Intra- and Inter-Host Assessment of Bartonella Diversity with Focus on Non-Hematophagous Bats and Associated Ectoparasites from Brazil

The relationship among bats, ectoparasites and associated microorganisms is important to investigate how humans can become exposed to zoonotic agents. Even though the diversity of Bartonella spp. in bats and ectoparasites has been previously reported, the occurrence of gltA genotypes within hosts has not been assessed so far. We aimed to investigate the genetic diversity of Bartonella spp. in non-hematophagous bats and associated ectoparasites by assessing cloned gltA Bartonella genotypes in intra- and inter-hosts levels, as well as by using three additional molecular markers. Overall, 13.5% (18/133) bat blood samples, 17.18% bat flies (11/64) and 23.8% (5/21) Macronyssidae mite pools showed to be positive for Bartonella spp. Seventeen positive samples were submitted to gltA-cloning and three clones were sequenced for each sample. We also obtained 11, seven and three sequences for nuoG, rpoB and ftsZ genes, respectively. None were positive for the other target genes. We found at least two genotypes among the three gltA-cloned sequences from each sample, and 13 between all the 51 sequences. Among the nuoG, rpoB and ftsZ sequences we found eight, five and three genotypes, respectively. In the phylogenetic analysis, the sequences were positioned mainly in groups related to Bartonella identified in rodents, bats and bat flies. Herein, we showed the genetic diversity of Bartonella in bat’s blood and associated ectoparasites samples at both intra- and inter-host levels.

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The relationship among freezing tolerance, vernalization requirement, Ppd alleles and winter hardiness in European wheat cultivars

The Journal of Agricultural Science ◽

10.1017/s0021859617000521 ◽

2017 ◽

Vol 155 (9) ◽

pp. 1353-1370 ◽

Cited By ~ 5

Author(s):

A. GORASH ◽

R. ARMONIENĖ ◽

Ž. LIATUKAS ◽

G. BRAZAUSKAS

Keyword(s):

Molecular Markers ◽

Western Europe ◽

Complex Trait ◽

Winter Hardiness ◽

Photoperiod Sensitivity ◽

The Other ◽

Wheat Cultivars ◽

Crucial Component ◽

Per Se ◽

The Relationship

SUMMARYWinter hardiness of wheat is a complex trait involving a system of structural, regulatory and developmental genes, which interact in a complex pathway. The objective of the present work was to study the relationship among the main traits determining the level of adaptation and the possibility for target manipulation of breeding material by using molecular markers and phenological parameters. Wheat cultivars from different ecoclimatic environments of Europe were included for analysis. Gene-specific assay showed that photoperiod sensitivity of the studied cultivars was determined by polymorphism in the Ppd-D1 allele. The study established the relationship among winter hardiness, LT50 (the temperature at which 50% of plants are killed), photoperiod sensitivity, vernalization duration and earliness per se genes in the environment of Lithuania. The cultivars from Northern and Western Europe exhibited stronger requirement for vernalization and photoperiod. Although the group of cultivars from the southern latitudes were characterized by earliness, they possessed a stronger level of LT50. The level of LT50 was found to be the most crucial component of winter hardiness, the other traits served as supplementary components.

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Detection, Quantitation, and Phylogenetic Analysis of Noroviruses in Japanese Oysters

Applied and Environmental Microbiology ◽

10.1128/aem.69.10.5782-5786.2003 ◽

2003 ◽

Vol 69 (10) ◽

pp. 5782-5786 ◽

Cited By ~ 122

Author(s):

Tomoko Nishida ◽

Hirokazu Kimura ◽

Mika Saitoh ◽

Michiyo Shinohara ◽

Masahiko Kato ◽

...

