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Amaranthus tricolor is a vegetable and ornamental amaranth, with high lysine, dietary fibre and squalene content. The red cultivar of A. tricolor possesses a high concentration of betalains, which has been used as natural food colorants. Here, we constructed the genome of A. tricolor , the first reference genome for the subgenus Albersia , combining PacBio HiFi, Nanopore ultra-long and Hi–C data. The contig N50 size was 906 kb, and 99.58% of contig sequence was anchored to the 17 chromosomes, totalling 520 Mb. We annotated 27,813 protein-coding genes with an average 1.3 kb coding sequence and 5.3 exons. We inferred that A. tricolor underwent a whole-genome duplication (WGD) and that the WGD shared by amaranths occurred in the last common ancestor of subfamily Amaranthoideae. Moreover, we comprehensively identified candidate genes in betalain biosynthesis pathway. Among them, DODAα1 and CYP76ADα1 , located in one topologically associated domain (TAD) of an active (A) compartment on chromosome 16, were more highly expressed in red leaves than in green leaves, and DODAα1 might be the rate-limiting enzyme gene in betalains biosynthesis. This study presents new genome resources and enriches our understanding of amaranth evolution, betalains production, facilitating molecular breeding improvements and the understanding of C4 plants evolution. [ABSTRACT FROM AUTHOR]

Background Due to the importance of chicken production and the remarkable influence of the gut microbiota on host health and growth, tens of thousands of metagenome-assembled genomes (MAGs) have been constructed for the chicken gut microbiome. However, due to the limitations of short-read sequencing and assembly technologies, most of these MAGs are far from complete, are of lower quality, and include contaminant reads. Results We generated 332 Gb of high-fidelity (HiFi) long reads from the 5 chicken intestinal compartments and assembled 461 and 337 microbial genomes, of which 53% and 55% are circular, at the species and strain levels, respectively. For the assembled microbial genomes, approximately 95% were regarded as complete according to the "RNA complete" criteria, which requires at least 1 full-length ribosomal RNA (rRNA) operon encoding all 3 types of rRNA (16S, 23S, and 5S) and at least 18 copies of full-length transfer RNA genes. In comparison with the short-read-derived chicken MAGs, 384 (83% of 461) and 89 (26% of 337) strain-level and species-level genomes in this study are novel, with no matches to previously reported sequences. At the gene level, one-third of the 2.5 million genes in the HiFi-derived gene catalog are novel and cannot be matched to the short-read-derived gene catalog. Moreover, the HiFi-derived genomes have much higher continuity and completeness, as well as lower contamination; the HiFi-derived gene catalog has a much higher ratio of complete gene structures. The dominant phylum in our HiFi-assembled genomes was Firmicutes (82.5%), and the foregut was highly enriched in 5 genera: Ligilactobacillus, Limosilactobacillus, Lactobacillus, Weissella , and Enterococcus , all of which belong to the order Lactobacillales. Using GTDB-Tk, all 337 species-level genomes were successfully classified at the order level; however, 2, 35, and 189 genomes could not be classified into any known family, genus, and species, respectively. Among these incompletely classified genomes, 9 and 49 may belong to novel genera and species, respectively, because their 16S rRNA genes have identities lower than 95% and 97% to any known 16S rRNA genes. Conclusions HiFi sequencing not only produced metagenome assemblies and gene structures with markedly improved quality but also recovered a substantial portion of novel genomes and genes that were missed in previous short-read-based metagenome studies. The novel genomes and species obtained in this study will facilitate gut microbiome and host–microbiota interaction studies, thereby contributing to the sustainable development of poultry resources. [ABSTRACT FROM AUTHOR]

Background The globe skimmer dragonfly (Pantala flavescens) is a notable Odonata insect distributed in nature fields and farmlands worldwide, and it is commonly recognized as a natural enemy because it preys on agricultural pests and health pests. As one of the sister groups of winged insects, odonatan species are key to understanding the evolution of insect wings. Findings We present a high-quality reference genome of P. flavescens , which is the first chromosome-level genome in the Palaeoptera (Odonata and Ephemeroptera). The assembled genome size was 662 Mb, with a contig N50 of 16.2 Mb. Via Hi-C scaffolding, 648 Mb (97.9%) of contig sequences were clustered, ordered, and assembled into 12 large scaffolds, each corresponding to a natural chromosome. The X chromosome was identified by sequence coverage depth. The repetitive sequences and gene density of the X chromosome are similar to those of autosomal sequences, but the X chromosome shows a much lower degree of heterozygosity. Our analysis shows that the effective population size experienced 3 declining events, which may have been caused by climate change and environmental pollution. Conclusions The genome of P. flavescens provides more information on the biology and evolution of insects and will help for the use of this species in pest control. [ABSTRACT FROM AUTHOR]

