The 3D GR was prepared by chemical vapor deposition using nickel nanoparticles as the template at a temperature of around 900 °C.

Golf ball-like MoS nanosheet arrays anchored onto carbon nanofibers for electrochemical detection of dopamine.

Arrays of molybdenum(IV) disulfide nanosheets resembling the shape of golf balls (MoS NSBs) were deposited on carbon nanofibers (CNFs), which are shown to enable superior electrochemical detection of dopamine without any interference by uric acid. The MoS NSBs have a diameter of ∼ 2 μm and are made up of numerous bent nanosheets. MoS NSBs are connected by the CNFs through the center of the balls.

Dating Whole Genome Duplication in and Potential Adaptive Values of Retained Gene Duplicates.

Whole-genome duplications (WGDs) are widespread in plants and frequently coincide with global climatic change events, such as the Cretaceous-Tertiary (KT) extinction event approximately 65 million years ago (mya). Ferns have larger genomes and higher chromosome numbers than seed plants, which likely resulted from multiple rounds of polyploidy. Here, we use diploid and triploid material from a model fern species, , for the detection of WGDs.

The identity of , as a new synonym of (Dennstaedtiaceae), based on morphology and DNA barcoding and the new distribution.

Based on field observations and examinations of herbarium specimens (including type material), consulting the original literature and molecular phylogenetic analysis of the and sequences, it is concluded that is conspecific with and is here formally treated as a synonym of it. Additionally is reported with new distribution records in Guangdong, Guangxi and the Hainan Island of China, respectively.