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Exposure to environmental chemicals is prevalent. While previous studies reported associations between multiple chemical exposures and metabolic syndrome (MetS), they did not comprehensively account for correlations among exposures. We used machine learning methods including Boruta algorithm and least absolute shrinkage and selection operator (LASSO) regression, combined with weighted quartiles sum (WQS) regression to investigate the associations of phenols, polycyclic aromatic hydrocarbons (PAHs), metals, and phthalates with MetS and its components. Data were drawn from the 2005–2012 National Health and Nutrition Examination Survey (NHANES). The mean (standard deviation (SD)) age of 2596 participants was 48.4 (17.9) years. After adjusting for age, sex, body mass index, race/ethnicity, marital status, education, poverty income ratio, physical activity, smoking, and alcohol, higher 2-Phenanthrene (2-PHE) and mono-(2-ethyl-5-hydroxyhexyl) phthalate (MEHHP) concentrations were associated with a higher odds of the MetS (odds ratio (OR) = 4.26, 95 % confidence interval (CI) 2.40–7.58 per ng/mL, and 3.24, 1.75–6.02 per ng/L, respectively). WQS index for environmental chemicals was positively associated with the MetS (OR = 1.31, 95 % CI 1.09–1.57). Moreover, we observed consistent and stronger positive associations with MetS (OR = 1.54, 95 % CI 1.04–2.30) in current smokers. Exposure to phenols, PAHs, metals, and phthalates was positively associated with an increase in metabolic syndrome and its components, which was more pronounced in current smokers.

Abstract Background Chinese indigenous pigs are popular with consumers for their juiciness, flavour and meat quality, but they have lower meat production. Insulin-like growth factor 2 (IGF2) is a maternally imprinted growth factor that promotes skeletal muscle growth by regulating cell proliferation and differentiation. A single nucleotide polymorphism (SNP) within intron 3 of porcine IGF2 disrupts a binding site for the repressor, zinc finger BED-type containing 6 (ZBED6), leading to up-regulation of IGF2 and causing major effects on muscle growth, heart size, and backfat thickness. This favorable mutation is common in Western commercial pig populations, but absent in most Chinese indigenous pig breeds. To improve meat production of Chinese indigenous pigs, we used cytosine base editor 3 (CBE3) to introduce IGF2-intron3-C3071T mutation into porcine embryonic fibroblasts (PEFs) isolated from a male Liang Guang Small Spotted pig (LGSS), and single-cell clones harboring the desired mutation were selected for somatic cell nuclear transfer (SCNT) to generate the founder line of IGF2 T/T pigs. Results We found the heterozygous progeny IGF2 C/T pigs exhibited enhanced expression of IGF2, increased lean meat by 18%–36%, enlarged loin muscle area by 3%–17%, improved intramuscular fat (IMF) content by 18%–39%, marbling score by 0.75–1, meat color score by 0.53–1.25, and reduced backfat thickness by 5%–16%. The enhanced accumulation of intramuscular fat in IGF2 C/T pigs was identified to be regulated by the PI3K-AKT/AMPK pathway, which activated SREBP1 to promote adipogenesis. Conclusions We demonstrated the introduction of IGF2-intron3-C3071T in Chinese LGSS can improve both meat production and quality, and first identified the regulation of IMF deposition by IGF2 through SREBP1 via the PI3K-AKT/AMPK signaling pathways. Our study provides a further understanding of the biological functions of IGF2 and an example for improving porcine economic traits through precise base editing.

Abstract Background Studies have shown that a direct association exists between the diet and blood uric acid concentrations. However, works on the association of dietary patterns with blood uric acid concentrations and hyperuricemia remain limited. Objective This study aims to evaluate the association of dietary patterns with blood uric acid concentrations and hyperuricemia. Methods The relationship between dietary patterns and hyperuricemia was explored through a nutritional epidemiological survey in China (n = 4855). Three statistical methods, including principal component analysis, reduced rank regression (RRR), and partial least squares regression, were used to extract dietary patterns. General linear regression and logistic regression analyses were utilized to explore the relationship of dietary patterns with blood uric acid concentrations and hyperuricemia. Results After adjusting for potential confounding factors, the score for the plant-based dietary pattern was found to be negatively correlated with blood uric acid levels (β = − 3.225) and that for the animal dietary pattern was discovered to be directly correlated with blood uric acid levels (β = 3.645). The participants in the highest quartile of plant-based dietary pattern scores were at a low risk of hyperuricemia (OR = 0.699; 95% CI: 0.561–0.870, P

