scholarly journals Mitochondrial Haplotype Analysis for Differentiation of Isolates of Phytophthora cinnamomi

2012 ◽  
Vol 102 (2) ◽  
pp. 229-239 ◽  
Author(s):  
F. N. Martin ◽  
M. D. Coffey
Keyword(s):  
Mating Type ◽  
Gene Order ◽  
Phytophthora Cinnamomi ◽  
Mitochondrial Haplotype ◽  
Data Set ◽  
Coding Regions ◽  
Mitochondrial Haplotypes ◽  
Phytophthora Spp ◽  
Intergenic Regions ◽  
Length Mutations

Although Phytophthora cinnamomi is heterothallic, there are few instances of successful crossing in laboratory experiments, and analysis of field populations indicates a clonally reproducing population. In the absence of sexual recombination, the ability to monitor mitochondrial haplotypes may provide an additional tool for identification of clonal isolates and analysis of population structure. To determine mitochondrial haplotypes for this species, seven mitochondrial loci spanning a total of 6,961 bp were sequenced for 62 isolates representing a geographically diverse collection of isolates with A1 and A2 mating type. Three of the regions were primarily intergenic regions between trnG and rns, rns and nad3, and nad6 and cox1, while the remaining loci spanned cox2, nad9, rps10, and secY coding regions and some of the flanking spacer regions. In total, 45 mitochondrial haplotypes were identified (75% of the total isolates examined) with differences due to single-nucleotide polymorphisms (SNPs, totaling 152 bp) and length mutations (17 indels >2 bp representing a total of 910 bp in length). SNPs were the predominate mutation in the four coding regions and their flanking intergenic regions, while both SNPs and length mutations were observed in the three primarily intergenic regions. Some of the length mutations in these regions were due to addition or loss of unique sequences while others were due to variable numbers of subrepeats (in the trnG-rns region, there were 3 to 12 copies of a 24-bp subrepeat sequence that differentiated 17 haplotypes). Network analysis of the haplotypes identified eight primary clades, with the most divergent clade representing primarily A1 isolates collected from Papua New Guinea. The isolate grouping in the network corresponded to mating type and previously published isozyme classifications, with three exceptions: a haplotype representing an A1 mating type (H29) was placed well within the A2 mating type haplotype grouping, one haplotype (H26) had isolates with two isozyme classifications, and one isozyme group was represented on separate network clades, suggesting that recombination has occurred in the past. Among the 62 isolates examined, several examples were identified of isolates recovered from different geographic regions having the same mitochondrial haplotype, suggesting movement of isolates via plant material. Analysis of the data set to determine whether fewer loci could be sequenced to classify haplotypes indicated that the trnG-rns and rns-nad6 loci would classify 87% of the haplotypes identified in this study, while additional sequencing of the nad9 or secY loci would further differentiate the remaining six haplotypes. Based on conservation of gene order in Phytophthora spp., the trnG-rns locus should be useful for mitochondrial haplotype classification in other species, as should the cox2, nad9, rps10, and secY loci. However, the rns-nad3 and nad6-cox1 loci span regions that can have a different gene order in some Phytophthora spp.

scholarly journals Population Structure of Phytophthora cinnamomi in South Africa

1997 ◽  
Vol 87 (8) ◽  
pp. 822-827 ◽  
Author(s):  
C. Linde ◽  
A. Drenth ◽  
G. H. J. Kemp ◽  
M. J. Wingfield ◽  
S. L. von Broembsen
Keyword(s):  
South Africa ◽  
Genetic Distance ◽  
South African ◽  
Mating Type ◽  
Phytophthora Cinnamomi ◽  
Regional Distribution ◽  
Specific Pattern ◽  
Fixation Index ◽  
The South ◽  
Hardy Weinberg Equilibrium

Phytophthora cinnamomi isolates collected from 1977 to 1986 and 1991 to 1993 in two regions in South Africa were analyzed using isozymes. A total of 135 isolates was analyzed for 14 enzymes representing 20 putative loci, of which four were polymorphic. This led to the identification of nine different multilocus isozyme genotypes. Both mating types of P. cinnamomi occurred commonly in the Cape region, whereas, predominantly, the A2 mating type occurred in the Mpumalanga region of South Africa. A2 mating type isolates could be resolved into seven multilocus isozyme genotypes, compared with only two multilocus isozyme genotypes for the A1 mating type isolates. Low levels of gene (0.115) and genotypic (2.4%) diversity and a low number of alleles per locus (1.43) were observed for the South African P. cinnamomi population. The genetic distance between the Cape and Mpumalanga P. cinnamomi populations was relatively low (Dm = 0.165), and no specific pattern in regional distribution of multilocus isozyme genotypes could be observed. The genetic distance between the “old” (isolated between 1977 and 1986) and “new” (isolated between 1991 and 1993) P. cinnamomi populations from the Cape was low (Dm = 0.164), indicating a stable population over time. Three of the nine multilocus isozyme genotypes were specific to the “old” population, and only one multilocus isozyme genotype was specific to the “new” population. Significant differences in allele frequencies, a high genetic distance (Dm = 0.581) between the Cape A1 and A2 mating type isolates, significant deviations from Hardy-Weinberg equilibrium, a low overall level of heterozygosity, and a high fixation index (0.71) all indicate that sexual reproduction occurs rarely, if at all, in the South African P. cinnamomi population.

