Gibberellins regulate masculinization through the SpGAI-SpSTM module in dioecious spinach

The sex of dioecious plants is mainly determined by genetic factors, but it can also be converted by environmental cues such as exogenous phytohormones. Gibberellic acids (GAs) are well-known inducers of flowering and sexual development, yet the pathway of gibberellin-induced sex conversion in dioecious spinach (Spinacia oleracea L.) remains elusive. Based on sex detection before and after GA3 application using T11A and SSR19 molecular markers, we confirmed and elevated the masculinization effect of GA on a single female plant through exogenous applications of GA3 , showing complete conversion and functional stamens. Silencing of GIBBERELLIC ACID INSENSITIVE (SpGAI), a single DELLA family protein that is a central GA signaling repressor, results in similar masculinization. We also show that SpGAI can physically interact with the spinach KNOX transcription factor SHOOT MERISTEMLESS (SpSTM), which is a homolog of the flower meristem identity regulator STM in Arabidopsis. The silencing of SpSTM also masculinized female flowers in spinach. Furthermore, SpSTM could directly bind the intron of SpPI to repress SpPI expression in developing female flowers. Overall, our results suggest that GA induces a female masculinization process through the SpGAI-SpSTM-SpPI regulatory module in spinach. These insights may help to clarify the molecular mechanism underlying the sex conversion system in dioecious plants while also elucidating the physiological basis for the generation of unisexual flowers so as to establish dioecy in plants.

[Analysis of distribution characteristics and influencing factors of chord μ in young myopia]

Objective: To explore and analyze the distribution characteristics of chord μ related parameters, as well as the pupil center's relative position to the coaxial corneal light reflex on the corneal surface, and the influencing factors in young myopia. Methods: This was a cross-sectional study. A total of 761 myopic patients (761 eyes) were collected from March 2021 to December 2021 in the Refractive Surgery Center of Tianjin Eye Hospital, including 388 males and 373 females, with an average age of (24±6) years. The relationship between age, sex, diopter, anterior and posterior corneal surface parameters, and chord μ related parameters was analyzed, including the x and y absolute values of the pupil center, chord μ length, and angle. The normality of the data was tested using the Kolmogorov-Smirnov test, and the influencing factors of chord μ were analyzed through Pearson and Spearman correlation analysis. Results: The equivalent spherical degree and chord μ length were (-5.47±1.66) D and (0.178±0.095) mm, respectively. The chord μ length followed an approximately normal distribution. The chord μ length of 266 eyes (35%) was distributed in the range of 0.120 to 0.200 mm, while the chord μ length of 479 eyes (63%) was<0.200 mm, and the chord μ length of 620 eyes (81%) was<0.260 mm. The chord μ angle distribution accounted for the largest proportion in the superior nasal quadrant (45.6%), followed by the superior temporal quadrant (34.3%), the inferior temporal quadrant (10.1%), and the inferior nasal quadrant (10.0%). High myopia (r=0.11, P=0.002) and high astigmatism (r=0.08, P=0.023) were associated with an increase in chord μ length. The higher the degree of myopia, the smaller the chord μ angle (r=-0.09, P=0.019). The larger the ISV (r=0.09, P=0.017), IVA (r=0.08, P=0.025), and IHD (r=0.08, P=0.039) on the anterior surface of the cornea, the longer the chord μ length. The higher the astigmatism of the posterior corneal surface, the greater the absolute value of the Y coordinate of the pupil center (r=0.07, P=0.044), and the longer the chord μ length (r=0.08, P=0.035), and the smaller the chord μ angle (r=-0.08, P=0.032). Conclusions: The chord μ length of young myopic individuals in China followed an approximately normal distribution, with the majority located in the superior nasal and superior temporal quadrants. High myopia, high astigmatism, and irregular corneal shape are the main factors related to an increase in chord μ length.

Genome-wide analysis of transposable elements and satellite DNA in Humulus scandens, a dioecious plant with XX/XY1Y2 chromosomes

Transposable elements (TEs) and satellite DNAs, two major categories of repetitive sequences, are expected to accumulate in non-recombining genome regions, including sex-linked regions, and contribute to sex chromosome evolution. The dioecious plant, Humulus scandens, can be used for studying the evolution of the XX/XY1Y2 sex chromosomes. In this study, we thoroughly examined the repetitive components of male and female H. scandens using next-generation sequencing data followed by bioinformatics analysis and florescence in situ hybridization (FISH). The H. scandens genome has a high overall repetitive sequence composition, 68.30% in the female and 66.78% in the male genome, with abundant long terminal repeat (LTR) retrotransposons (RTs), including more Ty3/Gypsy than Ty1/Copia elements, particularly two Ty3/Gypsy lineages, Tekay and Retand. Most LTR-RT lineages were found dispersed across the chromosomes, though CRM and Athila elements were predominately found within the centromeres and the pericentromeric regions. The Athila elements also showed clearly higher FISH signal intensities in the Y1 and Y2 chromosomes than in the X or autosomes. Three novel satellite DNAs were specifically distributed in the centromeric and/or telomeric regions, with markedly different distributions on the X, Y1, and Y2 chromosomes. Combined with FISH using satellite DNAs to stain chromosomes during meiotic diakinesis, we determined the synapsis pattern and distinguish pseudoautosomal regions (PARs). The results indicate that the XY1Y2 sex chromosomes of H. scandens might have originated from a centric fission event. This study improves our understanding of the repetitive sequence organization of H. scandens genome and provides a basis for further analysis of their chromosome evolution process.

[Research on indicators of ideological and political resource database construction for curriculum of "Epidemiology"]

Objective: To construct indicators of the ideological and political resource database construction for the curriculum of "Epidemiology". Methods: Two rounds of expert consultation were conducted in 15 experts from 4 universities and 1 textbook publishing house using the Delphi method, and the importance and feasibility scores of the indicators were calculated with the degree of concentration and coordination of experts' opinions. Results: In the two rounds of consultation, the experts' positive coefficient of the two questionnaires were both 100.00% (15/15), the authoritative coefficients of experts were both 0.83, and the Kendall's W was 0.27 (P<0.05) and 0.33 (P<0.05), respectively. Consensus was reached on 4 primary indicators and 31 secondary indicators. Conclusion: The process of this study is scientific, and the indicators for the construction of ideological and political resource database for the curriculum of "Epidemiology" are authoritative, which can promote the establishment of ideological and political resource database for the curriculum of "Epidemiology".

Lineage-specific amplification and epigenetic regulation of LTR-retrotransposons contribute to the structure, evolution, and function of Fabaceae species

BACKGROUND

Long terminal repeat (LTR)-retrotransposons (LTR-RTs) are ubiquitous and make up the majority of nearly all sequenced plant genomes, whereas their pivotal roles in genome evolution, gene expression regulation as well as their epigenetic regulation are still not well understood, especially in a large number of closely related species.

RESULTS

Here, we analyzed the abundance and dynamic evolution of LTR-RTs in 54 species from an economically and agronomically important family, Fabaceae, and also selected two representative species for further analysis in expression of associated genes, transcriptional activity and DNA methylation patterns of LTR-RTs. Annotation results revealed highly varied proportions of LTR-RTs in these genomes (5.1%~68.4%) and their correlation with genome size was highly positive, and they were significantly contributed to the variance in genome size through species-specific unique amplifications. Almost all of the intact LTR-RTs were inserted into the genomes 4 Mya (million years ago), and more than 50% of them were inserted in the last 0.5 million years, suggesting that recent amplifications of LTR-RTs were an important force driving genome evolution. In addition, expression levels of genes with intronic, promoter, and downstream LTR-RT insertions of Glycine max and Vigna radiata, two agronomically important crops in Fabaceae, showed that the LTR-RTs located in promoter or downstream regions suppressed associated gene expression. However, the LTR-RTs within introns promoted gene expression or had no contribution to gene expression. Additionally, shorter and younger LTR-RTs maintained higher mobility and transpositional potential. Compared with the transcriptionally silent LTR-RTs, the active elements showed significantly lower DNA methylation levels in all three contexts. The distributions of transcriptionally active and silent LTR-RT methylation varied across different lineages due to the position of LTR-RTs located or potentially epigenetic regulation.

CONCLUSION

Lineage-specific amplification patterns were observed and higher methylation level may repress the activity of LTR-RTs, further influence evolution in Fabaceae species. This study offers valuable clues into the evolution, function, transcriptional activity and epigenetic regulation of LTR-RTs in Fabaceae genomes.

