Genome assembly of Erythrophleum Fordii, a special "ironwood" tree in China.

OBJECTIVES: Erythrophleum is a genus in the Fabaceae family. The genus contains only about 10 species, and it is best known for its hardwood and medical properties worldwide. Erythrophleum fordii Oliv. is the only species of this genus distributed in China. It has superior wood and can be used in folk medicine, which leads to its overexploitation in the wild. For its effective conservation and elucidation of the distinctive genetic traits of wood formation and medical components, we present its first genome assembly. DATA DESCRIPTION: This work generated ~ 160.8 Gb raw Nanopore whole genome sequencing (WGS) long reads, ~ 126.0 Gb raw MGI WGS short reads and ~ 29.0 Gb raw RNA-seq reads using E. fordii leaf tissues. The de novo assembly contained 864,825,911 bp in the E. fordii genome, with 59 contigs and a contig N50 of 30,830,834 bp. Benchmarking Universal Single-Copy Orthologs (BUSCO) revealed 98.7% completeness of the assembly. The assembly contained 471,006,885 bp (54.4%) repetitive sequences and 28,761 genes that coded for 33,803 proteins. The protein sequences were functionally annotated against multiple databases, facilitating comparative genomic analysis.

Genome assembly of the pioneer species Plantago major L. (Plantaginaceae) provides insight into its global distribution and adaptation to metal-contaminated soil.

Plantago is a major genus belonging to the Plantaginaceae family and is used in herbal medicine, functional food, and pastures. Several Plantago species are also characterized by their global distribution, but the mechanism underpinning this is not known. Here, we present a high-quality, chromosome-level genome assembly of Plantago major L., a species of Plantago, by incorporating Oxford Nanopore sequencing and Hi-C technologies. The genome assembly size was approximately 671.27 Mb with a contig N50 length of 31.30 Mb. 31,654 protein-coding genes were identified from the genome. Evolutionary analysis showed that P. major diverged from other Lamiales species at ~62.18 Mya and experienced two rounds of WGD events. Notably, many gene families related to plant acclimation and adaptation expanded. We also found that many polyphenol biosynthesis genes showed high expression patterns in roots. Some amino acid biosynthesis genes, such as those involved in histidine synthesis, were highly induced under metal (Ni) stress that led to the accumulation of corresponding metabolites. These results suggest persuasive arguments for the global distribution of P. major through multiscale analysis. Decoding the P. major genome provides a valuable genomic resource for research on dissecting biological function, molecular evolution, taxonomy, and breeding.

Low density lipoprotein receptor (LDLR)-targeted lipid nanoparticles for the delivery of sorafenib and Dihydroartemisinin in liver cancers.

AIMS: Liver cancer is one of the leading causes of cancer mortality worldwide. Inspired by the biological structure and function of low-density lipoprotein (LDL), in this study, an ApopB-100 based targeted lipid nanoparticles was synthesized to improve the therapeutic efficacy in liver cancer treatment. MAIN METHODS: The biological composition of ApopB is similar to LDL which can effectively increase the targeting efficiency of nanoparticles in LDL receptor (LDLR)-overexpressed liver tumors. KEYFINDINGS: We have demonstrated that the co-administration of sorafenib (SRF) and Dihydroartemisinin (DHA) could exhibit synergistic anticancer effect in HepG2 liver cancer cells. DHA produced excessive cellular reactive oxygen species (ROS) and induced greater apoptosis of cancer cells. LDL-based SRF/DHA-loaded lipid nanoparticles (LD-SDN) showed remarkable decrease in the cell viability compared to that of either of single drug treated cancer cells. Combination of SRF+DHA resulted in predominant SubG1 proportion of cells. LD-SDN exhibited the highest SubG1 (%) of cells compared to that of any of the individual drugs. Most importantly, robust antitumor response and delayed tumor growth was observed for LD-SDN treated xenograft tumor model. Ki67 proliferation index of LD-SDN (22.1 ± 5.6%) is significantly lesser compared to that of either control (86.2 ± 6.9%) or SRF (75.4 ± 4.89%) or DHA (69.4 ± 6.9%). SIGNIFICANCES: These data provide strong evidence that LDL-mimetic lipid nanoformulations could be utilized as a biocompatible and tumor targeted platform for the delivery of multiple anticancer drugs in cancer treatment.

Endangered but genetically stable-Erythrophleum fordii within Feng Shui woodlands in suburbanized villages.

Feng Shui woodlands are naturally or artificially formed green areas in southern China. They are precious for maintaining ecosystem balance in modern semiurban environments. However, they are generally small and geographically isolated from each other, and the status of genetic diversity of the plant species within them has been almost neglected. Therefore, we studied the genetic diversity of the endangered Erythrophleum fordii in eight Feng Shui woodlands (a total of 1,061 individuals) in Guangzhou, a large city in southern China, using microsatellites. For comparison, one population with 33 individuals sampled in a nature reserve was also studied. Although our results indicate that significant demographic declines occurred historically in E. fordii, such declines have not resulted in consistent reductions in genetic variation over generations in Feng Shui populations in the recent past, and the levels of genetic variation in these populations were higher than or comparable to the genetic variation of the population in the nature reserve. In addition, our parentage and paternity analyses indicated widespread and potential long-distance pollen flow within one Feng Shui woodland, indicating the presence of an unbroken pollination network, which would at least partially alleviate the genetic erosion due to habitat fragmentation and the unequal gene contributions of E. fordii parents to their progenies when favorable recruitment habitats are absent under most of the parent trees. Overall, our results suggest that E. fordii in Feng Shui woodlands may not be driven to extinction in the near future. Nevertheless, uncontrolled fast urban development with a lack of awareness of Feng Shui woodlands will cause the local extinction of E. fordii, which has already happened in some Feng Shui woodlands.