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Complete mitochondrial genome of the leaf muntjac(Muntiacus putaoensis) and phylogenetics of the genus Muntiacus 被引量:3
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作者 Guo-Gang Li Ming-Xia Zhang +2 位作者 Kyaw Swa Kyaw-Win Maung Rui-Chang Quan 《Zoological Research》 CAS CSCD 2017年第5期310-316,共7页
The leaf muntjac (Muntiacus putaoensis) is an endemic deer species found in the east trans- Himalayan region. In recent years, population numbers have decreased due to heavy hunting and habitat loss, and little gene... The leaf muntjac (Muntiacus putaoensis) is an endemic deer species found in the east trans- Himalayan region. In recent years, population numbers have decreased due to heavy hunting and habitat loss, and little genetic data exists for this species, thus our knowledge of distribution rangs and population sizes likewise remain limited. We obtained mtDNA genes and the complete mitochondrial genome sequence of M. putaoensis using PCR, followed by direct sequencing. The complete mitogenome sequence was determined as a circular 16 349 bp mitochondrial genome, containing 13 protein-coding genes, two rRNA genes 22 tRNA genes, and one control region, the gene composition and order of which were similar to most other vertebrates so far reported. Most mitochondrial genes, except for ND6 and eight tRNAs, were encoded on the heavy strand. The overall base composition of the heavy strand was 33.1% A, 29.3% T, 24.2% C, and 13.4% G, with a strong AT bias of 62.4%. There were seven regions of gene overlap totaling 95 bp and 11 intergenic spacer regions totaling 74 bp. Phylogenetic analyses (ML and BI) among the Muntiacus genus based on the sequenced of mitogenome and ND4L-ND4 supported M. putaoensis as a member of Muntiacus, most closely related to M. vuquangensis. However, when analyses based on cyt b included two more muntjacs, M. truongsonensis was most closely related to M. putaoensis rather than M. vuquangensis, and together with M. rooseveltorum, likely forming a M. rooseveltorum complex of the species. This study will help in the exploration of the evolutionary history and taxonomic status of the leaf muntjac, as well as its protection as a genetic resource. 展开更多
关键词 MUNTIACUS Muntiacus putaoensis MITOGENOME phylogenetics
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Contribution of phylogenetics to understanding the evolution and epidemiology of dengue virus 被引量:1
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作者 Xi Yu Gong Cheng 《Animal Models and Experimental Medicine》 CAS CSCD 2022年第5期410-417,共8页
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
关键词 dengue virus(DENV) EVOLUTION FLAVIVIRUS phylogenetics
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Phylogenetics and Molecular Divergence of Tilapia Fish (Oreochromis Species) Using Mitochondrial D-Loop and Cytochrome b Regions 被引量:1
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作者 Ekerette Emmanuel Ekerette Ekei Victor Ikpeme +5 位作者 Ogbuagu Ugorji Udensi Michael Ohiokhuaobo Ozoje Owoidihe Monday Etukudo Anthony John Umoyen Samuel Olutunde Durosaro Matthew Wheto 《American Journal of Molecular Biology》 2018年第1期39-57,共19页
Understanding the level of genetic diversity in any population is an important requisite towards strategizing measures for conservation and improvement of stocks. This study focused on the assessment of phylogenetics ... Understanding the level of genetic diversity in any population is an important requisite towards strategizing measures for conservation and improvement of stocks. This study focused on the assessment of phylogenetics and molecular divergence of tilapia fish species obtained from two populations (Domita in South-South and Odeda in South-West, Nigeria) using the displacement loop (D-loop) and cytochrome b region of the mitochondrial deoxyribonucleic acid (mtDNA). A total of 28 samples (15 from South-South and 13 from South-West) were used for the genetic analysis. DNA was extracted from the tissue of all the samples using Quik-gDNATM miniPrep kit. The D-loop containing the hypervariable region was sequenced for all samples from the two populations, while cytochrome b (Cyt b) region of mtDNA was only sequenced for samples from South-South population. Chromatograms of the sequences were viewed and edited using Bioedit software. Multiple sequence alignment was carried out using molecular evolutionary genetic analysis (MEGA) software before subsequent genetic analyses. Phylogenetic analysis grouped the samples into two clusters based on population. Also, when the two mitochondrial regions were pooled together, they clustered into two major groups based on mitochondrial regions. Analysis of molecular variance (AMOVA) revealed 37.32% variation within population and 62.68% variation among population with a significant fixation index of 0.627 (p 0.05). The genetic distance inferred between D-loop regions of South-South and South-West populations was 0.243. Maternal lineage analysis revealed that the origin of tilapia fish from both populations could be traced to Oreochromis spirilus and Oreochromis leucostictus based on mitochondrial D-loop region. The findings of this study revealed molecular divergence among the tilapia populations and may serve as pivot information for the genetic improvement of this important species. 展开更多
