Dengue virus(DENV)is one of the most important arboviral pathogens in the tropics and subtropics,and nearly one-third of the world's population is at risk of infection.The transmission of DENV involves a sylvatic ...Dengue virus(DENV)is one of the most important arboviral pathogens in the tropics and subtropics,and nearly one-third of the world's population is at risk of infection.The transmission of DENV involves a sylvatic cycle between nonhuman primates(NHP)and Aedes genus mosquitoes,and an endemic cycle between human hosts and predominantly Aedes aegypti.DENV belongs to the genus Flavivirus of the family Flaviviridae and consists of four antigenically distinct serotypes(DENV-1-4).Phylogenetic analyses of DENV have revealed its origin,epidemiology,and the drivers that determine its molecular evolution in nature.This review discusses how phyloge-netic research has improved our understanding of DENV evolution and how it affects viral ecology and improved our ability to analyze and predict future DENV emergence.展开更多
Understanding the underlying mechanisms driving species assembly along elevational gradients is of great interest in ecology and biogeography.The Himalaya is one of the world’s hotspots of biodiversity,and the elevat...Understanding the underlying mechanisms driving species assembly along elevational gradients is of great interest in ecology and biogeography.The Himalaya is one of the world’s hotspots of biodiversity,and the elevational gradient of the central Himalaya in Nepal is one of the longest elevational gradients in the world.Mosses are important constituents of vegetation in the Himalaya,and knowledge of geographic patterns and ecological causes of phylogenetic structure of mosses along elevational gradients in the Himalaya is critical to understanding the assembly of plant diversity in general,and moss diversity in particular,in the Himalaya.Here,we investigate the relationships of phylogenetic structure metrics reflecting different evolutionary depths with elevation and climatic variables representing mean temperature and precipitation conditions,climate extremes,and climate seasonality for mosses distributed along an elevational gradient spanning about 5000 m in the central Himalaya,Nepal.For a given climatic variable,different metrics of phylogenetic structure show different spatial and climatic patterns,but all phylogenetic metrics standardized for species richness show that phylogenetic dispersion in moss assemblages tend to increase with increasing elevation and decreasing temperature.The standardized effect size of mean pairwise distance of moss assemblages shows a triphasic(zig-zag)pattern,which is generally consistent with the triphasic patterns previously found in angiosperms and ferns along the same elevational gradient.Our study shows that temperature-related variables and climate seasonality variables are more important drivers of phylogenetic dispersion in mosses in Nepal,compared with precipitation-related variables and climate extreme variables,respectively.展开更多
Inferring phylogenetic trees from molecular sequences is a cornerstone of evolutionary biology.Many standard phylogenetic methods(such as maximum-likelihood[ML])rely on explicit models of sequence evolution and thus o...Inferring phylogenetic trees from molecular sequences is a cornerstone of evolutionary biology.Many standard phylogenetic methods(such as maximum-likelihood[ML])rely on explicit models of sequence evolution and thus often suffer from model misspecification or inadequacy.The on-rising deep learning(DL)techniques offer a powerful alternative.Deep learning employs multi-layered artificial neural networks to progressively transform input data into more abstract and complex representations.DL methods can autonomously uncover meaningful patterns from data,thereby bypassing potential biases introduced by predefined features(Franklin,2005;Murphy,2012).Recent efforts have aimed to apply deep neural networks(DNNs)to phylogenetics,with a growing number of applications in tree reconstruction(Suvorov et al.,2020;Zou et al.,2020;Nesterenko et al.,2022;Smith and Hahn,2023;Wang et al.,2023),substitution model selection(Abadi et al.,2020;Burgstaller-Muehlbacher et al.,2023),and diversification rate inference(Voznica et al.,2022;Lajaaiti et al.,2023;Lambert et al.,2023).In phylogenetic tree reconstruction,PhyDL(Zou et al.,2020)and Tree_learning(Suvorov et al.,2020)are two notable DNN-based programs designed to infer unrooted quartet trees directly from alignments of four amino acid(AA)and DNA sequences,respectively.展开更多