Abstract Background Sedentary behaviours (SBs) are now considered a risk factor for depression. Older adults are sedentary most of the time and are at a high risk of depression. However, not all types of SBs have adverse effects on mental health. Passive SBs (such as watching TV) increase the risk of depression, whereas mentally active SBs (such as using the internet and reading) decrease the risk of depression. The aim of this study was to explore the associations between type of SBs (i.e., passive and mentally active SBs) and depression among people aged 60 years and older in the Hebei Province of China. Methods This cross-sectional study used data from the baseline survey of the Community-based Cohort Study on Nervous System Diseases. A total of 2679 older adults aged ≥60 years from the Hebei Province of China were included in this study. The type and time spent on SBs were self-reported. Watching TV was defined as a passive SB, whereas internet use, reading, and social SBs (including communicating with others and playing chess) were defined as mentally active SBs. Depression was evaluated using the Geriatric Depression Scale. The maximal possible score was 30 points, and ≥ 11 points indicated depression. Logistic regression analysis was used to assess the relationship between SBs and depression. Covariates included sex, age, education, employment, smoking, alcohol consumption, sleep duration, domestic work, physical exercise, body mass index (BMI), and chronic diseases. Results At baseline, the participants who spent two or more hours and 0 h on passive SBs (i.e., TV viewing) had a greater risk of depression (=0 h: adjusted OR = 2.09, 95% CI = 1.18–3.76; 2–3 h: OR = 2.21, 95% CI = 1.16–4.16; > 3 h: OR = 3.59, 95% CI = 1.93–6.68) than the participants who spent 1–2 h on passive SBs. The participants who spent > 1 h on mentally active SBs had a lower risk of depression (adjusted OR = 0.26, 95% CI = 0.06–0.71) than the participants who did not engage in mentally active SBs. Not all mentally active SBs were linked to depression. The participants who engaged in social SBs had a lower risk of depression (adjusted OR: 0.24, 95% CI: 0.06–0.66) than the participants who did not engage in social SBs. Conclusions Spending 2 h or more per day on passive SBs (watching TV) was associated with a high risk of depression among people aged 60 years and older in the Hebei Province of China. Mentally active SBs (predominantly social SBs) could reduce the risk of depression. Some participants with depression probably did not watch TV. These findings suggested that spending more time on social SBs (such as communicating with others and playing chess) rather than watching TV may have important public health implications for preventing and managing depression among older Chinese adults. Moreover, society should attend to the mental health of elderly adults who do not watch TV as they may be more prone to suffer from depressive symptoms.

Abstract In financial market, especially primary market, it is very costly and difficult to make a deal due to discovery difficulty, information asymmetry, lack of trust, complicated trading process and low liquidity. Blockchain is an innovative technology enabling new business models of distributed data storage, point‐to‐point transaction and decentralized autonomous organizations via consensus. The unique features of blockchain, ‘decentralization, highly transparent, enhanced security and immutability of information’, make it a good solution candidate to meet the needs of private equity exchange. This article focuses on analysing the technical basis of the blockchain financial model and the typical application scenarios of the blockchain in the financial market. It discusses the importance of applying key blockchain technology to the financial market, especially in the primary market. Research has found that the development of blockchain technology, especially the maturity of stabilized token technology, makes it possible for blockchain to become a supporting technology to support the next generation of infrastructure in the future financial market. At present, blockchain technology has been concentrated in the issuance, registration, clearing, settlement and derivatives management of private equity and other over‐the‐counter securities. The use of blockchain to build a decentralized primary market has not received enough attention in research and practice, and the use of blockchain technology to establish a primary market with diverse distribution methods is still in its infancy. On this basis, this article further analyses the current problems and the possibility of solving these problems in the application of blockchain in the primary market and points out several interesting directions for future research in this field.

