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1.
Restriction fragment patterns of mitochondrial DNA from sibling species of cyst nematodes Heterodera glycines and H. schachtii were examined. Fourteen restriction endonucleases recognizing four, five, and six base-pair sequences yielded a total of 90 scorable fragments of which 10% were shared by both species. Mitochondrial genome sizes for H. glycines and H. schachtii were estimated to be 22.5-23.5 kb and 23.0 kb, respectively. A single wild type mitochondrial genome was identified in all populations of H. glycines examined, although other mitochondrial genomes were present in some populations. The H. schachtii genome exhibited 57 scorable fragments, compared with 33 identified in the H. glycines wild type genome. The estimated nucleotide sequence divergence between the two species was p = 0.145. This estimate suggests these species diverged from a common ancestor 7.3-14.8 million years ago. 相似文献
2.
Perrine Hugon Dhamodharan Ramasamy Catherine Robert Carine Couderc Didier Raoult Pierre-Edouard Fournier 《Standards in genomic sciences》2013,8(3):500-515
Kallipyga massiliensis strain ph2T is the type strain of Kallipyga massiliensis gen. nov., sp. nov., the type species of the new genus Kallipyga within the family Clostridiales Incertae Sedis XI. This strain, whose genome is described here, was isolated from the fecal flora of a 26-year-old woman suffering from morbid obesity. K. massiliensis is an obligate anaerobic coccus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 1,770,679 bp long genome (1 chromosome but no plasmid) contains 1,575 protein-coding and 50 RNA genes, including 4 rRNA genes. 相似文献
3.
Klebsiella pneumoniae U25 is a multidrug resistant strain isolated
from a tertiary care hospital in Chennai, India. Here, we report the complete
annotated genome sequence of strain U25 obtained using PacBio RSII. This is the first
report of the whole genome of K. pneumoniaespecies from Chennai. It
consists of a single circular chromosome of size 5,491,870-bp and two plasmids of
size 211,813 and 172,619-bp. The genes associated with multidrug resistance were
identified. The chromosome of U25 was found to have eight antibiotic resistant genes
[blaOXA-1,blaSHV-28,
aac(6’)1b-cr,catB3, oqxAB,
dfrA1]. The plasmid pMGRU25-001 was found to have only one
resistant gene (catA1) while plasmid pMGRU25-002 had 20 resistant
genes [strAB, aadA1,aac(6’)-Ib,
aac(3)-IId,sul1,2,
blaTEM-1A,1B,blaOXA-9,
blaCTX-M-15,blaSHV-11, cmlA1,
erm(B),mph(A)]. A mutation in the porin OmpK36
was identified which is likely to be associated with the intermediate resistance to
carbapenems in the absence of carbapenemase genes. U25 is one of the few K.
pneumoniaestrains to harbour clustered regularly interspaced short
palindromic repeats (CRISPR) systems. Two CRISPR arrays corresponding to Cas3 family
helicase were identified in the genome. When compared to K.
pneumoniaeNTUHK2044, a transposase gene InsH of IS5-13
was found inserted. 相似文献
4.
5.
Carlos H Ni?o Nicolás Forero-Baena Luis E Contreras Diana Sánchez-Lancheros Katherine Figarella María H Ramírez 《Memórias do Instituto Oswaldo Cruz》2015,110(7):890-897
The intracellular parasite Trypanosoma cruzi is the aetiological
agent of Chagas disease, a public health concern with an increasing incidence rate.
This increase is due, among other reasons, to the parasite''s drug resistance
mechanisms, which require nicotinamide adenine dinucleotide (NAD+).
Furthermore, this molecule is involved in metabolic and intracellular signalling
processes necessary for the survival of T. cruzi throughout its life
cycle. NAD+ biosynthesis is performed by de novo and
salvage pathways, which converge on the step that is catalysed by the enzyme
nicotinamide mononucleotide adenylyltransferase (NMNAT) (enzyme commission
number: 2.7.7.1). The identification of the NMNAT of T.
cruzi is important for the development of future therapeutic strategies
to treat Chagas disease. In this study, a hypothetical open reading frame (ORF) for
NMNAT was identified in the genome of T. cruzi. The corresponding
putative protein was analysed by simulating structural models. The ORF was amplified
from genomic DNA by polymerase chain reaction and was further used for the
construction of a corresponding recombinant expression vector. The expressed
recombinant protein was partially purified and its activity was evaluated using
enzymatic assays. These results comprise the first identification of an NMNAT in
T. cruzi using bioinformatics and experimental tools and hence
represent the first step to understanding NAD+ metabolism in these
parasites. 相似文献
6.
