Understanding genome-wide diversity,inbreeding,and the burden of accumulated deleterious mutations in small and isolated populations is essential for predicting and enhancing population persistence and resilience.Howe...Understanding genome-wide diversity,inbreeding,and the burden of accumulated deleterious mutations in small and isolated populations is essential for predicting and enhancing population persistence and resilience.However,these effects are rarely studied in limestone karst plants.Here,we re-sequenced the nuclear genomes of 62 individuals of the Begonia masoniana complex(B.liuyanii,B.longgangensis,B.masoniana and B.variegata)and investigated genomic divergence and genetic load for these four species.Our analyses revealed four distinct clusters corresponding to each species within the complex.Notably,there was only limited admixture between B.liuyanii and B.longgangensis occurring in overlapping geographic regions.All species experienced historical bottlenecks during the Pleistocene,which were likely caused by glacial climate fluctuations.We detected an asymmetric historical gene flow between group pairs within this timeframe,highlighting a distinctive pattern of interspecific divergence attributable to karst geographic isolation.We found that isolated populations of B.masoniana have limited gene flow,the smallest recent population size,the highest inbreeding coefficients,and the greatest accumulation of recessive deleterious mutations.These findings underscore the urgency to prioritize conservation efforts for these isolated population.This study is among the first to disentangle the genetic differentiation and specific demographic history of karst Begonia plants at the whole-genome level,shedding light on the potential risks associated with the accumulation of deleterious mutations over generations of inbreeding.Moreover,our findings may facilitate conservation planning by providing critical baseline genetic data and a better understanding of the historical events that have shaped current population structure of rare and endangered karst plants.展开更多
Endangered species generally have small populations with low genetic diversity and a high genetic load.Thuja sutchuenensis is an endangered conifer endemic to southwestern China.It was once considered extinct in the w...Endangered species generally have small populations with low genetic diversity and a high genetic load.Thuja sutchuenensis is an endangered conifer endemic to southwestern China.It was once considered extinct in the wild,but in 1999 was rediscovered.However,little is known about its genetic load.We collected 67 individuals from five wild,isolated T.sutchuenensis populations,and used 636,151 SNPs to analyze the level of genetic diversity and genetic load in T.sutchuenensis to delineate the conservation units of T.sutchuenensis,based on whole transcriptome sequencing data,as well as target capture sequencing data.We found that populations of T.sutchuenensis could be divided into three groups.These groups had low levels genetic diversity and were moderately genetically differentiated.Our findings also indicate that T.sutchuenensis suffered two severe bottlenecks around the Last Glaciation Period and Last Glacial Maximum.Among Thuja species,T.sutchuenensis presented the lowest genetic load and hence might have purged deleterious mutations efficiently through purifying selection.However,distribution of fitness effects analysis indicated a high extinction risk for T.sutchuenensis.Multiple lines of evidence identified three management units for T.sutchuenensis.Although T.sutchuenensis possesses a low genetic load,low genetic diversity,suboptimal fitness,and anthropogenic pressures all present an extinction risk for this rare conifer.This might also hold true for many endangered plant species in the mountains all over the world.展开更多