A group of radiolarian fossils with a complete morphological gradient of increasing polarization are reported from upper Devonian successions in southwestern Tianshan, China. Specifically, the important transitional m...A group of radiolarian fossils with a complete morphological gradient of increasing polarization are reported from upper Devonian successions in southwestern Tianshan, China. Specifically, the important transitional mophotypes, Pylentonema transitorum sp. nov., Archocyrtium medium sp. nov. and Quadrapesus transitivus sp. nov, were found. Based on the fact that the new transitional radiolarian fossils resemble more closely to pylentonemids （cyrtoid nassellarians） than to entactinids （spumellarians） in morphology, they are assigned to pylentonemids. Pylentonemids share characters of both the Nassellaria （e.g., horned cephalis, basal opening with pylome） and Spumellaria （e.g., system of trabecular spicules）, and they are thus of evolutionary significance. The evolutionary trend from spumellarians to nassellarians is characterized by （1） internal spicule： from simple trabecular spicules to complicate components （A;Ir,II;D;V;Lr,Li;MB）; （2） polarization of the radiolarian tests due to rearrangment of spine, from radial to an axial symmetry; （3） the gradual formation of a basal opening （aperture, pylome, or podome）; and the transition from a pseudopylome, a primative pylome with a narrow margin on the outer shell, to a true pylome rimmed with a narrow, elevated impermite wall.展开更多
[Objective] This study aimed to explore the origin and evolution of poly- poids in Parakmeria Hu et Cheng through LEAFY gene clone and sequence analysis. [Method] In this study, LEAFY gene in Parakmeria species and it...[Objective] This study aimed to explore the origin and evolution of poly- poids in Parakmeria Hu et Cheng through LEAFY gene clone and sequence analysis. [Method] In this study, LEAFY gene in Parakmeria species and its relative genera was cloned and sequenced using molecular biology methods. With reference to LEAFY gene sequence published by NCBI, the origin pattern of polypoids in Parakmeria was explored and reasons for the distribution layout of different polypoids were analyzed through sequence alignment and phylogenetic analysis. [Result] Different Magnoliaceae species can be distinguished using the LEAFY gene, and there was a length polymorphism found in the 3＋ end of the LEAFY gene, which can be used to divide Magnoliaceae plants of different species or in different genera, thus of high application value. [Conclusion] Most Parakmeria tetraploids are produced by polyploidization of homologous chromosomes, while Parakmeria hexaploids are chiefly produced by both polyploidization of homologous chromosomes and heterologous hybridization.展开更多
The coat protein （CP） genes were cloned and sequenced from viral particles of 11 isolates of citrus tristeza virus （CTV） collected from wild citrus plants in China and 4 Chinese isolates from cultivated sweet oran...The coat protein （CP） genes were cloned and sequenced from viral particles of 11 isolates of citrus tristeza virus （CTV） collected from wild citrus plants in China and 4 Chinese isolates from cultivated sweet orange and pummelo varieties, respectively. By analyzing and comparing the nucleotide and amino acid sequences of CP genes, the 11 wild CTV isolates were found over 92% identical with 4 Chinese CTV isolates and 21 exotic CTV isolates from cultivated citrus. From 91 to 100% of the CTV CP gene sequences in wild type citrus plants were generally well conserved. Genetic evolution analysis indicated that the GC% of the CP gene was less than AT%, and more transition were found in the CP genes than transversion with the transition/transversion ratio ranging from 6.3 to 7.0 among species. The substitution frequency was the highest at the third codon, followed by the first and second codon. The ratio of non-synonymous mutations （du） to synonymous mutations （ds） was far lower than 1, suggesting that the CP gene might have experienced purifying selection in the evolution. Phylogenetic analysis revealed that the 11 CTV isolates in Chinese wild type citrus belonged to different phylogenetic clusters, and shared higher homology and closer relationships with other cultivated citrus CTV isolates from different countries, which indicated complicated genetic relationships among the CTV isolates. In addition, CTV isolates with similar biological characteristics usually located into the same clusters. Therefore, the conclusion was drawn that pathogenicity was critical to evolution and origin of CTV.展开更多
