Genetic origins and climate-induced erosion in economically important Asian walnuts.

The global climate is undergoing unprecedented changes, posing significant threats to species persistence. However, the spatiotemporal impacts on genetic diversity remain poorly understood, hindering species conservation and management. Walnuts, generally referred to as Juglans regia and J.

Comparative metabolomics of two nettle species unveils distinct high-altitude adaptation mechanisms on the Tibetan Plateau.

Background: The extreme high-altitude conditions of the Tibetan Plateau, characterized by intense solar radiation, low temperatures, and reduced oxygen levels, poses significant challenges to plant survival. Plants inhabiting this region have evolved specialized mechanisms to adapt to high-altitude environments. While most studies have focused on genomic and ecological perspectives, few have explored adaptive mechanisms in a metabolic context.

SOI: robust identification of orthologous synteny with the Orthology Index and broad applications in evolutionary genomics.

With the explosive growth of whole-genome datasets, accurate detection of orthologous synteny has become crucial for reconstructing evolutionary history. However, current methods for identifying orthologous synteny face great limitations, particularly in scaling with varied polyploidy histories and accurately removing out-paralogous synteny. In this study, we developed a scalable and robust approach, based on the Orthology Index (OI), to effectively identify orthologous synteny.

An integrative approach clarifies species delimitation and biogeographic history of (Urticaceae).

Integrative data from plastid and nuclear loci are increasingly utilized to resolve species boundaries and phylogenetic relationships within major angiosperm clades. (Urticaceae), an economically important genus, presents challenges in species delimitation due to its overlapping morphological traits and unstable taxonomic assignments. Here, we analyzed 14 morphological traits and generated 12 data matrices from the plastomes and nrDNA using genome skimming from the nine recognized morphospecies to clarify species boundaries and assess barcode performance in .

An Integrated Study of Ramie (), and Its Wild, Cultivated, and Feral Forms.

Feralization, the re-establishment of wild populations from domesticated ancestors, can involve multiple parallel character reversions and potentially also rampant gene flow with cultivated and/or naturally wild material. It hence poses great challenges for infraspecific classification, which may impede crop development, but studies on these issues are rare. Ramie (; Urticaceae) is an important fiber crop worldwide.

The origin and morphological character evolution of the paleotropical woody bamboos.

The woody bamboos (Bambusoideae) exhibit distinctive biological traits within Poaceae, such as highly lignified culms, rapid shoot growth, monocarpic mass flowering and nutlike or fleshy caryopses. Much of the remarkable morphological diversity across the subfamily exists within a single hexaploid clade, the paleotropical woody bamboos (PWB), making it ideal to investigate the factors underlying morphological evolution in woody bamboos. However, the origin and biogeographical history of PWB remain elusive, as does the effect of environmental factors on the evolution of their morphological characters.

Across two phylogeographic breaks: Quaternary evolutionary history of a mountain aspen () in the Hengduan Mountains.

Biogeographical barriers to gene flow are central to plant phylogeography. In East Asia, plant distribution is greatly influenced by two phylogeographic breaks, the Mekong-Salween Divide and Tanaka-Kaiyong Line, however, few studies have investigated how these barriers affect the genetic diversity of species that are distributed across both. Here we used 14 microsatellite loci and four chloroplast DNA fragments to examine genetic diversity and distribution patterns of 49 populations of , a species that spans both the Mekong-Salween Divide and the Tanaka-Kaiyong Line in southwestern China.

Conservation genomic investigation of an endangered conifer, , reveals low genetic diversity but also low genetic load.

Endangered species generally have small populations with low genetic diversity and a high genetic load. is an endangered conifer endemic to southwestern China. It was once considered extinct in the wild, but in 1999 was rediscovered.

Plastome phylogenomics and morphological traits analyses provide new insights into the phylogenetic position, species delimitation and speciation of Triplostegia (Caprifoliaceae).

Background: The genus Triplostegia contains two recognized species, T. glandulifera and T. grandiflora, but its phylogenetic position and species delimitation remain controversial.

Pervasive hybridization during evolutionary radiation of subgenus in mountains of southwest China.

Radiations are especially important for generating species biodiversity in mountainous ecosystems. The contribution of hybridization to such radiations has rarely been examined. Here, we use extensive genomic data to test whether hybridization was involved in evolutionary radiation within subgenus , whose members show strong geographic isolation in the mountains of southwest China.

The establishment of plants following long-distance dispersal.

Long-distance dispersal (LDD) beyond the range of a species is an important driver of ecological and evolutionary patterns, but insufficient attention has been given to postdispersal establishment. In this review, we summarize current knowledge of the post-LDD establishment phase in plant colonization, identify six key determinants of establishment success, develop a general quantitative framework for post-LDD establishment, and address the major challenges and opportunities in future research. These include improving detection and understanding of LDD using novel approaches, investigating mechanisms determining post-LDD establishment success using mechanistic modeling and inference, and comparison of establishment between past and present.

