Common mtDNA variations at C5178a and A249d/T6392C/G10310A decrease the risk of severe COVID-19 in a Han Chinese population from Central China

Background:Mitochondria have been shown to play vital roles during severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)infection and coronavirus disease 2019(COVID-19)development.Currently,it is unclear whether mitochondrial DNA(mtDNA)variants,which define mtDNA haplogroups and determine oxidative phosphorylation performance and reactive oxygen species production,are associated with COVID-19 risk.Methods:A population-based case-control study was conducted to compare the distribution of mtDNA variations defining mtDNA haplogroups between healthy controls(n=615)and COVID-19 patients(n=536).COVID-19 patients were diagnosed based on molecular diagnostics of the viral genome by qPCR and chest X-ray or computed tomography scanning.The exclusion criteria for the healthy controls were any history of disease in the month preceding the study assessment.MtDNA variants defining mtDNA haplogroups were identified by PCR-RFLPs and HVS-I sequencing and determined based on mtDNA phylogenetic analysis using Mitomap Phylogeny.Student’s t-test was used for continuous variables,and Pearson’s chi-squared test or Fisher’s exact test was used for categorical variables.To assess the independent effect of each mtDNA variant defining mtDNA haplogroups,multivariate logistic regression analyses were performed to calculate the odds ratios(OR)and 95%confidence intervals(CI)with adjustments for possible confounding factors of age,sex,smoking and diseases(including cardiopulmonary diseases,diabetes,obesity and hypertension)as determined through clinical and radiographic examinations.Results:Multivariate logistic regression analyses revealed that the most common investigated mtDNA variations(>10%in the control population)at C5178 a(in NADH dehydrogenase subunit 2 gene,ND2)and A249 d(in the displacement loop region,D-loop)/T6392 C(in cytochrome c oxidase I gene,CO1)/G10310 A(in ND3)were associated with a reduced risk of severe COVID-19(OR=0.590,95%CI 0.428–0.814,P=0.001;and OR=0.654,95%CI 0.457–0.936,P=0.020,respectively),while A4833 G(ND2),A4715 G(ND2),T3394 C(ND1)and G5417 A(ND2)/C16257 a(D-loop)/C16261 T(D-loop)were related to an increased risk of severe COVID-19(OR=2.336,95%CI 1.179–4.608,P=0.015;OR=2.033,95%CI 1.242–3.322,P=0.005;OR=3.040,95%CI 1.522–6.061,P=0.002;and OR=2.890,95%CI 1.199–6.993,P=0.018,respectively).Conclusions:This is the first study to explore the association of mtDNA variants with individual’s risk of developing severe COVID-19.Based on the case–control study,we concluded that the common mtDNA variants at C5178 a and A249 d/T6392 C/G10310 A might contribute to an individual’s resistance to developing severe COVID-19,whereas A4833 G,A4715 G,T3394 C and G5417 A/C16257 a/C16261 T might increase an individual’s risk of developing severe COVID-19.

The genome basis and whole-genome patterns of DNA variation of a major oil crop-oil palm Dura

Subject Code:C01The United Nations estimates that world population will increase to 11.2billion in the year 2100.Vegetative oil that serves as one of the major energy resources is essential to feeding human beings.Oil palm(Elaeis guineensis Jacq,Elaeis from ancient Greek,meaning'oil')produces more than 13times the yield of oil/year/hectare of soybean,one major human annual oil crop.In consequence,it represents a

Somatic CDKN2A copy number variations are associated with the prognosis of esophageal squamous cell dysplasia

Background:Somatic copy number variations(SCNVs)in the CDKN2A gene are among the most frequent events in the dysplasia-carcinoma sequence of esophageal squamous cell carcinoma.However,whether CDKN2A SCNVs are useful biomarkers for the risk stratification and management of patients with esophageal squamous cell dysplasia(ESCdys)is unknown.This study aimed to investigate the characteristics and prognostic value of CDKN2A SCNVs in patients with mild or moderate(m/M)ESCdys.Methods:This study conducted a prospective multicenter study of 205 patients with a baseline diagnosis of m/M ESCdys in five high-risk regions of China(Ci County,Hebei Province;Yanting,Sichuan Province;Linzhou,Henan Province;Yangzhong,Jiangsu Province;and Feicheng,Shandong Province)from 2005 to 2019.Genomic DNA was extracted from paraffin biopsy samples and paired peripheral white blood cells from patients,and a quantitative polymerase chain reaction assay,P16-Light,was used to detect CDKN2A copy number.The cumulative regression and progression rates of ESCdys were evaluated using competing risk models.Results:A total of 205 patients with baseline m/M ESCdys were enrolled.The proportion of ESCdys regression was significantly lower in the CDKN2A deletion cohort than in the diploid and amplification cohorts(18.8%[13/69]vs.35.0%[28/80]vs.51.8%[29/56],P<0.001).In the univariable competing risk analysis,the cumulative regression rate was statistically significantly lower(P=0.008),while the cumulative progression rate was higher(P=0.017)in ESCdys patients with CDKN2A deletion than in those without CDKN2A deletion.CDKN2A deletion was also an independent predictor of prognosis in ESCdys(P=0.004)in the multivariable analysis.Conclusion:The results indicated that CDKN2A SCNVs are associated with the prognosis of ESCdys and may serve as potential biomarkers for risk stratification.