Soybean(Glycine max L.)is a protein and oil crop grown worldwide.Its fitness may be reduced by deleterious mutations,whose identification and purging is desirable for crop breeding.In the published whole-genome re-seq...Soybean(Glycine max L.)is a protein and oil crop grown worldwide.Its fitness may be reduced by deleterious mutations,whose identification and purging is desirable for crop breeding.In the published whole-genome re-sequenced data of 2214 soybean accessions,including 221 wild soybean,1132 landrace cultivars and 861 improved soybean lines,we identified 115,275 deleterious single-nucleotide polymorphisms(SNPs).Numbers of deleterious alleles increased from wild soybeans to landraces and decreased from landraces to modern improved lines.Genes in selective-sweep regions showed fewer deleterious mutations than the remaining genes.Deleterious mutations explained 4.3%-48%more phenotypic variation than randomly selected SNPs for resistance to soybean cyst nematode race 2(SCN2),soybean cyst nematode race 3(SCN3)and soybean mosaic virus race 3(SMV3).These findings illustrate how mutation load has shifted during soybean domestication,expansion and improvement and provide candidate sites for breeding out deleterious mutations in soybean by genome editing and/or conventional breeding focused on the selection of progeny with fewer deleterious alleles.展开更多
AIM:To identify the prevalence of hepatitis B e antigen (HBeAg) and to assess the association of hepatitis B virus (HBV) core promoter mutations and viral load in Indonesian patients.METHODS:Sixty-four patients with c...AIM:To identify the prevalence of hepatitis B e antigen (HBeAg) and to assess the association of hepatitis B virus (HBV) core promoter mutations and viral load in Indonesian patients.METHODS:Sixty-four patients with chronic hepatitis,65 with liver cirrhosis and 50 with hepatocellular carcinoma were included in this study.HBeAg and hepatitis B e antibody (HBeAb) tests were performed using enzyme-linked immunosorbent assay and the mutations were analyzed by sequencing.Viral load was measured by real-time polymerase chain reaction.RESULTS:Of 179 patients,108 (60.3%) were HBeAg(-) and 86 (79.6%) of these HBeAg(-) patients had been seroconverted.The A1896 mutation was not found in HBeAg(+) patients,however,this mutation was detected in 70.7% of HBeAg(-) patients.This mutation was frequently found when HBeAg was not expressed (87.7%),compared to that found in HBeAg seroconverted patients (65.1%).The A1899 mutation was also more prevalent in HBeAg(-) than in HBeAg(+) patients (P=0.004).The T1762/A1764 mutation was frequently found in both HBeAg(+) and HBeAg(-) patients,however,the prevalence of this mutation did not significantly differ among the two groups (P=0.054).In HBeAg(+) patients,the T1762/A1764 mutation was correlated with lower HBV DNA (P < 0.001).The A1899 mutation did not correlate with HBV DNA (P=0.609).In HBeAg(-) patients,the T1762/A1764 mutation alone was not correlated with HBV DNA (P=0.095),however,the presence of either the T1762/A1764 or A1896 mutations was associated with increased HBV DNA (P < 0.001).CONCLUSION:The percentage of HBeAg(-) patients is high in Indonesia,and most of the HBeAg(-) patients had been seroconverted.The A1896 mutation was most likely the major cause of HBeAg loss.The T1762/A1764 mutation alone was associated with lower viral loads in HBeAg(+) patients,but not in HBeAg(-) patients.展开更多
要为明确高密度互通立交行驶环境下,主线车流量对出入口区段驾驶人精神负荷间的影响,在重庆市内环快速路高密度互通立交群进行自然驾驶实车试验,使用Physiolab生理检测仪连续采集驾驶人在行驶过程中的心电数据,用于统计各驾驶人的心率...要为明确高密度互通立交行驶环境下,主线车流量对出入口区段驾驶人精神负荷间的影响,在重庆市内环快速路高密度互通立交群进行自然驾驶实车试验,使用Physiolab生理检测仪连续采集驾驶人在行驶过程中的心电数据,用于统计各驾驶人的心率指标变化情况。本次试验基于主成分分析法选择心率变异率指标RMSSD(root mean square of successive differences)、LFnorm(low frequency norm)、HFnorm(high frequency norm)、LF(low frequency)/HF(high frequency)以及心率突变率指标HRMR(heat ratemutation rate)作为驾驶人精神负荷的评价指标,记为主成分F 1和主成分F 2,并建立评价模型。结果表明:驾驶人在小净距立交出入口区段行驶时,立交主线车流量的大小会影响驾驶人的精神负荷;当驾驶人驶入立交主线时,三次模型对入口段车流量与主成分F 2的拟合效果最好,呈开口向上的三次曲线,曲线谷值点出现在2级流量水平处,模型显著;当驾驶人驶出立交主线时,一次线性模型对出口段车流量与主成分F 1的拟合效果最好,模型显著。展开更多
在移动边缘计算(MEC)中,计算卸载可以有效缓解资源受限和提高网络服务质量。以任务执行时延、终端能耗和边缘服务器负载率的联合优化为目标,提出面向时延和能耗联合优化的MEC计算卸载策略。构建多目标约束的成本优化模型,引入多变异算子...在移动边缘计算(MEC)中,计算卸载可以有效缓解资源受限和提高网络服务质量。以任务执行时延、终端能耗和边缘服务器负载率的联合优化为目标,提出面向时延和能耗联合优化的MEC计算卸载策略。构建多目标约束的成本优化模型,引入多变异算子,以迭代关联概率更新变异算子,设计多变异差分进化(MDE)算法求解,实现计算卸载成本最优。为验证MDE算法的有效性,基于Autonomous Systems by Skitter公开数据集构建3个不同规模的实验网络,将MDE算法与随机计算卸载算法、能量优化计算卸载算法、多目标贪婪计算卸载等算法进行对比分析,MDE算法的执行成功率、卸载成功率、服务器负载均衡性分别平均提升了13.23%,12.96%,29.37%,MDE算法能实现MEC中高效、稳定的计算卸载。展开更多
基金supported by Key-Area Research and Development Program of Guangdong Province(Grant No.2022B1111230001)National Natural Science Foundation of China(31860048).