Genomic insights into the genotype-environment mismatch and conservation units of a Qinghai-Tibet Plateau endemic cypress under climate change.

Habitat loss induced by climate warming is a major threat to biodiversity, particularly to threatened species. Understanding the genetic diversity and distributional responses to climate change of threatened species is critical to facilitate their conservation and management. , a rare conifer found in the eastern Qinghai-Tibet Plateau (QTP) at 3000-3600 m.

Phylogenomics and evolutionary history of Oreocnide (Urticaceae) shed light on recent geological and climatic events in SE Asia.

Climate change and geological events have long been known to shape biodiversity, implying that these can likewise be viewed from a biological perspective. To study whether plants can shed light on this, and how they responded to climate change there, we examined Oreocnide, a genus widely distributed in SE Asia. Based on broad geographic sampling with genomic data, we employed an integrative approach of phylogenomics, molecular dating, historical biogeography, and ecological analyses.

Deep Insights Into the Plastome Evolution and Phylogenetic Relationships of the Tribe Urticeae (Family Urticaceae).

Urticeae , a tribe of Urticaceae well-known for their stinging trichomes, consists of more than 10 genera and approximately 220 species. Relationships within this tribe remain poorly known due to the limited molecular and taxonomic sampling in previous studies, and chloroplast genome (CP genome/plastome) evolution is still largely unaddressed. To address these concerns, we used genome skimming data-CP genome and nuclear ribosomal DNA (18S-ITS1-5.

Comparing the contents, functions and neonicotinoid take-up between floral and extrafloral nectar within a single species (Hemerocallis citrina Baroni).

Background And Aims: Many angiosperms can secrete both floral (FN) and extrafloral (EFN) nectar. However, much remains unclear about how EFN and FN differ in secretion, composition and ecological function, especially when both FN and EFN are secreted on flowers of the same species.

Methods: Hemerocallis citrina flowers secrete both FN and EFN.

Demographic history and identification of threats revealed by population genomic analysis provide insights into conservation for an endangered maple.

Recent advancements in whole genome sequencing techniques capable of covering nearly all the nucleotide variations of a genome would make it possible to set up a conservation framework for threatened plants at the genomic level. Here we applied a whole genome resequencing approach to obtain genome-wide data from 105 individuals sampled from the 10 currently known extant populations of Acer yangbiense, an endangered species with fragmented habitats and restricted distribution in Yunnan, China. To inform meaningful conservation action, we investigated what factors might have contributed to the formation of its extremely small population sizes and what threats it currently suffers at a genomic level.

Seeing through the hedge: Phylogenomics of Thuja (Cupressaceae) reveals prominent incomplete lineage sorting and ancient introgression for Tertiary relict flora.

The Eastern Asia (EA) - North America (NA) disjunction is a well-known biogeographic pattern of the Tertiary relict flora; however, few studies have investigated the evolutionary history of this disjunction using a phylogenomic approach. Here, we used 2369 single copy nuclear genes and nearly full plastomes to reconstruct the evolutionary history of the small Tertiary relict genus Thuja, which consists of five disjunctly distributed species. The nuclear species tree strongly supported an EA clade Thuja standishii-Thuja sutchuenensis and a "disjunct clade", where western NA species T.

Genome-wide analysis of butterfly bush (Buddleja alternifolia) in three uplands provides insights into biogeography, demography and speciation.

Understanding processes that generate and maintain large disjunctions within plant species can provide valuable insights into plant diversity and speciation. The butterfly bush Buddleja alternifolia has an unusual disjunct distribution, occurring in the Himalaya, Hengduan Mountains (HDM) and the Loess Plateau (LP) in China. We generated a high-quality, chromosome-level genome assembly of B.

Evolutionary legacy of a forest plantation tree species (): Implications for widespread afforestation.

Many natural systems are subject to profound and persistent anthropogenic influence. Human-induced gene movement through afforestation and the selective transportation of genotypes might enhance the potential for intraspecific hybridization, which could lead to outbreeding depression. However, the evolutionary legacy of afforestation on the spatial genetic structure of forest tree species has barely been investigated.

Characteristics and Mutational Hotspots of Plastomes in (Urticaceae).

is an economically important genus of the nettle family (Urticaceae). Previous systematic studies based on morphology, or using up to four plastome regions, have not satisfactorily resolved relationships within the genus. Here, we report 25 new plastomes for Urticaceae, including 12 plastomes from five species and 13 plastomes from other genera.

Development of 32 novel microsatellite loci in using genomic data.

Premise: A novel set of microsatellite markers was developed for (Juglandaceae), an endemic walnut species in southwestern China, to facilitate cultivar identification and future investigations into the genetic structure and domestication history of this species and its close relatives.

Methods And Results: We developed 32 microsatellite loci for using genomic data and used them to examine 60 individuals from three natural populations. A high level of polymorphism was detected by these primers, with up to eight alleles observed per locus, and an average of four alleles across populations.