Demographic history and identification of threats revealed by population genomic analysis provide insights into conservation for an endangered maple.

Recent advancements in whole genome sequencing techniques capable of covering nearly all the nucleotide variations of a genome would make it possible to set up a conservation framework for threatened plants at the genomic level. Here we applied a whole genome resequencing approach to obtain genome-wide data from 105 individuals sampled from the 10 currently known extant populations of Acer yangbiense, an endangered species with fragmented habitats and restricted distribution in Yunnan, China. To inform meaningful conservation action, we investigated what factors might have contributed to the formation of its extremely small population sizes and what threats it currently suffers at a genomic level. Our results revealed that A. yangbiense has low genetic diversity and comprises different numbers of genetic groups based on neutral (seven) and selected loci (13), with frequent gene flow between populations. Repeated bottleneck events, particularly the most recent one occurring within ~10,000 years before present, which decreased its effective population size (Ne ) < 200, and severe habitat fragmentation resulting from anthropogenic activities as well as a biased gender ratio of mature individuals in its natural habitat, might have together contributed to the currently fragmented and endangered status of A. yangbiense. The species has suffered from inbreeding and deleterious mutation load, both of which varied among populations but had similar patterns; that is, populations with higher FROH (frequency of runs of homozygosity) always carried a larger number of deleterious mutations in the homozygous state than in populations with lower FROH. In addition, based on our genetic differentiation results, and the distribution patterns of homozygous deleterious mutations in individuals, we recommend certain conservation actions regarding the genetic rescue of A. yangbiense. Overall, our study provides meaningful insights into the conservation genetics and a framework for the further conservation for the endangered A. yangbiense.

Chromosome-level genome assembly of the threatened resource plant Cinnamomum chago.

Cinnamomum chago is a tree species endemic to Yunnan province, China, with potential economic value, phylogenetic importance, and conservation priority. We assembled the genome of C. chago using multiple sequencing technologies, resulting in a high-quality, chromosomal-level genome with annotation information. The assembled genome size is approximately 1.06 Gb, with a contig N50 length of 92.10 Mb. About 99.92% of the assembled sequences could be anchored to 12 pseudo-chromosomes, with only one gap, and 63.73% of the assembled genome consists of repeat sequences. In total, 30,497 genes were recognized according to annotation, including 28,681 protein-coding genes. This high-quality chromosome-level assembly and annotation of C. chago will assist us in the conservation and utilization of this valuable resource, while also providing crucial data for studying the evolutionary relationships within the Cinnamomum genus, offering opportunities for further research and exploration of its diverse applications.

Rapid in-situ aerobic biodegradation of high salt and oily food waste employing constructed synthetic microbiome.

The high salt content of food waste (FW) severely limits microbial physiological activity and reduces its biodegradability. In this study, a salt-tolerant thermophilic bacterial agent that consists of four different substrate degradation functional strains was evaluated for efficient high salt and oily FW in solid-state aerobic biodegradation disposers. The phy-chemical properties, enzyme activities, microbial community structure, and function during the biodegradation process were evaluated under high salt (5%) stress. The results showed that the agent promoted the degradation rate, increased the matrix temperature, decreased the moisture content (MC), and enhanced enzyme activities without putrid smell. High-throughput sequencing indicated community structure succession between different groups and the positive contribution of the inoculated functional strains. During the FW biodegradation process, the Bacillus sp. inoculated was the dominant genus in the agent group. Furthermore, CCA further confirmed the positive effects of the four inoculated strains on high salt and oily FW aerobic biodegradation. Functional prediction and metabolite results both confirmed that the agent was more efficient in carbon, amino acid, and lipid metabolism, which demonstrated that the synthetic microbial consortium holds a potential advantage for efficiency and subsequent resource utilization for organic fertilizer.

Applying image clustering to phylogenetic analysis: A trial.

•Molecular phylogenetic analysis can be supplemented by image clustering analysis that uses pretrained machine learning tools.

Seed Germination and Seedling Growth Influenced by Genetic Features and Drought Tolerance in a Critically Endangered Maple.

Understanding the adaptation of plant species will help us develop effective breeding programs, guide the collection of germplasm, and improve the success of population restoration projects for threatened species. Genetic features correlate with species adaptation. Acer yangbiense is a critically endangered plant species with extremely small populations (PSESP). However, no information was available on its seed germination and seedling growth in populations with different genetic characteristics. In this study, we investigated seed germination and compared the performance of 566 seedlings in 10 maternal half-sib families cultivated in Kunming Botanical Garden. The results showed that A. yangbiense seeds required an average of 44 days to start germinating, with a 50% germination rate estimated to take about 47-76 days, indicating slow and irregular germination. There is a trade-off between the growth and survival in A. yangbiense seedlings, with fast growth coming at the cost of low survival. Groups that were able to recover from a recent bottleneck consistently had higher relative growth rates. High genetic diversity and low levels of inbreeding are likely to be responsible for their improved survival during drought conditions and rapid growth under optimal environmental conditions. Our results suggest that maternal genetic traits might be used as indicators for conservation and population restoration. These findings provide us with new information that could be applied to support ex situ conservation and reintroduction of threatened species.

Evidence for copurification of micronuclei in sucrose density gradient-enriched plasma membranes from cell lines.

