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.

Incomplete lineage sorting rather than hybridization explains the inconsistent phylogeny of the wisent.

The wisent or European bison is the largest European herbivore and is completely cross-fertile with its American relative. However, mtDNA genome of wisent is similar to that of cattle, which suggests that wisent emerged as a hybrid of bison and an extinct cattle-like species. Here, we analyzed nuclear whole-genome sequences of the bovine species, and found only a minor and recent gene flow between wisent and cattle.

Population genomic analysis reveals that homoploid hybrid speciation can be a lengthy process.

An increasing number of species are thought to have originated by homoploid hybrid speciation (HHS), but in only a handful of cases are details of the process known. A previous study indicated that Picea purpurea, a conifer in the Qinghai-Tibet Plateau (QTP), originated through HHS from P. likiangensis and P.

Characterization of the complete chloroplast genome of .

The whole chloroplast (cp) genome sequence of has been characterized from Illumina pair-end sequencing. The complete cp genome was 169,178 bp in length, containing a large single copy (LSC) region of 87,884 bp and a small single copy (SSC) region of 11,144 bp, which were separated by a pair of 35,075 bp inverted repeat (IR) regions. The genome contained 138 genes, including 88 protein-coding genes (87 PCG species), 37 tRNA genes (30 tRNA species), and eight ribosomal RNA genes (four rRNA species).

Demographic expansion and genetic load of the halophyte model plant Eutrema salsugineum.

The halophyte model plant Eutrema salsugineum (Brassicaceae) disjunctly occurs in temperate to subarctic Asia and North America. This vast, yet extremely discontinuous distribution constitutes an ideal system to examine long-distance dispersal and the ensuing accumulation of deleterious mutations as expected in expanding populations of selfing plants. In this study, we resequenced individuals from 23 populations across the range of E.

Interspecific Divergence of Two (Brassicaceae) Species in Eastern China.

How endemic species originated in eastern Asia has interested botanists for a long time. In this study, we combined experimental and computational modeling approaches to examine the morphological and genetic divergence and reproductive isolation of two tentative species of (Brassicaceae) endemic to eastern China, and . Most of the examined morphological characters (including hairs of leaf blades and stems, corolla length and width, and flower stalk length) were well-delineated between two species at the same ploidy level, and there was clear evidence of reproductive isolation between them (mainly due to post-pollination barriers) in the common garden environment.

The genomes of two Eutrema species provide insight into plant adaptation to high altitudes.

Eutrema is a genus in the Brassicaceae, which includes species of scientific and economic importance. Many Eutrema species are montane and/or alpine species that arose very recently, making them ideal candidates for comparative studies to understand both ecological speciation and high-altitude adaptation in plants. Here we provide de novo whole-genome assemblies for a pair of recently diverged perennials with contrasting altitude preferences, the high-altitude E.

Ancient polymorphisms and divergence hitchhiking contribute to genomic islands of divergence within a poplar species complex.

How genome divergence eventually leads to speciation is a topic of prime evolutionary interest. Genomic islands of elevated divergence are frequently reported between diverging lineages, and their size is expected to increase with time and gene flow under the speciation-with-gene-flow model. However, such islands can also result from divergent sorting of ancient polymorphisms, recent ecological selection regardless of gene flow, and/or recurrent background selection and selective sweeps in low-recombination regions.