Keyword(s):

Genetic Diversity ◽

Phylogenetic Analysis ◽

Virus Type ◽

Reverse Transcription ◽

Real Time Pcr ◽

The Other ◽

Capsid Gene ◽

Neighbor Joining ◽

Norwalk Virus ◽

Reverse Transcription Pcr

ABSTRACT Noroviruses (NVs) cause many cases of oyster- or clam-associated gastroenteritis in various countries. We collected 191 samples from Japanese oysters intended for raw consumption that had been harvested from the sea in two different areas between December 2001 and February 2002. To detect, quantitate, and phylogenetically analyze the NV genome in purified concentrates from the stomachs and digestive diverticula of these oysters, we amplified the NV capsid gene by reverse transcription-PCR. Phylogenetic analysis was performed by using the neighbor-joining method. We detected the NV genome in 17 of 191 oysters (9%). Phylogenetic analysis indicated genogroup I (Norwalk virus type) in 3 of the 17 oysters and genogroup II (Snow Mountain virus type) in the other 14. Both genogroups showed wide genetic diversity. To quantify the NV capsid gene in these oysters, we performed real-time PCR using genogroup-specific probes. More than 102 copies of the NV genome were detected in 11 of 17 oysters. The results suggested that about 10% of Japanese oysters intended for raw consumption harbored NVs, and more than 50% of those oysters in which NVs were detected had a large amount.

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The relationship between fall dormancy and germplasm source in North American alfalfa cultivars

Canadian Journal of Plant Science ◽

10.4141/cjps96-076 ◽

1996 ◽

Vol 76 (3) ◽

pp. 429-433 ◽

Cited By ~ 6

Author(s):

D. T. Fairey ◽

N. A. Fairey ◽

L. P. Lefkovitch

Keyword(s):

Genetic Diversity ◽

Regression Analysis ◽

Plant Height ◽

North American ◽

The Other ◽

Regression Coefficients ◽

Large Contribution ◽

Partial Regression ◽

Fall Dormancy ◽

The Relationship

Most of the genetic diversity of North American alfalfa cultivars has been accounted for by nine germplasm sources listed in descending order of winter hardiness as follows: Medicago sativa ssp. falcata, Ladak, M. sativa ssp. xvaria, Turkistan, Flemish, Chilean, Peruvian, Indian and African. In most instances, the breeder assigns a fall dormancy score and the relative proportions of each of the nine germplasm source for each cultivar at registration. The fall dormancy score (1 = dormant to 9 = non-dormant), determined by measuring plant height in October after harvest in early September, is used to indicate cultivar adaptation for different regions. This study examines the relationship between germplasm composition and plant height, the equivalence of fall dormancy. The signs on the partial regression coefficients of a multiple regression analysis of plant height on the proportional content of the nine sources of germplasm showed that the fall dormancy fell essentially into two classes, namely, a dormant category, comprising cultivars containing a large contribution of Falcata and Ladak, and a non-dormant category, in which Indian and African germplasm predominate. This does not necessarily preclude the influence of any of the other germplasm sources on fall dormancy, since they represent a rich source of diversity. However, nine distinct classes were not recognisable, perhaps because of the lack of an exact equivalence between fall dormancy class and plant height of the fall regrowth. Since these observations have not been derived in a common nursery, the latitude and latitude × cultivar effects have been disregarded. These limitations should be recognized when using the currently assigned fall dormancy ratings to predict cultivar adaptation. Key words: Alfalfa, fall dormancy, sources of germplasm

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A Molecular and Morphological Survey of Generic Limits of Acsmithia and Spiraeanthemum (Cunoniaceae)

Systematic Botany ◽

10.1600/036364409787602410 ◽

2009 ◽

Vol 34 (1) ◽

pp. 141-148 ◽

Cited By ~ 11

Author(s):

Yohan Pillon ◽

Helen C.F. Hopkins ◽

Jérôme Munzinger ◽

Mark W. Chase

Keyword(s):