Background
Acinetobacter baumannii is an important nosocomial pathogen that poses a serious health threat to immune-compromised patients. Due to its rapid ability to develop multidrug resistance (MDR), A. baumannii has increasingly become a focus of attention worldwide. To better understand the genetic variation and antibiotic resistance mechanisms of this bacterium at the genomic level, we reported high-quality draft genome sequences of 8 clinical isolates with various sequence types and drug susceptibility profiles.Results
We sequenced 7 MDR and 1 drug-sensitive clinical A. baumannii isolates and performed comparative genomic analysis of these draft genomes with 16 A. baumannii complete genomes from GenBank. We found a high degree of variation in A. baumannii, including single nucleotide polymorphisms (SNPs) and large DNA fragment variations in the AbaR-like resistance island (RI) regions, the prophage and the type VI secretion system (T6SS). In addition, we found several new AbaR-like RI regions with highly variable structures in our MDR strains. Interestingly, we found a novel genomic island (designated as GIBJ4) in the drug-sensitive strain BJ4 carrying metal resistance genes instead of antibiotic resistance genes inserted into the position where AbaR-like RIs commonly reside in other A. baumannii strains. Furthermore, we showed that diverse antibiotic resistance determinants are present outside the RIs in A. baumannii, including antibiotic resistance-gene bearing integrons, the blaOXA-23-containing transposon Tn2009, and chromosomal intrinsic antibiotic resistance genes.Conclusions
Our comparative genomic analysis revealed that extensive genomic variation exists in the A. baumannii genome. Transposons, genomic islands and point mutations are the main contributors to the plasticity of the A. baumannii genome and play critical roles in facilitating the development of antibiotic resistance in the clinical isolates.Electronic supplementary material
The online version of this article (doi:10.1186/1471-2164-15-1163) contains supplementary material, which is available to authorized users. 相似文献7.
The latifrons species-group (=Brachycallimerus
sensu Chapin 1924, Corporaal 1950; = flavofasciatus-group sensu Kolibáč 1998) of Callimerus Gorham is redefined and revised. Five species are recognized including one new species Callimerus cacuminis Yang & Yang sp. n. (type locality: Yunnan, China). Callimerus flavofasciatus Schenkling, 1902 is newly synonymized with Callimerus latifrons Gorham, 1876. Callimerus trifasciatus Schenkling, 1899a is transferred to the genus Corynommadius Schenkling, 1899a. Callimerus gorhami Corporaal, 1949 and Callimerus pallidus Gorham, 1892 are excluded from the latifrons species-group (their assignment to a species-group will be dealt with in a subsequent paper). A key to species of the latifrons species-group is given and habitus of each type specimen, male terminalia, and other diagnostic characters are illustrated. 相似文献
8.
James L Crainey Túllio RR da Silva Fernando Encinas Michel A Marín Ana Carolina P Vicente Sérgio LB Luz 《Memórias do Instituto Oswaldo Cruz》2016,111(1):79-81
We report here the first complete mitochondria genome of Onchocerca
volvulus from a focus outside of Africa. An O. volvulus
mitogenome from the Brazilian Amazonia focus was obtained using a combination of
high-throughput and Sanger sequencing technologies. Comparisons made between this
mitochondrial genome and publicly available mitochondrial sequences identified 46
variant nucleotide positions and suggested that our Brazilian mitogenome is more
closely related to Cameroon-origin mitochondria than West African-origin
mitochondria. As well as providing insights into the origins of Latin American
onchocerciasis, the Brazilian Amazonia focus mitogenome may also have value as an
epidemiological resource. 相似文献
9.
The development and rapid spread of chloroquine resistance (CQR) in
Plasmodium falciparum have triggered the identification of
several genetic target(s) in the P. falciparum genome. In
particular, mutations in the Pfcrt gene, specifically, K76T and
mutations in three other amino acids in the region adjoining K76 (residues 72, 74, 75
and 76), are considered to be highly related to CQR. These various mutations form
several different haplotypes and Pfcrt gene polymorphisms and the
global distribution of the different CQR- Pfcrt haplotypes in
endemic and non-endemic regions of P. falciparum malaria have been
the subject of extensive study. Despite the fact that the Pfcrt gene
is considered to be the primary CQR gene in P. falciparum , several
studies have suggested that this may not be the case. Furthermore, there is a poor
correlation between the evolutionary implications of the Pfcrt
haplotypes and the inferred migration of CQR P. falciparum based on
CQR epidemiological surveillance data. The present paper aims to clarify the existing
knowledge on the genetic basis of the different CQR- Pfcrt
haplotypes that are prevalent in worldwide populations based on the published
literature and to analyse the data to generate hypotheses on the genetics and
evolution of CQR malaria. 相似文献
10.
11.