关键词 phylogenetics Molecular Divergence MATERNAL LINEAGE TILAPIA FISH
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Progress in systematics and biogeography of Orchidaceae
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作者 Yajun Wang Hanchen Wang +4 位作者 Chao Ye Zhiping Wang Chongbo Ma Dongliang Lin Xiaohua Jin 《Plant Diversity》 SCIE CAS CSCD 2024年第4期425-434,共10页
Orchidaceae are one of the largest families of angiosperms in terms of species richness.In the last decade,numerous studies have delved into reconstructing the phylogenetic framework of Orchidaceae,leveraging data fro... Orchidaceae are one of the largest families of angiosperms in terms of species richness.In the last decade,numerous studies have delved into reconstructing the phylogenetic framework of Orchidaceae,leveraging data from plastid,mitochondrial and nuclear sources.These studies have provided new insights into the systematics,diversification and biogeography of Orchidaceae,establishing a robust foundation for future research.Nevertheless,pronounced controversies persist regarding the precise placement of certain lineages within these phylogenetic frameworks.To address these discrepancies and deepen our understanding of the phylogenetic structure of Orchidaceae,we provide a comprehensive overview and analysis of phylogenetic studies focusing on contentious groups within Orchidaceae since 2015,delving into discussions on the underlying reasons for observed topological conflicts.We also provide a novel phylogenetic framework at the subtribal level.Furthermore,we examine the tempo and mode underlying orchid species diversity from the perspective of historical biogeography,highlighting factors contributing to extensive speciation.Ultimately,we delineate avenues for future research aimed at enhancing our understanding of Orchidaceae phylogeny and diversity. 展开更多
关键词 Diversification Orchid phylogenetics Phylogenetic conflicts BIOGEOGRAPHY Taxonomy
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Morphological and molecular analyses of a Philine kinglipini outbreak in summer of 2022 in Jiaozhou Bay,China
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作者 Zelin DUAN Yanan YU +2 位作者 Jing WANG Junlong ZHANG Nansheng CHEN 《Journal of Oceanology and Limnology》 SCIE CAS CSCD 2024年第3期831-848,共18页
A sudden and unprecedented outbreak of molluscan Philine kinglipini occurred in summer 2022 in Jiaozhou Bay,Shandong,China,causing substantial damage to local mariculture industry of the Manila clam Ruditapes philippi... A sudden and unprecedented outbreak of molluscan Philine kinglipini occurred in summer 2022 in Jiaozhou Bay,Shandong,China,causing substantial damage to local mariculture industry of the Manila clam Ruditapes philippinarum.Although P.kinglipini has been found in many coastal regions of China,the molecular research of P.kinglipini has not been extensively studied,making it difficult to accurately identify and track P.kinglipini samples in field using molecular methods.Samples were collected during the outbreak and their morphological features and molecular sequences were analyzed.Results show that the causative species of the outbreak was P.kinglipini.The mitochondrial genome(mt DNA)of P.kinglipini was constructed for the first time,based on which phylogenetic analysis of the mt DNAs of P.kinglipini and related species in the order Cephalaspidea was carried out.As revealed by metabarcoding analysis of 18S rDNA V4,the seasonal change of P.kinglipini and closely related Philine species was striking with peaks between April and August.Therefore,metabarcoding analysis is applicable tool for monitoring the bloom development of P.kinglipini and related species.This study generated for the first time essential molecular marker sequences and mtDNA of P.kinglipini,which provided a reference for future characterization and monitoring of its outbreaks and for phylogenetic analysis of Philine species. 展开更多
关键词 marine species outbreaks metabarcoding analysis mitochondrial genome Philine kinglipini phylogenetics spatial-temporal dynamics
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Molecular phylogeny and taxonomy of Phlomoides(Lamiaceae subfamily Lamioideae)in China:Insights from molecular and morphological data
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作者 Yue Zhao Ya-Ping Chen +8 位作者 Bryan T.Drew Fei Zhao Maryam Almasi Orzimat T.Turginov Jin-Fei Xiao Abdul G.Karimi Yasaman Salmaki Xiang-Qin Yu Chun-Lei Xiang 《Plant Diversity》 SCIE CAS CSCD 2024年第4期462-475,共14页
