Structurally divergent and recurrently mutated regions of primate genomes.

We sequenced and assembled using multiple long-read sequencing technologies the genomes of chimpanzee, bonobo, gorilla, orangutan, gibbon, macaque, owl monkey, and marmoset. We identified 1,338,997 lineage-specific fixed structural variants (SVs) disrupting 1,561 protein-coding genes and 136,932 regulatory elements, including the most complete set of human-specific fixed differences. We estimate that 819.47 Mbp or ∼27% of the genome has been affected by SVs across primate evolution. We identify 1,607 structurally divergent regions wherein recurrent structural variation contributes to creating SV hotspots where genes are recurrently lost (e.g., CARD, C4, and OLAH gene families) and additional lineage-specific genes are generated (e.g., CKAP2, VPS36, ACBD7, and NEK5 paralogs), becoming targets of rapid chromosomal diversification and positive selection (e.g., RGPD gene family). High-fidelity long-read sequencing has made these dynamic regions of the genome accessible for sequence-level analyses within and between primate species.

The variation and evolution of complete human centromeres.

Human centromeres have been traditionally very difficult to sequence and assemble owing to their repetitive nature and large size1. As a result, patterns of human centromeric variation and models for their evolution and function remain incomplete, despite centromeres being among the most rapidly mutating regions2,3. Here, using long-read sequencing, we completely sequenced and assembled all centromeres from a second human genome and compared it to the finished reference genome4,5. We find that the two sets of centromeres show at least a 4.1-fold increase in single-nucleotide variation when compared with their unique flanks and vary up to 3-fold in size. Moreover, we find that 45.8% of centromeric sequence cannot be reliably aligned using standard methods owing to the emergence of new α-satellite higher-order repeats (HORs). DNA methylation and CENP-A chromatin immunoprecipitation experiments show that 26% of the centromeres differ in their kinetochore position by >500 kb. To understand evolutionary change, we selected six chromosomes and sequenced and assembled 31 orthologous centromeres from the common chimpanzee, orangutan and macaque genomes. Comparative analyses reveal a nearly complete turnover of α-satellite HORs, with characteristic idiosyncratic changes in α-satellite HORs for each species. Phylogenetic reconstruction of human haplotypes supports limited to no recombination between the short (p) and long (q) arms across centromeres and reveals that novel α-satellite HORs share a monophyletic origin, providing a strategy to estimate the rate of saltatory amplification and mutation of human centromeric DNA.

The structure, function and evolution of a complete human chromosome 8.

The complete assembly of each human chromosome is essential for understanding human biology and evolution1,2. Here we use complementary long-read sequencing technologies to complete the linear assembly of human chromosome 8. Our assembly resolves the sequence of five previously long-standing gaps, including a 2.08-Mb centromeric α-satellite array, a 644-kb copy number polymorphism in the ß-defensin gene cluster that is important for disease risk, and an 863-kb variable number tandem repeat at chromosome 8q21.2 that can function as a neocentromere. We show that the centromeric α-satellite array is generally methylated except for a 73-kb hypomethylated region of diverse higher-order α-satellites enriched with CENP-A nucleosomes, consistent with the location of the kinetochore. In addition, we confirm the overall organization and methylation pattern of the centromere in a diploid human genome. Using a dual long-read sequencing approach, we complete high-quality draft assemblies of the orthologous centromere from chromosome 8 in chimpanzee, orangutan and macaque to reconstruct its evolutionary history. Comparative and phylogenetic analyses show that the higher-order α-satellite structure evolved in the great ape ancestor with a layered symmetry, in which more ancient higher-order repeats locate peripherally to monomeric α-satellites. We estimate that the mutation rate of centromeric satellite DNA is accelerated by more than 2.2-fold compared to the unique portions of the genome, and this acceleration extends into the flanking sequence.

A high-quality bonobo genome refines the analysis of hominid evolution.

