Apolipoprotein D(ApoD),a member of the lipocalin superfamily of proteins,is involved in lipid transport and stress resistance.Whereas only a single copy of the ApoD gene is found in humans and some other vertebrates,t...Apolipoprotein D(ApoD),a member of the lipocalin superfamily of proteins,is involved in lipid transport and stress resistance.Whereas only a single copy of the ApoD gene is found in humans and some other vertebrates,there are typically several ApoD-like genes in insects.To date,there have been relatively few studies that have examined the evolution and functional differentiation of ApoD-like genes in insects,particularly hemi-metabolous insects.In this study,we identified 10 ApoD-like genes(NlApoD1−10)with distinct spatiotemporal expression patterns in Nilaparvata lugens(BPH),which is an important pest of rice.NlApoD1−10 were found to be distributed on 3 chromosomes in a tandem array of NlApoD1/2,NlApoD3−5,and NlApoD7/8,and show sequence and gene structural divergence in the coding regions,indicating that multiple gene duplication events occurred during evolution.Phylogenetic analysis revealed that NlApoD1−10 can be clustered into 5 clades,with NlApoD3−5 and NlApoD7/8 potentially evolving exclusively in the Delphacidae family.Functional screening using an RNA interference approach revealed that only NlApoD2 was essential for BPH development and survival,whereas NlApoD4/5 are highly expressed in testes,and might play roles in reproduction.Moreover,stress response analysis revealed that NlApoD3−5/9,NlApoD3−5,and NlApoD9 were up-regulated after treatment with lipopolysaccharide,H2O2,and ultraviolet-C,respectively,indicating their potential roles in stress resistance.展开更多
A series of stringent non-pharmacological and pharmacological interventions were implemented to contain the pandemic but the pandemic continues.Moreover,vaccination breakthrough infection and reinfection in convalesce...A series of stringent non-pharmacological and pharmacological interventions were implemented to contain the pandemic but the pandemic continues.Moreover,vaccination breakthrough infection and reinfection in convalescent coronavirus disease 2019(COVID-19)cases have been reported.Further,severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)variants emerged with mutations in spike(S)gene,the target of most current vaccines.Importantly,the mutations exhibit a trend of immune escape from the vaccination.Herein the scientific question that if the vaccination drives genetic or antigenic drifts of SARS-CoV-2 remains elusive.We performed correlation analyses to uncover the impacts of wide vaccination on epidemiological characteristics of COVID-19.In addition,we investigated the evolutionary dynamics and genetic diversity of SARS-CoV-2 under immune pressure by utilizing the Bayesian phylodynamic inferences and the lineage entropy calculation respectively.We found that vaccination coverage was negatively related to the infections,severe cases,and deaths of COVID-19 respectively.With the increasing vaccination coverage,the lineage diversity of SARS-CoV-2 dampened,but the rapid mutation rates of the S gene were identified,and the vaccination could be one of the explanations for driving mutations in S gene.Moreover,new epidemics resurged in several countries with high vaccination coverage,questioning their current pandemic control strategies.Hence,integrated vaccination and non-pharmacological interventions are critical to control the pandemic.Furthermore,novel vaccine preparation should enhance its capabilities to curb both disease severity and infection possibility.展开更多
An ancient genome duplication (PPP1) that predates divergence of the cereals has recently been recognized. We report here another potentially older large-scale duplication (PPP2) event that predates monocot-dicot dive...An ancient genome duplication (PPP1) that predates divergence of the cereals has recently been recognized. We report here another potentially older large-scale duplication (PPP2) event that predates monocot-dicot divergence in the genome of rice (Oryza sativa L.), as inferred from the age distribution of pairs of duplicate genes based on recent genome data for rice. Our results suggest that paleopolyploidy was widespread and played an important role in the evolution of rice.展开更多
This study compares results on reconstructing the ancestral state of characters and ancestral areas of distribution in Cornaceae to gain insights into the impact of using different analytical methods. Ancestral charac...This study compares results on reconstructing the ancestral state of characters and ancestral areas of distribution in Cornaceae to gain insights into the impact of using different analytical methods. Ancestral charac-ter state reconstructions were compared among three methods (parsimony, maximum likelihood, and stochastic character mapping) using MESQUITE and a full Bayesian method in BAYESTRAITS and inferences of ancestral area distribution were compared between the parsimony-based dispersal-vicariance analysis (DIVA) and a newly developed maximum likelihood (ML) method. Results indicated that among the six inflorescence and fruit char-acters examined, "perfect" binary characters (no homoplasy, no polymorphism within terminals, and no missing data) are little affected by choice of method, while homoplasious characters and missing data are sensitive to methods used. Ancestral areas at deep nodes of the phylogeny are substantially different between DIVA and ML and strikingly different between analyses including and excluding fossils at three deepest nodes. These results, while raising caution in making conclusions on trait evolution and historical biogeography using conventional methods, demonstrate a limitation in our current understanding of character evolution and biogeography. The biogeographic history favored by the ML analyses including fossils suggested the origin and early radiation of Cornus likely occurred in the late Cretaceous and earliest Tertiary in Europe and intercontinental disjunctions in three lineages involved movements across the North Atlantic Land Bridge (BLB) in the early and mid Tertiary. This result is congruent with the role of NALB for post-Eocene migration and in connecting tropical floras in North America and Africa, and in eastern Asia and South America. However, alternative hypotheses with an origin in eastern Asia and early Trans-Beringia migrations of the genus cannot be ruled out.展开更多
基金This work was supported by the Natural Science Foundation of Zhejiang Province(LQ22C140001)the National Natural Science Foundation of China(32230086).