Phlomoides,with 150-170 species,is the second largest and perhaps most taxonomically challenging genus within the subfamily Lamioideae(Lamiaceae).With about 60 species,China is one of three major biodiversity centers ... Phlomoides,with 150-170 species,is the second largest and perhaps most taxonomically challenging genus within the subfamily Lamioideae(Lamiaceae).With about 60 species,China is one of three major biodiversity centers of Phlomoides.Although some Phlomoides species from China have been included in previous molecular phylogenetic studies,a robust and broad phylogeny of this lineage has yet to be completed.Moreover,given the myriad new additions to the genus,the existing infrageneric classification needs to be evaluated and revised.Here,we combine molecular and morphological data to investigate relationships within Phlomoides,with a focus on Chinese species.We observed that plastid DNA sequences can resolve relationships within Phlomoides better than nuclear ribosomal internal and external transcribed spacer regions(nrITS and nrETS).Molecular phylogenetic analyses confirm the monophyly of Phlomoides,but most previously defined infrageneric groups are not monophyletic.In addition,morphological analysis demonstrates the significant taxonomic value of eight characters to the genus.Based on our molecular phylogenetic analyses and morphological data,we establish a novel section Notochaete within Phlomoides,and propose three new combinations as well as three new synonyms.This study presents the first molecular phylogenetic analyses of Phlomoides in which taxa representative of the entire genus are included,and highlights the phylogenetic and taxonomic value of several morphological characters from species of Phlomoides from China.Our study suggests that a taxonomic revision and reclassification for the entire genus is necessary in the future. 展开更多
关键词 Lamioideae Molecular phylogenetics MORPHOLOGY Phlomideae TAXONOMY
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Molecular Phylogeny, Species Delimitation and Taxonomic Revision of the Australian Spider Wasp Genus Heterodontonyx Haupt, 1935 (Hymenoptera: Pompilidae)
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作者 Mahin Sadat Chavoshi Jolfaei Juanita Rodriguez 《Advances in Entomology》 2024年第2期105-128,共24页
Heterodontonyx (Pompilidae: Pepsinae) is an understudied genus with Australasiandistribution and most species are endemic to Australia. There have recently been sometaxonomic changes involving the genera Heterodontony... Heterodontonyx (Pompilidae: Pepsinae) is an understudied genus with Australasiandistribution and most species are endemic to Australia. There have recently been sometaxonomic changes involving the genera Heterodontonyx and Cryptocheilus based on molecular and morphological evidence, however, phylogenetic relationships within Heterodontonyx, species delimitation and formal revision have not been conducted. Here, we construct a Maximum Likelihood phylogeny estimate of Heterodontonyx based on ITS1, 5.8S, ITS2 region of 30 samples representing seven Heterodontonyx morphospecies. bPTP species delimitation approach was employed and ultimately the taxonomic revision of the genus was carried out. Phylogenetic analyses strongly support the monophyly of Heterodontonyx and the species delimitation method recognizes eight species among which one new species is identified. 展开更多
关键词 Pompilidae Taxonomy Australian Pomplids phylogenetics
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Spatial phylogenetics of the Chinese angiosperm flora provides insights into endemism and conservation 被引量:9
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作者 Xiao-Xia Zhang Jian-Fei Ye +9 位作者 Shawn W.Laffan Brent D.Mishler Andrew H.Thornhill Li-Min Lu Ling-Feng Mao Bing Liu You-Hua Chen An-Ming Lu Joseph T.Miller Zhi-Duan Chen 《Journal of Integrative Plant Biology》 SCIE CAS CSCD 2022年第1期105-117,共13页
The flora of China is well known for its high diversity and endemism. Identifying centers of endemism and designating conservation priorities are essential goals for biodiversity studies.However, there is no comprehen... The flora of China is well known for its high diversity and endemism. Identifying centers of endemism and designating conservation priorities are essential goals for biodiversity studies.However, there is no comprehensive study from a rigorous phylogenetic perspective to understand patterns of diversity and endemism and to guide biodiversity conservation in China. We conducted a spatial phylogenetic analysis of the Chinese angiosperm flora at the generic level to identify centers of neo-and paleoendemism. Our results indicate that:(i) themajority of grid cells in China with significantly high phylogenetic endemism(PE) were located in the mountainous regions;(ii) four of the nine centers of endemism recognized, located in northern and western China, were recognized for the first time;(iii) arid and semiarid regions in Northwest China were commonly linked to significant PE, consistent with other spatial phylogenetic studies worldwide;and(iv) six highpriority conservation gaps were detected by overlaying the boundaries of China’s nature reserves on all significant PE cells. Overall, we conclude that the mountains of southern and northern China contain both paleo-endemics(ancient relictual lineages) and neo-endemics(recently diverged lineages). The areas we highlight as conservation priorities are important for broad-scale planning, especially in the context of evolutionary history preservation. 展开更多