The divergence of chimpanzee and bonobo provides one of the few examples of recent hominid speciation1,2. Here we describe a fully annotated, high-quality bonobo genome assembly, which was constructed without guidance from reference genomes by applying a multiplatform genomics approach. We generate a bonobo genome assembly in which more than 98% of genes are completely annotated and 99% of the gaps are closed, including the resolution of about half of the segmental duplications and almost all of the full-length mobile elements. We compare the bonobo genome to those of other great apes1,3-5 and identify more than 5,569 fixed structural variants that specifically distinguish the bonobo and chimpanzee lineages. We focus on genes that have been lost, changed in structure or expanded in the last few million years of bonobo evolution. We produce a high-resolution map of incomplete lineage sorting and estimate that around 5.1% of the human genome is genetically closer to chimpanzee or bonobo and that more than 36.5% of the genome shows incomplete lineage sorting if we consider a deeper phylogeny including gorilla and orangutan. We also show that 26% of the segments of incomplete lineage sorting between human and chimpanzee or human and bonobo are non-randomly distributed and that genes within these clustered segments show significant excess of amino acid replacement compared to the rest of the genome.

The pig pangenome provides insights into the roles of coding structural variations in genetic diversity and adaptation.

Structural variations have emerged as an important driving force for genome evolution and phenotypic variation in various organisms, yet their contributions to genetic diversity and adaptation in domesticated animals remain largely unknown. Here we constructed a pangenome based on 250 sequenced individuals from 32 pig breeds in Eurasia and systematically characterized coding sequence presence/absence variations (PAVs) within pigs. We identified 308.3-Mb nonreference sequences and 3438 novel genes absent from the current reference genome. Gene PAV analysis showed that 16.8% of the genes in the pangene catalog undergo PAV. A number of newly identified dispensable genes showed close associations with adaptation. For instance, several novel swine leukocyte antigen (SLA) genes discovered in nonreference sequences potentially participate in immune responses to productive and respiratory syndrome virus (PRRSV) infection. We delineated previously unidentified features of the pig mobilome that contained 490,480 transposable element insertion polymorphisms (TIPs) resulting from recent mobilization of 970 TE families, and investigated their population dynamics along with influences on population differentiation and gene expression. In addition, several candidate adaptive TE insertions were detected to be co-opted into genes responsible for responses to hypoxia, skeletal development, regulation of heart contraction, and neuronal cell development, likely contributing to local adaptation of Tibetan wild boars. These findings enhance our understanding on hidden layers of the genetic diversity in pigs and provide novel insights into the role of SVs in the evolutionary adaptation of mammals.

Integrated gene analyses of de novo variants from 46,612 trios with autism and developmental disorders.

Most genetic studies consider autism spectrum disorder (ASD) and developmental disorder (DD) separately despite overwhelming comorbidity and shared genetic etiology. Here, we analyzed de novo variants (DNVs) from 15,560 ASD (6,557 from SPARK) and 31,052 DD trios independently and also combined as broader neurodevelopmental disorders (NDDs) using three models. We identify 615 NDD candidate genes (false discovery rate [FDR] < 0.05) supported by ≥1 models, including 138 reaching Bonferroni exome-wide significance (P < 3.64e-7) in all models. The genes group into five functional networks associating with different brain developmental lineages based on single-cell nuclei transcriptomic data. We find no evidence for ASD-specific genes in contrast to 18 genes significantly enriched for DD. There are 53 genes that show mutational bias, including enrichments for missense (n = 41) or truncating (n = 12) DNVs. We also find 10 genes with evidence of male- or female-bias enrichment, including 4 X chromosome genes with significant female burden (DDX3X, MECP2, WDR45, and HDAC8). This large-scale integrative analysis identifies candidates and functional subsets of NDD genes.

Single-cell strand sequencing of a macaque genome reveals multiple nested inversions and breakpoint reuse during primate evolution.

