scholarly journals Genetic diversity analysis of Chinese Leishmania isolates and development of L. donovani complex-specific markers by RAPD

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Dongmei Yuan ◽  
Hanxiao Qin ◽  
Dali Chen ◽  
Jianping Chen
Keyword(s):  
Genetic Diversity ◽  
Random Amplified Polymorphic Dna ◽  
Phylogenetic Analyses ◽  
Data Matrix ◽  
Western China ◽  
Future Research ◽  
Specific Gene ◽  
Scar Markers ◽  
Gene Markers ◽  
Geographic Regions

Abstract Background Leishmaniasis is one of the most neglected tropical diseases in the world and remains endemic in some underdeveloped regions, including western China. The phylogeny and classification of Chinese Leishmania has not been completely clarified to date, especially within the Leishmania (L.) donovani complex, although phylogenetic analyses based on a series of gene markers have been performed. More analytic methods and data are still needed. Random amplified polymorphic DNA (RAPD) technology can sensitively identify slight intraspecific differences, and it is a powerful tool to seek species-specific markers. This work attempted to identify Chinese Leishmania isolates from diverse geographic regions at the genomic level. Meanwhile, specific markers of the L. donovani complex were also developed by RAPD. Methods RAPD was applied to 14 Chinese Leishmania isolates from diverse geographic regions and 3 WHO reference strains. The polymorphic sites of amplification were transformed into a data matrix, based on which genetic similarity was calculated, and a UPGMA dendrogram was constructed to analyse the genetic diversity of these Leishmania isolates. Meanwhile, the specific amplification loci of the L. donovani complex were TA-cloned, sequenced and converted into sequence characterized amplified region (SCAR) markers, which were validated preliminarily in 17 available Leishmania strains in this study and analysed by bioinformatics. Results The cluster analyses showed that the three Leishmania sp. isolates SC10H2, SD and GL clustered together and apart from others, the strains of the L. donovani complex clearly divided into two clades, and the three isolates Cy, WenChuan and 801 formed a subclade. Three specific SCAR markers of the L. donovani complex, i.e., 1-AD17, 2-A816 and 3-O13, were successfully obtained and validated on 17 available Leishmania strains in this study. Through bioinformatic analyses, Marker 1-AD17 may have more specificity for PCR detection of VL, and Marker 3-O13 has the potential to encode a protein. Conclusions The RAPD results verified that the undescribed Leishmania species causing visceral leishmaniasis (VL) in China was a unique clade distinguished from L. donovani and revealed that there was genetic differentiation among Chinese L. donovani. The identification of L. donovani-specific markers may help to provide a foundation for future research attempting to develop new specific diagnostic markers of VL and identify specific gene functions.

scholarly journals Genetic Diversity Analysis of Chinese Leishmania Isolates and Development of L. donovani Complex Specific Markers by RAPD

2020 ◽  
Author(s):  
Dongmei Yuan ◽  
Hanxiao Qin ◽  
Dali Chen ◽  
Jianping Chen
Keyword(s):  
Genetic Diversity ◽  
Neglected Tropical Diseases ◽  
Random Amplified Polymorphic Dna ◽  
Phylogenetic Analyses ◽  
Data Matrix ◽  
Specific Gene ◽  
Scar Markers ◽  
Bioinformatics Analyses ◽  
Gene Markers ◽  
Geographic Regions

