Molecular analysis of the complete set of length mutations found in the plastomes of Triticum–Aegilops species

Genome ◽  
2002 ◽  
Vol 45 (5) ◽  
pp. 956-962 ◽  
Author(s):  
Y Ogihara ◽  
T Ohsawa
Keyword(s):  
Hot Spots ◽  
Rflp Analysis ◽  
Single Copy ◽  
Aegilops Species ◽  
Nucleotide Sequence Level ◽  
Hypervariable Regions ◽  
Intergenic Regions ◽  
Complete Set ◽  
Chloroplast Dnas ◽  
Length Mutations

Precise location and nature of each of 14 length mutations detected among chloroplast DNAs of Triticum–Aegilops species by RFLP analysis were determined at the nucleotide sequence level. Each mutation was compared with at least three non-mutated wild-type plastomes as standards. These 14 length mutations were classified into 4 duplications and 10 deletions. One duplication occurred in the small single-copy region close to the border of the inverted repeat, and the remaining 13 length mutations took place in the large single-copy region. All length mutations occurred in the intergenic regions, suggesting that these length mutations do not affect plastid gene expression. Saltatory replication was the cause of all duplications, whereas intramolecular recombination mediated by short direct repeats played a substantial role in the deletions. Recurrent occurrences of certain deletion events were found in some AT-rich regions, which constituted hot spots for deletion. Out of four hypervariable regions detected among the grass plastomes, two (downstream of rbcL and a tRNA gene accumulated region) were still active after differentiation of Triticum and Aegilops complex.Key words: insertions–deletions, plastome, Triticum–Aegilops, deletion hot spots, molecular mechanism.

scholarly journals Evaluation of Four DNA Typing Techniques in Epidemiological Investigations of Bovine Tuberculosis

1998 ◽  
Vol 36 (1) ◽  
pp. 168-178 ◽  
Author(s):  
Debby Cousins ◽  
Suzette Williams ◽  
Ernesto Liébana ◽  
Alicia Aranaz ◽  
Annelies Bunschoten ◽  
...  
Keyword(s):  
Restriction Fragment ◽  
Dna Typing ◽  
Rflp Analysis ◽  
Direct Repeat ◽  
Single Copy ◽  
Epidemiological Evidence ◽  
Different Types ◽  
The Republic ◽  
Different Strains ◽  
Typing Technique

DNA fingerprinting techniques were used to type 273 isolates ofMycobacterium bovis from Australia, Canada, the Republic of Ireland, and Iran. The results of restriction fragment length polymorphism (RFLP) analysis with DNA probes from IS6110, the direct repeat (DR), and the polymorphic GC-rich sequence (PGRS) were compared with those of a new PCR-based method called spacer oligonucleotide typing (spoligotyping) developed for the rapid typing of Mycobacterium tuberculosis (J. Kamerbeek et al., J. Clin. Microbiol. 35:907–914, 1997). Eighty-five percent of the isolates harbored a single copy of IS6110, and 81.5% of these carried IS6110 on the characteristic 1.9-kb restriction fragment. RFLP analysis with IS6110 identified 23 different types, RFLP analysis with the DR probe identified 35 types, RFLP analysis with the PGRS probe identified 77 types, and the spoligotyping method identified 35 types. By combining all results, 99 different strains could be identified. Isolate clusters were frequently associated within herds or were found between herds when epidemiological evidence confirmed animal movements. RFLP analysis with IS6110 was sufficiently sensitive for the typing of isolates with more than three copies of IS6110, but RFLP analysis with the PGRS probe was the most sensitive typing technique for strains with only a single copy of IS6110. Spoligotyping may have advantages for the rapid typing of M. bovis, but it needs to be made more sensitive.

scholarly journals THE MOLECULAR BASIS OF GENETIC DIVERSITY AMONG CYTOPLASMS OF TRITICUM AND AEGILOPS SPECIES. II. ON THE ORIGIN OF POLYPLOID WHEAT CYTOPLASMS AS SUGGESTED BY CHLOROPLAST DNA RESTRICTION FRAGMENT PATTERNS

Genetics ◽  
1983 ◽  
Vol 104 (1) ◽  
pp. 155-171
Author(s):  
Koichiro Tsunewaki ◽  
Yasunari Ogihara
Keyword(s):  
Genetic Diversity ◽  
Chloroplast Dna ◽  
Restriction Fragment ◽  
Molecular Basis ◽  
Restriction Enzymes ◽  
Aegilops Species ◽  
Polyploid Wheat ◽  
Representative Species ◽  
Dna Restriction ◽  
Chloroplast Dnas