Susceptibility of low chill peach rootstocks to Phytophthora spp

1996 ◽  
Vol 36 (1) ◽  
pp. 111
Author(s):  
P Broadbent ◽  
MB Barkley ◽  
M Sriskanthadas ◽  
CJ Kaldor
Keyword(s):  
Nutrient Solution ◽  
Prunus Persica ◽  
Phytophthora Cinnamomi ◽  
New South ◽  
New South Wales ◽  
Phytophthora Spp ◽  
South Wales ◽  
Peach Rootstocks

Peach seedlings (Prunus persica L. Batsch cv. Ansbacher, Boyles, Clarke's Shanghai, Neilson (Fred Hill), Okinawa, O'Meara, Richens Nos 1,2 and 3, Tomm's Early and Tomm's Shanghai), which are commonly used as rootstocks for low chill peaches in coastal New South Wales, were all susceptible to Phytophthora cinnamomi and P. cambivora and to a lesser extent P. parasitica, P. citricola, P. cryptogea, and P. megasperma, when tested by stem inoculations in the glasshouse. Myrobalan H29C plum (P. cerasifera Ehrh.) cuttings showed more resistance than peach seedlings. Variety of seedling peach was highly significant in stem inoculation experiments, but the performance of each varied between experiments. Root inoculations in aerated nutrient solution showed all rootstocks were susceptible to P. cinnamomi, but Neilson (Fred Hill) peach was more tolerant than other seedling peaches and less tolerant than Myrobalan H29C plum. No recommendation could be made on a rootstock for low chill peaches more tolerant of root and collar rots and waterlogging.

scholarly journals Incidence of Phytophthora Root Rot of Fraser Fir in North Carolina and Sensitivity of Isolates of Phytophthora cinnamomi to Metalaxyl

Plant Disease ◽  
2000 ◽  
Vol 84 (6) ◽  
pp. 661-664 ◽  
Author(s):  
D. M. Benson ◽  
L. F. Grand
Keyword(s):  
North Carolina ◽  
Root Rot ◽  
Phytophthora Cinnamomi ◽  
Disease Incidence ◽  
The State ◽  
Systematic Sampling ◽  
Phytophthora Root Rot ◽  
Fraser Fir ◽  
Phytophthora Spp ◽  
Old Trees

A survey of Fraser fir Christmas trees in North Carolina for incidence of Phytophthora root rot was conducted during 1997 and 1998. Field sites (7- to 13-year-old trees) and nursery transplant beds (4- to 5-year-old trees) selected at random were surveyed based on foliar symptoms of Phytophthora root rot. Field sites were surveyed with a random transect method (>3,000 trees/field) or by counting all trees (<3,000 trees/field). Overall, incidence of Phytophthora root rot averaged 9% over the 58 field sites sampled, with a range of 0 to 75%. No relationship was found between number of years Fraser fir had been planted in the field site and disease incidence. Disease incidence did not increase as field sites were rotated through second or third crops of Fraser fir. Phytophthora spp. were recovered from 1.8% of asymptomatic trees sampled from 58 field sites across the state. P. cinnamomi accounted for 91% of the Phytophthora isolates recovered. In nursery transplant beds where a systematic sampling procedure was used, incidence of diseased trees averaged 2%, with a range of 0 to 12% across 16 locations. Recovery of Phytophthora spp. averaged 1.2% from root samples collected from 50 asymptomatic seedlings at each location. Isolates collected from the field and nursery transplant beds were grown on cornmeal agar incorporated with 0, 1, 1.25, 10, or 100 μg a.i. metalaxyl/ml. All 166 isolates of P. cinnamomi tested were sensitive to metalaxyl at 1 or 1.25 μg a.i. metalaxyl/ml. Although incidence of Phytophthora root rot has not increased in the state compared to a survey done in 1976 to 1977, the disease continues to limit production of Fraser fir in North Carolina.