[Objectives]This study was conducted to clarify the species,occurrence and distribution characteristics of sugarcane rust pathogens in low-latitude plateau sugarcane rust areas of Yunnan Province and the phylogenetic ...[Objectives]This study was conducted to clarify the species,occurrence and distribution characteristics of sugarcane rust pathogens in low-latitude plateau sugarcane rust areas of Yunnan Province and the phylogenetic relationship between the pathogens and that between them and other rust fungi of the genus Puccinia.[Methods]Fifty seven sugarcane rust samples collected from the sugarcane areas of Baoshan,Lincang,Menghai,Menglian,Ximeng,Lancang and Wenshan in Yunnan were subjected to molecular identification.[Results]The four sugarcane rust samples from Haiyin1 hao in Menghai,Yunnan Province belonged to orange rust of sugarcane,and the pathogen was Puccinia kuehnii Butler.;and other 53 samples of sugarcane rust belonged to brown rust of sugarcane,and the pathogen was Puccinia melanocephala Syd.et P.Syd.The rDNA sequences of other rust fungi from the genus Puccinia were downloaded from GenBank and used for the construction of an NJ tree for systematic evolution analysis together with the sequences obtained in this study.The results showed that the four P.kuehnii sequences obtained in this study were clustered with Puccinia polysora(GenBank accession number:GU058024)into one group,and they were close genetically;the 53 P.melanocephala sequences were clustered with P.nakanishikii(GenBank accession number:GU058002),P.rufipes(GenBank accession number:AJ296545),Aecidium deutziae(GenBank accession number:KU309317)and P.coronata(GenBank accession number:DQ354526)into one group,and they had a close genetic relationship;and the genetic relationship of the two species of sugarcane rust fungi identified in this study was relatively distant.[Conclusions]This study provides a scientific basis for sugarcane rust epidemic prediction,disease resistance breeding,and precise prevention and control.展开更多
Hepatitis C virus(HCV)infection represents an important public health problem worldwide.Reduction of HCV morbidity and mortality is a current challenge owned to several viral and host factors.Virus molecular evolution...Hepatitis C virus(HCV)infection represents an important public health problem worldwide.Reduction of HCV morbidity and mortality is a current challenge owned to several viral and host factors.Virus molecular evolution plays an important role in HCV transmission,disease progression and therapy outcome.The high degree of genetic heterogeneity characteristic of HCV is a key element for the rapid adaptation of the intrahost viral population to different selection pressures(e.g.,host immune responses and antiviral therapy).HCV molecular evolution is shaped by different mechanisms including a high mutation rate,genetic bottlenecks,genetic drift,recombination,temporal variations and compartmentalization.These evolutionary processes constantly rearrange the composition of the HCV intrahost population in a staging manner.Remarkable advances in the understanding of the molecular mechanism controlling HCV replication have facilitated the development of a plethora of direct-acting antiviral agents against HCV.As a result,superior sustained viral responses have been attained.The rapidly evolving field of anti-HCV therapy is expected to broad its landscape even further with newer,more potent antivirals,bringing us one step closer to the interferon-free era.展开更多
China is one of the most diverse countries, which have developed 88 indigenous pig breeds. Several studies showed that pigs were independently domesticated in multiple regions of the world. The purpose of this study w...China is one of the most diverse countries, which have developed 88 indigenous pig breeds. Several studies showed that pigs were independently domesticated in multiple regions of the world. The purpose of this study was to investigate the origin and evolution of Chinese pigs using complete mitochondrial genomic sequences （mtDNA） from Asian and European domestic pigs and wild boars. Thirty primer pairs were designed to determine the mtDNA sequences of Xiang pig, Large White, Lantang, Jinhua and Pietrain. The phylogenetic status of Chinese native pigs was investigated by comparing the mtDNA sequences of complete coding regions and D-loop regions respectively amongst Asian breeds, European breeds and wild boars. The analyzed results by two cluster methods contributed to the same conclusion that all pigs were classified into two major groups, European dade and Asian clade. It revealed that Chinese pigs were only recently diverged from each other and distinctly different from European pigs. Berkshire was clustered with Asian pigs and Chinese pigs were involved in the development of Berkshire breeding. The Malaysian wild boar had distant genetic relationship with European and Asian pigs. Jinhua and Lanyu pigs had more nucleotide diversity with Chinese pigs although they all belonged to the Asian major clade. Chinese domestic pigs were clustered with wild boars in Yangtze River region and South China.展开更多