关键词 categorical analysis of neo-and paleo-endemism Chinese angiosperm flora conservation priority phylogenetic endemism phylogenetic diversity spatial phylogenetics
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First report of complete mitochondrial genome in the subfamily Alleculinae and mitochondrial genome-based phylogenetics in Tenebrionidae(Coleoptera:Tenebrionoidea) 被引量:3
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作者 Chuan Wu Yong Zhou +2 位作者 Tian Tian Ting-Jing Li Bin Chen 《Insect Science》 SCIE CAS CSCD 2022年第4期1226-1238,共13页
Despite worldwide distribution and rich diversity,the knowledge of mitochondrial genome(mtgenome)characteristics within the family Tenebrionidae(Coleoptera)is still very limited,and phylogenetics remain unresolved for... Despite worldwide distribution and rich diversity,the knowledge of mitochondrial genome(mtgenome)characteristics within the family Tenebrionidae(Coleoptera)is still very limited,and phylogenetics remain unresolved for the family.In this study,the mtgenomes for 12 species are newly sequenced and annotated.Three of the species represent the first report of complete mtgenomes from the subfamily Alleculinae.Comparative analysis of 36 tenebrionid mtgenomes finds that gene composition and order are the same as a theoretical ancestral insect mtgenome,and AT bias,length variation,and codon usage are consistent with other reported beetle mtgenomes.Some intergenic overlap and gap sequences may contain phylogenetically informative information,whereas neither the conserved nor repeat sequences in the control region do.The subfamilies Lagriinae,Pimeliinae,Stenochiinae,and Alleculinae are found to be monophyletic,and the subfamilies Diaperinae and Tenebrioninae polyphyletic in our study.Furthermore,Lagriinae is sister to the rest of the subfamilies.At the tribal level,the tribes Lagriini in the subfamily Lagrrinae;Strongyliini in Stenochiinae;Cteniopodini in Alleculinae;and Triboliini,Opatrini,and Amarygmini in Tenebrioninae are monophyletic;while Diaperini in Diaperinae,and Tenebrionini in Tenebrioninae are polyphyletic. 展开更多
关键词 Alleculinac characteristics Colcopiera mtgenome phylogenetics Tenebrionidac
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Analysis of plastid and nuclear DNA data in plant phylogenetics——evaluation and improvement 被引量:2
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作者 WANG Wei LI HongLei CHEN ZhiDuan 《Science China(Life Sciences)》 SCIE CAS 2014年第3期280-286,共7页
Correct combination of plastid(cp)and nuclear(nr)DNA data for plant phylogenetic reconstructions is not a new issue,but with an increasing number of nrDNA loci being used,it is of ever greater practical concern.For ac... Correct combination of plastid(cp)and nuclear(nr)DNA data for plant phylogenetic reconstructions is not a new issue,but with an increasing number of nrDNA loci being used,it is of ever greater practical concern.For accurately reconstructing the phylogeny and evolutionary history of plant groups,correct treatment of phylogenetic incongruence is a vital step in the proper analysis of cpDNA and nrDNA data.We first evaluated the current status of analyzing cpDNA and nrDNA data by searching all articles published in the journal Systematic Botany between 2005 and 2011.Many studies combining cpDNA and nrDNA data did not rigorously assess the combinability of the data sets,or did not address in detail possible reasons for incongruence between the two data sets.By reviewing various methods,we outline a procedure to more accurately analyze and/or combine cpDNA and nrDNA data,which includes four steps:identifying significant incongruence,determining conflicting taxa,providing possible interpretations for incongruence,and reconstructing the phylogeny after treating incongruence.Particular attention is given to explanation of the cause of incongruence.We hope that our procedure will help raise awareness of the importance of rigorous analysis and help identify the cause of incongruence before combining cpDNA and nrDNA data. 展开更多
关键词 combined analysis plastid DNA INCONGRUENCE nuclear DNA phylogenetics
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Evolutionary fingerprint, phylogenetic and forest structure of tropical montane Atlantic cloud forests along an elevation gradient
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作者 Ravi Fernandes MARIANO Vanessa Leite REZENDE +7 位作者 Cléber Rodrigo de SOUZA Patrícia Vieira POMPEU Rubens Manoel dos SANTOS Carolina Njaime MENDES Aloysio Souza de MOURA Felipe Santana MACHADO Warley Augusto Caldas CARVALHO Marco Aurélio Leite FONTES 《Journal of Mountain Science》 SCIE CSCD 2024年第4期1259-1271,共13页