Qiuhui Li et al. report a pan-genome sequence study in Han Chinese genomes. They find 276 Mbp of DNA sequences (absent in the current human reference), and report that 46.646 Mbp common sequences improved the accuracy of variant calling and mapping rate when added to the reference genome.

Soil microorganisms promote material transformation and energy flow in the entire ecological environment and play a key role in the stability and development of grassland ecosystems. Studies on the impacts of grazing on the soil microbial community and the establishment of a reasonable grazing intensity are crucial to improve our knowledge of the mechanisms underlying grassland degradation and to accurately assess the influence of grazing management on grassland functions and the nutrient cycle. Based on the grassland grazing control experimental platform, we compared the structure and diversity characteristics of soil microbial communities under six grazing intensities (0.00, 0.23, 0.34, 0.46, 0.69, and 0.92 AU ha−1) (1 AU = 500 kg of adult cattle) on the Hulunbuir Leymus chinensis meadow steppe. The results showed that soil microbial biomass carbon (MBC) and nitrogen (MBN) decreased with increasing soil depth. The 0–10 cm soil layer of G0.34 had the highest MBC and MBN, and the G0.92 treatment had the lowest MBC and MBN. Heavy grazing significantly decreased the MBC and MBN contents in the soil surface layer. The soil bacterial diversity under light grazing treatment (0.23 AU ha−1) was higher than that under heavy grazing, and the fungal diversity under the no-grazing treatment was higher than that under the grazing treatment. Overgrazing reduced the bacterial species in the soil. The plant belowground biomass significantly (p = 0.039) influenced the bacterial community structure, and the soil pH (p = 0.032), total nitrogen (p = 0.011), and litter (p = 0.007) significantly influenced the fungal community. The effects of grazing on microbial communities were primarily driven by vegetation productivity, litter mass, and soil geophysical and chemical characteristics. This study deepened our understanding of the impacts of grazing practices on soil microbial communities on the meadow steppe, suggesting that moderate-disturbance grazing can promote the sustainable development of grassland vegetation-soil microorganisms.

Objectives Our study aimed to assess the association between the Dietary Inflammatory Index (DII) and depression in the elderly over 55 years in Northern China.Methods We analysed the data of 2022 Chinese adults aged 55 and over from a community-based neurological disease cohort study from 2018 to 2019. A validated semiquantitative food frequency questionnaire was used to assess eating habits at the time of inclusion. Multiple logistic regression was used for analysis, and social demographics, lifestyle and health-related factors were adjusted.Results Among the included population, the prevalence of depression was 23.39%. Mean (SD) and range of the DII in the included population were 1.70 (1.42) and −5.20 to +5.68. The risk of depression was significantly higher in participants in the most pro-inflammatory group (quartile 4) than in the participants in the most anti-inflammatory group (quartile 1) (OR 1.53; 1.37 to 1.82; p-trend=0.01). The subgroup analysis of body mass index (BMI) showed that there is a significant association between DII and the risk of depression in overweight and obese people (p＜0.05). The restricted cubic spline results show that the OR value of depression possesses an upward trend with the increase of the DII score.Conclusions Aged patients with depression present a higher potential for dietary inflammation. Pro-inflammatory diets might increase the risk of depressive symptoms. Further research in different populations is crucial to confirm the association between DII and depression.

BackgroundDepression is a common psychiatric disorder in older adults that affects their health-related quality of life. Two percent of adults over the age of 55 suffer from major depression, and the prevalence of depression increases with age. Even in the absence of major depressive disorder, 10–15% of older adults have clinically significant depressive symptoms.ObjectivesEpidemiological studies on the association between different gender eating patterns and depression show inconsistent associations. Our study examined whether different gender eating patterns are related to depression. We consider eating patterns individually and as a joint exposure to predefined eating patterns.MethodsPrincipal component analysis (PCA) was performed on the data of the 24-h diet recall dietary intake, and the dietary pattern was determined. Linear regression models are used to explore the relationship between different diets and depression of men and women; weighted quantile sum (WQS) regression, quantile g calculation (qgcomp) and Bayesian kernel machine regression (BKMR) are performed as Secondary analysis.ResultsIn the dietary patterns model, we found that the vegetable and fruit-based diet has a significant inhibitory effect in women, and the egg-milk-based diet has a significant inhibitory effect in men. We found that when all dietary factors are above the 55th percentile, there is a significant positive correlation between multiple dietary patterns and depression risk. We also determined a positive correlation between meat and obesity risk and a negative correlation between egg and milk and vegetables and fruits.ConclusionsIn the study population, after controlling for other baseline indicators and predictors of dietary pattern exposure, a fruit and vegetable-based diet was associated with a slightly healthier and lower risk of depression, while a meat-based dietary pattern associated with a higher risk of depression, and this association effect varies between genders.