[Introduction for One Health Joint Plan of Action (2022-2026)]

Four organizations, including the Food and Agriculture Organization of the United Nations, the United Nations Environment Programme, WHO, and the World Organization for Animal Health, recently launched a new One Health Joint Plan of Action (2022-2026) which was the first time that the Quadripartite had issued a joint action plan on One Health. The action plan aimed to address the health challenges in the human, animal, plant, and environment, focusing on improving capabilities in six action tracks including One Health capacities, emerging and re-emerging zoonotic diseases, neglected tropical and vector-borne diseases, food safety, antimicrobial resistance and environment. This introduction will give an overview and brief translation of the background, content, and the plan's value, to help readers understand the joint action plan quickly.

[A descriptive analysis of hyperlipidemia in adult twins in China]

Objective: To describe the distribution characteristics of hyperlipidemia in adult twins in the Chinese National Twin Registry (CNTR) and explore the effect of genetic and environmental factors on hyperlipidemia. Methods: Twins recruited from the CNTR in 11 project areas across China were included in the study. A total of 69 130 (34 565 pairs) of adult twins with complete information on hyperlipidemia were selected for analysis. The random effect model was used to characterize the population and regional distribution of hyperlipidemia among twins. The concordance rates of hyperlipidemia were calculated in monozygotic twins (MZ) and dizygotic twins (DZ), respectively, to estimate the heritability. Results: The age of all participants was (34.2±12.4) years. This study's prevalence of hyperlipidemia was 1.3% (895/69 130). Twin pairs who were men, older, living in urban areas, married,had junior college degree or above, overweight, obese, insufficient physical activity, current smokers, ex-smokers, current drinkers, and ex-drinkers had a higher prevalence of hyperlipidemia (P<0.05). In within-pair analysis, the concordance rate of hyperlipidemia was 29.1% (118/405) in MZ and 18.1% (57/315) in DZ, and the difference was statistically significant (P<0.05). Stratified by gender, age, and region, the concordance rate of hyperlipidemia in MZ was still higher than that in DZ. Further, in within-same-sex twin pair analyses, the heritability of hyperlipidemia was 13.04% (95%CI: 2.61%-23.47%) in the northern group and 18.59% (95%CI: 4.43%-32.74%) in the female group, respectively. Conclusions: Adult twins were included in this study and were found to have a lower prevalence of hyperlipidemia than in the general population study, with population and regional differences. Genetic factors influence hyperlipidemia, but the genetic effect may vary with gender and area.

[A descriptive analysis on hypertension in adult twins in China]

Objective: To describe the distribution characteristics of hypertension among adult twins in the Chinese National Twin Registry (CNTR) and to provide clues for exploring the role of genetic and environmental factors on hypertension. Methods: A total of 69 220 (34 610 pairs) of twins aged 18 and above with hypertension information were selected from CNTR registered from 2010 to 2018. Random effect models were used to describe the population and regional distribution of hypertension in twins. To estimate the heritability, the concordance rates of hypertension were calculated and compared between monozygotic twins (MZ) and dizygotic twins (DZ). Results: The age of all participants was (34.1±12.4) years. The overall self-reported prevalence of hypertension was 3.8%(2 610/69 220). Twin pairs who were older, living in urban areas, married, overweight or obese, current smokers or ex-smokers, and current drinkers or abstainers had a higher self-reported prevalence of hypertension (P<0.05). Analysis within the same-sex twin pairs found that the concordance rate of hypertension was 43.2% in MZ and 27.0% in DZ, and the difference was statistically significant (P<0.001). The heritability of hypertension was 22.1% (95%CI: 16.3%- 28.0%). Stratified by gender, age, and region, the concordance rate of hypertension in MZ was still higher than that in DZ. The heritability of hypertension was higher in female participants. Conclusions: There were differences in the distribution of hypertension among twins with different demographic and regional characteristics. It is indicated that genetic factors play a crucial role in hypertension in different genders, ages, and regions, while the magnitude of genetic effects may vary.

Impact of LTR-Retrotransposons on Genome Structure, Evolution, and Function in Curcurbitaceae Species

Long terminal repeat (LTR)-retrotransposons (LTR-RTs) comprise a major portion of many plant genomes and may exert a profound impact on genome structure, function, and evolution. Although many studies have focused on these elements in an individual species, their dynamics on a family level remains elusive. Here, we investigated the abundance, evolutionary dynamics, and impact on associated genes of LTR-RTs in 16 species in an economically important plant family, Cucurbitaceae. Results showed that full-length LTR-RT numbers and LTR-RT content varied greatly among different species, and they were highly correlated with genome size. Most of the full-length LTR-RTs were amplified after the speciation event, reflecting the ongoing rapid evolution of these genomes. LTR-RTs highly contributed to genome size variation via species-specific distinct proliferations. The Angela and Tekay lineages with a greater evolutionary age were amplified in Trichosanthes anguina, whereas a recent activity burst of Reina and another ancient round of Tekay activity burst were examined in Sechium edule. In addition, Tekay and Retand lineages belonging to the Gypsy superfamily underwent a recent burst in Gynostemma pentaphyllum. Detailed investigation of genes with intronic and promoter LTR-RT insertion showed diverse functions, but the term of metabolism was enriched in most species. Further gene expression analysis in G.pentaphyllum revealed that the LTR-RTs within introns suppress the corresponding gene expression, whereas the LTR-RTs within promoters exert a complex influence on the downstream gene expression, with the main function of promoting gene expression. This study provides novel insights into the organization, evolution, and function of LTR-RTs in Cucurbitaceae genomes.

[A descriptive analysis of tea consumption in adult twins in China]

Objective: To describe the distribution characteristics of tea consumption in adult twins recruited in the Chinese National Twin Registry (CNTR) and provide clues to genetic and environmental influences on tea consumption. Methods: Enrolled in CNTR during 2010-2018, 25 264 twin pairs aged 18 years and above were included in subsequent analysis. Random effect models were used to estimate tea consumption in the population and regional distribution characteristics. The concordance rate of the behavior and difference in consumption volume of tea within pairs were also described. Results: The mean age of all subjects was (35.38±12.45) years old. The weekly tea consumers accounted for 17.0%, with an average tea consumption of (3.36±2.44) cups per day. The proportion of weekly tea consumers was higher among males, 50-59 years old, southern, urban, educated, and the first-born in the twin pair (P<0.05), and lower among unmarried individuals (P<0.001). Within-pair analysis showed that the concordance rate of tea consumption of monozygotic (MZ) twins was higher than that of dizygotic (DZ) twins and the overall heritability of tea consumption was 13.45% (11.38%-15.51%). Stratified by the characteristics mentioned above, only in males, the concordance rate of MZ showed a tendency to be greater than that of DZ (all P<0.05). The differences in consumption volume of tea within twin pairs were minor in MZ among males (P<0.05), while the differences were not significant in female twins. Conclusion: There were discrepancies in the distribution of tea consumption among twins of different demographic and regional characteristics. Tea consumption was mainly influenced by environmental factors and slightly influenced by genetic factors. The size of genetic factors varied with gender, age, and region, and gender was a potential modified factor.

[Review of genome-wide association research of aging phenotypes]

"Active health" has been emphasized in "Healthy China 2030" in dealing with the challenges of population aging, so the anti-aging strategies are requires to be more precise and effective at both individual and population levels. Aging is influenced by both genetic and environmental factors. In the recent 20 years, the research of genetics of human ageing has been greatly facilitated owning to the development of high-throughput sequencing techniques, statistical methodology for multi-omics data, as well as the growing qualified evidence of large-scale population-based genomic research. This paper provides a review of genome-wide association research of aging.

[Heritability and genetic correlation of body mass index and coronary heart disease in Chinese adult twins]

Objective: To examine the heritability of body mass index (BMI) and coronary heart disease (CHD), and to explore whether genetic factors can explain their correlation. Methods: Participants were from 11 provinces/municipalities reqistered in the Chinese National Twin Registry (CNTR) from 2010 to 2018. Participants data were collected from face-to-face questionnaire survey. Bivariate structure equation model was used to estimate the heritability and the genetic correlation of BMI and CHD. Results: A total of 20 340 pairs of same-sex twins aged ≥25 years were included in this study. After adjusting for age and gender, the heritability of BMI and CHD was 0.52 (95%CI: 0.49-0.55) and 0.76 (95%CI: 0.69-0.81), respectively. Further, a genetic correlation was identified between BMI and CHD (r_A=0.10, 95%CI:0.02-0.17). Conclusion: In Chinese adult twin population, BMI and CHD are affected by genetic factors, and their correlation can be attributed to the common genetic basis.

