Physiological and transcriptome analysis of sex-specific responses to cadmium stress in poplars.

Soil cadmium (Cd) pollution is a serious ecological problem worldwide. Understanding Cd-detoxification mechanisms in woody plants will help to evaluate their tolerance ability and phytoremediation potential to Cd-polluted soils. This study investigated the growth, physiochemistry, Cd distribution, and transcriptome sequencing of male and female poplars under three Cd levels (0, 50, and 100 mg·kg).

Dryopteris×subdiffracta (Dryopteridaceae), a new natural hybrid fern from Guangxi, China.

A new natural hybrid fern, Dryopteris×subdiffracta (Dryopteridaceae), is reported from Guangxi, China. Molecular phylogenetic analysis based on DNA sequences from the low-copy nuclear marker and plastid genome revealed respectively that and are parents of the new hybrid, with as the maternal parent. Cytometric analysis of the nuclear DNA content indicated that might be a diploid hybrid.

Genomic, transcriptomic, and metabolomic analyses reveal convergent evolution of oxime biosynthesis in Darwin's orchid.

Angraecum sesquipedale, also known as Darwin's orchid, possesses an exceptionally long nectar spur. Charles Darwin predicted the orchid to be pollinated by a hawkmoth with a correspondingly long proboscis, later identified as Xanthopan praedicta. In this plant-pollinator interaction, the A.

Phylogeography of reveals the evolutionary patterns of a Cenozoic relict tree around the Sichuan Basin.

Environmental factors such as mountain tectonic movements and monsoons can enhance genetic differentiation by hindering inter- and intra-specific gene flow. However, the phylogeographic breaks detected within species may differ depending on the different molecular markers used, and biological traits may be a major confounding factor. is a vulnerable relict species distributed throughout the Sichuan Basin.

Evolution of Sex-linked Genes and the Role of Pericentromeric Regions in Sex Chromosomes: Insights from Diploid Willows.

The evolution of sex chromosomes can involve recombination suppression sometimes involving structural changes, such as inversions, allowing subsequent rearrangements, including inversions and gene transpositions. In the two major genus Salix clades, Salix and Vetrix, almost all species are dioecious, and sex-linked regions have evolved on chromosome 7 and 15, with either male or female heterogamety. We used chromosome conformation capture (Hi-C) and PacBio HiFi (high-fidelity) reads to assemble chromosome-level, gap-free X and Y chromosomes from both clades, S.

New insights on the phylogeny, evolutionary history, and ecological adaptation mechanism in cycle-cup oaks based on chloroplast genomes.

Cycle-cup oaks ( section ) are one of the principal components of forests in the tropical and subtropical climates of East and Southeast Asia. They have experienced relatively recent increases in the diversification rate, driven by changing climates and the Himalayan orogeny. However, the evolutionary history and adaptive mechanisms at the chloroplast genome level in cycle-cup oaks remain largely unknown.

The adaptive evolution of Quercus section Ilex using the chloroplast genomes of two threatened species.

Chloroplast (cp) genome sequences have been extensively used for phylogenetic and evolutionary analyses, as many have been sequenced in recent years. Identification of Quercus is challenging because many species overlap phenotypically owing to interspecific hybridization, introgression, and incomplete lineage sorting. Therefore, we wanted to gain a better understanding of this genus at the level of the maternally inherited chloroplast genome.

Content Determination and Chemical Clustering Analysis of Tanshinone and Salvianolic Acid in spp.

is one of the famous traditional Chinese medicines for treating cardiovascular and cerebrovascular diseases. Tanshinone and phenolic acids are the main active compounds of , whereas the distribution patterns of the two kinds of components are still unclear among spp. In this work, high-performance liquid chromatography was applied to analyze the distribution patterns of major components in the roots and leaves of 58 spp.

Allopolyploidization from two dioecious ancestors leads to recurrent evolution of sex chromosomes.

Polyploidization presents an unusual challenge for species with sex chromosomes, as it can lead to complex combinations of sex chromosomes that disrupt reproductive development. This is particularly true for allopolyploidization between species with different sex chromosome systems. Here, we assemble haplotype-resolved chromosome-level genomes of a female allotetraploid weeping willow (Salix babylonica) and a male diploid S.

Sex chromosome turnover plays an important role in the maintenance of barriers to post-speciation introgression in willows.

Almost all species in the genus (willow) are dioecious and willows have variable sex-determining systems, the role of this variation in maintaining species barriers is relatively untested. We first analyzed the sex determination systems (SDS) of two species, and , whose positions in the phylogeny make them important for understanding a sex chromosome turnover that has been detected in their relatives, and that changed the system from male (XX/XY) to female (ZW/ZZ) heterogamety. We show that both species have male heterogamety, with sex-linked regions (SLRs) on chromosome 15 (termed a 15XY system).

Genome-wide data reveal bi-direction and asymmetrical hybridization origin of a fern species .

Introduction: Natural hybridization is common and plays a crucial role in driving biodiversity in nature. Despite its significance, the understanding of hybridization in ferns remains inadequate. Therefore, it is imperative to study fern hybridization to gain a more comprehensive understanding of fern biodiversity.

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.

Understanding Arctic-Alpine Plants from Ecological and Evolutionary Perspectives.

Conditions in arctic and alpine ecosystems impose great challenges on the plants and other organisms that live there [...

Species delimitation 4.0: integrative taxonomy meets artificial intelligence.