Abstract Traditional rice landraces grown under on‐farm conservation conditions by indigenous farmers are extremely important for future crop improvement. However, little is known about how the natural selection and agriculture practices of indigenous farmers interact to shape and change the population genetics of rice landraces grown under on‐farm conservation conditions during the domestication. In this study, we sequenced DNA from 108 core on‐farm conserved rice landraces collected from the ethnic minority regions of Yunnan, China, including 56 accessions collected in 1980 and 52 accessions collected in 2007 and obtained 2,771,245 of credible SNPs. Our findings show that most genetic diversity was retained during the 27 years of domestication by on‐farm conservation. However, SNPs with marked allele frequency differences were found in some genome regions, particularly enriched in genic regions, indicating changes in genic regions may have played a much more prominent role in the short‐term domestication of 27 years. We identified 186 and 183 potential selective‐sweep regions in the indica and japonica genomes, respectively. We propose that on‐farm conserved rice landraces during the short‐term domestication had a highly polygenic basis with many loci responding to selection rather than a few loci with critical changes in response to selection. Moreover, loci affecting important agronomic traits and biotic or abiotic stress responses have been particularly targeted in selection. A genome‐wide association study identified 90 significant signals for six traits, 13 of which were in regions of selective sweeps. Moreover, we observed a number of significant and interesting associations between loci and environmental factors, which implies adaptation to local environment. Our results provide insights into short‐term evolutionary processes and shed light on the underlying mechanisms of on‐farm conservation.

ObjectivesThis study aimed to assess the relationship between dietary inflammatory index (DII) and sex steroids in children (6-11 years old) and adolescents (12-19 years old) in the U.S. National Health and Nutrition Examination Survey, 2015–2016.MethodsParticipants between the ages of 6-19 have 24-hour dietary intake data, serum sex hormones [total testosterone (TT), estradiol (E2)], and sex hormone-binding globulin (SHBG) available data (n = 1382). The free androgen index (FAI) is calculated as TT divided by SHBG and the ratio of TT to E2 (TT/E2). The constructed puberty state is defined as high levels of steroid hormones (TT≥50 ng/dL in men, E2≥20 pg/ml in women) or onset of menarche. Multiple linear regression analysis was stratified by gender-age and gender-pubertal status groups to evaluate the association between DII and sex hormone levels.ResultsAfter adjusting for covariates, the association between consecutive DII and sex hormone indicators by gender and age group. In male adolescents, DII was always negatively associated with TT (P-trend = 0.09), FAI (P-trend = 0.03) and E2 (P-trend = 0.01), and monotonically positively associated with SHBG (P-trend = 0.02).In female adolescents, with the increase of DII, a significant positive correlation with SHBG was observed (β 0.017, 95%CI: 0.009,0.053) (Table 3). Among female adolescents, a significant negative association between DII and TT and a significant positive association between SHBG were observed in this group. Moreover, DII was positively associated with SHBG of prepubertal males and negatively associated with FAI of prepubertal females.ConclusionsDII was associated with decreased levels of certain sex steroid hormones (TT, FAI, and E2) and increased levels of SHBG in adolescents or pubertal individuals, with the associations presenting somewhat sex-dependent pattern. However, there is little evidence that there is a significant association in children or prepubertal children. Further research needs to be carried out to verify our results.

