Cryptic divergences and repeated hybridizations within the endangered "living fossil" dove tree () revealed by whole genome resequencing.

The identification and understanding of cryptic intraspecific evolutionary units (lineages) are crucial for planning effective conservation strategies aimed at preserving genetic diversity in endangered species. However, the factors driving the evolution and maintenance of these intraspecific lineages in most endangered species remain poorly understood. In this study, we conducted resequencing of 77 individuals from 22 natural populations of , a "living fossil" dove tree endemic to central and southwest China.

The pan-genome and local adaptation of Arabidopsis thaliana.

Arabidopsis thaliana serves as a model species for investigating various aspects of plant biology. However, the contribution of genomic structural variations (SVs) and their associate genes to the local adaptation of this widely distribute species remains unclear. Here, we de novo assemble chromosome-level genomes of 32 A.

Evolutionary origin of genomic structural variations in domestic yaks.

Yak has been subject to natural selection, human domestication and interspecific introgression during its evolution. However, genetic variants favored by each of these processes have not been distinguished previously. We constructed a graph-genome for 47 genomes of 7 cross-fertile bovine species.

Chromosome-level de novo genome assembly of two conifer-parasitic wasps, Megastigmus duclouxiana and Megastigmus sabinae, reveals genomic imprints of adaptation to hosts.

Conifers make up about one third of global forests but are threatened by seed parasitoid wasp species. Many of these wasps belong to the genus Megastigmus, yet little is known about their genomic background. In this study, we provide chromosome-level genome assemblies for two oligophagous conifer parasitoid species of Megastigmus, which represent the first two chromosome-level genomes of the genus.

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.

A chromosome-level Populus qiongdaoensis genome assembly provides insights into tropical adaptation and a cryptic turnover of sex determination.

Populus species have long been used as model organisms to study the adaptability of trees and the evolution of sex chromosomes. As a species belonging to the section Populus and limited to tropical areas, the P. qiongdaoensis genome contains important information for tropical poplar studies and protection.

Genomic evidence for homoploid hybrid speciation between ancestors of two different genera.

Homoploid hybrid speciation (HHS) has been increasingly recognized as occurring widely during species diversification of both plants and animals. However, previous studies on HHS have mostly focused on closely-related species while it has been rarely reported or tested between ancestors of different genera. Here, we explore the likely HHS origin of Carpinus sect.

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.

Improved genome assembly provides new insights into genome evolution in a desert poplar (Populus euphratica).

Populus euphratica is well adapted to extreme desert environments and is an important model species for elucidating the mechanisms of abiotic stress resistance in trees. The current assembly of P. euphratica genome is highly fragmented with many gaps and errors, thereby impeding downstream applications.

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.

Genomic analyses of a "living fossil": The endangered dove-tree.

Davidia involucrata Baill, also known as the dove-tree, is a living fossil and an endangered species currently restricted to the mountains of southwestern and central China. It has a beautiful and innovative trait of high horticultural value: two white bracts covering the flower caputila. Here, we report on the chromosome-scale genome of this species using single-molecule real-time long reads and chromosome conformation capture (Hi-C) techniques.

A chromosome-level genome assembly of the Chinese tupelo Nyssa sinensis.

The deciduous Chinese tupelo (Nyssa sinensis Oliv.) is a popular ornamental tree for the spectacular autumn leaf color. Here, using single-molecule sequencing and chromosome conformation capture data, we report a high-quality, chromosome-level genome assembly of N.

A high-quality (kiwifruit) genome.

(kiwifruit) is a perennial horticultural crop species of the Actinidiaceae family with high nutritional and economic value. Two versions of the genomes have been previously assembled, based mainly on relatively short reads. Here, we report an improved chromosome-level reference genome of (v3.

Intergeneric Relationships within the Family Salicaceae based on Plastid Phylogenomics.

Many Salicaceae plants are recognized for their important role in the production of products such as wood, oils, and medicines, and as a model organism in life studies. However, the difference in plastid sequence, phylogenetic relationships, and lineage diversification of the family Salicaceae remain poorly understood. In this study, we compare 24 species representing 18 genera of the family.

The complete chloroplast genome of (Salicaceae) from Chile.

The chloroplast (cp) genome sequence of has been characterized from Illumina pair-end sequencing. The complete cp genome was 158,306 bp in length, containing a large single copy region (LSC) of 85,059 bp and a small single copy region (SSC) of 17,889 bp, which were separated by a pair of 27,679 bp inverted repeat regions (IRs). The genome contained 129 genes, including 85 protein-coding genes, 36 tRNA genes, and 8 rRNA genes.