Abstract Background: Leishmaniasis is one of the most neglected tropical diseases in the world and is still endemic in some underdeveloped regions including western of China. The phylogeny and classification of Chinese Leishmania has not yet been clarified, especially within Leishmania (L.) donovani complex, although phylogenetic analyses based on a series of gene markers were carried out. More different analytic method and data still be needed. Random amplified polymorphic DNA (RAPD) technology could identify slight intraspecific differences sensitively, and it always be a powerful tool to seek the species-specific markers. This work aimed to identify Chinese Leishmania isolates from diverse geographic regions at genomic level. Meanwhile, the specific markers of L. donovani complex were also developed by RAPD.Methods: The RAPD was applied on 14 Chinese Leishmania isolates from diverse geographic regions and 3 WHO reference strains. The polymorphic sites of amplification were transformed into data matrix, based on which genetic similarity were calculated and UPGMA dendrogram were constructed to analyze genetic diversity of these Leishmania isolates. Meanwhile, the specific amplification loci of L. donovani complex were TA-cloned, sequenced and converted into sequence characterized amplified regions (SCAR) markers, which were validated preliminarily in available 17 Leishmania strains in this study and analyzed by bioinformatics.Results: The cluster analyses showed that the three Leishmania sp. isolates SC10H2, SD and GL clustered together and apart from others, and the strains of L. donovani complex clearly divided into two clades and the three isolates Cy, WenChuan and 801 formed a subclade. Three specific SCAR markers of L. donovani complex, i.e. 1-AD17, 2-A816 and 3-O13, were successfully obtained and validated on available 17 Leishmania strains in this study. Through bioinformatics analyses, Marker 1-AD17 may have more specificity on PCR detection of VL and Marker 3-O13 has the potential of encoding protein.Conclusions: the RAPD result verified that the undescribed Leishmania species causing visceral Leishmaniasis (VL) in China was a unique clade distinguished from L. donovani, and revealed that there was genetic differentiation among Chinese L. donovani. The development of L. donovani specific markers may provide the foundation for developing new specific diagnostic markers of VL and the research of specific gene function.

scholarly journals Genetic diversity analysis of Chinese Leishmania isolates and development of L. donovani complex specific markers by RAPD

2020 ◽  
Author(s):  
Dongmei Yuan ◽  
Hanxiao Qin ◽  
Dali Chen ◽  
Jianping Chen
Keyword(s):  
Genetic Diversity ◽  
Neglected Tropical Diseases ◽  
Random Amplified Polymorphic Dna ◽  
Phylogenetic Analyses ◽  
Data Matrix ◽  
Specific Gene ◽  
Scar Markers ◽  
Bioinformatics Analyses ◽  
Gene Markers ◽  
Geographic Regions

Abstract Background: Leishmaniasis is one of the most neglected tropical diseases in the world and is still endemic in some underdeveloped regions including western of China. The phylogeny and classification of Chinese Leishmania has not yet been clarified, especially within Leishmania (L.) donovani complex, although phylogenetic analyses based on a series of gene markers were carried out. More different analytic method and data still be needed. Random amplified polymorphic DNA (RAPD) technology could identify slight intraspecific differences sensitively, and it always be a powerful tool to seek the species-specific markers. This work aimed to identify Chinese Leishmania isolates from diverse geographic regions at genomic level. Meanwhile, the specific markers of L. donovani complex were also developed by RAPD.Methods: The RAPD was applied on 14 Chinese Leishmania isolates from diverse geographic regions and 3 WHO reference strains. The polymorphic sites of amplification were transformed into data matrix, based on which genetic similarity were calculated and UPGMA dendrogram were constructed to analyze genetic diversity of these Leishmania isolates. Meanwhile, the specific amplification loci of L. donovani complex were TA-cloned, sequenced and converted into sequence characterized amplified regions (SCAR) markers, which were validated preliminarily in available 17 Leishmania strains in this study and analyzed by bioinformatics.Results: The cluster analyses showed that the three Leishmania sp. isolates SC10H2, SD and GL clustered together and apart from others, and the strains of L. donovani complex clearly divided into two clades and the three isolates Cy, WenChuan and 801 formed a subclade. Three specific SCAR markers of L. donovani complex, i.e. 1-AD17, 2-A816 and 3-O13, were successfully obtained and validated on available 17 Leishmania strains in this study. Through bioinformatics analyses, Marker 1-AD17 may have more specificity on PCR detection of VL and Marker 3-O13 has the potential of encoding protein.Conclusions: The RAPD result verified that the undescribed Leishmania species causing visceral Leishmaniasis (VL) in China was a unique clade distinguished from L. donovani, and revealed that there was genetic differentiation among Chinese L. donovani. The development of L. donovani specific markers may provide the foundation for developing new specific diagnostic markers of VL and the research of specific gene function.

