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Phylogeny and Biogeography of Common Toad(Bufo bufo) in Xinjiang, China

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Asian Herpetological Research 2021年第2期12卷 201-212页

作者： Siqi WANG Chunxia XU Jiaqi ZHANG Supen WANG Xuan LIU Xuejiao YANG Yiming LI Key Laboratory of Animal Ecology and Conservation Biology Institute of ZoologyChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China

The common toad, Bufo bufo(Linnaeus, 1758), is widely distributed in Europe and parts of Africa. Previous studies of the genetic relationships among B. bufo populations have not included Asian populations. Here, we investigated the phylogenetic relationships of B. bufo, including a population from Xinjiang, China, using 722 bp of the mitochondrial cytochrome b sequence and identified six subclades and 85 haplotypes in populations from 22 countries. Phylogenetic analyses and pedigree differentiation revealed that the subclade containing the Xinjiang population has undergone a relatively recent expansion. Combining our results with those of previous studies, we found that the common toad population of Xinjiang, China, belongs to the European-Caucasian lineage and that its closest relatives based on phylogenetic relationships were eastern European populations. Our research contributes to expanding knowledge of the geographic distribution of B. bufo and illuminates the lineage and genetic relationships of the B. bu fo population in Xinjiang, China. Future research should continue to update the geographic distribution of B. bufo and complete a genetic investigation of the full range of this species.

关键词： distribution genetic distance genetic structure haplotype mitochondrial DNA phylogenetic tree

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Diversity and genetic Structuration of Populations of <i>Plutella xylostella</i>(Lepidoptera, Plutellidae), Cabbage Farming Destroyer in Senegal

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Advances in Entomology 2022年第1期10卷 1-13页

作者： Toffène Diome Mamecor Faye Marième Seck Cheikh Tidiane Niass Mbacké Sembène genetic Team and Population Management Department of Animal Biology Faculty of Sciences and Technology Cheikh Anta Diop University Dakar Senegal Laboratory of Parasitology Department of Animal Biology Faculty of Sciences and Technology Cheikh Anta Diop University Dakar Senegal

Plutella xylostella, pointed out as the most dangerous destroyer of cabbage (Brassica olerarea), is a cosmopolitan species. In fact, owing to its large capacity of adaptation, P. xylestella colonizes any kind of area. This insect can bring about up to 90% of losses on cabbage farming. To control the insect, Senegalese farmers, very often, resort to high dose of chemical pesticides which are repetitively sprayed. The use of these chemical products gives rise to different varieties of resistant insects, which results in the emergence of different haplotypes between populations. It is in such a context that this study has been undertaken. Our objective is then to contribute to the knowledge of the genetic diversity of P. xylostella populations in Senegal. To hit the target, PCR- Sequencing method has been applied on samples from the five following localities: Diofior, Malika, Mboro, Santh Ndong, and Sebikotane. P. xylostella from Mboro is genetically different from the other populations. This fact could be due to a different way of using pesticides in this area vis-à-vis of the other localities. On the other hand, between populations of P. xylostella from Diofior, Malika, Santh Ndong, and Sebikotane, there is no significant genetic difference. In other respects, phylogenetic trees reveal the existence of two clades: one with individuals from Mboro and the other one with individuals from the other four localities. P. xylostella from Mboro distinguishes itself from other populations and then, can be regarded as a sub-population. Thus, the phylogenetic trees reveal the existence of two groups of P. xylostella in Senegal.

关键词： Brassica oleracea genetic Diversity genetic structure

Two genetically distinct units of Sinomanglietia glauca (Magnoliaceae) detected by chloroplast PCR-SSCP

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Journal of Systematics and Evolution 2009年第2期47卷 110-114页

作者： 1Zhi-Rong ZHANG 1Lai-Chun LUO 2Ding WU 1Zhi-Yong ZHANG 1(Laboratory of Subtropical Biodiversity,Jiangxi Agricultural University,Nanchang 330045,China) 2(Jingdezhen Comprehensive College,Jingdezhen 333000,China) Laboratory of Subtropical Biodiversity Jiangxi Agricultural University Nanchang 330045 China Jingdezhen Comprehensive College Jingdezhen 333000 China