Rhesus macaque is an Old World monkey that shared a common ancestor with human ∼25 Myr ago and is an important animal model for human disease studies. A deep understanding of its genetics is therefore required for both biomedical and evolutionary studies. Among structural variants, inversions represent a driving force in speciation and play an important role in disease predisposition. Here we generated a genome-wide map of inversions between human and macaque, combining single-cell strand sequencing with cytogenetics. We identified 375 total inversions between 859 bp and 92 Mbp, increasing by eightfold the number of previously reported inversions. Among these, 19 inversions flanked by segmental duplications overlap with recurrent copy number variants associated with neurocognitive disorders. Evolutionary analyses show that in 17 out of 19 cases, the Hominidae orientation of these disease-associated regions is always derived. This suggests that duplicated sequences likely played a fundamental role in generating inversions in humans and great apes, creating architectures that nowadays predispose these regions to disease-associated genetic instability. Finally, we identified 861 genes mapping at 156 inversions breakpoints, with some showing evidence of differential expression in human and macaque cell lines, thus highlighting candidates that might have contributed to the evolution of species-specific features. This study depicts the most accurate fine-scale map of inversions between human and macaque using a two-pronged integrative approach, such as single-cell strand sequencing and cytogenetics, and represents a valuable resource toward understanding of the biology and evolution of primate species.

Comprehensive analysis of m6A regulators characterized by the immune microenvironment in Duchenne muscular dystrophy.

BACKGROUND: Duchenne muscular dystrophy (DMD) is an X-linked, incurable, degenerative neuromuscular disease that is exacerbated by secondary inflammation. N6-methyladenosine (m6A), the most common base modification of RNA, has pleiotropic immunomodulatory effects in many diseases. However, the role of m6A modification in the immune microenvironment of DMD remains elusive. METHODS: Our study retrospectively analyzed the expression data of 56 muscle tissues from DMD patients and 26 from non-muscular dystrophy individuals. Based on single sample gene set enrichment analysis, immune cells infiltration was identified and the result was validated by flow cytometry analysis and immunohistochemical staining. Then, we described the features of genetic variation in 26 m6A regulators and explored their relationship with the immune mircoenvironment of DMD patients through a series of bioinformatical analysis. At last, we determined subtypes of DMD patients by unsupervised clustering analysis and characterized the molecular and immune characteristics in different subgroups. RESULTS: DMD patients have a sophisticated immune microenvironment that is significantly different from non-DMD controls. Numerous m6A regulators were aberrantly expressed in the muscle tissues of DMD and inversely related to most muscle-infiltrating immune cell types and immune response-related signaling pathways. A diagnostic model involving seven m6A regulators was established using LASSO. Furthermore, we determined three m6A modification patterns (cluster A/B/C) with distinct immune microenvironmental characteristics. CONCLUSION: In summary, our study demonstrated that m6A regulators are intimately linked to the immune microenvironment of muscle tissues in DMD. These findings may facilitate a better understanding of the immunomodulatory mechanisms in DMD and provide novel strategies for the treatment.

Amine-Assisted Simultaneous CO2 Absorption and Mineral Carbonation: Effect of Different Categories of Amines.

The hybrid technology of CO2 capture-mineral carbonation (CCMC) using alkaline streams has emerged in recent years. However, thus far, there has been no comprehensive study revealing the mechanisms of the simultaneous CCMC process regarding the choice of amine types and sensitivity of parameters. Combining with the analysis of multistep reaction mechanisms for different amines, we investigated a representative from each category in CCMC using calcium chloride to simulate the alkaline resource after leaching, i.e., primary (ethanolamine, MEA), secondary (diisopropanolamine, DIPA), tertiary (diethylethanolamine, DEAE), and triamine (diethylenetriamine, DETA), respectively. In the adsorption step, increasing the amine concentration beyond 2 mol/L reduced the absorption efficiency of DEAE due to the hydration mechanism, motivating a rational choice of concentration. In CCMC sections, when the amine concentration increased, only DEAE exhibited an increased carbonation efficiency of up to 100%, while DETA showed the lowest conversion. The carbonation of DEAE demonstrated the least sensitivity to temperature. The crystal transformation experiments suggested that over time, the produced vaterite could completely transform to calcite or aragonite, except those from DETA. Thus, with rationally chosen conditions, DEAE was demonstrated ideal for CCMC. These findings obtained in this work provided a theoretical foundation for designing future CCMC processes.