Phylogenetic Analysis ◽

Molecular Markers ◽

New Caledonia ◽

Intergenic Spacer ◽

Single Copy ◽

The Other ◽

New Combinations ◽

Sexual System ◽

Combined Analysis ◽

Independent Analysis

A phylogenetic analysis was conducted on the tribe Spiraeanthemeae (Cunoniaceae) to clarify relationships of Acsmithia and Spiraeanthemum. Three molecular markers, one plastid region (trnL intron and trnL-trnF intergenic spacer) and two nuclear single copy genes (ncpGS and PHYC), were sequenced for this purpose. The independent analysis of the three markers and a combined analysis all showed that Acsmithia is paraphyletic since Spiraeanthemum is nested within it. A morphological survey of all species in the tribe confirmed the existence of two groups within Acsmithia. One comprises the species from Australia, New Guinea, and A. densiflora from New Caledonia and is characterised by multiple ovules per carpel. The other group contains all the remaining New Caledonian species plus A. vitiensis from Fiji and is characterized by a single ovule per carpel. The study shows that characters previously used to distinguish Acsmithia and Spiraenthemum, phyllotaxy and sexual system, are homoplasious as in several other groups of Cunoniaceae. A broad circumscription of the genus Spiraeanthemum is adopted here that includes the species formerly placed in Acsmithia. Two new combinations are proposed: Spiraeanthemum collinum and Spiraeanthemum meridionale. Spiraeanthemum austrocaledonicum is considered a synonym of Spiraeanthemum densiflorum.

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Phylogenetic analysis, genetic diversity and relationships between the recently segregated species of Corynandra and Cleoserrata from the genus Cleome using DNA barcoding and molecular markers

Comptes Rendus Biologies ◽

10.1016/j.crvi.2016.02.005 ◽

2016 ◽

Vol 339 (3-4) ◽

pp. 123-132 ◽

Cited By ~ 5

Author(s):

Asif Shabodin Tamboli ◽

Swapnil Mahadeo Patil ◽

Avinash Ramchandra Gholave ◽

Suhas Kishor Kadam ◽

Shreya Vijaykumar Kotibhaskar ◽

...

Keyword(s):

Genetic Diversity ◽

Phylogenetic Analysis ◽

Molecular Markers ◽

Dna Barcoding

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Isolation of Candidatus Bartonella rousetti and Other Bat-associated Bartonellae from Bats and Their Flies in Zambia

Pathogens ◽

10.3390/pathogens9060469 ◽

2020 ◽

Vol 9 (6) ◽

pp. 469

Author(s):

Yongjin Qiu ◽

Masahiro Kajihara ◽

Ryo Nakao ◽

Evans Mulenga ◽

Hayato Harima ◽

...

Keyword(s):

Public Health ◽

Phylogenetic Analysis ◽

The Other ◽

Fruit Bats ◽

Public Health Importance ◽

Insectivorous Bats ◽

The Public ◽

Bat Flies

Bat-associated bartonellae, including Bartonella mayotimonensis and Candidatus Bartonella rousetti, were recently identified as emerging and potential zoonotic agents, respectively. However, there is no report of bat-associated bartonellae in Zambia. Thus, we aimed to isolate and characterize Bartonella spp. from bats and bat flies captured in Zambia by culturing and PCR. Overall, Bartonella spp. were isolated from six out of 36 bats (16.7%), while Bartonella DNA was detected in nine out of 19 bat flies (47.3%). Subsequent characterization using a sequence of five different genes revealed that three isolates obtained from Egyptian fruit bats (Rousettus aegyptiacus) were Ca. B. rousetti. The isolates obtained from insectivorous bats (Macronycteris vittatus) were divided into two previously unclassified bat-associated bartonellae. A phylogenetic analysis of the six genotypes of Bartonella gltA sequences from nine pathogen-positive bat flies revealed that three genotypes belonged to the same clades as bat-associated bartonellae, including Ca. B. rousetti. The other three genotypes represented arthropod-associated bartonellae, which have previously been isolated only from ectoparasites. We demonstrated that Ca. B. rousetti is maintained between bats (R. aegyptiacus) and bat flies in Zambia. Continuous surveillance of Bartonella spp. in bats and serological surveys in humans in Africa are warranted to evaluate the public health importance of bat-associated bartonellae.

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Genetic diversity and SNP’s from the chloroplast coding regions of virus-infected cassava

PeerJ ◽

10.7717/peerj.8632 ◽

2020 ◽

Vol 8 ◽

pp. e8632

Author(s):

Bruno Rossitto De Marchi ◽

Tonny Kinene ◽

Renate Krause-Sakate ◽

Laura M. Boykin ◽

Joseph Ndunguru ◽

...

