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.

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.

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.

The complete chloroplast genome sequence of the water fern (Pteridaceae).

This work determined and analyzed the complete chloroplast genome sequence of (Linnaeus) Brongniart 1822 (Pteridaceae). The results indicate that the total chloroplast genome size of is 149,399 bp in length, and the genome contains a large single-copy (LSC) region of 83,580 bp, a small single-copy (SSC) region of 21,241 bp, and a pair of inverted repeat (IR) regions of 22,289 bp. The GC content of is 36.

Protoplast technology enables the identification of efficient multiplex genome editing tools in Phalaenopsis.

Phalaenopsis orchids are popular ornamental plants worldwide. The application and optimization of efficient CRISPR-Cas genome editing toolkits in Phalaenopsis greatly accelerate the development of orchid gene function and breeding research. However, these methods are greatly hindered by the deficiency of a rapid screening system.

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.

Analysis of Comparative Transcriptome and Positively Selected Genes Reveal Adaptive Evolution in Leaf-Less and Root-Less Whisk Ferns.

While roots and leaves have evolved independently in lycophytes, ferns and seed plants, there is still confusion regarding the morphological evolution of ferns, especially in whisk ferns, which lack true leaves and roots and instead only exhibit leaf-like appendages and absorptive rhizoids. In this study, analyses of comparative transcriptomics on positively selected genes were performed to provide insights into the adaptive evolution of whisk fern morphologies. Significantly clustered gene families specific to whisk ferns were mainly enriched in Gene Ontology (GO) terms "binding proteins" and "transmembrane transporter activity", and positive selection was detected in genes involved in transmembrane transporter activities and stress response (e.

Corrigendum: Phylogeny and Taxonomy on Cryptic Species of Forked Ferns of Asia.

[This corrects the article DOI: 10.3389/fpls.2021.

Chromosome-Scale Assembly of the Genome Provides Insights Into the Molecular Mechanism of the Biosynthesis of the Medicinal Active Ingredient of .

Orchids constitute approximately 10% of flowering plant species. However, only about 10 orchid genomes have been published. Metabolites are the main way through which orchids respond to their environment.

Phylogenetic incongruence in orchids.

, which includes approximately 80 species, is one of the most ornamental and cultivated orchid genera. However, a lack of markers and sparse sampling have posed great challenges to resolving the phylogenetic relationships within the genus. In the present study, we reconstructed the phylogenetic relationships by utilizing one nuclear DNA (nrITS) and seven plastid genes (, , , , , , and ) from 70 species (varieties) in .

, 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.

Phylogeny and Taxonomy on Cryptic Species of Forked Ferns of Asia.

Cryptic species comprise two or more taxa that are grounded under a single name because they are more-or-less indistinguishable morphologically. These species are potentially important for detailed assessments of biodiversity, but there now appear to be many more cryptic species than previously estimated. One taxonomic group likely to contain many cryptic species is , a genus of forked ferns that occurs commonly along roadsides in Asia.

The complete chloroplast genome sequence of (Orchidaceae).

In the present study, we reported and characterized the complete chloroplast genome of a moth orchid, , which is endemic to South China. Its plastid genome size is 145,373 bp, consisting of a large single copy (LSC) region (84,996 bp), a small single-copy region (10,668 bp), and two inverted repeats (IRs) regions (24,855 bp). A total of 122 plastid genes were annotated, comprising 76 protein-coding genes, 38 tRNA genes, and 8 rRNA genes.

The complete chloroplast genome sequence of (Orchidaceae, Aeridinae).

The complete chloroplast genome sequence of was assembled and analyzed in this work. The total chloroplast genome size of was 148,124 bp in length, containing a large single-copy (LSC) region of 86,079 bp, a small single-copy (SSC) region of 10,799 bp, and a pair of inverted repeat (IR) regions of 25,623 bp. The GC content of was 36.

The genome of Cymbidium sinense revealed the evolution of orchid traits.

The Orchidaceae is of economic and ecological importance and constitutes ˜10% of all seed plant species. Here, we report a genome physical map for Cymbidium sinense, a well-known species belonging to genus Cymbidium that has thousands of natural variation varieties of flower organs, flower and leaf colours and also referred as the King of Fragrance, which make it arose into a unique cultural symbol in China. The high-quality chromosome-scale genome assembly was 3.

The chloroplast genome evolution of Venus slipper (Paphiopedilum): IR expansion, SSC contraction, and highly rearranged SSC regions.

Background: Paphiopedilum is the largest genus of slipper orchids. Previous studies showed that the phylogenetic relationships of this genus are not well resolved, and sparse taxon sampling documented inverted repeat (IR) expansion and small single copy (SSC) contraction of the chloroplast genomes of Paphiopedilum.

Results: Here, we sequenced, assembled, and annotated 77 plastomes of Paphiopedilum species (size range of 152,130 - 164,092 bp).

The complete chloroplast genome of (Orchidaceae).

Schltr., is a critically Endangered orchid (IUCN). In this study, we report the first complete chloroplast (cp) genome of to provide the underlying information for genetic breeding and conservation studies of this species.

The complete chloroplast genome of Rolfe (Orchidaceae: Coelogyninae).

In this study, the complete chloroplast genome of is presented, which represents first complete plastid genome of the genus in the subtribe Coelogyninae. The chloroplast genome size is 159,729 bp, including a GC content of 37.3% and 135 genes (89 protein-coding genes, 38 tRNA genes, 8 rRNA genes).

The complete chloroplast genome sequence of (Melastomataceae).

, a shrub endemic to Hong Kong and Guangdong, south China, growing on low-altitude hillsides, under the forest. The species is controversial in classification. Herein, we report the complete chloroplast genome sequence assembled from Illumina pair-end sequencing data, with aims to resolve its relationship with the related species.

Author Correction: The Apostasia genome and the evolution of orchids.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Functional analysis of a novel -glycosyltransferase in the orchid .

Flavonoids, which are a diverse class of phytonutrients, are used by organisms to respond to nearly all abiotic stresses and are beneficial for human health. Glycosyltransferase, used during the last step of flavonoid biosynthesis, is important in flavonoid enrichment. However, little is known about glycosyltransferase in the orchid ().

Complete chloroplast genome of an orchid species Lindl.

Lindl. is an ornamental plant and its native range is south China to north Vietnam. Here, we report the complete chloroplast (cp) genome sequence and the cp genome features of , which was assembled and characterized based on Illumina pair-end sequencing data.