Relationship between depressive disorders and biochemical indicators in adult men and women.

BACKGROUND: Depression is a psychiatric disorder with global public health concerns. Although a number of risk factors have been identified for depression, there is no clear relationship between biochemistry and depression. In this study, we assessed whether depressive disorders are significantly associated with biochemical indicators. METHODS: Our study included 17,561 adults (age ≥ 18 years) participating in the 2009-2018 National Health and Nutrition Examination Survey (NHANES). The relationship between depression and biochemical and obesity indicators was analyzed by logistic regression. RESULTS: As compared to the control group, men with depression showed significantly higher levels of gamma-glutamyl transferase, glucose, and triglycerides, and lower levels of albumin and total bilirubin. The depressed group had higher levels of alkaline phosphatase, bicarbonate, and sodium than the control group. CONCLUSION: Several biochemical and anthropometric indices were associated with depression in this study. It would be interesting to further analyze their cause-effect relationship. LIMITATIONS: This study is a cross-sectional study. The population is less restricted and does not exclude people with diabetes, pregnancy, etc., so it is less significant for a specific population. Dietary information was not included, as diet plays an important role in many indicators.

Recycling the High-Salinity Textile Wastewater by Quercetin-Based Nanofiltration Membranes with Minimal Water and Energy Consumption.

Effective recovery of dyes and salts from textile wastewater by nanofiltration (NF) remains a serious challenge due to the high consumption of water and energy caused by the limited performance of the available membranes. Herein, a novel strategy is described to prepare loose polyester NF membranes by using renewable quercetin as the aqueous monomer for fractionation of high salinity textile wastewater with minimal water and energy consumption. Compared with NF270, taken as the reference membrane, the QE-0.2/TMC-0.2 membrane significantly improved the efficiency for dye/salt fractionation by 288%. The water consumption was also decreased by 42.9%. The efficiency is attributed to an ultrahigh water permeance of 198 ± 2.1 L-1 m-2 h-1 bar-1 with a high selectivity of 123 (extremely low NaCl rejection of 1.6% and high Congo red rejection of 99.2%). The optimal quercetin-based membrane had an ultrathin separation layer of about 39 ± 1.2 nm with good hydrophilicity and negative charge density. Moreover, this work includes a novel method of comparison with a theoretically ideal membrane, which shows that both the energy and water consumption are near their theoretical minimum. This strategy is expected to save energy and minimize carbon emissions for membrane-based wastewater treatment systems.

Association of trimester-specific gestational weight gain with birth weight and fetal growth in a large community-based population.

BACKGROUND: Previous studies showed that the association of gestational weight gain (GWG) with fetal birthweight and offspring developmental growth was unclear. The aim of this study is to investigate the respective effect of 1 kg of GWG during three trimesters on birthweight and offspring growth from birth to 3 years of age. METHODS: We extracted the decoded information from the Maternal and Child Health Information Management System of Zhoushan Maternal and Child Health Hospital in Zhejiang, China from October 2001 to March 2015, and used multiple linear and logistic regression models. RESULTS: This study included 20,232 women with a full-term singleton birth and 15,557 newborns who took regular health check-ups. Compared to that in the 2nd and 3rd trimester, 1 kg GWG increasing in the 1st trimester had the strongest positive association with higher birthweight, body weight, and height from 1 to 36 months. Their associations with BMI after birth were similar among the three trimesters. In addition, some positive dose-response effects found between quartiles of GWG in the 1st trimester and offspring body weight, as well as BMI. The 1 kg GWG in 1st trimester played the strongest role in contributing to birth weight and benefiting to body growth among children aged up to 3 years. CONCLUSION: The 1 kg GWG in 1st trimester contributed more to birth weight and body development from birth to 3 years compared to the 2nd and 3rd trimesters. The possible beneficial effects of GWG in the 1st trimester on birthweight and offspring development in under/normal weight mothers are found.

