Multi-omics data provide insight into the adaptation of the glasshouse plant Rheum nobile to the alpine subnival zone.

Subnival glasshouse plants provide a text-book example of high-altitude adaptation with reproductive organs enclosed in specialized semi-translucent bracts, monocarpic reproduction and continuous survival under stress. Here, we present genomic, transcriptomic and metabolomic analyses for one such plant, the Noble rhubarb (Rheum nobile). Comparative genomic analyses show that an expanded number of genes and retained genes from two recent whole-genome duplication events are both relevant to subnival adaptation of this species. Most photosynthesis genes are downregulated within bracts compared to within leaves, and indeed bracts exhibit a sharp reduction in photosynthetic pigments, indicating that the bracts no longer perform photosynthesis. Contrastingly, genes related to flavonol synthesis are upregulated, providing enhanced defense against UV irradiation damage. Additionally, anatomically abnormal mesophyll combined with the downregulation of genes related to mesophyll differentiation in bracts illustrates the innovation and specification of the glass-like bracts. We further detect substantial accumulation of antifreeze proteins (e.g. AFPs, LEAs) and various metabolites (e.g. Proline, Protective sugars, procyanidins) in over-wintering roots. These findings provide new insights into subnival adaptation and the evolution of glasshouse alpine plants.

A high-quality Buxus austro-yunnanensis (Buxales) genome provides new insights into karyotype evolution in early eudicots.

BACKGROUND: Eudicots are the most diverse group of flowering plants that compromise five well-defined lineages: core eudicots, Ranunculales, Proteales, Trochodendrales, and Buxales. However, the phylogenetic relationships between these five lineages and their chromosomal evolutions remain unclear, and a lack of high-quality genome analyses for Buxales has hindered many efforts to address this knowledge gap. RESULTS: Here, we present a high-quality chromosome-level genome of Buxus austro-yunnanensis (Buxales). Our phylogenomic analyses revealed that Buxales and Trochodendrales are genetically similar and classified as sisters. Additionally, both are sisters to the core eudicots, while Ranunculales was found to be the first lineage to diverge from these groups. Incomplete lineage sorting and hybridization were identified as the main contributors to phylogenetic discordance (34.33%) between the lineages. In fact, B. austro-yunnanensis underwent only one whole-genome duplication event, and collinear gene phylogeny analyses suggested that separate independent polyploidizations occurred in the five eudicot lineages. Using representative genomes from these five lineages, we reconstructed the ancestral eudicot karyotype (AEK) and generated a nearly gapless karyotype projection for each eudicot species. Within core eudicots, we recovered one common chromosome fusion event in asterids and malvids, respectively. Further, we also found that the previously reported fused AEKs in Aquilegia (Ranunculales) and Vitis (core eudicots) have different fusion positions, which indicates that these two species have different karyotype evolution histories. CONCLUSIONS: Based on our phylogenomic and karyotype evolution analyses, we revealed the likely relationships and evolutionary histories of early eudicots. Ultimately, our study expands genomic resources for early-diverging eudicots.

The Chloranthus sessilifolius genome provides insight into early diversification of angiosperms.

Most extant angiosperms belong to Mesangiospermae, which comprises eudicots, monocots, magnoliids, Chloranthales and Ceratophyllales. However, phylogenetic relationships between these five lineages remain unclear. Here, we report the high-quality genome of a member of the Chloranthales lineage (Chloranthus sessilifolius). We detect only one whole genome duplication within this species and find that polyploidization events in different Mesangiospermae lineage are mutually independent. We also find that the members of all floral development-related gene lineages are present in C. sessilifolius despite its extremely simplified flower. The AP1 and PI genes, however, show a weak floral tissue-specialized expression. Our phylogenomic analyses suggest that Chloranthales and magnoliids are sister groups, and both are together sister to the clade comprising Ceratophyllales and eudicots, while the monocot lineage is sister to all other Mesangiospermae. Our findings suggest that in addition to hybridization, incomplete lineage sorting may largely account for phylogenetic inconsistencies between the observed gene trees.

The complete chloroplast genome sequence of Carpinus tibetana (Betulaceae).

The complete chloroplast genome of Carpinus tibetana was a circular DNA molecule of 158,762 bp in length, containing a large single copy region (LSC) of 87,825 bp and small single copy region (SSC) of 18,797 bp, which were separated by a pair of 26,071 bp and 26,069 bp inverted repeat regions (IRs). The all GC content of C. tibetana chloroplast genome was 36.47%. It encoded totally 127 genes, including 83 protein-coding genes, 35 tRNA genes and eight rRNA genes. The chloroplast genome of C. tibetana will provide useful genetic information for future conservation genetics and phylogenetic studies.

A chromosome-level genome assembly for the tertiary relict plant Tetracentron sinense oliv. (trochodendraceae).

Tetracentron sinense and Trochodendron aralioides are two Tertiary relict species of large trees in the family Trochodendraceae with narrow distributions on the mainland and islands of eastern Asia. They belong to the order Trochodendrales, which is one of the four early-diverged eudicot lineages. These two relict species provide a good system in which to examine genomic changes that occurred as they survived during repeated climatic oscillations in the Quaternary. We sequenced the genome of Te. sinense and compared it with that of Tr. aralioides. We found that Te. sinense has a smaller genome size (986.3 Mb) than that of Tr. aralioides (1610 Mb). Repetitive elements made the major contribution to the contrasting genome sizes in the two species, with most bursts of repeats occurring within the past four million years when the climate oscillated greatly. These species share two rounds of whole-genome duplications. The mainland species Te. sinense had a larger effective population size than the island species Tr. aralioides after the largest glaciation during the Quaternary climatic oscillation. However, soon after this recovery stage, the effective population sizes of both species continued to decrease, although the current effective population size of Te. sinense is still larger than that of Tr. aralioides. We recovered three distinctly diverged clades through resequencing the genomes of 50 individuals across the distributional range of Te. sinense in China. Our results provide an important genomic resource with which to examine early trait evolution in the core eudicots and assist efforts to conserve this relict tree species.

Complete chloroplast genome sequence of an alpine rhubarb Rheum likiangense.

Rheum likiangense Samuelsson (Polygonaceae) is an endangered alpine rhubarb in the Qinghai-Tibet Plateau. In this study we report the complete chloroplast genome sequence (plastome) of Rh. likiangense. The assembled plastome is 162,291 bp in length with 31,741 bp inverted repeat (IR) regions and 128 annotated genes, including 34 tRNA genes, 8 rRNA genes, and 86 protein-coding genes. Phylogenetic analyses based on the full plastome sequences suggest the close relationship of Rh. likiangense with Rh. acuminatum and Rh. nobile. The plastome reported here is highly useful for designing plastome SSR markers to conduct a further conservation genetic study of this endangered rhubarb.

Statistical analysis of the behavior of fracture toughness of compound bioceramic artificial bone.

We show the manufacturing procedure of the test specimen of the compound bioceramic artificial bone, conduct experiments to measure its fracture toughness, and conclude that the experiment data conform to the two-parameter Weibull distribution with scale parameter ß = 0.527369 and form parameter α = 5.24317. Furthermore, compound bioceramic artificial bone is of a high level of crack sensitivity and its data for the fracture toughness is has a high dispersion. We also analyze the evolution of the confidence level of the reliability of its fracture toughness. With the increase of the confidence level γ, the crack sensitivity increases, but the median, the discreteness, and the confidence intervals decrease. The size of the test specimen influences the experiment for the fracture toughness, the measured values and their dispersion, and there exists the conversion between size of the test specimen and that of the real device. We extend the results to introduce the statistic model of the size effect of the fracture toughness.