Environmental conditions can change markedly over geographical distances along elevation gradients,making them natural laboratories to study the processes that structure communities.This work aimed to assess the influ... Environmental conditions can change markedly over geographical distances along elevation gradients,making them natural laboratories to study the processes that structure communities.This work aimed to assess the influences of elevation on Tropical Montane Cloud Forest plant communities in the Brazilian Atlantic Forest,a historically neglected ecoregion.We evaluated the phylogenetic structure,forest structure(tree basal area and tree density)and species richness along an elevation gradient,as well as the evolutionary fingerprints of elevation-success on phylogenetic lineages from the tree communities.To do so,we assessed nine communities along an elevation gradient from 1210 to 2310 m a.s.l.without large elevation gaps.The relationships between elevation and phylogenetic structure,forest structure and species richness were investigated through Linear Models.The occurrence of evolutionary fingerprint on phylogenetic lineages was investigated by quantifying the extent of phylogenetic signal of elevation-success using a genus-level molecular phylogeny.Our results showed decreased species richness at higher elevations and independence between forest structure,phylogenetic structure and elevation.We also verified that there is a phylogenetic signal associated with elevation-success by lineages.We concluded that the elevation is associated with species richness and the occurrence of phylogenetic lineages in the tree communities evaluated in Mantiqueira Range.On the other hand,elevation is not associated with forest structure or phylogenetic structure.Furthermore,closely related taxa tend to have their higher ecological success in similar elevations.Finally,we highlight the fragility of the tropical montane cloud forests in the Mantiqueira Range in face of environmental changes(i.e.global warming)due to the occurrence of exclusive phylogenetic lineages evolutionarily adapted to environmental conditions(i.e.minimum temperature)associated with each elevation range. 展开更多
关键词 Atlantic Forest Cloud forest CONSERVATION Community ecology Montane forests Phylogenetic diversity Phylogenetic signal
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Phylogenetic study on Scenedesmacae with the description of a new genus Coccoidesmus gen.nov.(Chlorophyceae,Chlorophyta)and chloroplast genome analyses
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作者 Qinghua WANG Ying HOU +2 位作者 Yanhui LI Ying SHI Guoxiang LIU 《Journal of Oceanology and Limnology》 SCIE CAS CSCD 2024年第4期1272-1285,共14页
Members of the family Scenedesmaceae are some of the most common algal taxa in inland ecosystems,and they are widely distributed in freshwaters,aerial,and sub-aerial habitats.With the continuous updating of methods,th... Members of the family Scenedesmaceae are some of the most common algal taxa in inland ecosystems,and they are widely distributed in freshwaters,aerial,and sub-aerial habitats.With the continuous updating of methods,the classic morphological taxonomy of this family needs to be revised.In recent years,many genera of Scenedesmaceae have been established via the use of molecular methods.The phylogenetic relationships within Scenedesmaceae were analyzed using different molecular markers and morphological data,and the new freshwater genus Coccoidesmus Wang,Hou et Liu gen.nov.was described.Two new species in this genus were also described.Phylogenetic analysis based on tufA genes revealed that the new genus formed an independent clade closely related to Comasiella.However,these two genera are characterized by significant morphological differences in colony arrangement and cell shape.The chloroplast genome of the type species was assembled and annotated,and analyses of genome structure and sequences were conducted.More genome data could help clarify the phylogenetic relationships within this family. 展开更多
关键词 PHYLOGENETIC Scenedesmaceae Coccoidesmus morphology chloroplast genome
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Morphology and phylogenetic placement of Mallomonas vietnamica(Synurales,Chrysophyceae)from China
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作者 Junxue HAO Fangru NAN +4 位作者 Junping LÜ Qi LIU Xudong LIU Shulian XIE Jia FENG 《Journal of Oceanology and Limnology》 SCIE CAS CSCD 2024年第4期1325-1335,共11页
The newly described chrysophyte,Mallomonas vietnamica,is reported for the first time in China from specimens collected in Guizhou Province,SW China.The morphological characteristics were studied using light and scanni... The newly described chrysophyte,Mallomonas vietnamica,is reported for the first time in China from specimens collected in Guizhou Province,SW China.The morphological characteristics were studied using light and scanning electron microscopy.The species was described based on morphological characteristics,including cell size,scale size,dome,V-rib,and bristles.Subsequently,molecular sequencing of M.vietnamica was conducted and a phylogenetic tree was constructed based on concatenated SSU,LSU,and rbc L sequences.The phylogenetic tree led us to suggest raising a new section named Uncatusipedae for this species.This study provides new molecular data from the genus Mallomonas and enriches our understanding of the species diversity and geographical distribution of the genus Mallomonas in China. 展开更多