scholarly journals RNA Expression Analysis Using an AntisenseBacillus subtilis Genome Array

2001 ◽  
Vol 183 (24) ◽  
pp. 7371-7380 ◽  
Author(s):  
Jian-Ming Lee ◽  
Shehui Zhang ◽  
Soumitra Saha ◽  
Sonia Santa Anna ◽  
Can Jiang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dynamic Range ◽  
Expression Patterns ◽  
Transcript Level ◽  
Open Reading Frames ◽  
Biosynthetic Genes ◽  
Coding Regions ◽  
Intergenic Regions ◽  
Differential Gene ◽  
Novel Transcripts

ABSTRACT We have developed an antisense oligonucleotide microarray for the study of gene expression and regulation in Bacillus subtilis by using Affymetrix technology. Quality control tests of the B. subtilis GeneChip were performed to ascertain the quality of the array. These tests included optimization of the labeling and hybridization conditions, determination of the linear dynamic range of gene expression levels, and assessment of differential gene expression patterns of known vitamin biosynthetic genes. In minimal medium, we detected transcripts for approximately 70% of the known open reading frames (ORFs). In addition, we were able to monitor the transcript level of known biosynthetic genes regulated by riboflavin, biotin, or thiamine. Moreover, novel transcripts were also detected within intergenic regions and on the opposite coding strand of known ORFs. Several of these novel transcripts were subsequently correlated to new coding regions.

scholarly journals Phytophthora cinnamomi as a Contributor to White Oak Decline in Mid-Atlantic United States Forests

Plant Disease ◽  
2014 ◽  
Vol 98 (3) ◽  
pp. 319-327 ◽  
Author(s):  
M. E. McConnell ◽  
Y. Balci
Keyword(s):  
United States ◽  
Fine Roots ◽  
Phytophthora Cinnamomi ◽  
United States Department ◽  
Oak Decline ◽  
White Oak ◽  
Phytophthora Spp ◽  
Oak Trees ◽  
Root Health ◽  
The Impact

To evaluate Phytophthora cinnamomi as a cause of white oak (Quercus alba) decline in mid-Atlantic forests, sampling was conducted at 102 sites from 2011 to 2012. Soil and roots from healthy and declining white oak trees were collected. Phytophthora spp. were isolated using baiting and CFU of P. cinnamomi quantified using wet-sieving. Fine roots were scanned and measured. Phytophthora spp. were isolated from 43% of the sites. P. cinnamomi was common; six other species were isolated infrequently. Little difference in lesion size existed on white oak seedlings inoculated with 32 isolates of P. cinnamomi; only 13 isolates caused significant mortality. Soils from white oak versus nine other hosts did not have significantly different CFU. P. cinnamomi was restricted to United States Department of Agriculture hardiness zones six and seven and never found in zone five. The presence of Phytophthora spp. in soil can be associated with white oak fine root health. When Phytophthora spp. were present, white oak trees in zones five and six had less fine roots. In mid-Atlantic oak forests, however, environmental conditions appear to play a key role in determining the impact of P. cinnamomi on the root system. P. cinnamomi alone does not appear to be a causal factor of white oak decline.

scholarly journals Characterization and fungicides sensitivity of Phytophthora cinnamomi isolates causing avocado root rot in Zitácuaro, Michoacán

2021 ◽  
Vol 40 (1) ◽  
Author(s):  
Alejandra Mondragón-Flores ◽  
Patricia Manosalva ◽  
Salvador Ochoa-Ascencio ◽  
Marlene Díaz-Celaya ◽  
Gerardo Rodríguez-Alvarado ◽  
...  
Keyword(s):  
Growth Rate ◽  
Mating Type ◽  
Root Rot ◽  
Phytophthora Cinnamomi ◽  
Potassium Phosphite ◽  
Pathogenicity Tests