[A descriptive analysis on coronary heart disease in adult twins in China]

Objective: To describe the distribution characteristics of coronary heart disease in adult twins recruited from Chinese Twin Registry (CNTR), and provide clues and evidence for the effect of genetic and environmental influences on coronary heart disease. Methods: By using the data of CNTR during 2010-2018, a total of 34 583 twin pairs aged ≥18 years who completed questionnaire survey and had related information were included in the current study to analyze the population and area distribution characteristics of coronary heart disease. Random effect models were used to compare the differences between groups. The concordane rate of coronary heart disease were calculated respectively in monozygotic (MZ) twin pairs and dizygotic (DZ) twin pairs to estimate the heritability. Results: The twin pairs included in this analysis were aged (34.2±12.4) years. The overall prevalence rate of coronary heart disease in twin pairs was 0.7%. Twin pairs who were women, older, obese and lived in northern China had higher prevalence of coronary heart disease (P<0.05). Intra-pair analysis in the same-sex twin pairs found that the concordane rate of coronary heart disease was higher in MZ twin pairs (25.3%) than in DZ twins (7.4%), and the difference was statistically significant (P<0.001). The overall heritability of coronary heart disease was 19.3% (95%CI: 11.8%-26.8%). Stratified by gender, age and area, the concordane rate was still higher in MZ twin pairs than in DZ pairs. Participants who were women, aged 18-30 years or ≥60 years and lived in northern China had a higher heritability of coronary heart disease. Conclusion: The distribution of coronary heart disease in twin pairs differed in populations and areas. The prevalence of coronary heart disease was affected by genetic factors, but the effect varied with age, gender and area.

[A descriptive analysis on type 2 diabetes in twins in China]

Objective: To describe the distribution characteristics of type 2 diabetes in twins in Chinese National Twin Registry (CNTR), provide clues and evidence for revealing the influence of genetic and environmental factors for type 2 diabetes. Methods: Of all twins registered in the CNTR during 2010-2018, a total 18 855 twin pairs aged ≥30 years with complete registration information were included in the analysis. The random effect model was used to describe the population and area distribution characteristics and concordance of type 2 diabetes in twin pairs. Results: The mean age of the subjects was (42.8±10.2) years, the study subjects included 10 339 monozygotic (MZ) twin pairs and 8 516 dizygotic (DZ) twin pairs. The self-reported prevalence rate of type 2 diabetes was 2.2% in total population and there was no sighificant difference between MZ and DZ. Intra-twin pairs analysis showed that the concordance rate of type 2 diabetes was 38.2% in MZ twin pairs, and 16.0% in DZ twin pairs, the difference was statistically significant (P<0.001). The concordance rate of type 2 diabetes in MZ twin parts was higher than that in DZ twin pairs in both men and women, in different age groups and in different areas (P<0.05). Further stratified analysis showed that in northern China, only MZ twin pairs less than 60 years old were found to have a higher concordance rate of type 2 diabetes compared with DZ twin pairs (P<0.05). In southern China, the co-prevalence rate in male MZ twin pairs aged ≥60 years was still higher than that in DZ twin pairs (P<0.05). Conclusion: The twin pairs in this study had a lower self-reported prevalence of type 2 diabetes than the general population. The study results suggested that genetic factors play a role in type 2 diabetes prevalence in both men and women, in different age groups and in different areas, however, the effect might vary.

[Gene-lifestyle interaction on coronary heart disease in adult twins of China]

Objective: To explore the gene-lifestyle interaction on coronary heart disease (CHD) in adult twins of China. Methods: Participants were selected from twin pairs registered in the Chinese National Twin Registry (CNTR). Univariate interaction model was used to estimate the interaction, via exploring the moderation effect of lifestyle on the genetic variance of CHD. Results: A total of 20 477 same-sex twin pairs aged ≥25 years were recruited, including 395 CHD cases, and 66 twin pairs both had CHD. After adjustment for age and sex, no moderation effects of lifestyles, including current smoking, current drinking, physical activity, intake of vegetable and fruit, on the genetic variance of CHD were found (P>0.05), suggesting no significant interactions. Conclusion: There was no evidence suggesting statistically significant gene-lifestyle interaction on CHD in adult twins of China.

[Gene-body mass index interaction on coronary heart disease in Chinese adult twins]

Objective: To explore the gene-body mass index (BMI) interaction on coronary heart disease (CHD) in the Chinese adult twins. Methods: A total of 20 340 same-sex twin pairs registered in the Chinese National Twin Registry (CNTR) were enrolled in this study. Classical twin structure equation model was used to estimate the gene-BMI interaction on CHD. Results: After adjusting for age, we found that genetic variance of CHD differed as the function of BMI in male twins, which indicated the presence of a gene-BMI interaction on CHD (P=0.008).The genetic moderating effect (β_a) was -0.14 (95%CI: -0.22--0.04), indicating that for each logarithmic transformation value of BMI increase, genetic path parameters would decrease by 0.14, which would result in the decrease of genetic variance of CHD. And the heritability of CHD was 0.77 (95%CI: 0.65-0.86) among the male twins with lower BMI (<24.0 kg/m²), but 0.56 (95%CI: 0.33-0.74) among the male twins with high BMI (≥24.0 kg/m²). However, there was no evidence suggesting that BMI could moderate genetic variants of CHD in female. Conclusion: We found a significant gene-BMI interaction on CHD in the Chinese male adult twins in China, and the heritability of CHD was higher among the twins whose BMI was <24.0 kg/m².

DNA methylation is involved in sexual differentiation and sex chromosome evolution in the dioecious plant garden asparagus

DNA methylation is a crucial regulatory mechanism in many biological processes. However, limited studies have dissected the contribution of DNA methylation to sexual differentiation in dioecious plants. In this study, we investigated the variances in methylation and transcriptional patterns of male and female flowers of garden asparagus. Compared with male flowers, female flowers at the same stages showed higher levels of DNA methylation. Both male and female flowers gained DNA methylation globally from the premeiotic to meiotic stages. Detailed analysis revealed that the increased DNA methylation was largely due to increased CHH methylation. Correlation analysis of differentially expressed genes and differentially methylated regions suggested that DNA methylation might not have contributed to the expression variation of the sex-determining genes SOFF and TDF1 but probably played important roles in sexual differentiation and flower development of garden asparagus. The upregulated genes AoMS1, AoLAP3, AoAMS, and AoLAP5 with varied methylated CHH regions might have been involved in sexual differentiation and flower development of garden asparagus. Plant hormone signaling genes and transcription factor genes also participated in sexual differentiation and flower development with potential epigenetic regulation. In addition, the CG and CHG methylation levels in the Y chromosome were notably higher than those in the X chromosome, implying that DNA methylation might have been involved in Y chromosome evolution. These data provide insights into the epigenetic modification of sexual differentiation and flower development and improve our understanding of sex chromosome evolution in garden asparagus.

[Modification of physical activity on genetic effects of type 2 diabetes mellitus: a twin pairs cohort study in China]

Objective: To explore the modification effect of physical activity on the genetic effects of type 2 diabetes mellitus (T2DM). Methods: The univariate moderation model was fitted to calculate the modifying effect of physical activity on the genetic effects of T2DM based on the data of 12 107 pairs of same gender twins aged 30 years and older enrolled by the Chinese National Twin Registry in 11 provinces/cities in China. Results: After adjusting for age and gender, the heritability of T2DM was 0.56 (0.31-0.84). Qualified physical activity could attenuate the genetic effects of T2DM. The heritability of T2DM in twin pairs with qualified physical activity was 0.46 (0.06-0.88), which was lower than that in twin pairs without qualified physical activity during the same model [0.68(0.36-0.94)]. Conclusion: T2DM is a moderate genetic disease, physical activity can modify the genetic effects of T2DM.

[A descriptive analysis on body mass index distribution in adult twin pairs in China]

Objective: To describe the differences in body mass index (BMI) distribution in adult twins registered in Chinese National Twin Registry (CNTR), and provide evidence for the risk factor analysis and prevention and control of overweight or obesity. Methods: A total of 32 725 twin pairs aged 18 years and above who completed the questionnaire survey during 2010-2018 and had complete registered information in CNTR and normal body weight and length were included in the analysis on the population and region specific distributions of BMI of twin pairs and the difference in BMI in twin pairs. Results: The twin pairs included in the analysis were aged (34.6±12.4) years, the twin pairs of same gender accounted for 79.7%. The average BMI was 22.5 kg/m². The overall prevalence of obesity and overweight was 4.9% and 23.7%, respectively. Participants who were men, 50-59 years old, married, had lower education level, and lived in northern China had higher overweight rate and obesity rate (P<0.001). The difference in overweight or obesity prevalence between monozygotic (MZ) twin pars and dizygotic (DZ) twin pairs was not significant, but firstborn twin pairs had slightly higher rates of overweight and obesity than later-born twin pairs (P<0.05). The analysis in same gender-twin pairs indicated that the difference in BMI was associated with age (trend test: P<0.001), and the difference was more obvious in DZ twin pair in MZ pair and this difference increased with age. The concordant rate of BMI was higher in MZ twin pairs than DZ twin pairs (P<0.05). Conclusion: The distribution of BMI of twin pairs varied with population and region and BMI varied with age due to its genetic nature.