Introduction: This study investigated this association and the role of BMI in the inflammatory process in a large population-based observational study.Methods: A total of 1,865 elderly people (≥55 years) were followed from the Community Cohort Study of Nervous System Diseases (CCSNSD) cohort study from 2018 to 2019 (Mean [SD] age, 66.31 [0.32] years; 716 [38.4%] males). The semi-quantitative FFQ and geriatric depression scale (GDS) were used to evaluate the diet and depressive symptoms of the elderly, respectively. The multivariable logistic regression model estimated the OR and 95% CI between Empirical Dietary Inflammatory Index (E-DII) and depression. The interaction of E-DII and BMI on depressive events was tested, and the mediation analysis of BMI was performed.Results: As measured by E-DII, the mean (SE) value of the inflammatory potential of the diet in our study was 1.56 (0.12). E-DII ranged from 5.23 to 5.58. In comparison with the first quartile, the elderly from the second quartile (OR: 1.15 [95% CI: 1.09, 1.28]) to the fourth quartile (OR: 1.31 [95% CI: 1.16, 1.42]) have a higher risk of depression before adjustment for BMI. An interaction was observed between E-DII and BMI in terms of the risk of depression (PInteraction < 0.001). The whole related part is mediated by BMI (31.06%).Conclusion: Our findings indicate that the higher pro-inflammatory potential of diet is associated with a higher risk of depression, and this association may be mediated by BMI. Further research is needed to verify our findings and clarify the latent mechanism.

Understanding the effects of livestock grazing on ecosystem respiration (Re) of grassland ecosystems is critical for accurately assessing the feedback of grazing management to climate change. We examined ecosystem respiration in response to varying cattle grazing intensities during growing seasons from 2009 to 2018 in a meadow steppe ecosystem of eastern Inner Mongolia. We found that ungrazed swards had the highest mean annual Re rate, with seasonal CVs in Re ranging from 37.53% to 46.04% for all treatments. When all treatments were analysed as a whole, we identified a significant positive relationship between the annual Re rate and annual peak value of standing plant aboveground biomass. Our findings showed that controlling factors on the mean annual Re differed substantially with grazing intensity. In ungrazed and lightly-grazed plots (G0.00 and G0.23), the mean annual Re rate was controlled mainly by canopy height and/or rainfall, while it was controlled more predominantly by contents of NH4+-N and available phosphorus in moderately and heavily grazed plots. We detected significant positive relationships of the annual Re rate with rainfall, soil moisture, ammonium nitrogen, and soil available phosphorus during the entire study period, whereas significant negative relationships were detected between the annual ecosystem respiration rate and the mean growing season temperature, irrespective of grazing intensity. Our findings revealed that grazing could substantially simplify the relationship between the mean annual Re rate and biotic and abiotic parameters. It may be concluded that the relationship between the annual Re rate and the standing crop aboveground biomass was a principal mechanism underlying the effects of gradient grazing on the Re of Chinese meadow steppe ecosystems.

Summary: Pig has been proved to be a valuable large animal model used for research on diabetic disease. However, their translational value is limited given their distinct anatomy and physiology. For the last 30 years, we have been developing a laboratory Asian miniature pig inbred line (Bama miniature pig [BM]) from the primitive Bama xiang pig via long-term selective inbreeding. Here, we assembled a BM reference genome at full chromosome-scale resolution with a total length of 2.49 Gb. Comparative and evolutionary genomic analyses identified numerous variations between the BM and commercial pig (Duroc), particularly those in the genetic loci associated with the features advantageous to diabetes studies. Resequencing analyses revealed many differentiated gene loci associated with inbreeding and other selective forces. These together with transcriptome analyses of diabetic pig models provide a comprehensive genetic basis for resistance to diabetogenic environment, especially related to energy metabolism. : Biological Sciences; Gene Ontology; Genomic Analysis; Genomics; Omics; Sequence Analysis; Transcriptomics Subject Areas: Biological Sciences, Gene Ontology, Genomic Analysis, Genomics, Omics, Sequence Analysis, Transcriptomics

Summary: Decades of artificial selection have significantly improved performance and efficiency of animal production systems. However, little is known about the microevolution of genomes due to intensive breeding. Using whole-genome sequencing, we document dynamic changes of chicken genomes under divergent selection on adiposity over 19 generations. Directional selection reduced within-line but increased between-line genomic differences. We observed that artificial selection tended to result in recruitment of preexisting variations of genes related to adipose tissue growth. In addition, novel mutations contributed to divergence of phenotypes under selection but contributed significantly less than preexisting genomic variants. Integration of 15 generations genome sequencing, genome-wide association study, and multi-omics data further identified that genes involved in signaling pathways important to adipogenesis, such as autophagy and lysosome (URI1, MBL2), neural system (CHAT), and endocrine (PCSK1) pathways, were under strong selection. Our study provides insights into the microevolutionary dynamics of domestic animal genomes under artificial selection.