<em>Phytophthora cinnamomi</em> is the pathogen most frequently associated with avocado root rot. In Zitácuaro, Michoacán, production has increased by 19.8%; however, there are no studies of root rot in this area. The objective of the study was to characterize the isolates obtained from avocado roots and assess the sensitivity to fungicides. Samples from 5 avocado orchards were collected, sampling 5 trees per orchard (a total of 25 samples). The samples isolated were characterized morphological and molecularly. Mating type was analyzed using reference isolates of<em> P. cinnamomi</em> A1 (isolate from camelia) and A2 (isolate from avocado). To confirm the pathogenicity, tests were performed on avocado fruits with the isolates. The sensitivity of 15 isolates to potassium phosphite and to metalaxyl-M at different concentrations was evaluated<em> in vitro</em>. In a subgroup of six isolates, it was evaluated whether there was a relationship between growth rate and potassium phosphite sensitivity. Fifteen isolates were obtained with coenocytic coraloid mycelium, chlamydospores, sporangia without papilla, ovoid to ellipsoid, with internal proliferation, heterothallic with mating type A2, with amphigynous antheridia and plerotic oospores, characteristics consistent with <em>P. cinnamomi</em>. The inoculated isolates were pathogenic on avocado fruits. The isolates were more sensitive to potassium phosphite than to metalaxyl-M, with mean EC50 values of 24.62 and 0.215 ?g mL-1 of i.a., respectively. No relationship was observed between growth rate and potassium phosphite sensitivity. It is necessary to obtain a greater number of<em> P. cinnamomi</em> isolates for virulence studies.

scholarly journals Non-Coding RNAs in Bacteria

2018 ◽  
Author(s):  
Amanda Carvalho Garcia ◽  
Vera Lúcia Pereira dos Santos ◽  
Teresa Cristina Santos Cavalcanti ◽  
Luiz Martins Collaço ◽  
Iara José Taborda de Messias ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Physiological Responses ◽  
Coding Regions ◽  
Short Rnas ◽  
Genes Encoding ◽  
Intergenic Regions ◽  
In Trans ◽  
Rna Interaction ◽  
In Cis ◽  
Target Rna

Genes encoding regulatory RNAs known as short RNAs (sRNAs) or non-coding sRNAs (ncRNAs), modulate physiological responses through different mechanisms, through RNA-RNA interaction or RNA-protein interaction. These molecules transcribed in trans and in cis relative to the target RNA. They are located between the coding regions of proteins, i.e., in the intergenic regions of the genome and show signals of promoters and termini sequences generally Rho-independent. The size of the ncRNAs genes ranges from ~ 50 to ~ 500 nucleotides and several transcripts are processed by RNase with smaller end products, which modulate physiological responses through different mechanisms, by RNA-RNA interaction or RNA-protein interactions and some interactions may be stabilized by the Hfq chaperone. The Riboswitches constitute another class of ncRNAs, located in the 5'UTR region of an mRNA that promote transcriptional regulation through their interaction with a linker molecule. Recently, in prokaryotes, CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) regions have described, which repeats of sequences of palindromic bases are. Each replicate consists of short segments of "spacer DNA" from exposures prior to a bacteriophage virus or exogenous plasmid. The CRISPR system consists of an immune system of resistance to exogenous molecules.

scholarly journals Pandoravirus celtis illustrates the microevolution processes at work in the giant Pandoraviridae genomes

2018 ◽  
Author(s):  
Matthieu Legendre ◽  
Jean-Marie Alempic ◽  
Nadège Philippe ◽  
Audrey Lartigue ◽  
Sandra Jeudy ◽  
...  
Keyword(s):  
De Novo ◽  
Gene Repertoire ◽  
Protein Coding ◽  
Genomic Changes ◽  
Coding Regions ◽  
Protein Coding Genes ◽  
Intergenic Regions ◽  
Mere Existence ◽  
Increasing Functions ◽  
Similar Gene

AbstractWith genomes of up to 2.7 Mb propagated in µm-long oblong particles and initially predicted to encode more than 2000 proteins, members of the Pandoraviridae family display the most extreme features of the known viral world. The mere existence of such giant viruses raises fundamental questions about their origin and the processes governing their evolution. A previous analysis of six newly available isolates, independently confirmed by a study including 3 others, established that the Pandoraviridae pan-genome is open, meaning that each new strain exhibits protein-coding genes not previously identified in other family members. With an average increment of about 60 proteins, the gene repertoire shows no sign of reaching a limit and remains largely coding for proteins without recognizable homologs in other viruses or cells (ORFans). To explain these results, we proposed that most new protein-coding genes were created de novo, from pre-existing non-coding regions of the G+C rich pandoravirus genomes. The comparison of the gene content of a new isolate, P. celtis, closely related (96% identical genome) to the previously described P. quercus is now used to test this hypothesis by studying genomic changes in a microevolution range. Our results confirm that the differences between these two similar gene contents mostly consist of protein-coding genes without known homologs (ORFans), with statistical signatures close to that of intergenic regions. These newborn proteins are under slight negative selection, perhaps to maintain stable folds and prevent protein aggregation pending the eventual emergence of fitness-increasing functions. Our study also unraveled several insertion events mediated by a transposase of the hAT family, 3 copies of which are found in P. celtis and are presumably active. Members of the Pandoraviridae are presently the first viruses known to encode this type of transposase.

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