Ancient allopolyploidy and specific subgenomic evolution drove the radiation of poplars and willows.

Allopolyploidy involves the fusion of genomes from different lineages through hybridization and chromosome doubling. However, detecting early allopolyploidy events and understanding the specific subgenomic evolution that contributes to the origin of adaptive innovations for species radiation can be challenging. Here, we present genomes representing all three subfamilies of Salicaceae, a woody model clade, and collect epigenetic and transcriptomic samples.

Predicting Range Shifts of Five (Betulaceae) Species in China Under Future Climate Scenarios.

Climate change poses significant challenges to forest biodiversity by altering species distributions. This study employed the MaxEnt model to predict the current and potential future suitable habitats of five species in China under four Shared Socioeconomic Pathways. Model accuracy was high, with temperature seasonality identified as the most influential variable.

A haplotype-resolved chromosomal-level genome assembly of Oxalis articulata.

Oxalis articulata is a widely distributed perennial herb known for its adaptability to diverse environmental conditions. Here, we report the first haplotype-resolved, chromosome-scale genome assembly for O. articulata (Oxalidaceae), generated through PacBio HiFi long reads and Hi-C technology.

Chromosome fusions shaped karyotype evolution and evolutionary relationships in the model family Brassicaceae.

The ancestral crucifer karyotype and 22 conserved genomic blocks (CGBs) facilitate phylogenomic analyses in the Brassicaceae. Chromosomal rearrangements reshuffled CGBs of ancestral chromosomes during karyotype evolution. Here, we identify eight protochromosomes representing the common ancestral karyotype (ACBK) of the two Brassicoideae supertribes: Camelinodae (Lineage I) and Brassicodae (Lineage II).

Construction of the super pan-genome for the genus reveals structural variations linked to phenotypic diversity.

Kiwifruits, belonging to the genus , are acknowledged as one of the most successfully domesticated fruits in the twentieth century. Despite the rich wild resources and diverse phenotypes within this genus, insights into the genomic changes are still limited. Here, we conducted whole-genome sequencing on seven representative materials from highly diversified sections of , leading to the assembly and annotation of 14 haplotype genomes with sizes spanning from 602.

Domestication history and genetic changes for the newly evolved flower color in the ornamental plant (Brassicaceae).

(sweet alyssum) is a popular ornamental plant that displays a range of flower colors, particularly white and purple. However, the genetic underpinning and evolutionary history of flower colors have remained unknown. To address this, we performed a assembly of a chromosome-level genome for this species and conducted comparative population genomic analyses of both domestic and wild representatives.

Chromosome-level genome assembly of Helwingia omeiensis: the first genome in the family Helwingiaceae.

Helwingia, a shrub of the monotypic cosmopolitan family Helwingiaceae, is distinguished by its inflorescence, in which flowers are borne on the midrib of the leaf-a trait not commonly observed in related plant families. Previous studies have investigated the development of this unusual structure using comparative anatomical methods. However, the scarcity of genomic data has hindered our understanding of the origins and evolutionary history of this uncommon trait at the molecular level.

A high-quality chromosome-level Eutrema salsugineum genome, an extremophile plant model.

Background: Eutrema salsugineum (2n = 14), a halophyte in the family Brassicaceae, is an attractive model to study abiotic stress tolerance in plants. Two versions of E. salsugineum genomes that previously reported were based on relatively short reads; thus, the repetitive regions were difficult to characterize.

Phylotranscriptomics of Swertiinae (Gentianaceae) reveals that key floral traits are not phylogenetically correlated.

Establishing how lineages with similar traits are phylogenetically related remains critical for understanding the origin of biodiversity on Earth. Floral traits in plants are widely used to explore phylogenetic relationships and to delineate taxonomic groups. The subtribe Swertiinae (Gentianaceae) comprises more than 350 species with high floral diversity ranging from rotate to tubular corollas and possessing diverse nectaries.

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.

Out of the Qinghai-Tibet plateau: Genomic biogeography of the alpine monospecific genus Megadenia (Biscutelleae, Brassicaceae).

Numerous high-elevation alpine plants of the Qinghai-Tibet Plateau (QTP) also have disjunct distribution in adjacent low-altitude mountains. The out-of-QTP versus into-the-QTP hypothesis of alpine plants provide strong evidence for the highly disputed assumption of the massive ice sheet developed in the central plateau during the Last Glacial Maximum (LGM). In this study, we sequenced the genomes of most known populations of Megadenia, a monospecific alpine genus of Brassicaceae distributed primarily in the QTP, though rarely found in adjacent low-elevation mountains of north China and Russia (NC-R).

The chromosome-level genome assembly of Gentiana dahurica (Gentianaceae) provides insights into gentiopicroside biosynthesis.

Gentiana dahurica Fisch. is a perennial herb of the family Gentianaceae. This species is used as a traditional Tibetan medicine because of its rich gentiopicroside constituents.