[Epidemiological characteristics of COVID-19 cases in outbreak in Xinfadi market in Beijing]

Objective: To understand the epidemiological characteristics of COVID-19 cases, including asymptomatic cases and symptomatic cases, in the outbreak in Xinfadi market in Beijing. Methods: Data and epidemiological survey reports of COVID-19 cases in Xinfadi market in Beijing were extracted from China's Infectious Disease Information System. Epidemiological characteristics of symptomatic cases and asymptomatic cases were analyzed and compared by using software SPSS 19.0. Results: From June 11 to July 10, 2020, a total of 368 laboratory-confirmed COVID-19 cases reported in the outbreak in Xinfadi market, in which, 335 (91.03%) were symptomatic and 33 (8.97%) were asymptomatic. The cases were distributed in 11 districts, and most cases (252/368, 68.48%) were reported in Fengtai district. The incidence curve of the cases showed a typical outbreak pattern, the case number peaked on 13 June. The median age of the cases were 43 years (Q_R: 31-51). The asymptomatic cases (M=32, Q_R: 29-46) were younger than the symptomatic cases (M=43, Q_R: 31-52), the difference was significant (Z=2.416, P=0.016). The ratio of male to female was 1.26∶1. Most cases (236/368, 64.13%) were engaged in catering service and public place service. About 73.91% of the cases (272/368) had direct exposures in Xinfadi market. About 54.08%(199/368) of cases were detected through nucleic acid testing and screening. Mild and moderate cases accounted for 99.10% (332/335) of the total cases, and no death occurred. Conclusion: The COVID-19 cases in the outbreak in Xinfadi market were mainly engaged in catering service and public place service. The asymptomatic cases were younger than the symptomatic cases.

[Current status of COVID-19 pandemic and progress in response strategy]

As the approaching of autumn and winter in northern hemisphere, COVID-19, mainly transmitted through respiratory droplets and close contact, has posed new challenge to the countries across the world. This paper summarizes the current status of COVID-19 pandemic and related responses performed in terms of the variation of SARS-CoV-2, global situation reports, herd immunity and the influence of asymptomatic infection on COVID-19 prevention and control in China, as well as vaccine development progress and case treatment for the purpose of providing reference to further improve the COVID-19 prevention and control strategy in China.

[Nutritional risk screening and related factors of cancer patients in community of Shanghai, 2018-2019]

Objective: To study the risk of malnutrition and related factors of cancer patients in community of Shanghai. Methods: From October 2018 to January 2019, four communities, Pengpu New Village Street, Pengpu Town, Jiangning Road Street, and Caojiadu Street, from 14 communities in Jing 'an District, Shanghai City, were selected by using a random cluster sampling method based on the Shanghai Cancer Registration and reporting system. All cases of malignant tumors and benign tumors of the central nervous system were included. A total of 4 396 questionnaires were distributed. After the exclusion of 9 invalid questionnaires, 3 310 valid questionnaires were included with a rate of 99.73%. A self-designed questionnaire was used to collect data including basic demographic characteristics, history of malignant, physical and psychological pain, nutritional demands and cognitive status. Malnutrition Universal Screening Tools (MUST) was used to analyze the nutritional risk of cancer patients in the community. Multivariate logistic regression model was applied to analyze potential factors. Results: Among the 3 310 cancer patients who completed the survey, the average age of study participants was (64.05±13.02), and 1 467 cases (44.32%) were males. The incidence rate of nutritional risk was 12.84% (425/3 310). The result of logistic regression analysis showed that compared with male, other cancer patients and no physical pain, the risk factors of the occurrence of nutritional included: female (OR=1.53,95%CI:1.23-1.92), head and neck malignant tumors (OR=1.42,95%CI:1.07-1.90), bronchus/lung malignant tumors (OR=1.93,95%CI:1.43-2.61), liver, biliary/pancreatic malignant tumors (OR=2.11,95%CI:1.21-3.65) and upper gastrointestinal malignant tumors (OR=6.04,95%CI:4.31-8.46), patients with physical pain (OR=1.39,95%CI:1.02-1.89). Conclusion: Nutritional risk of cancer patients is higher in community of Shanghai. Gender, location of tumors and physical pain are associated with the occurrence of nutritional risk.

[Association between perceived built environment attributes and adults' leisure-time physical activity in four cities of China]

Objective: To explore the associations between perceived built environment attributes and adults' leisure-time physical activity in four cities of China. Methods: Multistage cluster random sampling method was used to select adults aged 25 to 64 in Hangzhou, Suzhou, Chengdu, and Qingdao. Data were collected from June 2017 to July 2018. The perception of the urban built environment was assessed by the neighborhood environment walkability scale-abbreviated (NEWS-A), and the physical activity was assessed by the International Physical Activity Questionnaire. Generalized linear mixed models were used to explore the relationship between the perceived built environment and leisure-time physical activities. Results: A total of 3 789 participants were included in the analysis. After adjusting for potential confounders, better access to public services (OR=1.34, 95%CI: 1.02-1.75) and higher aesthetic quality (OR=1.37, 95%CI: 1.09-1.73) were positively associated with the possibility of engaging in leisure-time physical activity in the past week. Similarly, these two attributes were positively associated with leisure-time walking. Higher scores on the perception of street connectivity were positively associated with leisure-time walking [exp(β)=1.09, 95%CI: 1.00-1.19]. Higher residential density [exp(β)=1.000 4, 95%CI:1.000 0-1.000 8], better access to physical activity destinations[exp(β)=1.09, 95%CI: 1.00-1.19], and better aesthetics [exp(β)=1.11, 95%CI:1.00-1.22] were associated with higher leisure-time physical activity. Similarly, these three attributes were positively associated with the possibility of meeting the WHO recommendations. Conclusion: Changing some urban built environment attributes may increase leisure-time physical activity.

[Bivariate heritability estimation of resting heart rate and common chronic disease based on extended pedigrees]

OBJECTIVE

To estimate the univariate heritability of resting heart rate and common chronic disease such as hypertension, diabetes, and dyslipidemia based on extended pedigrees in Fujian Tulou area and to explore bivariate heritability to test for the genetic correlation between resting heart rate and other relative phenotypes.

METHODS

The study was conducted in Tulou area of Nanjing County, Fujian Province from August 2015 to December 2017. The participants were residents with Zhang surname and their relatives from Taxia Village, Qujiang Village, and Nanou Village or residents with Chen surname and their relatives from Caoban Village, Tumei Village, and Beiling Village. The baseline survey recruited 1 563 family members from 452 extended pedigrees. The pedigree reconstruction was based on the family information registration and the genealogy booklet. Univariate and bivariate heritability was estimated using variance component models for continuous variables, and susceptibility-threshold model for binary variables.

RESULTS

The pedigree reconstruction identified 1 seven-generation pedigree, 2 five-generation pedigrees, 23 four-generation pedigrees, 186 three-generation pedigrees, and 240 two-generation pedigrees. The mean age of the participants was 57.2 years and the males accounted for 39.4%. The prevalence of hypertension, diabetes, dyslipidemia in this population was 49.2%, 10.0%, and 45.2%, respectively. The univariate heritability estimation of resting heart rate, hypertension, and dyslipidemia was 0.263 (95%CI: 0.120－0.407), 0.404 (95%CI: 0.135－0.673), and 0.799 (95%CI: 0.590－1), respectively. The heritability of systolic blood pressure, diastolic blood pressure, fasting glucose, total cholesterol, triglyceride, high-density lipoprotein cholesterol, and low-density lipoprotein cholesterol was 0.379, 0.306, 0.393, 0.452, 0.568, 0.852, and 0.387, respectively. In bivariate analysis, there were phenotypic correlations between resting heart rate with hypertension, diabetes, diastolic blood pressure, fasting glucose, and triglyceride. After taking resting heart rate into account, there were strong genetic correlations between resting heart rate with fasting glucose (genetic correlation 0.485, 95%CI: 0.120－1, P<0.05) and diabetes (genetic correlation 0.795, 95%CI: 0.181－0.788, P<0.05).

CONCLUSION

Resting heart rate was a heritable trait and correlated with several common chronic diseases and related traits. There was strong genetic correlation between resting heart rate with fasting glucose and diabetes, suggesting that they may share common genetic risk factors.