S-locus genes were cloned from three Brassica napus and three B. campestris lines by using PCR walking and homologuesequence methods. A phylogenetic gene tree was constructed based on the six cloned genes and fifty-on...S-locus genes were cloned from three Brassica napus and three B. campestris lines by using PCR walking and homologuesequence methods. A phylogenetic gene tree was constructed based on the six cloned genes and fifty-one previouslyreported SLG/SRK genes of Brassica and Raphanus. The SLGs from R. sativus were dispersed in the phylogenetic treeintermingling with SLG/SRKs from B. oleracea, B. napus and B. campestris. The SLG/SRK genes of classⅡclusteredindependently in one group. The SLG/SRK genes of classⅠshowed to be more divergent than classⅡgenes. Theseresults suggested that the divergence of classⅠand classⅡ should have occurred before the differentiation of thegenera Brassica and Raphanus. In addition, SLG and SRK of the same S haplotypes belonged to the same class. Itsuggested that class-Ⅰ and class-Ⅱ group divergence occurred first, and then SLG and SRK diverged. The three SC SRKgenes from B. napus and B. campestris were grouped into one cluster, displaying difference from the SC SLG of B.oleracea. These three SC SRK genes were close to SI SRK of SI1300, SI271 and guanyou in phylogenetic relationships.These results indicated that SC and SI genes diverged more recently. It is not clear yet whether the differentiation of SCand SI genes was earlier than the differentiation of Brassica and Raphanus. Studies based on more genes are necessaryfor a comprehensive elucidation of the phylogenetic relationships in Brassicaceae.展开更多
Cymbidium,which includes approximately 80 species,is one of the most ornamental and cultivated orchid genera.However,a lack of markers and sparse sampling have posed great challenges to resolving the phylogenetic rela...Cymbidium,which includes approximately 80 species,is one of the most ornamental and cultivated orchid genera.However,a lack of markers and sparse sampling have posed great challenges to resolving the phylogenetic relationships within the genus.In the present study,we reconstructed the phylogenetic relationships by utilizing one nuclear DNA(nrITS)and seven plastid genes(rbcL,trnS,trnG,matK,trnL,psbA,and atpI)from 70 species(varieties)in Cymbidium.We also examined the occurrence of phylogenetic conflict between nuclear(nrITS)and plastid loci and investigated how phylogenetic conflict bears on taxonomic classification within the genus.We found that phylogenetic conflict and low support values may be explained by hybridization and a lack of informative characteristics.Our results do not support previous classification of the subgenera and sections within Cymbidium.Discordance between gene trees and network analysis indicate that reticulate evolution occurred in the genus Cymbidium.Overall,our study indicates that Cymbidium has undergone a complex evolution.展开更多
Litsea,a non-monophyletic group of the tribe Laureae(Lauraceae),plays important roles in the tropical and subtropical forests of Asia,Australia,Central and North America,and the islands of the Pacific.However,intergen...Litsea,a non-monophyletic group of the tribe Laureae(Lauraceae),plays important roles in the tropical and subtropical forests of Asia,Australia,Central and North America,and the islands of the Pacific.However,intergeneric relationships between Litsea and Laurus,Lindera,Parasassafras and Sinosassafras of the tribe Laureae remain unresolved.In this study,we present phylogenetic analyses of seven newly sequenced Litsea plastomes,together with 47 Laureae plastomes obtained from public databases,representing six genera of the Laureae.Our results highlight two highly supported monophyletic groups of Litsea taxa.One is composed of 16 Litsea taxa and two Lindera taxa.The 18 plastomes of these taxa were further compared for their gene structure,codon usage,contraction and expansion of inverted repeats,sequence repeats,divergence hotspots,and gene evolution.The complete plastome size of newly sequenced taxa varied between 152,377 bp(Litsea auriculata)and 154,117 bp(Litsea pierrei).Seven of the 16 Litsea plastomes have a pair of insertions in the IRa(trnL-trnH)and IRb(ycf2)regions.The 18 plastomes of Litsea and Lindera taxa exhibit similar gene features,codon usage,oligonucleotide repeats,and inverted repeat dynamics.The codons with the highest frequency among these taxa favored A/T endings and each of these plastomes had nine divergence hotspots,which are located in the same regions.We also identified six protein coding genes(accD,ndhJ,rbcL,rpoC2,ycf1 and ycf2)under positive selection in Litsea;these genes may play important roles in adaptation of Litsea species to various environments.展开更多