scholarly journals Analysis of Genetic Diversity of Fusarium tupiense, the Main Causal Agent of Mango Malformation Disease in Southern Spain

Plant Disease ◽  
2016 ◽  
Vol 100 (2) ◽  
pp. 276-286 ◽  
Author(s):  
M. Crespo ◽  
F. M. Cazorla ◽  
A. de Vicente ◽  
E. Arrebola ◽  
J. A. Torés ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Sequence Data ◽  
Random Amplified Polymorphic Dna ◽  
Phylogenetic Analyses ◽  
Southern Spain ◽  
Fusarium Fujikuroi ◽  
Dna Sequence Data ◽  
Fusarium Fujikuroi Species Complex ◽  
Polymerase Chain ◽  
Mango Malformation

Mango malformation disease (MMD) has become an important global disease affecting this crop. The aim of this study was to identify the main causal agents of MMD in the Axarquía region of southern Spain and determine their genetic diversity. Fusarium mangiferae was previously described in the Axarquía region but it represented only one-third of the fusaria recovered from malformed trees. In the present work, fusaria associated with MMD were analyzed by arbitrary primed polymerase chain reaction (ap-PCR), random amplified polymorphic DNA (RAPD), vegetative compatibility grouping (VCG), a PCR screen for mating type idiomorph, and phylogenetic analyses of multilocus DNA sequence data to identify and characterize the genetic diversity of the MMD pathogens. These analyses confirmed that 92 of the isolates were F. tupiense, which was previously only known from Brazil and Senegal. In addition, two isolates of a putatively novel MMD pathogen were discovered, nested within the African clade of the Fusarium fujikuroi species complex. The F. tupiense isolates all belonged to VCG I, which was first described in Brazil, and the 11 isolates tested showed pathogenicity on mango seedlings. Including the prior discovery of F. mangiferae, three exotic MMD pathogenic species have been found in southern Spain, which suggests multiple independent introductions of MMD pathogens in the Axarquía region.

Phylogeography of the rare Gymnocarpos przewalskii (Caryophyllaceae): indications of multiple glacial refugia in north-western China

2012 ◽  
Vol 60 (1) ◽  
pp. 20 ◽  
Author(s):  
S. M. Ma ◽  
M. L. Zhang ◽  
S. C. Sanderson
Keyword(s):  
Tarim Basin ◽  
Phylogenetic Analyses ◽  
Glacial Refugia ◽  
Gansu Province ◽  
Western China ◽  
Phylogeographic Structure ◽  
Quaternary Climate ◽  
Geographic Regions ◽  
Gymnocarpos Przewalskii ◽  
North Western

We investigated the phylogeography of Gymnocarpos przewalskii Maxim. (Caryophyllaceae), a rare relictual shrub restricted to north-western China, in the context of Quaternary climate oscillations. Three cpDNA regions (psbA–trnH, ycf6–psbM and rpl32–trnL (UAG)) were sequenced for 160 individuals from 16 populations. High genetic diversity (hT = 0.930, hS = 0.425) and a significant phylogeographic structure (NST > GST, P < 0.01) were identified; 31 different cpDNA haplotypes were detected. Phylogenetic analyses showed that the haplotypes were clustered into five clades, consistent with their distributions in the following four geographic regions: the Tarim Basin, Hami Basin, the western Yumen of Gansu Province and an easternmost region, consisting of populations in the Wulate Rear Banner region in Inner Mongolia, the Jinta and Jingyuan regions in Gansu Province and the Zhongwei region in Ningxia. The existence of regional divergence was supported by AMOVA, which revealed that ~63% of variation was due to differences among the four geographic regions. Four independent glacial refugia were inferred, in the western Tarim Basin, Hami Basin, the Liuyuan region in western Gansu and the easternmost region mentioned. Population bottlenecks and postglacial recolonisation were identified in the northern Tarim Basin, western Yumen and the Jinta region in Gansu Province.