Agricultural intensification has increased crop productivity but simplified production and reduced cropping system diversity. In recent decades, the intensified wheat–maize rotation in the North China Plain has sharply decreased the groundwater table, with associated environmental and biodiversity issues. Understanding whether increasing cropping system diversity stabilizes productivity, improves resilience, and reduces adverse environmental impacts is critical. This study quantified the water requirements of nine staple crops from 1960 to 2020, established 15 alternative crop rotations, and evaluated the resilience of each rotation in the Cangzhou area, a typical groundwater deletion funnel area. The results showed that reducing cropping density (harvests per year) from 2 to 1.5 decreased the average annual water requirement and irrigation demand by 14 % and 33 %, respectively. Summer soybean alternated with maize and rotated with wheat did not reduce groundwater use but increased profitability and protein production. Spring mung bean–summer millet-based multi-rotations had higher precipitation coupling degrees (8 % in wet years, 17 % in normal years, and 56 % in dry years) and profitability (1.1–2.4 times) than the wheat–maize rotation. The spring potato–summer millet rotation in one year had the greatest profitability, the highest equivalent yield to wheat, and the highest water use efficiency (WUE), while spring maize rotated with winter wheat–summer soybean performed best for protein content, energy output, and WUEs. This study identified 11 alternative rotations with a higher comprehensive evaluation index than the conventional wheat–maize rotation based on entropy-TOPSIS considering 12 indicators. Spring mungbean is not suitable for inclusion in the crop rotation when solely cultivated in one year due to mismatched rainfall. Beyond wheat and maize, soybean, millet, and potato are promising crops for innovative multi-year multi-crop rotations to enhance crop diversification, maximize system outputs, and minimize groundwater and energy depletion. This study's analysis could be extended to develop robust and diverse crop rotations with multiple co-benefits in other water-stressed agricultural regions. • Water requirements of nine staple crops from 1960 to 2020 was quantified. • 15 diversified crop rotations were redesigned and established. • Multi-dimensional outcomes of each rotation were evaluated for synergies and tradeoff. • Reducing cropping density mitigated groundwater table decline. • Wheat-maize rotations involving soybean, millet and potato achieved multiple co-benefits. [ABSTRACT FROM AUTHOR]

Background: Anaerobic digestion (AD) is important in treating of food waste, and thousands of metagenome-assembled genomes (MAGs) have been constructed for the microbiome in AD. However, due to the limitations of the short-read sequencing and assembly technologies, most of these MAGs are grouped from hundreds of short contigs by binning algorithms, and the errors are easily introduced., Results: In this study, we constructed a total of 60 non-redundant microbial genomes from 64.5 Gb of PacBio high-fidelity (HiFi) long reads, generated from the digestate samples of a full-scale biogas plant fed with food waste. Of the 60 microbial genomes, all genomes have at least one copy of rRNA operons (16S, 23S, and 5S rRNA), 54 have ≥18 types of standard tRNA genes, and 39 are circular complete genomes. In comparison with the published short-read derived MAGs for AD, we found 23 genomes with average nucleotide identity less than 95% to any known MAGs. Besides, our HiFi-derived genomes have much higher average contig N50 size, slightly higher average genome size and lower contamination. GTDB-Tk classification of these genomes revealed two genomes belonging to novel genus and four genomes belonging to novel species, since their 16S rRNA genes have identities lower than 95 and 97% to any known 16S rRNA genes, respectively. Microbial community analysis based on the these assembled genomes reveals the most predominant phylum was Thermotogae (70.5%), followed by Euryarchaeota (6.1%), and Bacteroidetes (4.7%), and the most predominant bacterial and archaeal genera were Defluviitoga (69.1%) and Methanothrix (5.4%), respectively. Analysis of the full-length 16S rRNA genes identified from the HiFi reads gave similar microbial compositions to that derived from the 60 assembled genomes., Conclusion: High-fidelity sequencing not only generated microbial genomes with obviously improved quality but also recovered a substantial portion of novel genomes missed in previous short-read based studies, and the novel genomes will deepen our understanding of the microbial composition in AD of food waste., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Jiang, Li, Wang, Shen, Wang, Wang, Xu, Yuan, Lei, Chen, Yang, Deng and Fan.)