基金National Key Research and Development Plan of China,Grant/Award Number:2018YFA0507202,2020YFC1200100 and 2021YFC2300200National Natural Science Foundation of China,Grant/Award Number:31825001,32188101,81730063,81961160737 and 82102389+5 种基金Provincial Innovation Team for the Prevention and Control of Highly Pathogenic Pathogens,Institute of Medical Biology,Chinese Academy of Medical Sciences,Grant/Award Number:202105AE160020Shenzhen San-Ming Project for Prevention and Research on Vector-borne Diseases,Grant/Award Number:SZSM201611064Shenzhen Science and Technology Project,Grant/Award Number:JSGG20191129144225464Tsinghua University Spring Breeze Fund,Grant/Award Number:2020Z99CFG017Young Elite Scientists Sponsorship Program,Grant/Award Number:2021QNRC001Yunnan Cheng Gong Expert Work-Station,Grant/Award Number:202005AF150034。
文摘Dengue virus(DENV)is one of the most important arboviral pathogens in the tropics and subtropics,and nearly one-third of the world's population is at risk of infection.The transmission of DENV involves a sylvatic cycle between nonhuman primates(NHP)and Aedes genus mosquitoes,and an endemic cycle between human hosts and predominantly Aedes aegypti.DENV belongs to the genus Flavivirus of the family Flaviviridae and consists of four antigenically distinct serotypes(DENV-1-4).Phylogenetic analyses of DENV have revealed its origin,epidemiology,and the drivers that determine its molecular evolution in nature.This review discusses how phyloge-netic research has improved our understanding of DENV evolution and how it affects viral ecology and improved our ability to analyze and predict future DENV emergence.
文摘Understanding the underlying mechanisms driving species assembly along elevational gradients is of great interest in ecology and biogeography.The Himalaya is one of the world’s hotspots of biodiversity,and the elevational gradient of the central Himalaya in Nepal is one of the longest elevational gradients in the world.Mosses are important constituents of vegetation in the Himalaya,and knowledge of geographic patterns and ecological causes of phylogenetic structure of mosses along elevational gradients in the Himalaya is critical to understanding the assembly of plant diversity in general,and moss diversity in particular,in the Himalaya.Here,we investigate the relationships of phylogenetic structure metrics reflecting different evolutionary depths with elevation and climatic variables representing mean temperature and precipitation conditions,climate extremes,and climate seasonality for mosses distributed along an elevational gradient spanning about 5000 m in the central Himalaya,Nepal.For a given climatic variable,different metrics of phylogenetic structure show different spatial and climatic patterns,but all phylogenetic metrics standardized for species richness show that phylogenetic dispersion in moss assemblages tend to increase with increasing elevation and decreasing temperature.The standardized effect size of mean pairwise distance of moss assemblages shows a triphasic(zig-zag)pattern,which is generally consistent with the triphasic patterns previously found in angiosperms and ferns along the same elevational gradient.Our study shows that temperature-related variables and climate seasonality variables are more important drivers of phylogenetic dispersion in mosses in Nepal,compared with precipitation-related variables and climate extreme variables,respectively.
基金supported by the National Key R&D Program of China(2022YFD1401600)the National Science Foundation for Distinguished Young Scholars of Zhejang Province,China(LR23C140001)supported by the Key Area Research and Development Program of Guangdong Province,China(2018B020205003 and 2020B0202090001).
文摘Inferring phylogenetic trees from molecular sequences is a cornerstone of evolutionary biology.Many standard phylogenetic methods(such as maximum-likelihood[ML])rely on explicit models of sequence evolution and thus often suffer from model misspecification or inadequacy.The on-rising deep learning(DL)techniques offer a powerful alternative.Deep learning employs multi-layered artificial neural networks to progressively transform input data into more abstract and complex representations.DL methods can autonomously uncover meaningful patterns from data,thereby bypassing potential biases introduced by predefined features(Franklin,2005;Murphy,2012).Recent efforts have aimed to apply deep neural networks(DNNs)to phylogenetics,with a growing number of applications in tree reconstruction(Suvorov et al.,2020;Zou et al.,2020;Nesterenko et al.,2022;Smith and Hahn,2023;Wang et al.,2023),substitution model selection(Abadi et al.,2020;Burgstaller-Muehlbacher et al.,2023),and diversification rate inference(Voznica et al.,2022;Lajaaiti et al.,2023;Lambert et al.,2023).In phylogenetic tree reconstruction,PhyDL(Zou et al.,2020)and Tree_learning(Suvorov et al.,2020)are two notable DNN-based programs designed to infer unrooted quartet trees directly from alignments of four amino acid(AA)and DNA sequences,respectively.