文摘Understanding genome-wide diversity,inbreeding,and the burden of accumulated deleterious mutations in small and isolated populations is essential for predicting and enhancing population persistence and resilience.However,these effects are rarely studied in limestone karst plants.Here,we re-sequenced the nuclear genomes of 62 individuals of the Begonia masoniana complex(B.liuyanii,B.longgangensis,B.masoniana and B.variegata)and investigated genomic divergence and genetic load for these four species.Our analyses revealed four distinct clusters corresponding to each species within the complex.Notably,there was only limited admixture between B.liuyanii and B.longgangensis occurring in overlapping geographic regions.All species experienced historical bottlenecks during the Pleistocene,which were likely caused by glacial climate fluctuations.We detected an asymmetric historical gene flow between group pairs within this timeframe,highlighting a distinctive pattern of interspecific divergence attributable to karst geographic isolation.We found that isolated populations of B.masoniana have limited gene flow,the smallest recent population size,the highest inbreeding coefficients,and the greatest accumulation of recessive deleterious mutations.These findings underscore the urgency to prioritize conservation efforts for these isolated population.This study is among the first to disentangle the genetic differentiation and specific demographic history of karst Begonia plants at the whole-genome level,shedding light on the potential risks associated with the accumulation of deleterious mutations over generations of inbreeding.Moreover,our findings may facilitate conservation planning by providing critical baseline genetic data and a better understanding of the historical events that have shaped current population structure of rare and endangered karst plants.
基金This study was financially supported by National Natural Science Foundation of China(grant No.U20A2080,31622015)the Institutional Research Fund from Sichuan University(2021SCUNL102)Fundamental Research Fund for the Central Universities of China(SCU 2021D006,SCU 2022D003).
文摘Endangered species generally have small populations with low genetic diversity and a high genetic load.Thuja sutchuenensis is an endangered conifer endemic to southwestern China.It was once considered extinct in the wild,but in 1999 was rediscovered.However,little is known about its genetic load.We collected 67 individuals from five wild,isolated T.sutchuenensis populations,and used 636,151 SNPs to analyze the level of genetic diversity and genetic load in T.sutchuenensis to delineate the conservation units of T.sutchuenensis,based on whole transcriptome sequencing data,as well as target capture sequencing data.We found that populations of T.sutchuenensis could be divided into three groups.These groups had low levels genetic diversity and were moderately genetically differentiated.Our findings also indicate that T.sutchuenensis suffered two severe bottlenecks around the Last Glaciation Period and Last Glacial Maximum.Among Thuja species,T.sutchuenensis presented the lowest genetic load and hence might have purged deleterious mutations efficiently through purifying selection.However,distribution of fitness effects analysis indicated a high extinction risk for T.sutchuenensis.Multiple lines of evidence identified three management units for T.sutchuenensis.Although T.sutchuenensis possesses a low genetic load,low genetic diversity,suboptimal fitness,and anthropogenic pressures all present an extinction risk for this rare conifer.This might also hold true for many endangered plant species in the mountains all over the world.
基金supported by the National Natural Science Foundation of China(32172002,32070242)Shenzhen Science and Technology Program(KQTD2016113010482651)+1 种基金Special Funds for Science Technology Innovation and Industrial Development of Shenzhen Dapeng New District(RC201901-05,PT201901-19)the USDA Agricultural Research Service Research Participation Program of the Oak Ridge Institute for Science and Education(ORISE)(DE-AC05-06OR23100).
文摘Soybean(Glycine max L.)is a protein and oil crop grown worldwide.Its fitness may be reduced by deleterious mutations,whose identification and purging is desirable for crop breeding.In the published whole-genome re-sequenced data of 2214 soybean accessions,including 221 wild soybean,1132 landrace cultivars and 861 improved soybean lines,we identified 115,275 deleterious single-nucleotide polymorphisms(SNPs).Numbers of deleterious alleles increased from wild soybeans to landraces and decreased from landraces to modern improved lines.Genes in selective-sweep regions showed fewer deleterious mutations than the remaining genes.Deleterious mutations explained 4.3%-48%more phenotypic variation than randomly selected SNPs for resistance to soybean cyst nematode race 2(SCN2),soybean cyst nematode race 3(SCN3)and soybean mosaic virus race 3(SMV3).These findings illustrate how mutation load has shifted during soybean domestication,expansion and improvement and provide candidate sites for breeding out deleterious mutations in soybean by genome editing and/or conventional breeding focused on the selection of progeny with fewer deleterious alleles.