Sucrose density gradient-enriched membrane preparations and membrane fraction enrichment through affinity purification techniques are commonly used in proteomic analysis. However, published proteomic profiles characterized by the above methods show the presence of nuclear proteins in addition to membrane proteins. While shuttling of nuclear proteins across cellular compartments and their transient residency at membrane interfaces could explain some of these observations, the presence of nuclear proteins in proteomic profiles generated with crude and enriched membranes could be the result of nonspecific contamination of nuclear debris during cell fractionation procedures. We hypothesized that micronuclei arising from the genomic instability inherent to cancer cells may copurify with plasma membrane fractions on sucrose gradients. Using sucrose gradient-enriched plasma membranes from breast cancer cell lines derived from the MCF-7 cell line, we provide experimental evidence to indicate that micronuclei are present in fresh preparations of plasma membranes. The origin of these micronuclei was traced to budding of nuclei in intact cells. Furthermore, mass spectrometric analysis confirmed the presence of nuclear proteins as well as membrane and associated signaling proteins in sucrose gradient-enriched preparations.

De novo genome assembly of the endangered Acer yangbiense, a plant species with extremely small populations endemic to Yunnan Province, China.

BACKGROUND: Acer yangbiense is a newly described critically endangered endemic maple tree confined to Yangbi County in Yunnan Province in Southwest China. It was included in a programme for rescuing the most threatened species in China, focusing on "plant species with extremely small populations (PSESP)". FINDINGS: We generated 64, 94, and 110 Gb of raw DNA sequences and obtained a chromosome-level genome assembly of A. yangbiense through a combination of Pacific Biosciences Single-molecule Real-time, Illumina HiSeq X, and Hi-C mapping, respectively. The final genome assembly is ∼666 Mb, with 13 chromosomes covering ∼97% of the genome and scaffold N50 sizes of 45 Mb. Further, BUSCO analysis recovered 95.5% complete BUSCO genes. The total number of repetitive elements account for 68.0% of the A. yangbiense genome. Genome annotation generated 28,320 protein-coding genes, assisted by a combination of prediction and transcriptome sequencing. In addition, a nearly 1:1 orthology ratio of dot plots of longer syntenic blocks revealed a similar evolutionary history between A. yangbiense and grape, indicating that the genome has not undergone a whole-genome duplication event after the core eudicot common hexaploidization. CONCLUSION: Here, we report a high-quality de novo genome assembly of A. yangbiense, the first genome for the genus Acer and the family Aceraceae. This will provide fundamental conservation genomics resources, as well as representing a new high-quality reference genome for the economically important Acer lineage and the wider order of Sapindales.

Tubedown associates with cortactin and controls permeability of retinal endothelial cells to albumin.

Tubedown (Narg1, Tbdn), a member of the Nat1 family of proteins, associates with the acetyltransferase Ard1 and exerts an angiostatic function in adult retinal-blood-vessel homeostasis. The purpose of the present study was to gain a better understanding of the nature of the Tbdn protein complex and how it might exert a homeostatic influence on blood vessels. Immunoprecipitation of Tbdn from endothelial cells followed by gel electrophoresis and liquid-chromatography-tandem-mass-spectrometry identified the actin-cytoskeleton-binding protein cortactin as a co-immunopurifying species. Western blotting confirmed the association between Tbdn and cortactin. Immunofluorescence confocal microscopy revealed that Tbdn colocalizes with cortactin and F-actin in cytoplasmic regions and at the cortex of cultured endothelial cells. Because cortactin is known to regulate cellular permeability through its interaction with the actin cytoskeleton, a process that is crucial for endothelial cell homeostasis, the role of Tbdn on endothelial cell permeability was examined. Knockdown of Tbdn expression in endothelial cells led to the co-suppression of Ard1 protein expression and to a significant increase in cellular permeability measured by the transit of FITC-albumin across the cellular monolayer. Furthermore, the proliferative retinal neovascularization and thickening resulting from induction of Tbdn knockdown in endothelium in transgenic mice was associated with a significant increase in extravasation or leakage of albumin from abnormal retinal blood vessels in vivo. These results provide evidence that an association occurs between Tbdn and cortactin, and that Tbdn is involved in the regulation of retinal-endothelial-cell permeability to albumin. This work implicates a functional role for Tbdn in blood-vessel permeability dynamics that are crucial for vascular homeostasis.

Bacterial identification by protein mass mapping combined with an experimentally derived protein mass database.

A protein mass mapping approach using mass spectrometry (MS) combined with an experimentally derived protein mass database is presented for rapid and effective identification of bacterial species. A prototype mass database from the protein extracts of nine bacterial species has been created by off-line high-performance liquid chromatography (HPLC) matrix-assisted laser desorption/ionization (MALDI) MS, in which the microbiological parameter of bacterial growth time is considered. A numerical method using a statistical weight factor algorithm is devised for matching the protein masses of an unknown bacterial sample against the database. The sum of these weight factors produces a corresponding summed weight factor score for each bacterial species listed in the database, and the database species producing the highest score represents the identity of the respective unknown bacterium. The applicability and reliability of this protein mass mapping approach has been tested with seven bacterial species in a single-blind study by both direct MALDI MS and HPLC electrospray ionization MS methods, and identification results with 100% accuracy are obtained. Our studies have demonstrated that the protein mass database can be rapidly established and readily adopted with relatively less dependency on experimental factors. Furthermore, it is shown that a number of proteins can be detected using a protein sample amount equivalent to an extract of less than 1000 cells, demonstrating that this protein mass mapping approach can potentially be highly sensitive for rapid bacterial identification.