scholarly journals An identification tool for the Australian weedy Sporobolus species based on random amplified polymorphic DNA (RAPD) profiles

2005 ◽  
Vol 56 (2) ◽  
pp. 157 ◽  
Author(s):  
Sangita Shrestha ◽  
Stephen W. Adkins ◽  
Glenn C. Graham ◽  
Donald S. Loch
Keyword(s):  
Genetic Diversity ◽  
Genetic Markers ◽  
Native Species ◽  
Random Amplified Polymorphic Dna ◽  
Data Matrix ◽  
High Genetic Diversity ◽  
Considerable Difficulty ◽  
Major Cluster ◽  
Weedy Species ◽  
Species Specific

Based on morphological features alone, there is considerable difficulty in identifying the 5 most economically damaging weed species of Sporobolus [viz. S. pyramidalis P. Beauv., S. natalensis (Steud.) Dur and Schinz, S. fertilis (Steud.) Clayton, S. africanus (Poir.) Robyns and Tourney, and S. jacquemontii Kunth.] found in Australia. A polymerase chain reaction (PCR)-based random amplified of polymorphic DNA (RAPD) technique was used to create a series of genetic markers that could positively identify the 5 major weeds from the other less damaging weedy and native Sporobolus species. In the initial RAPD profiling experiment, using arbitrarily selected primers and involving 12 species of Sporobolus, 12 genetic markers were found that, when used in combination, could consistently identify the 5 weedy species from all others. Of these 12 markers, the most diagnostic were UBC51490 for S. pyramidalis and S. natalensis; UBC43310, 2000, 2100 for S. fertilis and S. africanus; and OPA20850 and UBC43470 for S. jacquemontii. Species-specific markers could be found only for S. jacquemontii. In an effort to understand why there was difficulty in obtaining species-specific markers for some of the weedy species, a RAPD data matrix was created using 40 RAPD products. These 40 products amplified by 6 random primers from 45 individuals belonging to 12 species, were then subjected to numerical taxonomy and multivariate system (NTSYS pc version 1.70) analysis. The RAPD similarity matrix generated from the analysis indicated that S. pyramidalis was genetically more similar to S. natalensis than to other species of the ‘S. indicus complex’. Similarly, S. jacquemontii was more similar to S. pyramidalis, and S. fertilis was more similar to S. africanus than to other species of the complex. Sporobolus pyramidalis, S. jacquemontii, S. africanus, and S. creber exhibited a low within-species genetic diversity, whereas high genetic diversity was observed within S. natalensis, S. fertilis, S. sessilis, S. elongates, and S. laxus. Cluster analysis placed all of the introduced species (major and minor weedy species) into one major cluster, with S. pyramidalis and S. natalensis in one distinct subcluster and S. fertilis and S. africanus in another. The native species formed separate clusters in the phenograms. The close genetic similarity of S. pyramidalis to S. natalensis, and S. fertilis to S. africanus may explain the difficulty in obtaining RAPD species-specific markers. The importance of these results will be within the Australian dairy and beef industries and will aid in the development of integrated management strategy for these weeds.

Phylogenetic analysis and genetic diversity of Phytophthora palmivora causing black pod disease of cocoa in Malaysia.