12.
P. Castagnone-Sereno C. Piotte P. Abad M. Bongiovanni A. Dalmasso 《Journal of nematology》1991,23(3):316-320
Several Meloidogyne incognita geographic populations were characterized by analysis of the restriction fragment length polymorphisms (RFLP) obtained after digestion of their total DNA and hybridization with a [³²P]-labeled probe. The probe consisted of a 1.7-kb-repeated DNA sequence, isolated from a M. incognita genomic library, that hybridized to multiple BamH I fragments in the genome of each isolate. The patterns showed sufficient polymorphism to enable the accurate differentiation of all the populations tested. 相似文献
13.
14.
Santiago R. Ron Pablo J. Venegas Eduardo Toral Morley?Read Diego?A.?Ortiz Andrea L. Manzano 《ZooKeys》2012,(229):1-52
We present a new phylogeny, based on DNA sequences of mitochondrial and nuclear genes, for frogs of the genus Osteocephalus with emphasis in the Osteocephalus buckleyi species complex. Genetic, morphologic, and advertisement call data are combined to define species boundaries and describe new species. The phylogeny shows strong support for: (1) a basal position of Osteocephalus taurinus + Osteocephalus oophagus, (2) a clade containing phytotelmata breeding species, and (3) a clade that corresponds to the Osteocephalus buckleyi species complex. Our results document a large proportion of hidden diversity within a set of populations that were previously treated as a single, widely distributed species, Osteocephalus buckleyi. Individuals assignable to Osteocephalus buckleyi formed a paraphyletic group relative to Osteocephalus verruciger and Osteocephalus cabrerai and contained four species, one of which is Osteocephalus buckleyi
sensu stricto and three are new. Two of the new species are shared between Ecuador and Peru (Osteocephalus vilmae
sp. n. and Osteocephalus cannatellai
sp. n.) and one is distributed in the Amazon region of southern Peru (Osteocephalus germani
sp. n.) We discuss the difficulties of using morphological characters to define species boundaries and propose a hypothesis to explain them. 相似文献
15.
Shunkei Enoki Akinori Shimizu Chisato Hayashi Hirotake Imanishi Osamu Hashizume Kazuyuki Mekada Hitoshi Suzuki Tetsuo Hashimoto Kazuto Nakada Jun-Ichi Hayashi 《Experimental Animals》2014,63(1):21-30
Previous reports have shown that transmitochondrial mito-mice with nuclear DNA from
Mus musculus and mtDNA from M. spretus do not express
respiration defects, whereas those with mtDNA from Rattus norvegicus
cannot be generated from ES cybrids with mtDNA from R. norvegicus due to
inducing significant respiration defects and resultant losing multipotency. Here, we
isolated transmitochondrial cybrids with mtDNA from various rodent species classified
between M. spretus and R. norvegicus, and compared the
O2 consumption rates. The results showed a strong negative correlation
between phylogenetic distance and reduction of O2 consumption rates, which
would be due to the coevolution of nuclear and mitochondrial genomes and the resultant
incompatibility between the nuclear genome from M. musculus and the
mitochondrial genome from the other rodent species. These observations suggested that
M. caroli was an appropriate mtDNA donor to generate transmitochondrial
mito-mice with nuclear DNA from M. musculus. Then, we generated ES
cybrids with M. caroli mtDNA, and found that these ES cybrids expressed
respiration defects without losing multipotency and can be used to generate
transmitochondrial mito-mice expressing mitochondrial disorders. 相似文献
16.
Restriction digests of amplified DNA from the mitochondrial genome and the nuclear ribosomal internally transcribed spacer region have been evaluated as genetic markers for species groups in Heterorhabditis. Six RFLP profiles have been identified. These profiles supported groupings determined by cross-breeding studies and were in agreement with less definitive groupings based on other biochemical and molecular methods. Digestion patterns of both amplification products provided strong evidence for the recognition of species groups, which include Irish, NW European, tropical, and a H. bacteriophora complex. The H. bacteriophora complex could be further resolved into three genotypes represented by H. zealandica, the H. bacteriophora, Brecon (Australian) type isolate for H. bacteriophora, and a grouping composed of isolates NC1, V16, HI82, and HP88. All cultures obtained of the H. megidis isolate were identical to the NW European group. These results could be used to aid monitoring of field release of Heterorhabditis as well as allowing a rapid initial assessment of taxonomic grouping. 相似文献
17.