文摘Apolipoprotein D(ApoD),a member of the lipocalin superfamily of proteins,is involved in lipid transport and stress resistance.Whereas only a single copy of the ApoD gene is found in humans and some other vertebrates,there are typically several ApoD-like genes in insects.To date,there have been relatively few studies that have examined the evolution and functional differentiation of ApoD-like genes in insects,particularly hemi-metabolous insects.In this study,we identified 10 ApoD-like genes(NlApoD1−10)with distinct spatiotemporal expression patterns in Nilaparvata lugens(BPH),which is an important pest of rice.NlApoD1−10 were found to be distributed on 3 chromosomes in a tandem array of NlApoD1/2,NlApoD3−5,and NlApoD7/8,and show sequence and gene structural divergence in the coding regions,indicating that multiple gene duplication events occurred during evolution.Phylogenetic analysis revealed that NlApoD1−10 can be clustered into 5 clades,with NlApoD3−5 and NlApoD7/8 potentially evolving exclusively in the Delphacidae family.Functional screening using an RNA interference approach revealed that only NlApoD2 was essential for BPH development and survival,whereas NlApoD4/5 are highly expressed in testes,and might play roles in reproduction.Moreover,stress response analysis revealed that NlApoD3−5/9,NlApoD3−5,and NlApoD9 were up-regulated after treatment with lipopolysaccharide,H2O2,and ultraviolet-C,respectively,indicating their potential roles in stress resistance.
基金We thank the important work of SARS-CoV-2 genome data producers globally and especially the COVID-19 genomics UK(COG-UK)consortium contributing sequence data to the GISAID database.This work was supported by the Beijing Natural Science Foundation(M22029)National Key R&D Program of China(2021YFC2301300)+5 种基金Strategic Priority Research Program of the Chinese Academy of Sciences(CAS)(XDB29010102)and National Natural Science Foundation of China(NSFC)(82161148010)J.Y.is supported by Special Program of China Postdoctoral Science Foundation(2020T130123ZX)Y.B.is supported by the NSFC Outstanding Young Scholars(31822055)Youth Innovation Promotion Association of CAS(Y2021034)Innovation Team and Talents Cultivation Program of National Administration of Traditional Chinese Medicine(ZYYCXTD-D-202208).
文摘A series of stringent non-pharmacological and pharmacological interventions were implemented to contain the pandemic but the pandemic continues.Moreover,vaccination breakthrough infection and reinfection in convalescent coronavirus disease 2019(COVID-19)cases have been reported.Further,severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)variants emerged with mutations in spike(S)gene,the target of most current vaccines.Importantly,the mutations exhibit a trend of immune escape from the vaccination.Herein the scientific question that if the vaccination drives genetic or antigenic drifts of SARS-CoV-2 remains elusive.We performed correlation analyses to uncover the impacts of wide vaccination on epidemiological characteristics of COVID-19.In addition,we investigated the evolutionary dynamics and genetic diversity of SARS-CoV-2 under immune pressure by utilizing the Bayesian phylodynamic inferences and the lineage entropy calculation respectively.We found that vaccination coverage was negatively related to the infections,severe cases,and deaths of COVID-19 respectively.With the increasing vaccination coverage,the lineage diversity of SARS-CoV-2 dampened,but the rapid mutation rates of the S gene were identified,and the vaccination could be one of the explanations for driving mutations in S gene.Moreover,new epidemics resurged in several countries with high vaccination coverage,questioning their current pandemic control strategies.Hence,integrated vaccination and non-pharmacological interventions are critical to control the pandemic.Furthermore,novel vaccine preparation should enhance its capabilities to curb both disease severity and infection possibility.
文摘An ancient genome duplication (PPP1) that predates divergence of the cereals has recently been recognized. We report here another potentially older large-scale duplication (PPP2) event that predates monocot-dicot divergence in the genome of rice (Oryza sativa L.), as inferred from the age distribution of pairs of duplicate genes based on recent genome data for rice. Our results suggest that paleopolyploidy was widespread and played an important role in the evolution of rice.
文摘This study compares results on reconstructing the ancestral state of characters and ancestral areas of distribution in Cornaceae to gain insights into the impact of using different analytical methods. Ancestral charac-ter state reconstructions were compared among three methods (parsimony, maximum likelihood, and stochastic character mapping) using MESQUITE and a full Bayesian method in BAYESTRAITS and inferences of ancestral area distribution were compared between the parsimony-based dispersal-vicariance analysis (DIVA) and a newly developed maximum likelihood (ML) method. Results indicated that among the six inflorescence and fruit char-acters examined, "perfect" binary characters (no homoplasy, no polymorphism within terminals, and no missing data) are little affected by choice of method, while homoplasious characters and missing data are sensitive to methods used. Ancestral areas at deep nodes of the phylogeny are substantially different between DIVA and ML and strikingly different between analyses including and excluding fossils at three deepest nodes. These results, while raising caution in making conclusions on trait evolution and historical biogeography using conventional methods, demonstrate a limitation in our current understanding of character evolution and biogeography. The biogeographic history favored by the ML analyses including fossils suggested the origin and early radiation of Cornus likely occurred in the late Cretaceous and earliest Tertiary in Europe and intercontinental disjunctions in three lineages involved movements across the North Atlantic Land Bridge (BLB) in the early and mid Tertiary. This result is congruent with the role of NALB for post-Eocene migration and in connecting tropical floras in North America and Africa, and in eastern Asia and South America. However, alternative hypotheses with an origin in eastern Asia and early Trans-Beringia migrations of the genus cannot be ruled out.