Sinomanglietia glauca is a critically endangered species described from Jiangxi Province in the 1990s.Recently two populations were discovered from Yongshun County of west Hunan Province,about 450 km away from those in Jiangxi.Because of the new findings and the poor reproducibility inherent to RAPD and ISSR markers of previous studies,the population structure of this rare species was reanalyzed with chloroplast PCR-SSCP(single-stranded conformation polymorphism),including all of four recorded populations.The results showed that two distinct haplotypes characterized Jiangxi and Hunan populations separately,with no genetic variation occurring within regions.We postulated that this surprising pattern might result from habitat fragmenta-tion and demographic bottlenecks during and/or after the Quaternary glaciation.On the basis of the pronounced genetic structure,two evolutionarily significant units(ESUs) were recommended for effective conservation of S.glauca.

关键词： chloroplast genome genetic structure PCR-SSCP Sinomanglietia glauca

genetic Characterization of Nile Tilapia (Oreochromis niloticus) Strains from Senegal for Sustainable Local Aquaculture Production

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Open Journal of genetics 2023年第1期13卷 1-22页

作者： Mbaye Tine Ramatoulaye Fall Hamet Diaw Diadhiou Mbacké Sembene UFR of Agricultural Sciences Aquaculture and Food Technologies (UFR S2ATA) Gaston Berger University (UGB) Saint-Louis Senegal The National Agency for Aquaculture (ANA) Dakar Senegal ISRA/Oceanographic Research Center Dakar-Thiaroye Dakar Senegal Department of Animal Biology Faculty of Science and Technology Cheikh Anta Diop University (UCAD) Dakar Senegal

The optimization of aquaculture production requires the selection of efficient strains. Thus, genetic improvement has become one of the important levers to boost the development of aquaculture. The objective of this study was to carry out genetic characterization of Nile tilapia Oreochromis niloticus, one of the most cultivated fish species in Senegal, in order to select an efficient strain to optimize local fish production. Thus, fish from five different populations (Richard-Toll, ANA, ITACA, Mbodiene and Sauvage) were analyzed, with 15 individuals per population. genetic diversity and population structure were assessed using molecular genetic analyses by sequence characterized amplified region (SCAR) and microsatellite (SSR) markers. The analyses of the SCARII marker were conducted on four populations (ANA, ITACA, Sauvage and Mbodiene) while microsatellite analyses were conducted on all five populations. The results show high levels of polymorphism of SSR markers, and a high level of observed heterozygosity (Ho), indicating a high within-population genetic variability. These results are in agreement with the AMOVA results, which indicated a high within-population genetic variability (94%). The genetic structure analysis by DAPC indicates that the five populations analyzed are structured into four groups, which are highly heterogeneous because they share common allele individuals. The analysis of the genetic structure by AMOVA showed a low degree of differentiation between the populations (6%), in agreement with the genetic differentiation index (Fst = 0.059). The heterogeneity of studied populations implies a genetic flow over time, which may have existed between the original populations. The overall negative Tajima D values and low genetic differentiation indicate an excess of rare mutations in the populations studied, resulting from a recent population expansion from a limited number of initial breeders isolated in locale hatcheries. Thus, further studies with a much larger panel of markers are required to be

关键词： Oreochromis niloticus Polymorphism Heterozygosity genetic Diversity genetic structure

Incidence,genomic diversity,and evolution of strawberry mottle virus in China

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BIOCELL 2021年第4期45卷 1137-1151页

作者： LINGJIAO FAN CHENGYONG HE MENGMENG WU DEHANG GAO ZHENFEI DONG SHENGFAN HOU ZEKUN FENG HONGQING WANG College of Horticulture China Agricultural UniversityBeijing100193China