Although species are central units for biological research, recent findings in genomics are raising awareness that what we call species can be ill-founded entities due to solely morphology-based, regional species descriptions. This particularly applies to groups characterized by intricate evolutionary processes such as hybridization, polyploidy, or asexuality. Here, challenges of current integrative taxonomy (genetics/genomics + morphology + ecology, etc.

Different reference genomes determine different results: Comparing SNP calling in RAD-seq of Engelhardia roxburghiana using different reference genomes.

Advances in next-generation sequencing (NGS) have significantly reduced the cost and improved the efficiency of obtaining single nucleotide polymorphism (SNP) markers, particularly through restriction site-associated DNA sequencing (RAD-seq). Meanwhile, the progression in whole genome sequencing has led to the utilization of an increasing number of reference genomes in SNP calling processes. This study utilized RAD-seq data from 242 individuals of Engelhardia roxburghiana, a tropical tree of the walnut family (Juglandaceae), with SNP calling conducted using the STACKS pipeline.

Gap-free X and Y chromosome assemblies of Salix arbutifolia reveal an evolutionary change from male to female heterogamety in willows, without a change in the position of the sex-determining locus.

In the Vetrix clade of Salix, a genus of woody flowering plants, sex determination involves chromosome 15, but an XY system has changed to a ZW system. We studied the detailed genetic changes involved. We used genome sequencing, with chromosome conformation capture (Hi-C) and PacBio HiFi reads to assemble chromosome level gap-free X and Y of Salix arbutifolia, and distinguished the haplotypes in the 15X- and 15Y-linked regions, to study the evolutionary history of the sex-linked regions (SLRs).

Genomic insights into the clonal reproductive : mitochondrial and chloroplast genomes of the cochineal cactus for enhanced understanding of structural dynamics and evolutionary implications.

Background: The cochineal cactus (), notable for its substantial agricultural and industrial applications, predominantly undergoes clonal reproduction, which presents significant challenges in breeding and germplasm innovation. Recent developments in mitochondrial genome engineering offer promising avenues for introducing heritable mutations, potentially facilitating selective sexual reproduction through the creation of cytoplasmic male sterile genotypes. However, the lack of comprehensive mitochondrial genome information for species hinders these efforts.

sp. nov.: unraveling a critical evolutionary link in East Asian from Central China integrating morphology, phylogeny, and plastid genomics.

Introduction: L., representing the largest genus within the mint family, is noted for its global distribution of approximately 1000 species, with East Asia, and particularly China, recognized as a critical center of diversity for the genus.

Methods: Our research was conducted through extensive fieldwork in Guidong County, Hunan Province, China, where we identified a previously undescribed species of .

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.

Genome Size in the Species Complex (Caryophyllaceae), with Special Focus on Northern Europe and the Arctic.

The main aim of the present study has been the completion of genome size data for the diverse arctic-alpine species complex, with special focus on the unexplored arctic taxon , the north-European and from Gotland (Sweden). Altogether, 46 individuals of these three Nordic taxa have been sampled from seven different regions and their genome size estimated using flow cytometry. Three other alpine taxa in the complex (, subsp.

Cliff-edge forests: Xerothermic hotspots of local biodiversity and models for future climate change.

Cliffs are remarkable environments that enable the existence of microclimates. These small, isolated sites, decoupled from the regional macroclimate, play a significant role in maintaining species biodiversity, particularly in topographically homogeneous landscapes. Our study investigated the microclimate of south-exposed forests situated at the edge of sandstone cliffs in the western part of the North Alpine Foreland Basin in Switzerland and its role in local forest community composition.

Complete Chloroplast Genomes of Four Oaks from the Section Improve the Phylogenetic Analysis and Understanding of Evolutionary Processes in the Genus .

is a valuable genus ecologically, economically, and culturally. They are keystone species in many ecosystems. Species delimitation and phylogenetic studies of this genus are difficult owing to frequent hybridization.

Deciphering the Plastomic Code of Chinese Hog-Peanut ( Benth., Leguminosae): Comparative Genomics and Evolutionary Insights within the Phaseoleae Tribe.

The classification and phylogenetic relationships within the Phaseoleae tribe (Leguminosae) have consistently posed challenges to botanists. This study addresses these taxonomic intricacies, with a specific focus on the Glycininae subtribe, by conducting a comprehensive analysis of the highly conserved plastome in Benth., a critical species within this subtribe.

Structured and unstructured intraspecific propagule trait variation across environmental gradients in a widespread mangrove.

Increasing studies have shown the importance of intraspecific trait variation (ITV) on ecological processes. However, the patterns and sources of ITV are still unclear, especially in the propagules of coastal vegetation. Here, we measured six hypocotyl traits for 66 genealogies of from 26 sites and analyzed how ITV in these traits was distributed across geography and genealogy through variance partitioning.

Evolution and chemical diversity of the volatile compounds in Salvia species.

Introduction: The plant essential oils are composed of volatile compounds and have significant value in preventing and treating neurological diseases, anxiety, depression, among others. The genus Salvia has been shown to be an important medicinal resource, especially the aerial parts of genus Salvia, which are rich in volatile compounds; however, the chemical diversity and distribution patterns of volatile compounds in Salvia species are still unknown.

Objective: The work is performed to analyse the chemical diversity and distribution patterns of volatile compounds in genus Salvia.