关键词 CHRYSOPHYTA Mallomonas vietnamica phylogenetic study TAXONOMY
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Temperate Stutzerimonas Phage Encoding Toxin-Antitoxin System Genes Represents a Novel Genus
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作者 ZHANG Hong GUO Ruizhe +14 位作者 GAO Chen ZHENG Kaiyang XIONG Yao DONG Yue LIU Yundan WANG Ziyue CHEN Ying WANG Hongmin SHAO Hongbing SUNG Yeong Yik MOK Wen Jye WONG Li Lian MCMINN Andrew WANG Min LIANG Yantao 《Journal of Ocean University of China》 SCIE CAS CSCD 2024年第4期1087-1101,共15页
Stutzerimonas have been extensively studied due to their remarkable metabolic and physiological diversity.However,research on its phages is currently limited.In this study,we isolated a novel double-stranded DNA(dsDNA... Stutzerimonas have been extensively studied due to their remarkable metabolic and physiological diversity.However,research on its phages is currently limited.In this study,we isolated a novel double-stranded DNA(dsDNA)phage,vB_SstM-PG1,from the marine environment that infects Stutzerimonas stutzeri G1.Its dsDNA genome is 37204 bp long with a G/C content of 64.14%and encodes 54 open reading frames.The phage possesses a tail packaging structure that is different from known Stutzerimonas stutzeri phages and exhibits structural protein characteristics similar to those of temperate phages.In addition,two genes of toxin-antitoxin system,including YdaS_antitoxin and HEPN_SAV_6107,were found in the vB_SstM-PG1 genome and play important roles in regulating host growth and metabolism.With phylogenetic tree and comparative genomic analysis,it has been determined that vB_SstM-PG1 is not closely related to any phages previously identified in the GenBank database.Instead,it has a connection with enigmatic,uncultured viruses.Specifically,the vB_SstM-PG1 virus exhibits an average nucleotide identity of over 70%with six uncultivated viruses identified in the IMG/VR v4 database.This significant finding has resulted in the identification of a novel viral genus known as Metabovirus. 展开更多
关键词 Stutzerimonas vB_SstM-PG1 Metabovirus temperate phage genomic and phylogenetic analysis
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An unprotected vulnerable relict subtropical conifer-Keteleeria evelyniana: Its forests, populations, growth and endangerment by invasive alien plant species in China
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作者 Cindy Q.Tang Min-Rui Du +10 位作者 Huan-Chong Wang You-Cai Shi Jia-Le Zeng Shu-Li Xiao Peng-Bin Han Jian-Ran Wen Shi-Qian Yao Ming-Chun Peng Chong-Yun Wang Yong-Ping Li Jordi López-Pujol 《Plant Diversity》 SCIE CAS CSCD 2024年第5期648-660,共13页
Relict subtropical coniferous forests in China face severe fragmentation,resulting in declining populations,and some are under significant threat from invasive alien species.Despite the crucial importance of understan... Relict subtropical coniferous forests in China face severe fragmentation,resulting in declining populations,and some are under significant threat from invasive alien species.Despite the crucial importance of understanding forest dynamics,knowledge gaps persist,particularly regarding the impact of invasive plants on vulnerable natives like Keteleeria evelyniana.In this study,we investigated the impact of invasive plants on the regeneration of forests dominated by K.evelyniana,a subtropical relict species in southwestern China.For this purpose,we characterized forest dynamics of 160 forest plots featuring K.evelyniana as the primary dominant species and determined whether the presence of invasive plants was correlated with regeneration of K.evelyniana.We identified four distinct forest types in which K.evelyniana was dominant.We found that radial growth of K.evelyniana trees is faster in younger ageclasses today than it was for older trees at the same age.The population structure of K.evelyniana in each forest type exhibited a multimodal age-class distribution.However,three forest types lacked established saplings younger than 10 years old,a situation attributed to the dense coverage of the invasive alien Ageratina adenophora.This invasive species resulted in a reduction of understory species diversity.Additionally,our analysis uncovered a significant negative correlation in phylogenetic relatedness(net relatedness index)between native and invasive alien plant species in eastern Yunnan.This suggests closely related invasive species face heightened competition,hindering successful invasion.Taken together,our findings indicate that successful establishment and habitat restoration of K.evelyniana seedling/saplings require effective measures to control invasive plants. 展开更多
关键词 Keteleeria evelyniana Age structure Regeneration Species diversity Invasive alien species Phylogenetic relatedness
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Epidemiological Surveillance: Genetic Diversity of Rotavirus Group A in the Pearl River Delta, Guangdong, China in 2019
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作者 JIANG Jie Ying LIANG Dan +9 位作者 WANG Li XIAO Yun LIANG Yu Feng KE Bi Xia SU Juan XIAO Hong WANG Tao ZOU Min LI Hong Jian KE Chang Wen 《Biomedical and Environmental Sciences》 SCIE CAS CSCD 2024年第3期278-293,共16页