Strawberry mottle virus(SMoV)is one of the most common viruses infecting strawberries,causing losses to fruit yield and quality.In this study,165 strawberry leaf samples were collected from six provinces of China,46 of which tested positive for SMoV.The complete genome sequences of 11 SMoV isolates were obtained from Liaoning(DGHY3,DGHY16-2,DGHY17,DGHY20-2,DGHY21,DGHY26-2),Shandong(SDHY1,SDHY5,SDHY31-2,SDHY33-2),and Beijing(BJMX7).The RNA1 and RNA2 nucleotide identities between the 11 Chinese isolates were 95.4-99.3%and 96.3-99.6%,respectively,and they shared 78.4-96.6%and 84.8-93.5%identities with the available SMoV isolates in GenBank.Recombination analysis revealed that Chinese isolate SDHY33-2 and Canadian isolates Ontario and Simcoe were recombinants,and recombination events frequently occurred in the 3’UTR of SMoV.Phylogenetic analysis showed that in an RNA1 tree,most Chinese isolates clustered into the same group while isolate DGHY17 clustered into another group together with Czech isolate C and three Canadian isolates.In an RNA2 tree,all Chinese isolates clustered into a single group.The phylogenetic analysis based on nucleotide sequences was consistent with the results based on coat protein(CP)and RNA-dependent RNA polymerase(RdRp).Further evolutionary analysis indicated that negative selection drives SMoV evolution,and gene flow plays a major role in genetic differentiation.Additionally,reassortment and recombination also influence the evolution of SMoV.To our knowledge,this is the first report of the complete genome of SMoV isolates from China and a detailed analysis of the SMoV population structure.

关键词： Viral occurrence Complete genome Molecular variation genetic structure

Mitochondrial DNA sequence diversity in three ethnic populations from the South-west Iran:a preliminary study

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Frontiers in Biology 2011年第5期6卷 422-432页

作者： Elham DAVOUDI-DEHAGHANI Ali Mohammad FOROUGHMAND Babak SAFFARI Massoud HOUSHMAND Hamid GALEHDARI Mehdi SHAFA SHARIAT PANAHI Majid YAVARIAN Mohammad Hossein SANATI Somayeh TORFI Department of genetics Shahid Chamran UniversityAhvaz 61357-43337Iran Medical genetics Department Tehran University of Medical SciencesTehran 14155-6447Iran Human genetic Research Group Iranian Academic Center for EducationCulture&Research(ACECR)Fars Province BranchShiraz 71347Iran National Institute for genetic Engineering and Biotechnology Tehran 14155-6343Iran Hematology Research Center School of MedicineShiraz University of Medical SciencesShiraz 71937Iran

To investigate the genetic structure of human populations in the South-west region of Iran,mitochondrial first hypervariable DNA sequences were obtained from 50 individuals representing three different ethnic groups from Khuzestan Province.Studied groups were Shushtari Persians and Chahar Lang Bakhtiyaries from Indo-Europeanspeaking populations and Bani Torof Arabs from Semitic-speaking linguistic families.genetic analysis of mtDNA data showed high similarity of Chahar Lang Bakhtiyaries with other Iranian Indo-European-speaking populations while Shushtaries and Bani Torofs had a closer affinity with Semitic-speaking groups rather than to other Iranian populations.The relationship of Chahar Lang Bakhtiyaries and Bani Torof Arabs with their neighbor populations can be explained by linguistic and geographic proximity.Whereas,the greater similarity of Shushtari Persians with West Asian Arabs is probably according to high gene flow between them.This article represents a preliminary study of three major ethnic groups of South-west Iran which investigates the potential genetic substructure of the region.

关键词： diversity mitochondrial DNA first hypervariable sequence Iran genetic structure population

genetic differentiation of Arthrobacter population from heavy metal-contaminated environment

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Frontiers in Biology 2007年第1期2卷 30-34页

作者： ZHANG Hanbo REN Weimin SHAO Qiyong DUAN Changqun Department of Biology Yunnan UniversityKunming 650091China Department of Environmental Science Yunnan UniversityKunming 650091China