[Advances on the asymptomatic infection of COVID-19]

The COVID-19 outbreak in China has been gradually controlled. At present, the management and risk assessment of asymptomatic infected cases has become an urgent problem to be addressed. Asymptomatic case is mainly detected by close contact screening, cluster epidemic investigation, infection source tracking investigation, and active detection of target population. Currently, research on the spread risk from asymptomatic cases was limited, and lacking the data relates to the distribution of asymptomatic cases in large community population. Pathogen detection using PCR is suitable for screening in close contacts of confirmed cases and should be started as early as possible. The antibody test is more suitable for screening in general population where the source of infection is unclear. The management of asymptomatic cases now in China focuses on isolation and medical observation according to the guideline of "early detection, early report, early isolation and early treatment" .

[Correlation between fasting plasma glucose, HbA1c and DNA methylation in adult twins]

OBJECTIVE

To explore the cytidine-phosphate-guanosine (CPG) sites associated with fas-ting plasma glucose (FPG) and glycated haemoglobin (HbA1c) in twins.

METHODS

In the study, 169 pairs of monozygotic twins were recruited in Qingdao, Zhejiang, Jiangsu, Sichuan and Heilongjiang in June to December of 2013 and June 2017 to October 2018. The methylation was detected by Illumina Infinium HumanMethylation450 BeadChip and Illumina Infinium MethylationEPIC BeadChip. According to the Linear Mixed Effect model (LME model), fasting plasma glucose and HbA1c were taken as the main effects, the methylation level (β value) was taken as the dependent variable, continuous variables, such as age, body mass index (BMI), blood pressure, components of blood cells, surrogate variables generated by SVA, and categorical variables, such as gender, smoking and drinking status, hypoglycemic drugs taking, were included in the fixed effect model as covariates, and the identity numbers (ID) of the twins was included in the random effect model. The intercept was set as a random. Regression analysis was carried out to find out the CpG sites related to fasting blood glucose or HbA1c, respectively.

RESULTS

In this study, 338 monozygotic twins (169 pairs) were included, with 412 459 CpG loci. Among them, 114 pairs were male, and 55 pairs were female, with an average age of (48.2±11.9) years. After adjustment of age, gender, BMI, blood pressure, smoking, drinking, blood cell composition, and other covariates, and multiple comparison test, 7 CpG sites (cg19693031, cg01538969, cg08501915, cg04816311, ch.8.1820050F, cg06721411, cg26608667) were found related to fasting blood glucose, 3 of which (cg08501915, ch.8.1820050f, cg26608667) were the newly found sites in this study; whereas 10 CpG sites (cg19693031, cg04816311, cg01538969, cg01339781, cg01676795, cg24667115, cg09029192, cg20697417, ch.4.1528651F, cg16097041) were found related to HbA1c, and 4 of which(cg01339781, cg24667115, cg20697417, and ch.4.1528651f) were new. We found that cg19693031 in TXNIP gene was the lowest P-value site in the association analysis between DNA methylation and fas-ting plasma glucose and HbA1c (P_FPG=2.42×10^-19, FDR_FPG<0.001; P_HbA1c=1.72×10^-19, FDR_HbA1c<0.001).

CONCLUSION

In this twin study, we found new CpG sites related to fasting blood glucose and HbA1c, and provided some clues that partly revealed the potential mechanism of blood glucose metabolism in terms of DNA methylation, but it needed further verification in external larger samples.

[Heritability of alcohol intake among adult twins, calculate by the structural equation model]

Objective: To explore the genetic and environmental effects on alcohol intake. Methods: Data on 9 231 pairs of adult twins of the same sex was collected from the Chinese National Twin Registry (CNTR), between 2015 and 2018 and used in this study. Structural equation model was used to estimate the effects of genetic and environmental factors on alcohol intake. Results: A total of 9 231 pairs of twins were included in the analysis, of which 6 085 pairs were monozygotic (MZ). The average age of MZ was (36.91±13.07) years old, and males accounted for 56.80%. The average age of dizygotic twins (DZ) was (35.22±12.48) years old, and males accounted for 55.91%. There were 350 pairs of alcohol-drinking twins were with high-risk, accounting for 1.90% and another 367 pairs (1.99%) were with medium-risk. Alcohol-drinkers with medium-risk were affected by additive genetics, common and unique environmental factors, seen among the twins. The overall heritability appeared as 24.3% (95%CI: 0 to 56.8%). Furthermore, 50.7% of the variation (95%CI: 20.4%-79.0%) could be explained by the common environmental factors and 24.9% (95%CI: 18.3%-36.5%) by unique environmental factors. High-risk related drinking behavior was affected by both common and unique environmental factors. The common environmental component appeared as 75.6% (95%CI: 69.6%-80.8%) and unique environmental component as 24.4% (95%CI: 19.2%-30.4%), respectively. Gender difference was seen in the heritability of those with medium or high-risk drinking behaviors. The heritability of men was 30.8% (95%CI: 9.8%-53.5%), while in women it was mainly affected by the environment. Conclusion: Both alcohol drinkers with medium and high-risk drinking behaviors were mainly affected by the environment factors and gender. With the increase of drinking volume, the effect of environment on drinking behaviors became more obvious.

[Advances on presymptomatic or asymptomatic carrier transmission of COVID-19]

COVID-19 is rapidly spreading. Patients in incubation period and healthy carriers are possible sources for transmission. However, such sources of infection cannot be effectively identified due to the symptoms absent. The research evidence is very lacking so far, although there are a few studies suggesting that presymptomatic or asymptomatic carrier may cause COVID-19 transmission. Nearly half of the literature is in the state of preprint without peer review. The question of "the degree to which presymptomatic or asymptomatic infections can transmit" is not fully understood. There is an urgent need to screen infected carriers in larger close contacts or in the general population, and assess their risk for transmission.

[Heritability of coronary heart disease, based on the data from the Chinese adult twins]

Objective: To analyze the heritability of coronary heart disease (CHD) among the Chinese twin adults. Methods: A total of 20 477 same-sex twin pairs aged 25 years and older from the Chinese National Twin Registry were interviewed. Structure equation model was used to estimate the heritability of CHD. Results: After adjusting for age and gender, the overall heritability of CHD was 0.75(0.68-0.81). Stratified analyses showed that genetic factors play a more important role in CHD incidence in ≥40 years or female twins. While the development of CHD was mainly influenced by environmental factors in 25-39 years or male twins. Conclusion: CHD is influenced by both genetic and environmental factors and the heritability is high.

Chromosome-level genome assembly, annotation and evolutionary analysis of the ornamental plant Asparagus setaceus

Asparagus setaceus is a popular ornamental plant cultivated in tropical and subtropical regions globally. Here, we constructed a chromosome-scale reference genome of A. setaceus to facilitate the investigation of its genome characteristics and evolution. Using a combination of Nanopore long reads, Illumina short reads, 10× Genomics linked reads, and Hi-C data, we generated a high-quality genome assembly of A. setaceus covering 710.15 Mb, accounting for 98.63% of the estimated genome size. A total of 96.85% of the sequences were anchored to ten superscaffolds corresponding to the ten chromosomes. The genome of A. setaceus was predicted to contain 28,410 genes, 25,649 (90.28%) of which were functionally annotated. A total of 65.59% of the genome was occupied by repetitive sequences, among which long terminal repeats were predominant (42.51% of the whole genome). Evolutionary analysis revealed an estimated divergence time of A. setaceus from its close relative A. officinalis of ~9.66 million years ago, and A. setaceus underwent two rounds of whole-genome duplication. In addition, 762 specific gene families, 96 positively selected genes, and 76 resistance (R) genes were detected and functionally predicted in A. setaceus. These findings provide new knowledge about the characteristics and evolution of the A. setaceus genome, and will facilitate comparative genetic and genomic research on the genus Asparagus.

[Birth weight predicts physical indicators in adulthood: a large population-based study in Chinese twins]

Objective: To quantitate the association between birth weight and phenotypes of physical indicators in adulthood, i.e. BMI and waist circumference (WC) and to what degree genetic or environmental factors affect birth weight-obesity association. Methods: A total of 6 623 gender matched twin pairs aged 25 to 79 years were recruited through the Chinese National Twin Registry. The twins reported their own birth weight, current height and weight, and WC using a self-administered questionnaire. BMI was calculated according to the self-reports of body height and weight. Within twin-pair design was used to quantitate the association between birth weight and phenotypes related to obesity while bivariate structural equation models were used to decompose the phenotype correlation. Results: After adjusted for multiple factors, twin-pair analyses within monozygotic (MZ) showed that, on average, a 1.0 kg increase in birth weight corresponded to an increase of 0.33 kg/m(2) in BMI and 0.95 cm in WC in adulthood (P<0.001). Bivariate structural equation models showed significant positive unique environmental correlation between birth weight and the two obesity-related phenotypes. Conclusion: The study supported the role of twin-specific supply line factors on relationship between birth weight and physical indicators in adulthood.

