Decoding endosperm endophytes in Pinus armandi: a crucial indicator for host response to climate change.

Background: Plant-associated microorganisms significantly contribute to plant survival in diverse environments. However, limited information is available regarding the involvement of endophytes in responding to climate change and their potential to enhance host plants' adaptation to future environmental shifts. Pinus armandi, endemic to China and widely distributed in climate-sensitive regions, serves as an ideal subject for investigating microbiome interactions that assist host plants in climate change response.

Evaluating the impact of movement representation techniques on recovery outcomes in post-orthopaedic surgery individuals: a systematic review and meta-analysis.

Background: Although movement representation techniques has originally been used in neurological rehabilitation, growing researches suggests that it may also introduce advantageous effects to individuals with orthopaedic injuries. This systematic review and meta-analysis aimed to investigate the effects of these techniques on pain, range of motion, muscle strength, functional performance and fear of movement in individuals after orthopaedic surgeries.

Method: Five electronic databases were searched until April 2024.

DNA methylation dynamics in gymnosperm duplicate genes: implications for genome evolution and stress adaptation.

Duplicate genes are pivotal in driving evolutionary innovation, often exhibiting expression divergence that offers a system to investigate the role of DNA methylation in transcriptional regulation. However, previous studies have predominantly focused on angiosperms, leaving the methylation patterns in major lineages of land plants still unclear. This study explores DNA methylation evolution in duplicate genes across representative gymnosperm species with large genomes, spanning over 300 million years, using genomic, transcriptomic, and high-depth DNA methylomic data.

The effect of emotional cues on attentional bias to food cues in women with body weight dissatisfaction.

The eating behavior of individuals is susceptible to various factors. Emotion is an important factor that influences eating behaviors, especially in women who care about their body weight and dissatisfied with their bodies. This study explored the effect of emotional cues on attentional bias toward food in women with body weight dissatisfaction (BWD).

The effect of avatar identity on spontaneous perspective-taking in patients with schizophrenia.

Controversy exists regarding whether the spontaneity of altercentric intrusion is impaired in patients with schizophrenia during implicit visual perspective-taking tasks. This study explored the characteristics of spontaneous visual perspective-taking in patients with schizophrenia and the effect of an avatar identity on their perspective-taking. We recruited 65 patients with schizophrenia and 65 healthy participants to complete 4 visual perspective-taking experiments for uncued other-avatar and self-avatar tasks and cued other-avatar and self-avatar tasks.

Convergent Patterns of Karyotype Evolution Underlying Karyotype Uniformity in Conifers.

Karyotype diversity plays an important role in speciation and diversification. However, gymnosperms, particularly conifers, exhibit remarkable karyotype uniformity. To explore the evolutionary processes shaping karyotypes in gymnosperms, the karyotype evolutionary history is reconstructed through comparative genomic analyses.

Phylogenomic analyses shed new light on the spatiotemporal evolution of global larches: Implications for the dynamics of boreal forests.

As the Earth warms, understanding the long-term dynamics of forest ecosystems is essential for guiding forest management and biodiversity conservation. Insights from past dynamics may provide valuable lessons for managing today's forests. Here, we investigated the spatiotemporal evolution of global larches to gain further insights into how boreal forests change over time.

Genomic insights into adaptive evolution of the species-rich cosmopolitan plant genus Rhododendron.

The species-rich cosmopolitan genus Rhododendron offers a good system for exploring the genomic mechanisms underlying adaptation to diverse habitats. Here, we report high-quality chromosomal-level genome assemblies of nine species, representing all five subgenera, different altitudinal distributions, and all flower color types of this genus. Further comprehensive genomic analyses indicate diverse adaptive strategies employed by Rhododendron, particularly adaptation to alpine and subalpine habitats by expansion/contraction of gene families involved in pathogen defense and oxidative phosphorylation, genomic convergent evolution, and gene copy-number variation.

Phylotranscriptomic and ecological analyses reveal the evolution and morphological adaptation of Abies.

Coniferous forests are under severe threat of the rapid anthropogenic climate warming. Abies (firs), the fourth-largest conifer genus, is a keystone component of the boreal and temperate dark-coniferous forests and harbors a remarkably large number of relict taxa. However, the uncertainty of the phylogenetic and biogeographic history of Abies significantly impedes our prediction of future dynamics and efficient conservation of firs.