Keyword(s):

Genetic Diversity ◽

Phylogenetic Analysis ◽

East Africa ◽

Target Genes ◽

Rna Extraction ◽

Plant Viruses ◽

Sub Saharan Africa ◽

Cassava Mosaic Disease ◽

Chloroplast Genomes ◽

Cassava Varieties

Cassava is a staple food crop in sub-Saharan Africa; it is a rich source of carbohydrates and proteins which currently supports livelihoods of more than 800 million people worldwide. However, its continued production is at stake due to vector-transmitted diseases such as Cassava mosaic disease and Cassava brown streak disease. Currently, the management and control of viral diseases in cassava relies mainly on virus-resistant cultivars of cassava. Thus, the discovery of new target genes for plant virus resistance is essential for the development of more cassava varieties by conventional breeding or genetic engineering. The chloroplast is a common target for plant viruses propagation and is also a potential source for discovering new resistant genes for plant breeding. Non-infected and infected cassava leaf samples were obtained from different locations of East Africa in Tanzania, Kenya and Mozambique. RNA extraction followed by cDNA library preparation and Illumina sequencing was performed. Assembling and mapping of the reads were carried out and 33 partial chloroplast genomes were obtained. Bayesian phylogenetic analysis from 55 chloroplast protein-coding genes of a dataset with 39 taxa was performed and the single nucleotide polymorphisms for the chloroplast dataset were identified. Phylogenetic analysis revealed considerable genetic diversity present in chloroplast partial genome among cultivated cassava of East Africa. The results obtained may supplement data of previously selected resistant materials and aid breeding programs to find diversity and achieve resistance for new cassava varieties.

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Caracterización molecular de una población de ganado Caqueteño y su relación filogenética con razas bovinas criollas colombianas

Ciencia y Tecnología Agropecuaria ◽

10.21930/rcta.vol7_num1_art:57 ◽

2006 ◽

Vol 7 (1) ◽

pp. 33 ◽

Cited By ~ 2

Author(s):

Gloria Patricia Barrera ◽

Rodrigo Martínez ◽

Rafael Torrijos ◽

Francisco Ramón

Keyword(s):

Molecular Markers ◽

Genetic Distance ◽

Bos Indicus ◽

Racial Group ◽

The Other ◽

Fixation Index ◽

Blood Samples ◽

Creole Cattle ◽

Zebu Breed

El objetivo fue determinar si una población de la raza bovina criolla Caqueteño (CAQ) representa una agrupación racial diferente de las demás poblaciones criollas bovinas colombianas. A tal fin se realizó extracción de ADN a partir de muestras de sangre tomadas a 80 animales Caqueteño; además, se usaron 126 muestras de ADN pertenecientes a seis razas criollas colombianas, 19 muestras de ADN tomadas de animales Cebú (Bos indicus) y 14 de una raza española autóctona. Para caracterizar la población se utilizaron 14 marcadores moleculares tipo microsatélite para los cuales se identificaron los genotipos mediante PCR y electroforesis. En la población CAQ se encontró un número promedio de alelos (NPA= 9,21) superior a las demás razas evaluadas, que variaron entre NPA= 4,57 y NPA= 8,57 para las razas Sanmartinero y BON, respectivamente. La endogamia, definida mediante el índice de fijación (Fis), fue similar a otras razas criollas (0,14) y se encuentra dentro de los parámetros reportados en otros trabajos. Los menores valores de distancias genéticas fueron encontrados entre la población CAQ y las razas BON (0,15) y Romosinuano (0,17) y se constató una distancia considerable con la raza Cebú (0,27). En general, los análisis genotípicos muestran que el biotipo CAQ presenta uniformidad racial con introgresión moderada de la raza cebú, por lo que puede considerarse como un grupo racial definido que puede ser utilizado para un programa de conservación. The molecular characterization of a population of Caqueteño cattle and their phylogenetic relationship with Colombian creole cattle breedsThe object of this work was to determine whether a population of Caqueteño creole cattle (CAC) represented a racial grouping different to other Colombian creole populations. DNA was thus extracted from blood-samples taken from 80 CAC animals; 126 samples of DNA from six Colombian creole breeds, 19 DNA samples from zebu animals (Bos indicus) and 14 from an autochthonous Spanish breed were also used. 14 micro-satellite molecular markers were used for characterising the population, their genotypes being identified by PCR and electrophoresis. A greater average number of alleles (ana=9.21) was found in the CAC population than in the other breeds being evaluated, varying from ana=4.57 to ana=8.57 for Sanmartinero and BON breeds, respectively. Endogamy, defined by fixation index (Fis), was similar to other creole breeds (0.14), coming within parameters reported in other paper. The smallest genetic distance values were found between the CAC population and BON (0.15) and Romosinuano (0.17) breeds, though a considerable distance was found from the zebu breed (0.27). Genotyping analysis generally revealed that the CAC biotype presented racial uniformity, the zebu breed having moderate introgression, meaning that it could be considered to be a well defined racial group which could be used for a conservation program.