Nuclear Integrants of Organellar DNA Contribute to Genome Structure and Evolution in Plants

The transfer of genetic material from the mitochondria and plastid to the nucleus gives rise to nuclear integrants of mitochondrial DNA (NUMTs) and nuclear integrants of plastid DNA (NUPTs). This frequently occurring DNA transfer is ongoing and has important evolutionary implications. In this review, based on previous studies and the analysis of NUMT/NUPT insertions of more than 200 sequenced plant genomes, we analyzed and summarized the general features of NUMTs/NUPTs and highlighted the genetic consequence of organellar DNA insertions. The statistics of organellar DNA integrants among various plant genomes revealed that organellar DNA-derived sequence content is positively correlated with the nuclear genome size. After integration, the nuclear organellar DNA could undergo different fates, including elimination, mutation, rearrangement, fragmentation, and proliferation. The integrated organellar DNAs play important roles in increasing genetic diversity, promoting gene and genome evolution, and are involved in sex chromosome evolution in dioecious plants. The integrating mechanisms, involving non-homologous end joining at double-strand breaks were also discussed.

Cytogenetic and genomic organization analyses of chloroplast DNA invasions in the nuclear genome of Asparagus officinalis L. provides signatures of evolutionary complexity and informativity in sex chromosome evolution

BACKGROUND

The transfer of chloroplast DNA into nuclear genome is a common process in plants. These transfers form nuclear integrants of plastid DNAs (NUPTs), which are thought to be driving forces in genome evolution, including sex chromosome evolution. In this study, NUPTs in the genome of a dioecious plant Asparagus officinalis L. were systematically analyzed, in order to investigate the characteristics of NUPTs in the nuclear genome and the relationship between NUPTs and sex chromosome evolution in this species.

RESULTS

A total of 3155 NUPT insertions were detected, and they represented approximated 0.06% of the nuclear genome. About 45% of the NUPTs were organized in clusters. These clusters were derived from various evolutionary events. The Y chromosome contained the highest number and largest proportion of NUPTs, suggesting more accumulation of NUPTs on sex chromosomes. NUPTs were distributed widely in all of the chromosomes, and some regions preferred these insertions. The highest density of NUPTs was found in a 47 kb region in the Y chromosome; more than 75% of this region was occupied by NUPTs. Further cytogenetic and sequence alignment analysis revealed that this region was likely the centromeric region of the sex chromosomes. On the other hand, the male-specific region of the Y chromosome (MSY) and the adjacent regions did not have NUPT insertions.

CONCLUSIONS

These results indicated that NUPTs were involved in shaping the genome of A. officinalis through complicated process. NUPTs may play important roles in the centromere shaping of the sex chromosomes of A. officinalis, but were not implicated in MSY formation.

Characterization of the complete chloroplast genome of Asparagus setaceus

Asparagus setaceus is an important ornamental plant and is important to study the sex chromosome evolution in genus Asparagus. Here the complete chloroplast (cp) genome sequence of A. setaceus was determined. The cpDNA is 156,978 bp in length, contains a large single copy region of 85,311 bp and a small single copy region of 18,641 bp, which was separated by a pair of inverted repeat regions of 26,513 bp each. The cp genome contains 132 genes, including 88 protein-coding genes, 6 ribosomal RNA genes, and 38 transfer RNA genes. Phylogenetic analysis indicates that A. setaceus is closely related to Asparagus officinalis and Asparagus schoberioides.

[Analysis on the heritability of diabetes, based on data from the Chinese adult twins]

Objective: To analyze the heritability of diabetes among the Chinese twin adults. Methods: A total of 10 253 same-sex twin pairs aged 25 years and older, were selected from the Chinese National Twin Registry (CNTR) program. Heritability of diabetes was calculated by using the structural equation model. Results: After adjusted for age and gender, the overall heritability rates of diabetes were 0.41 (0.15-0.75), 0.83 (0.72-0.91) and 0.34 (0.04-0.73) in the <45 and ≥45 years twin pairs, respectively. After adjusted for age, rates of heritability appeared as 0.37 (0.05-0.78) and 0.88 (0.79-0.94) in men and women, respectively. Conclusions: Diabetes is affected by both genetic and environmental factors. The genetic effect of diabetes seemed stronger on female than that on male twins but was dying down along with ageing.

[Fujian Tulou Family Cohort Study: study design and characteristics of participants and pedigrees in baseline investigation]

Objective: To describe the study design, the characteristics of participants as well as the pedigrees included in the baseline survey of Fujian Tulou Family Cohort Study. Methods: Fujian Tulou Family Cohort Study was a prospective open cohort study with a biological sample bank. A baseline survey was conducted in Tulou areas of Nanjing county in Fujian province from 2015 to 2018, including questionnaire survey, physical and biochemical indicators examinations, and blood sample collection in adults aged ≥18 years. In addition, family relationship of the participants was also recorded. The pedigree information of the juveniles under 18 years old were also collected. Results: The baseline survey included 2 727 individuals in two clans, of whom 2 373 (87.0%) were adults, and 2 126 participants completed questionnaires, physical examinations and biochemical tests. The average age of the 2 126 participants was (57.9±13.3) years, with 39.4% being males. The current smoking rates in male and female participants were 41.2% and 2.1%, respectively. The corresponding rates of current alcohol consumption were 19.0% and 2.6%. For common chronic diseases, the prevalence rates were 51.3% for hypertension, 9.7% for diabetes and 26.7% for hyperlipemia according to the self-reported disease diagnoses, health examination results and biochemical examination results in class Ⅱ or Ⅲ hospitals. Based on the family relationship information and genealogical data, 710 pedigrees were finally identified, consisting of 5 087 family members. The numbers of five, four, three, and two generations pedigrees were 3, 88, 238 and 381, respectively. The pairs of the first to the fifth degree relatives were 12 039, 2 662, 1 511, 202 and 31, respectively. Conclusion: The establishment of Fujian Tulou Family Cohort provides valuable resources for exploring the genetic risk factors, environmental risk factors and gene-environment interactions contributing to the risk of common chronic diseases.

The landscape of transposable elements and satellite DNAs in the genome of a dioecious plant spinach (Spinacia oleracea L.)

Background

Repetitive sequences, including transposable elements (TEs) and satellite DNAs, occupy a considerable portion of plant genomes. Analysis of the repeat fraction benefits the understanding of genome structure and evolution. Spinach (Spinacia oleracea L.), an important vegetable crop, is also a model dioecious plant species for studying sex determination and sex chromosome evolution. However, the repetitive sequences of the spinach genome have not been fully investigated.

Results

We extensively analyzed the repetitive components of draft spinach genome, especially TEs and satellites, by different strategies. A total of 16,002 full-length TEs were identified. Among the most abundant long terminal repeat (LTR) retrotransposons (REs), Copia elements were overrepresented compared with Gypsy ones. Angela was the most dominating Copia lineage; Ogre/Tat was the most abundant Gypsy lineage. The mean insertion age of LTR-REs was 1.42 million years; approximately 83.7% of these elements were retrotransposed during the last two million years. RepeatMasker totally masked about 64.05% of the spinach genome, with LTR-REs, non-LTR-REs, and DNA transposons occupying 49.2, 2.4, and 5.6%, respectively. Fluorescence in situ hybridization (FISH) analysis showed that most LTR-REs dispersed all over the chromosomes, by contrast, elements of CRM lineage were distributed at the centromeric region of all chromosomes. In addition, Ogre/Tat lineage mainly accumulated on sex chromosomes, and satellites Spsat2 and Spsat3 were exclusively located at the telomeric region of the short arm of sex chromosomes.

Conclusions

We reliably annotated the TE fraction of the draft genome of spinach. FISH analysis indicates that Ogre/Tat lineage and the sex chromosome-specific satellites DNAs might participate in sex chromosome formation and evolution. Based on FISH signals of microsatellites, together with 45S rDNA, a fine karyotype of spinach was established. This study improves our knowledge of repetitive sequence organization in spinach genome and aids in accurate spinach karyotype construction.

Electronic supplementary material

The online version of this article (10.1186/s13100-019-0147-6) contains supplementary material, which is available to authorized users.