Claudia Mendon?a Bezerra Luciano Pamplona de Góes Cavalcanti Rita de Cássia Moreira de Souza Silvia Ermelinda Barbosa Samanta Cristina das Chagas Xavier Ana Maria Jansen Relrison Dias Ramalho Liléia Diotaiut 《Memórias do Instituto Oswaldo Cruz》2014,109(7):887-898
The role played by different mammal species in the maintenance of Trypanosoma
cruzi is not constant and varies in time and place. This study aimed to
characterise the importance of domestic, wild and peridomestic hosts in the
transmission of T. cruzi in Tauá, state of Ceará, Caatinga area,
Brazil, with an emphasis on those environments colonised by Triatoma
brasiliensis. Direct parasitological examinations were performed on
insects and mammals, serologic tests were performed on household and outdoor mammals
and multiplex polymerase chain reaction was used on wild mammals. Cytochrome b was
used as a food source for wild insects. The serum prevalence in dogs was 38% (20/53),
while in pigs it was 6% (2/34). The percentages of the most abundantly infected wild
animals were as follows: Thrichomys laurentius 74% (83/112)
and Kerodon rupestris 10% (11/112). Of the 749 triatomines
collected in the household research, 49.3% (369/749) were positive for T.
brasiliensis, while 6.8% were infected with T. cruzi
(25/369). In captured animals, T. brasiliensis shares a
natural environment with T. laurentius, K.
rupestris, Didelphis albiventris, Monodelphis
domestica, Galea spixii, Wiedomys
pyrrhorhinos, Conepatus semistriatus and Mus
musculus. In animals identified via their food
source, T. brasiliensis shares a natural environment with
G. spixii, K. rupestris, Capra hircus, Gallus
gallus, Tropidurus oreadicus and Tupinambis merianae.
The high prevalence of T. cruzi in household and peridomiciliar
animals reinforces the narrow relationship between the enzootic cycle and humans in
environments with T. brasiliensis and characterises it as
ubiquitous. 相似文献
18.
The sensitivity of acetylcholinesterases (ACHE) isolated from the plant-parasitic nematodes Meloidogyne arenaria, M. incognita, and Heterodera glycines and the free-living nematode Caenorhabditis elegans to carbamate and organophosphate nematicides was examined. The AChE from plant-parasitic nematode species were more sensitive to carbamate inhibitors than was AChE from C. elegans, but response to the organophosphates was approximately equivalent. The sulfur-containing phosphate nematicides were poor inhibitors of nematode acetylcholinesterase, but treatment with an oxidizing agent greatly improved inhibition. Behavioral bioassays with living nematodes revealed a poor relationship between enzyme inhibition and expression of symptoms in live nematodes. 相似文献
19.
The use of plant-covers oat (Arena sativa L.), rhodesgrass (Chloris gayana Kunth), soybean (Glycine max [L.] Merr.), and marigold (Tagetes patula L.) during pineapple inter-cycle planting periods was investigated at two sites (Kunia and Whitmore, Oahu, HI) as a potential means to reduce population densities of Rotylenchulus reniformis, Helicotylenchus dihystera, and Paratylenchus spp. Clean fallow and fallow covered with pineapple-plant residues (mulch) were the controls without plant-cover. Regardless of treatments, population densities of R. reniformis declined with time at both sites to low residue levels by the end of the 6-month period. Treatment means of R. reniformis population densities in the plant-cover treatments were lower than the controls'' (P = 0.05). The plant-cover treatments also effected higher rates of R. reniformis population decline at both sites during the period, being 2.0 to 2.2 times that of the mulch control and 1.2 to 1.4 times that of the fallow control. Plant-covers'' effect on H. dihystera during the same period at both sites was variable, resulting in decreased, unchanged, or increased population densities. The change was especially obvious in the oat-cover treatment, where H. dihystera population densities increased 9 to 15-fold at both sites. Population of Paratylenchus spp. was absent or present at low levels at the sites throughout the period. Biological activities antagonistic to R. reniformis at Kunia were estimated at the end of 6 months by comparing the extent of nematode''s reproduction (on cowpea seedlings) in the treatment soils that had been subjected to autoclaving or freezing temperature. Although higher indices of antagonistic activities were observed in soils with prior plant-cover treatments than in soils from the controls, none of the treatments resulted in conferring soils the increased ability to suppress re-introduced R. reniformis populations or enhance subsequent pineapple-plant growth. 相似文献
20.
Littoral dipluran Parajapyx pauliani Pagés, 1959 was redescribed based on the specimens collected in Hainan Island, South China. The littoral habitat was confirmed for the species, as the first report of arenicolous dipluran in China. DNA barcoding fragment was sequenced for five Parajapyx species (18 individuals) from China, and this is the first report on DNA barcodes used for dipluran identification. The mean intra- and interspecific divergencesare 1.9% and 19.1% respectively. Synonymy of Parajapyx paucidentis and Parajapyx isabellae was confirmed. 相似文献