2021 ◽  
Author(s):  
Wael Alsultan ◽  
Ganesan Vadamalai ◽  
Halimi Mohd Saud ◽  
Ahmad Khairulmazmi ◽  
Mui Yun Wong ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Random Amplified Polymorphic Dna ◽  
Phylogenetic Analyses ◽  
Inter Simple Sequence Repeat ◽  
Its Rdna ◽  
Phytophthora Palmivora ◽  
High Genetic Diversity ◽  
Study Results ◽  
Black Pod ◽  
Black Pod Disease

Black pod, caused by Phytophthora spp., occurs worldwide and is a major problem to cocoa farmers in Malaysia. Limited studies addressed causal agents of black pod disease of cocoa in Malaysia as well as their genetic diversity. Therefore, this study was initiated to isolate and identify Phytophthora from the main cocoa plantations infected by black pod in Malaysia using sequence analyses of the ITS rDNA, EF-1α, and COX I gene regions. A total of 36 Phytophthora isolates were obtained from infected cocoa plantations from five states of Malaysia in 2016 and 14 isolates in 2013. Six Phytophthora isolates obtained from durian crop in 2013 were also used in this study. Results of phylogenetic analyses of combined dataset of the ITS rDNA, COX I and EF-1α confirmed that all Phytophthora isolates belonged to P. palmivora. P. palmivora isolates obtained from cocoa and durian clustered into different subclades based on the three regions examined. The study also examined the genetic diversity within a population of 56 P. palmivora isolates using random amplified polymorphic DNA (RAPD) and Inter-simple sequence repeat (ISSR) markers. The results of both markers indicated relatively high diversity among P. palmivora isolates. The complete separation was based on host and year of isolation. The study suggests that one species of Phytophthora viz. P. palmivora, is responsible for black pod of cocoa in Malaysia. However, the relatively high genetic diversity and separation of isolates into different clades may suggest that P. palmivora has been introduced into Malaysia via different sources.

Low levels of genetic diversity in red pine confirmed by random amplified polymorphic DNA markers

1992 ◽  
Vol 22 (9) ◽  
pp. 1332-1337 ◽  
Author(s):  
A. Mosseler ◽  
K.N. Egger ◽  
G.A. Hughes
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Rapd Markers ◽  
Black Spruce ◽  
Random Amplified Polymorphic Dna ◽  
Red Pine ◽  
Gene Markers ◽  
Island Populations ◽  
Oligonucleotide Primers ◽  
Low Levels

Random amplified polymorphic DNA (RAPD) markers were used to characterize genetic variation in disjunct Newfoundland populations of red pine (Pinusresinosa Ait.) for comparison with individuals from throughout the mainland range of red pine. Red pine demonstrated a largely monomorphic profile for 69 arbitrary oligonucleotide primers. DNA samples from white spruce (Piceaglauca (Moench) Voss) and black spruce (Piceamariana (Mill.) B.S.P.) that were screened together with red pine for 11 oligonucleotide primers showed abundant polymorphisms, confirming the genetic heterogeneity that characterizes these Boreal Zone spruces. Results with RAPD markers correspond with genetic diversity estimates using isozyme gene markers for both spruce species and red pine. RAPD markers provided further confirmation of low levels of genetic variation for a random sample of the red pine genome. A period of between 8000 and 10 000 years of isolation on the island of Newfoundland has resulted in very little detectable genetic differentiation of island populations from mainland populations, and the mainland populations have not recovered from losses of genetic diversity following a hypothesized genetic bottleneck that may have been experienced during glacial episodes of the Holocene. The low levels of genetic variation observed in red pine demonstrate the long time periods required for recovery following a loss of genetic diversity in long-lived, long-generation organisms like trees.

scholarly journals Population Genetics of Bactrocera minax (Diptera: Tephritidae) in China Based on nad4 Gene Sequence

Insects ◽  
2019 ◽  
Vol 10 (8) ◽  
pp. 236
Author(s):  
Feng Hong ◽  
Lizhi Gao ◽  
Hong-Liang Han ◽  
Pan Wang ◽  
Jia Wang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Southern China ◽  
Phylogenetic Analyses ◽  
Discrete Distribution ◽  
Central China ◽  
Western China ◽  
Species Dispersal ◽  
Haplotype Networks ◽  
Nad4 Gene