Chinese herbal medicines (CHMs), with a wide range of bioactive components, are considered to be an important source for new drug discovery. However, the process to isolate and obtain those bioactive components to develop new drugs always consumes a large amount of organic solvents with high toxicity and non-biodegradability. Natural deep eutectic solvents (NADES), a new type of green and designable solvents composed of primary plant-based metabolites, have been used as eco-friendly substitutes for traditional organic solvents in various fields. Due to the advantages of easy preparation, low production cost, low toxicity, and eco-friendliness, NADES have been also applied as extraction solvents, media, and drug delivery agents in CHMs in recent years. Besides, the special properties of NADES have been contributed to elucidating the traditional processing (also named Paozhi in Chinese) theory of CHMs, especially processing with honey. In this paper, the development process, preparation, classification, and applications for NADES in CHMs have been reviewed. Prospects in the future applications and challenges have been discussed to better understand the possibilities of the new solvents in the drug development and other uses of CHMs., Competing Interests: Author MW was employed by the company SU Biomedicine BV. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Li, Rao, Ye, Wang, Yang, Wang, Guo, Xiong and Cui.)

Ipomoea cairica is a perennial creeper that has been widely introduced as a garden ornamental across tropical, subtropical, and temperate regions. Because it grows extremely fast and spreads easily, it has been listed as an invasive species in many countries. Here, we constructed the chromosome-level reference genome of Ipomoea cairica by Pacific Biosciences HiFi and Hi-C sequencing, with the assembly size of 733.0 Mb, the contig N50 of 43.8 Mb, the scaffold N50 of 45.7 Mb, and the Benchmarking Universal Single-Copy Orthologs complete rate of 98.0%. Hi-C scaffolding assigned 97.9% of the contigs to 15 pseudo-chromosomes. Telomeric repeat analysis reveals that 7 of the 15 pseudo-chromosomes are gapless and telomere to telomere. The transposable element content of Ipomoea cairica is 73.4%, obviously higher than that of other Ipomoea species. A total of 38,115 protein-coding genes were predicted, with the Benchmarking Universal Single-Copy Orthologs complete rate of 98.5%, comparable to that of the genome assembly, and 92.6% of genes were functional annotated. In addition, we identified 3,039 tRNA genes and 2,403 rRNA genes in the assembled genome. Phylogenetic analysis showed that Ipomoea cairica formed a clade with Ipomoea aquatica, and they diverged from each other 8.1 million years ago. Through comparative genome analysis, we reconfirmed that a whole genome triplication event occurred specific to Convolvulaceae family and in the ancestor of the genus Ipomoea and Cuscuta. This high-quality reference genome of Ipomoea cairica will greatly facilitate the studies on the molecular mechanisms of its rapid growth and invasiveness., (© The Author(s) 2022. Published by Oxford University Press on behalf of Genetics Society of America.)

Lead (Pb) in lipstick products has become an increasing concern, which can cause safety problems to human body directly with diet. To investigate the Pb exposure and potential health risk level of typical popular lip cosmetics in Chinese e-commerce market, Python crawler was introduced to identify and select 34 typical popular lip cosmetics, including 12 lipsticks, 13 lip glosses, and 9 lip balms. And then this study used ICP-MS to determine the content of Pb. Furthermore, the ingestion health risk assessment method issued by United States Environmental Protection Agency (USEPA) and Monte Carlo simulation algorithm were applied to assess the probabilistic health risks of adults exposure. Finally, taking the possible exposure of children contacting with lip products, the health risk assessment of children blood Pb was carried out. The results showed that the concentration of Pb in lip products ranged from 0 to 0.5237 mg/kg, which was far lower than the limit set by various countries. The probabilistic non-carcinogenic risks and carcinogenic risks were 4.93 ×10 -7 ~2.82 ×10 -3 and 1.68 ×10 -12 ~9.59 ×10 -9 , respectively, which were in an acceptable level. The results of blood Pb assessment suggested that the Pb content of lip cosmetics had no obvious influence on blood Pb concentration of children, and background Pb exposure is the main factor affecting children's blood Pb level (BLL). Overall, the samples of lip products are selected by Python crawler in this study, which are more objective and representative. This study focuses on deeper study of Pb, especially for the health risk assessment of blood Pb in children exposed to lip products. These results perhaps could provide useful information for the safety cosmetics usage for people in China and even the global world., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Li, Fang, Liu, Zhang, Liu, Jiang, Yang, Yang, Song and Liu.)