Genome-wide characterization of microsatellites and genetic diversity assessment of spinach in the Chinese germplasm collection

Spinach is a nutritional leafy green vegetable, and it also serves as a model species for studying sex chromosome evolution. Genetic marker development and genome structure analysis are important in breeding practice and theoretical evolution studies of spinach. In this study, the frequency and distribution of different microsatellites in the recently released draft spinach genome were characterized. A total of 261,002 perfect microsatellites were identified (estimated frequency: ~262.1 loci/Mbp). The most abundant microsatellites were tetranucleotide and trinucleotide, accounting for 33.2% and 27.7% of the total number of microsatellites, respectively. A total of 105 primer pairs were designed and screened, and 34 were polymorphic among the detected spinach cultivars. Combined with seven primer sets developed previously, 41 primer pairs were used to investigate genetic diversity among 43 spinach cultivars in China. The average polymorphism information content value of the 41 markers was 0.43, representing an intermediate level. The spinach cultivars had a low genetic diversity, and no detectable common factors were shared by each group in the UPGMA dendrogram. This study's findings facilitate further investigations on the organization of the microsatellites in spinach genome and provide clues for future breeding applications of spinach in China.

[Correlation between blood pressure and DNA methylation in adult twins]

OBJECTIVE

To explore the DNA methylation sites correlated with blood pressure (systolic blood pressure, diastolic blood pressure, mean arterial pressure, pulse pressure) in adult twin population.

METHODS

A total of 476 twins from the Chinese National Twin Registry were selected as the research population. Questionnaires were used to collect demographic characteristics, lifestyle, disease status and other information, and blood pressure, height, weight and other anthropometric indicators were measured. The genome-wide DNA methylation of whole blood samples was detected by using Infinium HumanMethylation450 BeadChip. The DNA methylation sites correlated with blood pressure were analyzed by constructing mixed effect model with adjusting potential confounding factors, and the significant level was false discovery rate <0.05.

RESULTS

After data quality control, 465 twins (122 pairs of monozygotic twins, 104 pairs of dizygotic twins, 13 individuals from 13 pairs of twins) aged (44.8±13.2) years were finally enrolled. There were more males and more monozygotic twins, and the current smokers and current regular drinkers both accounted for more than 30%. No significant CpG site was found after multiple testing in the correlation study between genome-wide DNA methylation and blood pressure by using the collected twins. However, the cg07761116 located on chromosome 10 had low P value in the correlation analysis of 3 blood pressure indices (systolic blood pressure, diastolic blood pressure, mean arterial pressure), suggesting that this site might be correlated with blood pressure. The other 7 sites had low P value in the correlation analysis of the two blood pressure indices, respectively, which pointed to genes involved in neurological development, protein homeostasis, inflammatory reaction and other pathways.

CONCLUSION

There is no sufficient evidence to support any DNA methylation site correlated with blood pressure, which may be caused by insufficient sample size and other reasons. This study could provide a reference for subsequent similar twin studies, and subsequent studies can focus on the cg07761116 located on chromosome 10 and other sites with low P values.

[Association between obesity and DNA methylation among the 7-16 year-old twins]

Objective: On whole-genome scale, we tried to explore the correlation between obesity-related traits and DNA methylation sites, based on discordant monozygotic twin pairs. Methods: A total of 90 pairs of 6-17 year-old twins were recruited in Chaoyang district, Yanqing district and Fangshan district in Beijing in 2016. Information on twins was gathered through a self-designed questionnaire and results: from physical examination, including height, weight and waist circumference of the subjects under study. DNA methylation detection was chosen on the Illumina Human Methylation EPIC BeadChip. R 3.3.1 language was used to read the DNA methylation signal under quality control on samples and probes. Ebayes function of empirical Bayes paired moderated t-test was used to identify the differential methylated CpG sites (DMCs). VarFit function of empirical Bayes paired moderated Levene test was used to identify the differentially variables CpG sits (DVCs) in obese and normal groups. Results According to the obesity discordance criteria, we collected 23 pairs of twins (age range 7 to 16 years), including 12 male pairs. A total of 817 471 qualified CpG loci were included in the genome-wide correlation analysis. According to the significance level of FDR set as <0.05, no positive sites would meet this standard. When DMC CpG site cg05684382, with the smallest P value (1.26E-06) as on chromosome 12, the DVC CpG site cg26188191 with the smallest P value (6.44E-06) appeared in CMIP gene on chromosome 16. Conclusions: In this study, we analyzed the genome-wide DNA methylation and its correlation with obesity traits. After multiple testing corrections, no positive sites were found to have associated with obesity. However, results from the correlation analysis demonstrated sites cg05684382 (chr: 12) and cg26188191 (chr: 16) might have played a role in the development of obesity. This study provides a methodologic reference for the studies on discordance twins related problems.

Development of a high-rate submerged anaerobic membrane bioreactor

Typically, anaerobic membrane bioreactors are operated at an organic loading rate (OLR) less than 10 kg chemical oxygen demand (COD)/m³d. This paper discusses the development and performance of a high-rate submerged anaerobic membrane bioreactor (SAnMBR) for a high-strength synthetic industrial wastewater treatment. An OLR as high as 41 kg COD/m³ d was achieved with excellent COD removal efficiency (>99%). The membrane was operated at constant fluxes (9.4-9.9 ± 0.5 L/m² h) and the change in trans-membrane pressure (TMP) was monitored to characterize the membrane performance. The results showed a low TMP (<5 kPa) under steady-state operation with only biogas sparging and relaxation as control strategy for over 300 days, implying no significant fouling was developed. Inorganic fouling was the dominant fouling mechanism occurred at the end of the study. The results suggest that the newly developed SAnMBR configuration can treat high-strength wastewater at lower capital expenditure while still providing superior effluent quality for water reuse or system closure.

Comparative transcriptome analysis reveals differentially expressed genes associated with sex expression in garden asparagus (Asparagus officinalis)

BACKGROUND

Garden asparagus (Asparagus officinalis) is a highly valuable vegetable crop of commercial and nutritional interest. It is also commonly used to investigate the mechanisms of sex determination and differentiation in plants. However, the sex expression mechanisms in asparagus remain poorly understood.

RESULTS

De novo transcriptome sequencing via Illumina paired-end sequencing revealed more than 26 billion bases of high-quality sequence data from male and female asparagus flower buds. A total of 72,626 unigenes with an average length of 979 bp were assembled. In comparative transcriptome analysis, 4876 differentially expressed genes (DEGs) were identified in the possible sex-determining stage of female and male/supermale flower buds. Of these DEGs, 433, including 285 male/supermale-biased and 149 female-biased genes, were annotated as flower related. Of the male/supermale-biased flower-related genes, 102 were probably involved in anther development. In addition, 43 DEGs implicated in hormone response and biosynthesis putatively associated with sex expression and reproduction were discovered. Moreover, 128 transcription factor (TF)-related genes belonging to various families were found to be differentially expressed, and this finding implied the essential roles of TF in sex determination or differentiation in asparagus. Correlation analysis indicated that miRNA-DEG pairs were also implicated in asparagus sexual development.

CONCLUSIONS

Our study identified a large number of DEGs involved in the sex expression and reproduction of asparagus, including known genes participating in plant reproduction, plant hormone signaling, TF encoding, and genes with unclear functions. We also found that miRNAs might be involved in the sex differentiation process. Our study could provide a valuable basis for further investigations on the regulatory networks of sex determination and differentiation in asparagus and facilitate further genetic and genomic studies on this dioecious species.

Identification of male-specific AFLP and SCAR markers in the dioecious plant Humulus scandens

In this study, 17 male-specific amplified fragment length polymorphism (AFLP) markers were identified between male and female Humulus scandens plants. BLAST analysis revealed that 7 of the 17 sex-linked sequences were highly similar to retrotransposons. Two stable male-specific sequence-characterized amplified regions (SCAR) markers were developed. These AFLP and SCAR markers are novel molecular probes that can be used efficiently to identify the genetic gender of H. scandens and may provide a basis for further investigations on the evolution of sex chromosomes.

[Mendelian randomization analysis of the relationship between obesity and DNA methylation]

Objective: To explore the association between DNA methylation and body mass index (BMI) using Mendelian randomization analysis. Methods: A total of 469 participants were selected from the Chinese National Twin Registry in 2013, who were living in Shandong, Jiangsu, Zhejiang, and Sichuan provinces, and at least 18 years of age. A questionnaire survey and physical examination were conducted to collect demographic, clinical, and behavioral information. Peripheral blood cells were collected to detect genotype and methylation status. Association analyses between DNA methylation and BMI and between CpGs and cis-SNP were conducted. With rs748212 as the instrumental variable, the association between cg15053022 and BMI was explored using the Mendelian randomization method. Results: A total of 469 participants were selected. The mean age of participants was (44.8±13.2) years and the BMI was (25.0±3.8) kg/m(2). Nine BMI-related DNA methylation sites were found and DNA methylation site cg15053022 in the ATP4A gene was negatively associated with cis-SNP rs748212 (β=-0.020); the mean methylation level of AA, AC, and CC were 0.212±0.025, 0.242±0.024, and 0.264±0.028, respectively. rs748212 was associated with BMI (β=0.04, P=0.007) and closely related to cg15053022 (F=237.66, P=0.143). Mendelian randomization analysis showed lower methylation levels at cg15053022 were associated with higher BMI (β=-1.97, P<0.001). Conclusion: This study supported the impact of cg15053022 methylation in the ATP4A gene on BMI using Mendelian randomization analysis and provided the basis for using Mendelian randomization analysis in methylation studies.