基金Supported by MRIN Funding (Budget No.cc041/2009)
文摘AIM:To identify the prevalence of hepatitis B e antigen (HBeAg) and to assess the association of hepatitis B virus (HBV) core promoter mutations and viral load in Indonesian patients.METHODS:Sixty-four patients with chronic hepatitis,65 with liver cirrhosis and 50 with hepatocellular carcinoma were included in this study.HBeAg and hepatitis B e antibody (HBeAb) tests were performed using enzyme-linked immunosorbent assay and the mutations were analyzed by sequencing.Viral load was measured by real-time polymerase chain reaction.RESULTS:Of 179 patients,108 (60.3%) were HBeAg(-) and 86 (79.6%) of these HBeAg(-) patients had been seroconverted.The A1896 mutation was not found in HBeAg(+) patients,however,this mutation was detected in 70.7% of HBeAg(-) patients.This mutation was frequently found when HBeAg was not expressed (87.7%),compared to that found in HBeAg seroconverted patients (65.1%).The A1899 mutation was also more prevalent in HBeAg(-) than in HBeAg(+) patients (P=0.004).The T1762/A1764 mutation was frequently found in both HBeAg(+) and HBeAg(-) patients,however,the prevalence of this mutation did not significantly differ among the two groups (P=0.054).In HBeAg(+) patients,the T1762/A1764 mutation was correlated with lower HBV DNA (P < 0.001).The A1899 mutation did not correlate with HBV DNA (P=0.609).In HBeAg(-) patients,the T1762/A1764 mutation alone was not correlated with HBV DNA (P=0.095),however,the presence of either the T1762/A1764 or A1896 mutations was associated with increased HBV DNA (P < 0.001).CONCLUSION:The percentage of HBeAg(-) patients is high in Indonesia,and most of the HBeAg(-) patients had been seroconverted.The A1896 mutation was most likely the major cause of HBeAg loss.The T1762/A1764 mutation alone was associated with lower viral loads in HBeAg(+) patients,but not in HBeAg(-) patients.
文摘要为明确高密度互通立交行驶环境下,主线车流量对出入口区段驾驶人精神负荷间的影响,在重庆市内环快速路高密度互通立交群进行自然驾驶实车试验,使用Physiolab生理检测仪连续采集驾驶人在行驶过程中的心电数据,用于统计各驾驶人的心率指标变化情况。本次试验基于主成分分析法选择心率变异率指标RMSSD(root mean square of successive differences)、LFnorm(low frequency norm)、HFnorm(high frequency norm)、LF(low frequency)/HF(high frequency)以及心率突变率指标HRMR(heat ratemutation rate)作为驾驶人精神负荷的评价指标,记为主成分F 1和主成分F 2,并建立评价模型。结果表明:驾驶人在小净距立交出入口区段行驶时,立交主线车流量的大小会影响驾驶人的精神负荷;当驾驶人驶入立交主线时,三次模型对入口段车流量与主成分F 2的拟合效果最好,呈开口向上的三次曲线,曲线谷值点出现在2级流量水平处,模型显著;当驾驶人驶出立交主线时,一次线性模型对出口段车流量与主成分F 1的拟合效果最好,模型显著。
文摘在移动边缘计算(MEC)中,计算卸载可以有效缓解资源受限和提高网络服务质量。以任务执行时延、终端能耗和边缘服务器负载率的联合优化为目标,提出面向时延和能耗联合优化的MEC计算卸载策略。构建多目标约束的成本优化模型,引入多变异算子,以迭代关联概率更新变异算子,设计多变异差分进化(MDE)算法求解,实现计算卸载成本最优。为验证MDE算法的有效性,基于Autonomous Systems by Skitter公开数据集构建3个不同规模的实验网络,将MDE算法与随机计算卸载算法、能量优化计算卸载算法、多目标贪婪计算卸载等算法进行对比分析,MDE算法的执行成功率、卸载成功率、服务器负载均衡性分别平均提升了13.23%,12.96%,29.37%,MDE算法能实现MEC中高效、稳定的计算卸载。