Objective This study aimed to understand the epidemic status and phylogenetic relationships of rotavirus group A(RVA)in the Pearl River Delta region of Guangdong Province,China.Methods This study included individuals ... Objective This study aimed to understand the epidemic status and phylogenetic relationships of rotavirus group A(RVA)in the Pearl River Delta region of Guangdong Province,China.Methods This study included individuals aged 28 days–85 years.A total of 706 stool samples from patients with acute gastroenteritis collected between January 2019 and January 2020 were analyzed for 17 causative pathogens,including RVA,using a Gastrointestinal Pathogen Panel,followed by genotyping,virus isolation,and complete sequencing to assess the genetic diversity of RVA.Results The overall RVA infection rate was 14.59%(103/706),with an irregular epidemiological pattern.The proportion of co-infection with RVA and other pathogens was 39.81%(41/103).Acute gastroenteritis is highly prevalent in young children aged 0–1 year,and RVA is the key pathogen circulating in patients 6–10 months of age with diarrhea.G9P[8](58.25%,60/103)was found to be the predominant genotype in the RVA strains,and the 41 RVA-positive strains that were successfully sequenced belonged to three different RVA genotypes in the phylogenetic analysis.Recombination analysis showed that gene reassortment events,selection pressure,codon usage bias,gene polymorphism,and post-translational modifications(PTMs)occurred in the G9P[8]and G3P[8]strains.Conclusion This study provides molecular evidence of RVA prevalence in the Pearl River Delta region of China,further enriching the existing information on its genetics and evolutionary characteristics and suggesting the emergence of genetic diversity.Strengthening the surveillance of genotypic changes and gene reassortment in RVA strains is essential for further research and a better understanding of strain variations for further vaccine development. 展开更多
关键词 Infectious diarrheal disease ROTAVIRUS Phylogenetic analysis Gene rearrangement Codon usage bias Genetic diversity
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A novel pathogen Fusarium cuneirostrum causing common bean(Phaseolus vulgaris)root rot in China
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作者 Dong Deng Wenqi Wu +2 位作者 Canxing Duan Suli Sun Zhendong Zhu 《Journal of Integrative Agriculture》 SCIE CSCD 2024年第1期166-176,共11页
Several fungal pathogens cause root rot of common bean,among which Fusarium spp.are the most common pathogens causing Fusarium root rot(FRR)worldwide.FRR has been becoming an increasingly severe disease of common bean... Several fungal pathogens cause root rot of common bean,among which Fusarium spp.are the most common pathogens causing Fusarium root rot(FRR)worldwide.FRR has been becoming an increasingly severe disease of common bean in China,but the species of Fusarium spp.have remained unclear.Thus,this study was performed to identify the pathogen causing common bean root rot in Liangcheng County,Inner Mongolia,China.Nineteen Fusarium-like isolates were obtained after pathogen isolation and purification.The pathogenicity test indicated that eight isolates caused severe disease symptoms on common bean,while 11 other isolates were not pathogenic.The eight pathogenic isolates,FCL1–FCL8,were identified as Fusarium cuneirostrum by morphological characterization and phylogenetic analysis using partial sequences of EF-1α,ITS,28S,and IGS regions.Host range test showed that the representative F.cuneirostrum isolate FCL3 was also pathogenic to mung bean,while not pathogenic to adzuki bean,chickpea,cowpea,faba bean,pea,and soybean.Moreover,50 common bean and 50 mung bean cultivars were screened for resistance to FRR,and seven highly resistant or resistant cultivars of common bean were identified,while no resistant cultivars of mung bean were screened.This study revealed that F.cuneirostrum was one of common bean FRR pathogens in Inner Mongolia and it could induce mung bean root rot as well.To our knowledge,this is the first report of F.cuneirostrum causing FRR of common bean in China. 展开更多
关键词 Fusarium cuneirostrum fusarium root rot PATHOGENICITY molecular phylogenetic analysis Phaseolus vulgaris
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Deterministic processes drive turnover-dominated beta diversity of breeding birds along the central Himalayan elevation gradient
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作者 Zhifeng Ding Jianchao Liang +3 位作者 Le Yang Cong Wei Huijian Hu Xingfeng Si 《Avian Research》 SCIE CSCD 2024年第2期163-171,共9页