Cloning and characterization of ChiMYB in Chrysanthemum indicum with an emphasis on salinity stress tolerance

v-myb avianmyeloblastosis viral oncogene homolog (MYB) transcription factors are key regulators of stress responsive gene expression in plants. In this study, the MYB gene, ChiMYB (GenBank accession No. KT948997), was isolated from Chrysanthemum indicum, and was functionally characterized with an emphasis on salinity stress tolerance. The full ChiMYB cDNA sequence (948 bp) encoded a typical R2R3 MYB transcription factor that contained 315 amino acid residues and two MYB domains. The temporal expression pattern of ChiMYB was noted in C. indicum, and the highest level was detected in the roots, followed by leaves and stems. ChiMYB expression was induced by NaCl treatments, and transient expression of the fusion of ChiMYB and green fluorescent protein (GFP) indicated that the protein was targeted to the nuclei of onion epidermal cells. Arabidopsis plants overexpressing ChiMYB displayed improved tolerance to drought and salt stress. When under salt stress conditions, transgenic Arabidopsis plants had higher survival rates than non-transgenic wild-type plants. Chlorophyll content, intercellular CO₂ concentration, photosynthetic rate, and stomatal conductance were higher in the transgenic Arabidopsis plants than in non-transgenic control plants. Further investigation revealed that ChiMYB was able to regulate the expression of RD29A, RAB18, COR15, ABI1, and ABA genes, which are involved in salt stress signaling pathways. Our findings demonstrated that ChiMYB is essential for plant responses to salt stress, and it may have great potential for the improvement of salt tolerance in crops.

Genes encoding Δ(8)-sphingolipid desaturase from various plants: identification, biochemical functions, and evolution

∆(8)-sphingolipid desaturase catalyzes the C8 desaturation of a long chain base, which is the characteristic structure of various complex sphingolipids. The genes of 20 ∆(8)-sphingolipid desaturases from 12 plants were identified and functionally detected by using Saccharomyces cerevisiae system to elucidate the relationship between the biochemical function and evolution of this enzyme. Results showed that the 20 genes all can encode a functional ∆(8)-sphingolipid desaturase, which catalyzes different ratios of two products, namely, 8(Z) and 8(E)-C18-phytosphingenine. The coded enzymes could be divided into two groups on the basis of biochemical functions: ∆(8)-sphingolipid desaturase with a preference for an E-isomer product and ∆(8)-sphingolipid desaturase with a preference for a Z-isomer product. The conversion rate of the latter was generally lower than that of the former. Phylogenetic analysis revealed that the 20 desaturases could also be clustered into two groups, and this grouping is consistent with that of the biochemical functions. Thus, the biochemical function of ∆(8)-sphingolipid desaturase is correlated with its evolution. The two groups of ∆(8)-sphingolipid desaturases could arise from distinct ancestors in higher plants. However, they might have initially evolved from ∆(8)-sphingolipid desaturases in lower organisms, such as yeasts, which can produce E-isomer products only. Furthermore, almost all of the transgenic yeasts harboring ∆(8)-sphingolipid desaturase genes exhibit an improvement in aluminum tolerance. Our study provided new insights into the biochemical function and evolution of ∆(8)-sphingolipid desaturases in plants.

[Influences of genetic and environmental factors on smoking related behaviors among male twin adults in China]

OBJECTIVE

To analyze the influences of genetic and environmental factors on smoking behavior, smoking cessation and onset age of smoking less than 20 years in male twin adults.

METHODS

A face-to-face questionnaire was conducted to collect data from 6 458 pair male twins aged ≥25 years registered in 9 provinces(municipality)in China. The heritability of three smoking related behaviors were calculated by using structural equation models.

RESULTS

The ACE models were the best models of the three dimensions of smoking, i.e. smoking behavior, smoking cessation and onset age of smoking less than 20 years for male twins, and the corresponding heritability of these behaviors were 0.26(0.19-0.34), 0.27(0.19-0.37)and 0.05(0.00-0.14), respectively. When adjusted for area and age, the heritability of these three behaviors were 0.26(0.19-0.34), 0.31(0.00-0.74)and 0.05(0.00-0.14), respectively.

CONCLUSIONS

All the three smoking related behaviors were affected by genetic factors, but environment factors had more effect on them. For smoking cessation, the heritability was highest, but the influence of environmental factors was lowest. Meanwhile, for onset age of smoking, the influence of environmental factors was highest.

DPTEdb, an integrative database of transposable elements in dioecious plants

Dioecious plants usually harbor ‘young’ sex chromosomes, providing an opportunity to study the early stages of sex chromosome evolution. Transposable elements (TEs) are mobile DNA elements frequently found in plants and are suggested to play important roles in plant sex chromosome evolution. The genomes of several dioecious plants have been sequenced, offering an opportunity to annotate and mine the TE data. However, comprehensive and unified annotation of TEs in these dioecious plants is still lacking. In this study, we constructed a dioecious plant transposable element database (DPTEdb). DPTEdb is a specific, comprehensive and unified relational database and web interface. We used a combination of de novo, structure-based and homology-based approaches to identify TEs from the genome assemblies of previously published data, as well as our own. The database currently integrates eight dioecious plant species and a total of 31 340 TEs along with classification information. DPTEdb provides user-friendly web interfaces to browse, search and download the TE sequences in the database. Users can also use tools, including BLAST, GetORF, HMMER, Cut sequence and JBrowse, to analyze TE data. Given the role of TEs in plant sex chromosome evolution, the database will contribute to the investigation of TEs in structural, functional and evolutionary dynamics of the genome of dioecious plants. In addition, the database will supplement the research of sex diversification and sex chromosome evolution of dioecious plants.

Database URL: http://genedenovoweb.ticp.net:81/DPTEdb/index.php

Repetitive sequences and epigenetic modification: inseparable partners play important roles in the evolution of plant sex chromosomes

The present review discusses the roles of repetitive sequences played in plant sex chromosome evolution, and highlights epigenetic modification as potential mechanism of repetitive sequences involved in sex chromosome evolution. Sex determination in plants is mostly based on sex chromosomes. Classic theory proposes that sex chromosomes evolve from a specific pair of autosomes with emergence of a sex-determining gene(s). Subsequently, the newly formed sex chromosomes stop recombination in a small region around the sex-determining locus, and over time, the non-recombining region expands to almost all parts of the sex chromosomes. Accumulation of repetitive sequences, mostly transposable elements and tandem repeats, is a conspicuous feature of the non-recombining region of the Y chromosome, even in primitive one. Repetitive sequences may play multiple roles in sex chromosome evolution, such as triggering heterochromatization and causing recombination suppression, leading to structural and morphological differentiation of sex chromosomes, and promoting Y chromosome degeneration and X chromosome dosage compensation. In this article, we review the current status of this field, and based on preliminary evidence, we posit that repetitive sequences are involved in sex chromosome evolution probably via epigenetic modification, such as DNA and histone methylation, with small interfering RNAs as the mediator.

Relationship between urinary protein changes in lupus nephritis and renal pathology

This study investigated the relationship between urinary protein excretion in lupus nephritis New Zealand black mice and renal pathology. A total of 328 lupus nephritis New Zealand black mice were established by a backcross hybridization method, and renal pathology was determined. The urinary protein excretion of the backcross mice over 24 h was compared and analyzed. Urinary protein excretion over 24 h differed significantly across different pathological types (1.9, 2.4, 2.9 and 4.9 g in types II, III, IV, and V, respectively) in the backcross mice (P < 0.05). Moreover, it correlated with pathology grade (r = 0.391, P = 0.0001) as well as activity index, chronic index, renal tubular interstitial activity index, and renal tubular interstitial lesions (P < 0.05) but not with vascular lesions (P = 0.683). Urinary protein excretion from lupus nephritis is closely associated with renal pathology. Urinary protein changes can be used to determine lupus nephritis pathology and have some clinical significance for treatment and prognosis.