Non-random arrangement of synonymous codons in archaea coding sequences.

Non-random arrangement of synonymous codons in coding sequences has been recently reported in eukaryotic and bacterial genomes, but the case in archaeal genomes is largely undetermined. Here, we systematically investigated 122 archaeal genomes for their synonymous codon co-occurrence patterns. We found that in most archaeal coding sequences, the order of synonymous codons is not arranged randomly, but rather some successive codon pairs appear significantly more often than expected. Importantly, such codon pairing bias (CPB) pattern in archaea does not seem to completely follow the co-tRNA codon pairing (CCP) rule previously reported for eukaryotes, but largely obeys an identical codon pairing (ICP) rule. Further, synonymous codon permutation test demonstrated that in many archaeal genomes, random mutation alone is unable to cause the observed high level of ICP bias, which strongly indicates that selection force has been involved to shape synonymous codon orders, potentially meeting a global requirement to optimize translation rate.

Association of serum 25-hydroxyvitamin d concentrations with all-cause and cause-specific mortality among individuals with depression: A cohort study.

BACKGROUND: Limited evidence exists on the relationship between vitamin D status and mortality in depressed patients. METHODS: This study investigates serum 25-hydroxyvitamin D [25(OH)D] concentrations in 8417 adults with depression among the National Health and Nutrition Examination Survey (NHANES, 2005-2018). Mortality outcomes were assessed through National Death Index records up to December 31, 2019. Cox proportional risk models estimated risk ratios (HR) and 95 % confidence intervals (CI) for all-cause, cardiovascular disease (CVD), and cancer mortality. Restricted cubic spline analyses explored the nonlinear association of serum 25(OH)D levels with mortality, using the likelihood ratio test for nonlinearity. RESULTS: The weighted mean serum 25(OH)D level was 66.40 nmol/L (95 % CI: 65.8, 67.0), with 36.3 % having deficient vitamin D (<50 nmol/L [20 ng/mL]). Over an average 7.16-year follow-up, 935 deaths were documented, including 296 CVD deaths and 191 cancer deaths. Higher serum 25(OH)D levels were associated with reduced all-cause mortality (HRs 0.55-1.00, p trend = 0.006) and cancer-specific mortality (HRs 0.36-1.00, p trend = 0.015) after multivariate adjustment. The relationship between serum 25(OH)D and all-cause mortality exhibited a nonlinear pattern (P for nonlinearity <0.001), with a 34 % lower risk for each unit increase in natural log-transformed 25(OH)D levels. Significant interactions were observed with age, antidepressant use, and diabetes status. CONCLUSIONS: Higher serum 25(OH)D levels were associated with decreased all-cause and cancer-specific mortality in depressed adults, particularly among younger individuals and those using antidepressants or without diabetes. Further research is essential to understand mechanisms and interventions related to vitamin D in depression.

Comparative transcriptome analysis between rhesus macaques ( Macaca mulatta) and crab-eating macaques ( M. fascicularis).

Understanding gene expression variations between species is pivotal for deciphering the evolutionary diversity in phenotypes. Rhesus macaques ( Macaca mulatta, MMU) and crab-eating macaques ( M. fascicularis, MFA) serve as crucial nonhuman primate biomedical models with different phenotypes. To date, however, large-scale comparative transcriptome research between these two species has not yet been fully explored. Here, we conducted systematic comparisons utilizing newly sequenced RNA-seq data from 84 samples (41 MFA samples and 43 MMU samples) encompassing 14 common tissues. Our findings revealed a small fraction of genes (3.7%) with differential expression between the two species, as well as 36.5% of genes with tissue-specific expression in both macaques. Comparison of gene expression between macaques and humans indicated that 22.6% of orthologous genes displayed differential expression in at least two tissues. Moreover, 19.41% of genes that overlapped with macaque-specific structural variants showed differential expression between humans and macaques. Of these, the FAM220A gene exhibited elevated expression in humans compared to macaques due to lineage-specific duplication. In summary, this study presents a large-scale transcriptomic comparison between MMU and MFA and between macaques and humans. The discovery of gene expression variations not only enhances the biomedical utility of macaque models but also contributes to the wider field of primate genomics.