Six samples containing extremely high concen-tration of Pb,Zn,and Cd were obtained from the layers of 5−10 cm and 25−30 cm three tailing piles,with ages of about 10,20 and more than 80 years,respectively.Then,48 bacterial strains were obtained from these samples,and sub-sequently their phylogenetic positions were determined by analysis on the partial sequence of 16S rRNA gene(fragment length ranging from 474 to 708 bp).These isolates were members of the Arthrobacter genus,phylogenetically close to A.keyseri and A.ureafaciens,with sequence ranging from 99.1%to 100%.Furthermore,genetic variation between sub-populations from different samples was revealed by analysis on their randomly amplified polymorphic DNA profile.Nei genetic distance showed that the greatest differentiation occurred between subpopulation A and C.Notably,either genetic distance between subpopulations from the layers of 5−10 cm and 25−30 cm of each tailing pile or between same layers of different tailing pile increased with the history of tailings.Moreover,correlation analysis showed that soluble Pb has a significantly negative relationship with Nei’gene diversity of subpopulation.It was assumed that soluble Pb may be respon-sible for the reduced genetic diversity of the Arthrobacter popu-lation.Our data provided evidence that genetic differentiation of microbial populations was consistent with the changes of environmental factors,particularly heavy metals.

关键词： lead-zinc mine tailings Arthrobacter phylogenetic analysis randomly amplified polymorphic DNA genetic structure

Molecular genetic analysis of Dongzhou-period ancient human of Helingeer in Inner Mongolia,China

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Frontiers in Biology 2008年第1期3卷 9-12页

作者： Yuqin FU Chengzhi XIE Han ZHAO Xuelian XU Yinqiu CUI Quanchao ZHANG Hui ZHOU Hong ZHU Ancient DNA Laboratory Research Center for Chinese Frontier ArchaeologyJilin UniversityChangchun 130012China College of Life Science Jilin UniversityChangchun 130023China College of Life Science Jilin Agricultural UniversityChangchun 130118China

The mtDNA hypervariable region I(HVR-I)of 10 ancient individuals from Dongzhou-period ancient human populations in Helingeer county of Inner Mongolia were amplified and sequenced to investigate the genetic structure.The relationships between the ancient population and related extant populations,as well as its possible origin at the molecular level,were also studied.Moreover,phylogenetic analysis and multi-dimensional scaling analysis were also performed based on the mtDNA data of the ancient population in Helingeer and the related Eurasian population.The results showed that the ancient population in Helingeer were closer to the northern Asian populations than to the other compared populations in matrilineal lineage.Combining the research results of archaeology and anthropology as well as molecular biology,we inferred that they were nomads who migrated from Mongolia plateau and cis-Baikal region to Helingeer in Inner Mongolia,China.

关键词： ancient DNA mtDNA genetic structure phylogenetic analysis

genetic Variation in Triticum turgidum L. ssp. turgidum Landraces from China Assessed by EST-SSR Markers

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Agricultural Sciences in China 2008年第9期7卷 1029-1036页

作者： LI Wei DONG Pan WEI Yu-ming CHENG Guo-yue ZHENG You-liang Key Laboratory of Crop genetic Resources and Improvement in Southwest China Ministry of Education/Sichuan Agricultural University Ya＇an 625014 P.R.China Triticeae Research Institute Sichuan Agricultural University Dujiangyan 611830 P.R.China College of Agronomy Sichuan Agricultural University Ya＇an 625014 P.R.China

It was helpful for the wheat improvement to evaluate the genetic resources of Triticum turgidum L. ssp. turgidum landraces. In this study, 68 turgidum landraces accessions, belonging to four geographic populations in China, were investigated by using EST-SSR markers. A total of 63 alleles were detected on 22 EST-SSR loci, and the number of alleles on each locus ranged from 1 to 5, with an average of 2.9. The results of the analysis of molecular variance （AMOVA） indicated that 92.5% of the total variations was attributed to the genetic variations within population, whereas only 7.5% variations among populations. Although the four populations had similar genetic diversity parameters, Sichuan population was yet distinguished from other populations when comparing the population samples in pairs. Significant correlations were detected by the statistic analysis among six genetic diversity parameters among each other. The selection difference between heterozygosty and homozygosty was also observed among different EST-SSR locus. The genetic similarity （GS） ranged from 0.18 to 0.98, with the mean of 0.72, and all accessions could be clustered into 7 groups. The dendrogram suggested that the genetic relationships among turgidum accessions evaluated by EST-SSR markers were unrelated to their geographic distributions. These results implied that turgidum landraces from China had the unique characters of genetic diversity.

关键词： T. turgidum L. ssp. turgidum EST-SSR markers genetic variation genetic structure

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