Reciprocal expression of MADS-box genes and DNA methylation reconfiguration initiate bisexual cones in spruce.

The naturally occurring bisexual cone of gymnosperms has long been considered a possible intermediate stage in the origin of flowers, but the mechanisms governing bisexual cone formation remain largely elusive. Here, we employed transcriptomic and DNA methylomic analyses, together with hormone measurement, to investigate the molecular mechanisms underlying bisexual cone development in the conifer Picea crassifolia. Our study reveals a "bisexual" expression profile in bisexual cones, especially in expression patterns of B-class, C-class and LEAFY genes, supporting the out of male model.

Diploid species phylogeny and evolutionary reticulation indicate early radiation of Ephedra in the Tethys coast.

Reconstructing a robust species phylogeny and disentangling the evolutionary and biogeographic history of the gymnosperm genus Ephedra, which has a large genome and rich polyploids, remain a big challenge. Here we reconstructed a transcriptome-based phylogeny of 19 diploid Ephedra species, and explored evolutionary reticulations in this genus represented by 50 diploid and polyploid species, using four low-copy nuclear and nine plastid genes. The diploid species phylogeny indicates that the Mediterranean species diverged first, and the remaining species split into three clades, including the American species (Clade A), E.

Tracing the geographic origin of endangered plant species using transcriptome-derived SNPs: An example of Cathaya argyrophylla.

Genetic markers have emerged as one of the most promising tools for species identification and geographic traceability in biodiversity conservation and international trade of biological products. However, traditional molecular markers rarely have sufficient resolution at lower taxonomic levels, especially for discriminating closely related forest tree species and their populations. In this study, we developed a panel of RNA-Seq based single nucleotide polymorphism (SNP) markers for tracing the geographic origin of an endangered conifer, Cathaya argyrophylla, which is a paleoendemic restricted to four mountain regions in subtropical China.

A Comprehensive Evolutionary Study of Chloroplast RNA Editing in Gymnosperms: A Novel Type of G-to-A RNA Editing Is Common in Gymnosperms.

Although more than 9100 plant plastomes have been sequenced, RNA editing sites of the whole plastome have been experimentally verified in only approximately 21 species, which seriously hampers the comprehensive evolutionary study of chloroplast RNA editing. We investigated the evolutionary pattern of chloroplast RNA editing sites in 19 species from all 13 families of gymnosperms based on a combination of genomic and transcriptomic data. We found that the chloroplast C-to-U RNA editing sites of gymnosperms shared many common characteristics with those of other land plants, but also exhibited many unique characteristics.

Phylogeny and evolution of Cupressaceae: Updates on intergeneric relationships and new insights on ancient intergeneric hybridization.

After the merger of the former Taxodiaceae and Cupressaceae s.s., currently the conifer family Cupressaceae (sensu lato) comprises seven subfamilies and 32 genera, most of which are important components of temperate and mountainous forests.

The Cycas genome and the early evolution of seed plants.

Cycads represent one of the most ancient lineages of living seed plants. Identifying genomic features uniquely shared by cycads and other extant seed plants, but not non-seed-producing plants, may shed light on the origin of key innovations, as well as the early diversification of seed plants. Here, we report the 10.

Phylotranscriptomics reveals the evolutionary history of subtropical East Asian white pines: further insights into gymnosperm diversification.

Floristic composition within a geographic area is driven by a wide array of factors from local biotic interactions to biogeographical processes. Subtropical East Asia is a key biodiversity hotspot of the world, and harbors the most families of extant gymnosperms and a large number of endemic genera with ancient origins, but rare phylogenetic studies explored whether it served as a diversification center for gymnosperms. Here, we investigated the evolutionary and biogeographical history of subtropical East Asian white pines using an integrative approach that combines phylotranscriptomic and ecological analyses.

New insights into the phylogeny and evolution of Podocarpaceae inferred from transcriptomic data.