Gastrodia elata is an obligate mycoheterotrophic plant with highly reduced leaves and bracts in scape. Here, Yuan et al sequence and analyze its 1.06 Gb genome which provides insights in adaptation to a lifestyle of heterotrophy.

Bivalve molluscs have evolved various characteristics to adapt to benthic filter-feeding. Here, Li et al investigate the genome, transcriptomes and proteomes of scallop Chlamys farreri, revealing evidences of molecular adaptations to semi-sessile life and neurotoxins.

MicroRNAs (miRNAs) are small non-coding RNAs that can regulate their target genes at the post-transcriptional level. Skeletal muscle comprises different fiber types that can be broadly classified as red, intermediate, and white. Recently, a set of miRNAs was found expressed in a fiber type-specific manner in red and white fiber types. However, an in-depth analysis of the miRNA transcriptome differences between all three fiber types has not been undertaken. Herein, we collected 15 porcine skeletal muscles from different anatomical locations, which were then clearly divided into red, white, and intermediate fiber type based on the ratios of myosin heavy chain isoforms. We further illustrated that three muscles, which typically represented each muscle fiber type (i.e., red: peroneal longus (PL), intermediate: psoas major muscle (PMM), white: longissimus dorsi muscle (LDM)), have distinct metabolic patterns of mitochondrial and glycolytic enzyme levels. Furthermore, we constructed small RNA libraries for PL, PMM, and LDM using a deep sequencing approach. Results showed that the differentially expressed miRNAs were mainly enriched in PL and played a vital role in myogenesis and energy metabolism. Overall, this comprehensive analysis will contribute to a better understanding of the miRNA regulatory mechanism that achieves the phenotypic diversity of skeletal muscles.

Jujube (Ziziphus jujuba Mill.) belongs to the Rhamnaceae family and is a popular fruit tree species with immense economic and nutritional value. Here, we report a draft genome of the dry jujube cultivar 'Junzao' and the genome resequencing of 31 geographically diverse accessions of cultivated and wild jujubes (Ziziphus jujuba var. spinosa). Comparative analysis revealed that the genome of 'Dongzao', a fresh jujube, was ~86.5 Mb larger than that of the 'Junzao', partially due to the recent insertions of transposable elements in the 'Dongzao' genome. We constructed eight proto-chromosomes of the common ancestor of Rhamnaceae and Rosaceae, two sister families in the order Rosales, and elucidated the evolutionary processes that have shaped the genome structures of modern jujubes. Population structure analysis revealed the complex genetic background of jujubes resulting from extensive hybridizations between jujube and its wild relatives. Notably, several key genes that control fruit organic acid metabolism and sugar content were identified in the selective sweep regions. We also identified S-locus genes controlling gametophytic self-incompatibility and investigated haplotype patterns of the S locus in the jujube genomes, which would provide a guideline for parent selection for jujube crossbreeding. This study provides valuable genomic resources for jujube improvement, and offers insights into jujube genome evolution and its population structure and domestication.

Among forager honey bees, scouts seek new resources and return to the colony, enlisting recruits to collect these resources. Differentially expressed genes between these behaviors and genetic variability in scouting phenotypes have been reported. Whole-genome sequencing of 44 Apis mellifera scouts and recruits was undertaken to detect variants and further understand the genetic architecture underlying the behavioral differences between scouts and recruits. The median coverage depth in recruits and scouts was 10.01 and 10.7 X, respectively. Representation of bacterial species among the unmapped reads reflected a more diverse microbiome in scouts than recruits. Overall, 1,412,705 polymorphic positions were analyzed for associations with scouting behavior, and 212 significant (p-value < 0.0001) associations with scouting corresponding to 137 positions were detected. Most frequent putative transcription factor binding sites proximal to significant variants included Broad-complex 4, Broad-complex 1, Hunchback, and CF2-II. Three variants associated with scouting were located within coding regions of ncRNAs including one codon change (LOC102653644) and 2 frameshift indels (LOC102654879 and LOC102655256). Significant variants were also identified on the 5'UTR of membrin, and 3'UTRs of laccase 2 and diacylglycerol kinase theta. The 60 significant variants located within introns corresponded to 39 genes and most of these positions were > 1000 bp apart from each other. A number of these variants were mapped to ncRNA LOC100578102, solute carrier family 12 member 6-like gene, and LOC100576965 (meprin and TRAF-C homology domain containing gene). Functional categories represented among the genes corresponding to significant variants included: neuronal function, exoskeleton, immune response, salivary gland development, and enzymatic food processing. These categories offer a glimpse into the molecular support to the behaviors of scouts and recruits. The level of association between genomic variants and scouting behavior observed in this study may be linked to the honey bee's genomic plasticity and fluidity of transition between castes.