Clinical assessment and genomic landscape of a consanguineous family with three Kallmann syndrome descendants

Although some genes that cause Kallmann syndrome （KS） have been identified by traditional linkage analysis and candidate gene techniques, the syndrome＇s molecular etiology in the majority of patients remains poorly understood. In this paper, we present the clinical assessments of a consanguineous Hart Chinese family with three KS descendants. To understand the molecular etiology of KS from a genome-wide perspective, we investigated the genome-wide profile of structural variation in this family using the Affymetrix Genome-Wide Human SNP Array 6.0 platform. The results revealed that the three affected individuals had common copy number variants （microdeletions） on chromosomes lp21.1, 2q32.2, 8q21.13, 14q21.2 and Xp22.31. Moreover, the copy number variants on Xp22.31 were located in the intron of KAL 1, which causes X-linked KS. Two PCR assays were performed on these regions to validate the results obtained using the chips. In addition, genomic microdeletions in this region were verified in one of 29 Han Chinese sporadic KS cases and one of four other family cases, but not in 26 Han Chinese sporadic normosmic idiopathic hypogonadotropic hypogonadism cases and 100 unrelated Han Chinese normal controls. Our results provide a novel insight into the relative contributions of certain copy number variants to KS＇s molecular etiology and generate a list of interesting candidate regions for further studies.

Phylogenetic biogeography and taxonomy of disjunctly distributed bryophytes

More than 200 research papers on the molecular phylogeny and phylogenetic biogeography ofbryophytes have been published since the beginning of this millenium. These papers corroborated assumptions of a complex genetic structure of morphologically circumscribed bryophytes, and raised reservations against many morphologically justified species concepts, especially within the mosses. However, many molecular studies allowed for corrections and modifications of morphological classification schemes. Several studies reported that the phylogenetic structure of disjunctly distributed bryophyte species reflects their geographical ranges rather than morphological disparities. Molecular data led to new appraisals of distribution ranges and allowed for the reconstruction of refugia and migration routes. Intercontinental ranges of bryophytes are often caused by dispersal rather than geographical vicariance. Many distribution patterns of disjunct bryophytes are likely formed by processes such as short distance dispersal, rare long distance dispersal events, extinction, recolonization and diversification.

Genome-wide DNA methylation variations upon engineered nanomaterials and their implications in nanosafety assessment

Subject Code:B07With the support by the National Natural Science Foundation of China,the National'973'Program,and the Strategic Priority Research Program of the Chinese Academy of Sciences,the research team led by Prof.Liu Sijin(刘思金)at the State Key Laboratory of Environmental Chemistry and Ecotoxicology,Research Center for Eco-Environmental Sciences,Chinese Academy of Sciences,uncovered the

Strategic Conservation of Orchard Germplasm Based on Indigenous Knowledge and Genetic Diversity:a Case Study of Sour Orange Populations in China

To effectively conserve sour orange （Citrus aurantium L.） germplasm on two islands at the estuary of the Yangtze River in China, we estimated genetic variation and relationships of the known parental trees and their proposed descendents （young trees） using the fingerprints of random amplified polymorphic DNA （RAPD）. Results based on RAPD analyses showed considerable genetic diversity in the parental populations （He = 0.202）. The overall populations including the parental and young trees showed slightly higher genetic diversity （He = 0.298） than the parents, with about 10% variation between populations. An unweighted pair group method with arithmetic mean analysis dendrogram based on cluster analysis of the Jaccard similarity among individuals demonstrated a more complicated relationship of the parental and young trees from the two islands, although the young trees showed a clear association with parental trees. This indicates a significant contribution of parental trees in establishing the sour orange populations on the two islands. According to farmers＇ knowledge, conservation of only one or two parental trees would be sufficient because they believed that the whole populations were generated from a single mother tree. However, this study suggests that preserving most parental trees and some selected young trees with distant genetic relationships should be an effective conservation strategy for sour orange germplasm on the two islands.