Phylogenies of an increasing number of taxa have been resolved with the development of phylogenomics. However, the intergeneric relationships of Podocarpaceae, the second largest family of conifers comprising 19 genera and approximately 187 species mainly distributed in the Southern Hemisphere, have not been well disentangled in previous studies, even when genome-scale data sets were used. Here we used 993 nuclear orthologous groups (OGs) and 54 chloroplast OGs (genes), which were generated from 47 transcriptomes of Podocarpaceae and its sister group Araucariaceae, to reconstruct the phylogeny of Podocarpaceae.

Spatiotemporal Evolution of the Global Species Diversity of Rhododendron.

Evolutionary radiation is a widely recognized mode of species diversification, but its underlying mechanisms have not been unambiguously resolved for species-rich cosmopolitan plant genera. In particular, it remains largely unknown how biological and environmental factors have jointly driven its occurrence in specific regions. Here, we use Rhododendron, the largest genus of woody plants in the Northern Hemisphere, to investigate how geographic and climatic factors, as well as functional traits, worked together to trigger plant evolutionary radiations and shape the global patterns of species richness based on a solid species phylogeny.

NS1: A Key Protein in the "Game" Between Influenza A Virus and Host in Innate Immunity.

Since the influenza pandemic occurred in 1918, people have recognized the perniciousness of this virus. It can cause mild to severe infections in animals and humans worldwide, with extremely high morbidity and mortality. Since the first day of human discovery of it, the "game" between the influenza virus and the host has never stopped.

Both Conifer II and Gnetales are characterized by a high frequency of ancient mitochondrial gene transfer to the nuclear genome.

Background: Mitochondrial gene transfer/loss is common in land plants, and therefore the fate of missing mitochondrial genes has attracted more and more attention. The gene content of gymnosperm mitochondria varies greatly, supplying a system for studying the evolutionary fate of missing mitochondrial genes.

Results: Here, we studied the tempo and pattern of mitochondrial gene transfer/loss in gymnosperms represented by all 13 families, using high-throughput sequencing of both DNA and cDNA.

Phylogenomic and ecological analyses reveal the spatiotemporal evolution of global pines.

How coniferous forests evolved in the Northern Hemisphere remains largely unknown. Unlike most groups of organisms that generally follow a latitudinal diversity gradient, most conifer species in the Northern Hemisphere are distributed in mountainous areas at middle latitudes. It is of great interest to know whether the midlatitude region has been an evolutionary cradle or museum for conifers and how evolutionary and ecological factors have driven their spatiotemporal evolution.

Phylotranscriptomics reveals the complex evolutionary and biogeographic history of the genus Tsuga with an East Asian-North American disjunct distribution.

The disjunct distribution between East Asia and North America is one of the best established biogeographic patterns. A robust phylogeny is fundamental for understanding the biogeographic histories of taxa with this distribution pattern. Tsuga (hemlock) is a genus of Pinaceae with a typical intercontinental disjunct distribution in East Asia and eastern and western North America, and its phylogeny has not been completely reconstructed in previous studies.

Unbiased Subgenome Evolution in Allotetraploid Species of Ephedra and Its Implications for the Evolution of Large Genomes in Gymnosperms.

The evolutionary dynamics of polyploid genomes and consequences of polyploidy have been studied extensively in angiosperms but very rarely in gymnosperms. The gymnospermous genus Ephedra is characterized by a high frequency of polyploidy, and thus provides an ideal system to investigate the evolutionary mode of allopolyploid genomes and test whether subgenome dominance has occurred in gymnosperms. Here, we sequenced transcriptomes of two allotetraploid species of Ephedra and their putative diploid progenitors, identified expressed homeologs, and analyzed alternative splicing and homeolog expression based on PacBio Iso-Seq and Illumina RNA-seq data.

The complete mitochondrial genome of Taxus cuspidata (Taxaceae): eight protein-coding genes have transferred to the nuclear genome.

Background: Gymnosperms represent five of the six lineages of seed plants. However, most sequenced plant mitochondrial genomes (mitogenomes) have been generated for angiosperms, whereas mitogenomic sequences have been generated for only six gymnosperms. In particular, complete mitogenomes are available for all major seed plant lineages except Conifer II (non-Pinaceae conifers or Cupressophyta), an important lineage including six families, which impedes a comprehensive understanding of the mitogenomic diversity and evolution in gymnosperms.