Comparative genomics of macaques and integrated insights into genetic variation and population history.

The crab-eating macaques ( Macaca fascicularis ) and rhesus macaques ( M. mulatta ) are widely studied nonhuman primates in biomedical and evolutionary research. Despite their significance, the current understanding of the complex genomic structure in macaques and the differences between species requires substantial improvement. Here, we present a complete genome assembly of a crab-eating macaque and 20 haplotype-resolved macaque assemblies to investigate the complex regions and major genomic differences between species. Segmental duplication in macaques is ∼42% lower, while centromeres are ∼3.7 times longer than those in humans. The characterization of ∼2 Mbp fixed genetic variants and ∼240 Mbp complex loci highlights potential associations with metabolic differences between the two macaque species (e.g., CYP2C76 and EHBP1L1 ). Additionally, hundreds of alternative splicing differences show post-transcriptional regulation divergence between these two species (e.g., PNPO ). We also characterize 91 large-scale genomic differences between macaques and humans at a single-base-pair resolution and highlight their impact on gene regulation in primate evolution (e.g., FOLH1 and PIEZO2 ). Finally, population genetics recapitulates macaque speciation and selective sweeps, highlighting potential genetic basis of reproduction and tail phenotype differences (e.g., STAB1 , SEMA3F , and HOXD13 ). In summary, the integrated analysis of genetic variation and population genetics in macaques greatly enhances our comprehension of lineage-specific phenotypes, adaptation, and primate evolution, thereby improving their biomedical applications in human diseases.

The relationship between slack resources and organizational resilience: The moderating role of dual learning.

Slack resources and organizational learning are key elements in building organizational resilience. This paper constructs an impact model of organizational resilience and investigates the impact of slack resources on organizational resilience using data from Chinese-listed companies, as well as verifying the moderating effect of organizational dual learning through hierarchical analysis. The findings show that: Firstly, both absorbed slack resources and unabsorbed slack resources promote organizational resilience. Secondly, organizational learning has a moderating effect on the relationship between slack resources and organizational resilience, where organizational exploitative learning positively moderates the relationship between unabsorbed slack resources and organizational resilience, while organizational exploitative learning negatively moderates the relationship between absorbed slack resources and organizational resilience. Accordingly, organizations should pay attention to the composition of slack resources and the coordination between slack resources and organizational dual learning in order to improve organizational resilience.

Exploring the promotion of green technology innovation in the new energy vehicle industry: An evolutionary game analysis.

This paper aims to explore how to promote green technology innovation (GTI) among new energy vehicle (NEV) manufacturers and the strategic changes among the government, manufacturers, and consumers. From the perspective of evolutionary game theory, a tripartite evolutionary game model is established to analyze the influence of key factors on the tripartite strategies in the context of the government's willingness to subsidize gradually decreases. The main findings are as follows: (1) government subsidies provided to manufacturers better promote their willingness to participate in GTI. The relationship between government subsidies and GTI is not linear, and the government cannot blindly increase the level of subsidies. (2) The willingness of NEV manufacturers to engage in GTI is influenced by price and consumer purchase preferences. The higher the price of new energy vehicle using green technology (NEVG) is not better, and lowering the price of NEVGs can promote manufacturers' participation in GTI and consumers' purchase of NEVGs. (3) Increasing the mileage of NEVGs and consumers' green consumption preferences will effectively increase consumers' willingness to purchase. Accordingly, this study suggests that to enhance manufacturers' participation in GTI, the government should increase subsidies and encourage green consumption among consumers. In addition, manufacturers should focus on improving the mileage of NEVGs and reducing their prices to make them more accessible to consumers.