基金This work was supported by the National Nature Science Foundation of China(No.40232019).
文摘A group of radiolarian fossils with a complete morphological gradient of increasing polarization are reported from upper Devonian successions in southwestern Tianshan, China. Specifically, the important transitional mophotypes, Pylentonema transitorum sp. nov., Archocyrtium medium sp. nov. and Quadrapesus transitivus sp. nov, were found. Based on the fact that the new transitional radiolarian fossils resemble more closely to pylentonemids （cyrtoid nassellarians） than to entactinids （spumellarians） in morphology, they are assigned to pylentonemids. Pylentonemids share characters of both the Nassellaria （e.g., horned cephalis, basal opening with pylome） and Spumellaria （e.g., system of trabecular spicules）, and they are thus of evolutionary significance. The evolutionary trend from spumellarians to nassellarians is characterized by （1） internal spicule： from simple trabecular spicules to complicate components （A;Ir,II;D;V;Lr,Li;MB）; （2） polarization of the radiolarian tests due to rearrangment of spine, from radial to an axial symmetry; （3） the gradual formation of a basal opening （aperture, pylome, or podome）; and the transition from a pseudopylome, a primative pylome with a narrow margin on the outer shell, to a true pylome rimmed with a narrow, elevated impermite wall.
基金Supported by the National Natural Science Foundation of China(NSFC31160432)the Key Project of Department of Education,Yunnan Province(2011Z108)~~
文摘[Objective] This study aimed to explore the origin and evolution of poly- poids in Parakmeria Hu et Cheng through LEAFY gene clone and sequence analysis. [Method] In this study, LEAFY gene in Parakmeria species and its relative genera was cloned and sequenced using molecular biology methods. With reference to LEAFY gene sequence published by NCBI, the origin pattern of polypoids in Parakmeria was explored and reasons for the distribution layout of different polypoids were analyzed through sequence alignment and phylogenetic analysis. [Result] Different Magnoliaceae species can be distinguished using the LEAFY gene, and there was a length polymorphism found in the 3＋ end of the LEAFY gene, which can be used to divide Magnoliaceae plants of different species or in different genera, thus of high application value. [Conclusion] Most Parakmeria tetraploids are produced by polyploidization of homologous chromosomes, while Parakmeria hexaploids are chiefly produced by both polyploidization of homologous chromosomes and heterologous hybridization.
基金supported by the National Natural Science Foundation of China (30900977)the Key Project 210111 of Chinese Ministry of Education and Natural Science Foundation Project of CQ CSTC (2009BB1310)
文摘The coat protein （CP） genes were cloned and sequenced from viral particles of 11 isolates of citrus tristeza virus （CTV） collected from wild citrus plants in China and 4 Chinese isolates from cultivated sweet orange and pummelo varieties, respectively. By analyzing and comparing the nucleotide and amino acid sequences of CP genes, the 11 wild CTV isolates were found over 92% identical with 4 Chinese CTV isolates and 21 exotic CTV isolates from cultivated citrus. From 91 to 100% of the CTV CP gene sequences in wild type citrus plants were generally well conserved. Genetic evolution analysis indicated that the GC% of the CP gene was less than AT%, and more transition were found in the CP genes than transversion with the transition/transversion ratio ranging from 6.3 to 7.0 among species. The substitution frequency was the highest at the third codon, followed by the first and second codon. The ratio of non-synonymous mutations （du） to synonymous mutations （ds） was far lower than 1, suggesting that the CP gene might have experienced purifying selection in the evolution. Phylogenetic analysis revealed that the 11 CTV isolates in Chinese wild type citrus belonged to different phylogenetic clusters, and shared higher homology and closer relationships with other cultivated citrus CTV isolates from different countries, which indicated complicated genetic relationships among the CTV isolates. In addition, CTV isolates with similar biological characteristics usually located into the same clusters. Therefore, the conclusion was drawn that pathogenicity was critical to evolution and origin of CTV.