Bactrocera minax (Enderlein) (Diptera: Tephritidae) is an important citrus pest in Asia with a non-uniform distribution. In some locations, it had been reported to occur but was either eradicated or disappeared itself. To understand species dispersal of B. minax, we collected and analyzed 359 individuals from 18 localities in China. One mitochondrial DNA gene fragment (nad4) was used to investigate the genetic diversity and population genetic structure of B. minax. The populations were divided by phylogenetic analyses and statistical parsimony haplotype networks into three branches: a Central China (CC) branch, a Western China (WC) branch, and a Southern China (SC) branch. A total of 93 variable sites (15.6% of the 595 bp alignment) and 91 unique haplotypes were observed in the 359 individuals scored from the nad4 gene of the 18 B. minax populations. This indicated that B. minax had a high level of genetic diversity. These populations also showed a discrete distribution in both the scatter plots of genetic versus geographical distance for pairwise population comparisons and the median-joining network of haplotypes, which revealed the strong genetic structure of B. minax.

Genetic diversity of root-knot nematodes from Brazil and development of SCAR markers specific for the coffee-damaging species

Genome ◽  
2002 ◽  
Vol 45 (5) ◽  
pp. 862-870 ◽  
Author(s):  
Onivaldo Randig ◽  
Michel Bongiovanni ◽  
Regina M.D.G Carneiro ◽  
Philippe Castagnone-Sereno
Keyword(s):  
Genetic Diversity ◽  
Multiplex Pcr ◽  
Rapd Markers ◽  
Phylogenetic Analyses ◽  
The Other ◽  
Scar Markers ◽  
Meloidogyne Hapla ◽  
Root Knot Nematodes ◽  
Sequence Characterized Amplified Region ◽  
Scar Primers

RAPD markers were used to characterize the genetic diversity and relationships of root-knot nematodes (RKN) (Meloidogyne spp.) in Brazil. A high level of infraspecific polymorphism was detected in Meloidogyne arenaria, Meloidogyne exigua, and Meloidogyne hapla compared with the other species tested. Phylogenetic analyses showed that M. hapla and M. exigua are more closely related to one another than they are to the other species, and illustrated the early divergence of these meiotically reproducing species from the mitotic ones. To develop a PCR-based assay to specifically identify RKN associated with coffee, three RAPD markers were further transformed into sequence-characterized amplified region (SCAR) markers specific for M. exigua, Meloigogyne incognita and Meloidogyne paranaensis, respectively. After PCR using the SCAR primers, the initial polymorphism was retained as the presence or absence of amplification. Moreover, multiplex PCR using the three pairs of SCAR primers in a single reaction enabled the unambiguous identification of each species, even in mixtures. Therefore, it is concluded that the method developed here has potential for application in routine diagnostic procedures.Key words: diagnostic, multiplex PCR, phylogeny, RAPD, root-knot nematodes.

scholarly journals Population Biology of Pseudoperonospora humuli in Oregon and Washington

Plant Disease ◽  
2006 ◽  
Vol 90 (10) ◽  
pp. 1283-1286 ◽  
Author(s):  
Hee Youn Chee ◽  
Mark E. Nelson ◽  
Gary G. Grove ◽  
Kenneth C. Eastwell ◽  
Stephen T. Kenny ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variation ◽  
Population Biology ◽  
Random Amplified Polymorphic Dna ◽  
Dna Amplification ◽  
Pseudoperonospora Humuli ◽  
Band Profile ◽  
Geographic Regions ◽  
Unique Band

Pseudoperonospora humuli populations from Oregon and Washington were analyzed for genetic variation using random amplified polymorphic DNA (RAPD) and DNA amplification fingerprinting (DAF) markers. The genetic structure of the Oregon and Washington populations differed considerably. There was little genetic diversity in Washington, with only five RAPD and six DAF groups detected among 40 isolates tested. One genotype was predominant in Washing-ton. In contrast, 18 RAPD and 34 DAF groups were found among the 40 isolates tested from Oregon. No unique band profile associated with host cultivar was observed. It is suggested that the distinct difference in population structure between the two geographic regions might be due to climatic differences resulting in a higher frequency of sexual reproduction of P. humuli in Oregon than in Washington.

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