Adipose tissue is not only a storage organ involved in fuel metabolism, but also an endocrine organ involved in the regulation of insulin sensitivity, thermogenesis, immunity, and inflammation. There are anatomical, cellular, molecular and physiological differences among adipose tissues deposited in different body sites. However, current understanding of the intrinsic differences between the sub-compartments of the subcutaneous adipose tissue remains rudimentary. Here, we analyzed the genome-wide DNA methylation differences between the porcine superficial and deep backfat tissues using methylated DNA immunoprecipitation combined with high-throughput sequencing. We show that the genes with differentially methylated regions in their promoter are mainly involved in the processes of “lipid metabolism” and “regulation of immune-related cytokines”. Compared with the deep backfat tissue, the promoters of genes related to the ‘positive regulation of cytokine production’ were significantly hypermethylated in the superficial backfat tissue, which reflects the intrinsic functional and metabolic differences between the sub-compartments of the subcutaneous adipose tissue. This study provides epigenetic evidence for functionally relevant methylation differences between different layers of porcine backfat tissues.

To tackle the exponentially increasing throughput of Next-Generation Sequencing (NGS), most of the existing short-read aligners can be configured to favor speed in trade of accuracy and sensitivity. SOAP3-dp, through leveraging the computational power of both CPU and GPU with optimized algorithms, delivers high speed and sensitivity simultaneously. Compared with widely adopted aligners including BWA, Bowtie2, SeqAlto, CUSHAW2, GEM and GPU-based aligners BarraCUDA and CUSHAW, SOAP3-dp was found to be two to tens of times faster, while maintaining the highest sensitivity and lowest false discovery rate (FDR) on Illumina reads with different lengths. Transcending its predecessor SOAP3, which does not allow gapped alignment, SOAP3-dp by default tolerates alignment similarity as low as 60%. Real data evaluation using human genome demonstrates SOAP3-dp's power to enable more authentic variants and longer Indels to be discovered. Fosmid sequencing shows a 9.1% FDR on newly discovered deletions. SOAP3-dp natively supports BAM file format and provides the same scoring scheme as BWA, which enables it to be integrated into existing analysis pipelines. SOAP3-dp has been deployed on Amazon-EC2, NIH-Biowulf and Tianhe-1A.

Previous studies have indicated two main domestic pig dispersal routes in East Asia: one is from the Mekong region, through the upstream region of the Yangtze River (URYZ) to the middle and upstream regions of the Yellow River, the other is from the middle and downstream regions of the Yangtze River to the downstream region of the Yellow River, and then to northeast China. The URYZ was regarded as a passageway of the former dispersal route; however, this assumption remains to be further investigated. We therefore analyzed the hypervariable segements of mitochondrial DNA from 513 individual pigs mainly from Sichuan and the Tibet highlands and 1,394 publicly available sequences from domestic pigs and wild boars across Asia. From the phylogenetic tree, most of the samples fell into a mixed group that was difficult to distinguish by breed or geography. The total network analysis showed that the URYZ pigs possessed a dominant position in haplogroup A and domestic pigs shared the same core haplotype with the local wild boars, suggesting that pigs in group A were most likely derived from the URYZ pool. In addition, a region-wise network analysis determined that URYZ contains 42 haplotypes of which 22 are unique indicating the high diversity in this region. In conclusion, our findings confirmed that pigs from the URYZ were domesticated in situ.