基金Supported by China Agriculture Research System of MOF and MARA(CARS-170303)Joint Special Project of Basic Agricultural Research in Yunnan Province(2018FG001-029)+1 种基金"Yunling Industrial Technology Leading Talents"Training Project(2018LJRC56)Special Fund for the Construction of Modern Agricultural Industry Technology System in Yunnan Province(YNGZTX-4-92)。
文摘[Objectives]This study was conducted to clarify the species,occurrence and distribution characteristics of sugarcane rust pathogens in low-latitude plateau sugarcane rust areas of Yunnan Province and the phylogenetic relationship between the pathogens and that between them and other rust fungi of the genus Puccinia.[Methods]Fifty seven sugarcane rust samples collected from the sugarcane areas of Baoshan,Lincang,Menghai,Menglian,Ximeng,Lancang and Wenshan in Yunnan were subjected to molecular identification.[Results]The four sugarcane rust samples from Haiyin1 hao in Menghai,Yunnan Province belonged to orange rust of sugarcane,and the pathogen was Puccinia kuehnii Butler.;and other 53 samples of sugarcane rust belonged to brown rust of sugarcane,and the pathogen was Puccinia melanocephala Syd.et P.Syd.The rDNA sequences of other rust fungi from the genus Puccinia were downloaded from GenBank and used for the construction of an NJ tree for systematic evolution analysis together with the sequences obtained in this study.The results showed that the four P.kuehnii sequences obtained in this study were clustered with Puccinia polysora(GenBank accession number:GU058024)into one group,and they were close genetically;the 53 P.melanocephala sequences were clustered with P.nakanishikii(GenBank accession number:GU058002),P.rufipes(GenBank accession number:AJ296545),Aecidium deutziae(GenBank accession number:KU309317)and P.coronata(GenBank accession number:DQ354526)into one group,and they had a close genetic relationship;and the genetic relationship of the two species of sugarcane rust fungi identified in this study was relatively distant.[Conclusions]This study provides a scientific basis for sugarcane rust epidemic prediction,disease resistance breeding,and precise prevention and control.
基金Supported by Project Salud 2012-C01-181585,CONACYT and PAPIIT TA200112,Dirección General de Asuntos del Personal Academico,Universidad Nacional Autónoma de México(in part)Argentine National Agency for Scientific and Technology Promotion(PICT 2012 No804)National Research Council(CONICET,PIP 2010 No51)
文摘Hepatitis C virus(HCV)infection represents an important public health problem worldwide.Reduction of HCV morbidity and mortality is a current challenge owned to several viral and host factors.Virus molecular evolution plays an important role in HCV transmission,disease progression and therapy outcome.The high degree of genetic heterogeneity characteristic of HCV is a key element for the rapid adaptation of the intrahost viral population to different selection pressures(e.g.,host immune responses and antiviral therapy).HCV molecular evolution is shaped by different mechanisms including a high mutation rate,genetic bottlenecks,genetic drift,recombination,temporal variations and compartmentalization.These evolutionary processes constantly rearrange the composition of the HCV intrahost population in a staging manner.Remarkable advances in the understanding of the molecular mechanism controlling HCV replication have facilitated the development of a plethora of direct-acting antiviral agents against HCV.As a result,superior sustained viral responses have been attained.The rapidly evolving field of anti-HCV therapy is expected to broad its landscape even further with newer,more potent antivirals,bringing us one step closer to the interferon-free era.
文摘China is one of the most diverse countries, which have developed 88 indigenous pig breeds. Several studies showed that pigs were independently domesticated in multiple regions of the world. The purpose of this study was to investigate the origin and evolution of Chinese pigs using complete mitochondrial genomic sequences （mtDNA） from Asian and European domestic pigs and wild boars. Thirty primer pairs were designed to determine the mtDNA sequences of Xiang pig, Large White, Lantang, Jinhua and Pietrain. The phylogenetic status of Chinese native pigs was investigated by comparing the mtDNA sequences of complete coding regions and D-loop regions respectively amongst Asian breeds, European breeds and wild boars. The analyzed results by two cluster methods contributed to the same conclusion that all pigs were classified into two major groups, European dade and Asian clade. It revealed that Chinese pigs were only recently diverged from each other and distinctly different from European pigs. Berkshire was clustered with Asian pigs and Chinese pigs were involved in the development of Berkshire breeding. The Malaysian wild boar had distant genetic relationship with European and Asian pigs. Jinhua and Lanyu pigs had more nucleotide diversity with Chinese pigs although they all belonged to the Asian major clade. Chinese domestic pigs were clustered with wild boars in Yangtze River region and South China.