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Characterization of Carambola (Averrhoa carambola L.) Plant Collection of Cibinong Plant Germplasm Garden Based on Phenotypic and Genetic Characters

Biosaintifika Journal of Biology & Biology Education ◽

10.15294/biosaintifika.v8i1.5199 ◽

2016 ◽

Vol 8 (1) ◽

pp. 119

Author(s):

Dody Priadi ◽

Ambar Yuswi Perdani ◽

Yuli Sulistyowati ◽

Fiqolbi Nuro Pohan ◽

Enung Sri Mulyaningsih

Keyword(s):

Phylogenetic Analysis ◽

Rapd Markers ◽

The Other ◽

Plant Production ◽

Averrhoa Carambola ◽

Phenotypic Characters ◽

Plant Collection ◽

The Relationship ◽

Genetic Characters

Indonesia as a rich biodiversity country has many superior fruit plant germplasms such as sweet star fruit or carambola (Averrhoa carambola L.). Some varieties of carambola which collected at the Germplasm Garden of Research Center for Biotechnology-LIPI have been used for parent trees of fruit plant production. Therefore, they have to be characterized both phenotypically and genetically. The objective of the study was to analyze the relationship between eight varieties of carambola i.e. Malaysia, Penang, Rawasari, Bangkok, Sembiring, Dewabaru, Demak and Dewimurni at the germplasm garden based on phenotypic and genetic characters. Phenotypic characters were observed directly in the field, whereas genetic characters were observed with RAPD markers using 10 primers. Phylogenetic analysis was done using NT-SYS software showed that there were three clusters of carambola varieties. Meanwhile, Malaysia and Penang varieties have closed relationships (96%) compared with the other varieties. The result of the study would be dedicated to updating and completing the existing fruit plant collection database of Plants Germplasm Garden.

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Genetic diversity and molecular markers of five snapper species

Chinese Journal of Agricultural Biotechnology ◽

10.1017/s1479236207001210 ◽

2007 ◽

Vol 4 (1) ◽

pp. 39-46 ◽

Cited By ~ 2

Author(s):

Liu Li ◽

Liu Chu-Wu

Keyword(s):

Genetic Diversity ◽

Molecular Markers ◽

Simple Sequence Repeats ◽

Microsatellite Loci ◽

Random Amplified Polymorphic Dna ◽

Genetic Distances ◽

The Other ◽

Information Contents ◽

The Mean ◽

Simple Sequence

AbstractIn order to protect and develop valuable snappers (Lutjanus spp.), genetic diversity and molecular markers of five species (Lutjanus vitta, L. fulvus, L. fulviflamma, L. sebae and L. stellatus) were detected and analysed using random amplified polymorphic DNA (RAPD) and simple sequence repeats (SSR) techniques. The polymorphic loci ratio (P) (86.00–92.11%), the mean intraspecies genetic distances (D) (0.1775–0.3431) and the intraspecies genetic diversity indexes (Hi) (0.1022–0.1634) were calculated using the RAPD technique. The genetic diversities of L. fulviflamma and L. vitta were richest in terms of P, and D and Hi, respectively. The results of SSR showed that low effective numbers of alleles (1.7893–3.6591), medium average heterozygosities (0.332–0.676) and medium polymorphism information contents (PIC) (0.302–0.641) occurred in five species of snappers, indicating comparatively rich genetic diversity among these fish. Nine molecular markers in the products amplified by primers OPA8 and OPP10, and six molecular markers in 11 microsatellite loci were found to be useful as specific markers to identify five species of snappers. Two neighbour-joining (NJ) dendrograms based on the results of RAPD and SSR suggested that L. stellatus and L. sebae are closely related and clustered in one branch, with L. vitta, L. fulviflamma and L. fulvus in the other.

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