A chromosome-level genome assembly of an alpine plant Crucihimalaya lasiocarpa provides insights into high-altitude adaptation.

It remains largely unknown how plants adapt to high-altitude habitats. Crucihimalaya (Brassicaceae) is an alpine genus occurring in the Qinghai-Tibet Plateau characterized by cold temperatures and strong ultraviolet radiation. Here, we generated a chromosome-level genome for C.

Genome evolution of the psammophyte for desert adaptation and further speciation.

Deserts exert strong selection pressures on plants, but the underlying genomic drivers of ecological adaptation and subsequent speciation remain largely unknown. Here, we generated de novo genome assemblies and conducted population genomic analyses of the psammophytic genus (Brassicaceae). Our results indicated that this bispecific genus had undergone an allopolyploid event, and the two parental genomes were derived from two ancestral lineages with different chromosome numbers and structures.

Hydrogen sulfide treatment at the late growth stage of extends chronological lifespan.

Previous studies demonstrated that lifelong treatment with a slow HS releasing donor extends yeast chronological lifespan (CLS), but it is not clear when the action of HS benefits to CLS during yeast growth. Here, we show that short HS treatments by using NaHS as a fast HS releasing donor at 96 hours after inoculation extended yeast CLS while NaHS treatments earlier than 72 hours after inoculation failed to do so. To reveal the mechanism, we analyzed the transcriptome of yeast cells with or without the early and late NaHS treatments.

A chromosome-scale reference genome of Lobularia maritima, an ornamental plant with high stress tolerance.

Lobularia maritima (L.) Desv. is an ornamental plant cultivated across the world.

Hybrid speciation via inheritance of alternate alleles of parental isolating genes.

It is increasingly realized that homoploid hybrid speciation (HHS), which involves no change in chromosome number, is an important mechanism of speciation. HHS will likely increase in frequency as ecological and geographical barriers between species are continuing to be disrupted by human activities. HHS requires the establishment of reproductive isolation between a hybrid and its parents, but the underlying genes and genetic mechanisms remain largely unknown.

The chromosome-level genome sequence and karyotypic evolution of Megadenia pygmaea (Brassicaceae).

Karyotypic changes in chromosome number and structure are drivers in the divergent evolution of diverse plant species and lineages. This study aimed to reveal the origins of the unique karyotype (2n = 12) and phylogenetic relationships of the genus Megadenia (Brassicaceae). A high-quality chromosome-scale genome was assembled for Megadenia pygmaea using Nanopore long reads and high-throughput chromosome conformation capture (Hi-C).

The Genome Sequence of Alpine Identifies Species-Specific Whole-Genome Duplication.

(Brassicaceae), a plant found the high mountains of southwest China at high altitudes (3000-4800 m), is used as a vegetable or medicine. Here, we report a draft genome for this species. The assembly genome of is 883 Mb, and 61.

A chromosome-scale genome assembly of , an important medicinal plant used in traditional Chinese medicine: An genome.

(2 = 14) is an important medicinal plant in China. Its dried leaves and roots (called Isatidis Folium and Isatidis Radix, respectively) are broadly used in traditional Chinese medicine for curing diseases caused by bacteria and viruses such as influenza and viral pneumonia. Various classes of compounds isolated from this species have been identified as effective ingredients.

The complete chloroplast genome of .

, a herbaceous plant, has been used in medicines as an alternative febrifuge and anthelmintic. In this study, the complete chloroplast DNA sequence of was assembled. It is 153,429 bp in length, including a large single-copy region of 83,613 bp and a small single-copy region of 18,038 bp separated by a pair of inverted repeat regions of 25,889 bp each.

The complete chloroplast genome of (Gentianaceae).

, is an alpine medicinal endemic to the Qinghai-Tibetan Plateau. In this study, the complete chloroplast DNA sequence of was assembled，and its genome is 149,064 bp in length, including a large single-copy region (LSC) of 81,158 bp and a small single-copy region (SSC) of 17,034 bp, which was separated by a pair of 25,436 bp inverted repeat regions (IRs). A total of 130 genes are detected, including 86 protein-coding genes, 37 tRNA genes, and 7 rRNA genes.

Ancient introgression drives adaptation to cooler and drier mountain habitats in a cypress species complex.

Introgression may act as an important source of new genetic variation to facilitate the adaptation of organisms to new environments, yet how introgression might enable tree species to adapt to higher latitudes and elevations remains unclear. Applying whole-transcriptome sequencing and population genetic analyses, we present an example of ancient introgression from a cypress species () that occurs at higher latitude and elevation on the Qinghai-Tibet Plateau into a related species (), which has likely aided the latter species to extend its range by colonizing cooler and drier mountain habitats during postglacial periods. We show that 16 introgressed candidate adaptive loci could have played pivotal roles in response to diverse stresses experienced in a high-elevation environment.