基金supported by the Outstanding Youth Science Funds(39825117)Bohai University Science Funds(BJ2004001),P.R.China
文摘S-locus genes were cloned from three Brassica napus and three B. campestris lines by using PCR walking and homologuesequence methods. A phylogenetic gene tree was constructed based on the six cloned genes and fifty-one previouslyreported SLG/SRK genes of Brassica and Raphanus. The SLGs from R. sativus were dispersed in the phylogenetic treeintermingling with SLG/SRKs from B. oleracea, B. napus and B. campestris. The SLG/SRK genes of classⅡclusteredindependently in one group. The SLG/SRK genes of classⅠshowed to be more divergent than classⅡgenes. Theseresults suggested that the divergence of classⅠand classⅡ should have occurred before the differentiation of thegenera Brassica and Raphanus. In addition, SLG and SRK of the same S haplotypes belonged to the same class. Itsuggested that class-Ⅰ and class-Ⅱ group divergence occurred first, and then SLG and SRK diverged. The three SC SRKgenes from B. napus and B. campestris were grouped into one cluster, displaying difference from the SC SLG of B.oleracea. These three SC SRK genes were close to SI SRK of SI1300, SI271 and guanyou in phylogenetic relationships.These results indicated that SC and SI genes diverged more recently. It is not clear yet whether the differentiation of SCand SI genes was earlier than the differentiation of Brassica and Raphanus. Studies based on more genes are necessaryfor a comprehensive elucidation of the phylogenetic relationships in Brassicaceae.
基金funded by The National Key Research and Development Program of China(Nos.2018YFD1000401 and 2018YFD1000400)the Natural Science Foundation of Guangdong Province(No.2017A030312004)the Science and Technology Plan Project of Shenzhen(No.JCYJ20170817151501595).
文摘Cymbidium,which includes approximately 80 species,is one of the most ornamental and cultivated orchid genera.However,a lack of markers and sparse sampling have posed great challenges to resolving the phylogenetic relationships within the genus.In the present study,we reconstructed the phylogenetic relationships by utilizing one nuclear DNA(nrITS)and seven plastid genes(rbcL,trnS,trnG,matK,trnL,psbA,and atpI)from 70 species(varieties)in Cymbidium.We also examined the occurrence of phylogenetic conflict between nuclear(nrITS)and plastid loci and investigated how phylogenetic conflict bears on taxonomic classification within the genus.We found that phylogenetic conflict and low support values may be explained by hybridization and a lack of informative characteristics.Our results do not support previous classification of the subgenera and sections within Cymbidium.Discordance between gene trees and network analysis indicate that reticulate evolution occurred in the genus Cymbidium.Overall,our study indicates that Cymbidium has undergone a complex evolution.
基金supported by the National Natural Science Foundation of China(Grant No.32060710,31970223,31860005,31860620)Applied Basic Research Projects of Yunnan(Grant No.2019FB057).
文摘Litsea,a non-monophyletic group of the tribe Laureae(Lauraceae),plays important roles in the tropical and subtropical forests of Asia,Australia,Central and North America,and the islands of the Pacific.However,intergeneric relationships between Litsea and Laurus,Lindera,Parasassafras and Sinosassafras of the tribe Laureae remain unresolved.In this study,we present phylogenetic analyses of seven newly sequenced Litsea plastomes,together with 47 Laureae plastomes obtained from public databases,representing six genera of the Laureae.Our results highlight two highly supported monophyletic groups of Litsea taxa.One is composed of 16 Litsea taxa and two Lindera taxa.The 18 plastomes of these taxa were further compared for their gene structure,codon usage,contraction and expansion of inverted repeats,sequence repeats,divergence hotspots,and gene evolution.The complete plastome size of newly sequenced taxa varied between 152,377 bp(Litsea auriculata)and 154,117 bp(Litsea pierrei).Seven of the 16 Litsea plastomes have a pair of insertions in the IRa(trnL-trnH)and IRb(ycf2)regions.The 18 plastomes of Litsea and Lindera taxa exhibit similar gene features,codon usage,oligonucleotide repeats,and inverted repeat dynamics.The codons with the highest frequency among these taxa favored A/T endings and each of these plastomes had nine divergence hotspots,which are located in the same regions.We also identified six protein coding genes(accD,ndhJ,rbcL,rpoC2,ycf1 and ycf2)under positive selection in Litsea;these genes may play important roles in adaptation of Litsea species to various environments.