Beta diversity,the variation of community composition among sites,bridges alpha and gamma diversity and can reveal the mechanisms of community assembly through applying distance-decay models and/or partitioning beta d... Beta diversity,the variation of community composition among sites,bridges alpha and gamma diversity and can reveal the mechanisms of community assembly through applying distance-decay models and/or partitioning beta diversity into turnover and nestedness components from functional and phylogenetic perspectives.Mountains as the most natural experiment system provide good opportunities for exploring beta diversity patterns and the underlying ecological processes.Here,we simultaneously consider distance-decay models and multiple di-mensions of beta diversity to examine spatial variations of bird communities,and to evaluate the relative importance of niche-based and neutral community assembly mechanisms along a 3600-m elevational gradient in the central Himalayas,China.Our results showed that species turnover dominates taxonomic,functional,and phylogenetic beta diversity.We observed strongest evidence of spatial distance decays in taxonomic similarities of birds,followed by its phylogenetic and functional analogues.Turnover component was highest in taxonomic beta diversity,while nestedness component was highest in functional beta diversity.Further,all correlations of assemblage similarity with climatic distance were higher than that with spatial distances.Standardized values of overall taxonomic,functional,and phylogenetic beta diversity and their turnover components increase with increasing elevational distance,while the standardized values of taxonomic and phylogenetic nestedness decreased with increasing elevational distance.Our results highlighted the niche-based deterministic processes in shaping elevational bird diversity patterns that were determined by the relative roles of decreasing trend of environmental filtering and increasing trend of limiting similarity along elevation distances. 展开更多
关键词 Beta diversity BIRD Community assembly Functional trait HIMALAYA Nestedenss Phylogenetic distance TURNOVER
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New record of the feather star Palaeocomatella hiwia(Echinodermata:Crinoidea:Comatulida)from Zhenbei Seamount in South China Sea:new insights into the taxonomic position of Palaeocomatella
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作者 Shao’e SUN Zijie MEI +2 位作者 Zhongli SHA Jing WANG Nansheng CHEN 《Journal of Oceanology and Limnology》 SCIE CAS CSCD 2024年第1期244-251,共8页
One specimen belonging to the family Comatellinae was collected from the Zhenbei Seamount(332.5–478.2 m)in the South China Sea in July 2022.Based on the morphological characters,the specimen was identified as Palaeoc... One specimen belonging to the family Comatellinae was collected from the Zhenbei Seamount(332.5–478.2 m)in the South China Sea in July 2022.Based on the morphological characters,the specimen was identified as Palaeocomatella hiwia McKnight,1977.It is first recorded from China Sea and redescribed in detail.This specimen differs from the original description from New Zealand for never showing syzygy at br4+5 or br5+6 on interior and br1+2 on exterior arms.However,it is much conform to the redescription to specimens from Indonesia,with only differences in position of the second syzygy and distalmost pinnule comb.Specimen is deposited in the Institute of Oceanology,Chinese Academy of Sciences.Phylogenetic analyses based on the mitochondrial c oxidase subunit I(COI)and 16S rRNA genes indicated that P.hiwia was nested within the tribe Phanogeniini and clustered with Aphanocomaster pulcher.Furthermore,P.hiwia showed same morphological features in terms of mouth placement,comb location,and number of comb teeth rows as other genera of Phanogeniini.Therefore,we suggest that the genus Palaeocomatella should be put in the tribe Phanogeniini. 展开更多
关键词 new record Palaeocomatella hiwia McKnight 1977 South China Sea phylogenetic relationship TAXONOMY
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Benthodytes occidentpalauta sp.nov.,a new species of deep-sea holothuroid(Elasipodida:Psychropotidae)from the west of Kyushu-Palau Ridge in the Western Pacific Ocean
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作者 Chongzhen YUAN Chunsheng WANG Dongsheng ZHANG 《Journal of Oceanology and Limnology》 SCIE CAS CSCD 2024年第1期252-262,共11页
Benthodytes occidentpalauta sp.nov.was collected from the Kyushu-Palau Ridge at a depth of 5481 m in 2021.This new species is characterized by a gelatinous body wall,violet skin,six pairs of dorsal papillae,and a roug... Benthodytes occidentpalauta sp.nov.was collected from the Kyushu-Palau Ridge at a depth of 5481 m in 2021.This new species is characterized by a gelatinous body wall,violet skin,six pairs of dorsal papillae,and a rough mid-ventral surface without tube feet.The dorsal deposits are rod-shaped and tripartite.Two types of papillae deposits as crosses with four arms with central bipartite apophyses.Ventral deposits are rods.Tentacle ossicles are rod-shaped with end protrusions.Gonad deposits are rodshaped,tripartite,and cross-shaped.The phylogenetic analyses based on cytochrome oxidase subunit 1(COI)and 16S individually and a concatenated dataset of COI and 16S genes of this species support that B.occidentpalauta sp.nov.belongs to Benthodytes. 展开更多
关键词 HOLOTHUROIDEA Benthodytes cytochrome oxidase subunit 1(COI) 16S phylogenetic analysis
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