Myopia is the most common ocular disorder worldwide, and high myopia in particular is one of the leading causes of blindness. Genetic factors play a critical role in the development of myopia, especially high myopia. Recently, the exome sequencing approach has been successfully used for the disease gene identification of Mendelian disorders. Here we show a successful application of exome sequencing to identify a gene for an autosomal dominant disorder, and we have identified a gene potentially responsible for high myopia in a monogenic form. We captured exomes of two affected individuals from a Han Chinese family with high myopia and performed sequencing analysis by a second-generation sequencer with a mean coverage of 30× and sufficient depth to call variants at ∼97% of each targeted exome. The shared genetic variants of these two affected individuals in the family being studied were filtered against the 1000 Genomes Project and the dbSNP131 database. A mutation A672G in zinc finger protein 644 isoform 1 (ZNF644) was identified as being related to the phenotype of this family. After we performed sequencing analysis of the exons in the ZNF644 gene in 300 sporadic cases of high myopia, we identified an additional five mutations (I587V, R680G, C699Y, 3'UTR+12 C>G, and 3'UTR+592 G>A) in 11 different patients. All these mutations were absent in 600 normal controls. The ZNF644 gene was expressed in human retinal and retinal pigment epithelium (RPE). Given that ZNF644 is predicted to be a transcription factor that may regulate genes involved in eye development, mutation may cause the axial elongation of eyeball found in high myopia patients. Our results suggest that ZNF644 might be a causal gene for high myopia in a monogenic form.

DNA methylation plays an important role in biological processes in human health and disease. Recent technological advances allow unbiased whole-genome DNA methylation (methylome) analysis to be carried out on human cells. Using whole-genome bisulfite sequencing at 24.7-fold coverage (12.3-fold per strand), we report a comprehensive (92.62%) methylome and analysis of the unique sequences in human peripheral blood mononuclear cells (PBMC) from the same Asian individual whose genome was deciphered in the YH project. PBMC constitute an important source for clinical blood tests world-wide. We found that 68.4% of CpG sites and 80% displayed allele-specific expression (ASE). These data demonstrate that ASM is a recurrent phenomenon and is highly correlated with ASE in human PBMCs. Together with recently reported similar studies, our study provides a comprehensive resource for future epigenomic research and confirms new sequencing technology as a paradigm for large-scale epigenomics studies.

We describe an algorithm, ReAS, to recover ancestral sequences for transposable elements (TEs) from the unassembled reads of a whole genome shotgun. The main assumptions are that these TEs must exist at high copy numbers across the genome and must not be so old that they are no longer recognizable in comparison to their ancestral sequences. Tested on the japonica rice genome, ReAS was able to reconstruct all of the high copy sequences in the Repbase repository of known TEs, and increase the effectiveness of RepeatMasker in identifying TEs from genome sequences.

We report improved whole-genome shotgun sequences for the genomes of indica and japonica rice, both with multimegabase contiguity, or almost 1,000-fold improvement over the drafts of 2002. Tested against a nonredundant collection of 19,079 full-length cDNAs, 97.7% of the genes are aligned, without fragmentation, to the mapped super-scaffolds of one or the other genome. We introduce a gene identification procedure for plants that does not rely on similarity to known genes to remove erroneous predictions resulting from transposable elements. Using the available EST data to adjust for residual errors in the predictions, the estimated gene count is at least 38,000-40,000. Only 2%-3% of the genes are unique to any one subspecies, comparable to the amount of sequence that might still be missing. Despite this lack of variation in gene content, there is enormous variation in the intergenic regions. At least a quarter of the two sequences could not be aligned, and where they could be aligned, single nucleotide polymorphism (SNP) rates varied from as little as 3.0 SNP/kb in the coding regions to 27.6 SNP/kb in the transposable elements. A more inclusive new approach for analyzing duplication history is introduced here. It reveals an ancient whole-genome duplication, a recent segmental duplication on Chromosomes 11 and 12, and massive ongoing individual gene duplications. We find 18 distinct pairs of duplicated segments that cover 65.7% of the genome; 17 of these pairs date back to a common time before the divergence of the grasses. More important, ongoing individual gene duplications provide a never-ending source of raw material for gene genesis and are major contributors to the differences between members of the grass family.