ABSTRACT In attempts to identify the phylogenetic donors of cytoplasm to Emmer-Dinkel and Timopheevi groups of wheat (Triticum), and the Aegilops kotschyi-Ae. variabilis complex, the restriction fragment patterns of chloroplast DNAs of representative species were compared with those of their putative diploid ancestors. The following seven restriction enzymes were used; BamHI, EcoRI, HindIII, KpnI, PstI, SmaI and XhoI. The restriction fragment patterns of an Emmer and a Dinkel (common) wheat were identical with those of Ae. longissima, and different from those of Ae. aucheri, Ae. bicornis, Ae. searsii, Ae. sharonensis, Ae. speltoides, and T. urartu by 4 to 12 fragments. The restriction fragment patterns of a Timopheevi wheat were identical with those of Ae. aucheri, and different from those of all other diploids by four to nine fragments. The restriction fragment patterns of Ae. variabilis were identical to those of Ae. bicornis and Ae. searsii, and different from those of all other species. Thus, we have concluded that Ae. longissima, Ae. aucheri and Ae. bicornis (or Ae. searsii) were the cytoplasm donors to the Emmer-Dinkel and the Timopheevi groups, and the Ae. kotschyi-Ae. variabilis complex, respectively. A diphyletic origin of Emmer and Timopheevi groups is supported by the present results.

scholarly journals ANALYSIS OF RFLP LOCI IN WALNUTS: INHERITANCE, INTRA- AND INTERSPECIFIC VARIATION, AND CULTIVAR IDENTIFICATION.

HortScience ◽  
1992 ◽  
Vol 27 (6) ◽  
pp. 574b-574
Author(s):  
R. Fjellstrom ◽  
D. E. Parfitt
Keyword(s):  
Rflp Analysis ◽  
Interspecific Variation ◽  
Single Copy ◽  
Interspecific Backcross ◽  
Rflp Markers ◽  
Backcross Population ◽  
Low Copy Number ◽  
English Walnut ◽  
Genomic Probes ◽  
Relationship Of

RFLP analysis was employed to study the inheritance of and genetic diversity identified by cloned walnut genomic probes. An interspecific backcross population of (J. hindsii × J. regia) × J. regia was used to determine the inheritance of thirty low copy number RFLP cloned probes. Of these probes, approximately 20% correspond to single copy loci, 40% correspond to single major loci with multiple minor loci, and 40% correspond to two major loci. Twenty of these probes were used to analyze variability within and between 13 walnut species (Juglans spp.). Substantial genetic variation was identified within many wild walnut species, while limited variation was identified within butternut (J. cinerea) and the widely cultivated English walnut (J. regia). Extensive polymorphism was found between walnut species, allowing a phylogenetic relationship of walnuts based upon RFLP markers to be developed. Identification of clonally propagated walnut cultivars by RFLP typing was readily performed in black walnut (J. nigra) accessions, was more difficult in English walnut accessions, and rarely possible in butternut accessions.

scholarly journals Serotyping of Adenoviruses on Conjunctival Scrapings by PCR and Sequence Analysis

1999 ◽  
Vol 37 (6) ◽  
pp. 1839-1845 ◽  
Author(s):  
Satoshi Takeuchi ◽  
Norihiko Itoh ◽  
Eiichi Uchio ◽  
Koki Aoki ◽  
Shigeaki Ohno
Keyword(s):  
Dna Sequences ◽  
Direct Sequencing ◽  
Rflp Analysis ◽  
Amino Acid Homology ◽  
Hypervariable Regions ◽  
Pcr Rflp ◽  
Causative Agents ◽  
Sequence Method ◽  
Primer Sets ◽  
Acute Conjunctivitis

To detect and identify adenovirus (Ad), we investigated hypervariable regions (HVRs) of Ad by using a combination of PCR and direct sequencing (PCR-sequence) method. Primers for nested PCR to amplify the conserved region in the hexon protein containing HVRs were designed based on hexon gene sequences derived from GenBank. These two primer sets amplified a DNA fragment of 7 HVRs from 16 prototypes of Ad, which were divided into five subgenera, including seven serotypes that are the predominant causative agents of acute conjunctivitis in Japan, and from 31 recent conjunctival scraping specimens from patients with adenoviral conjunctivitis. HVR DNA sequences were determined by means of universal sequence primers. Analysis of the predicted amino acid homology of HVRs among Ad prototypes suggested three regions, HVR4, -5, and -7, to be candidates for the neutralization epitopes. The clinical serotype of specimens was determined by the PCR-sequence method with reference to these three HVRs. The serotype determined according to this method was identical to that obtained by culture isolation and the neutralization test (NT) in all scraping samples, whereas the results of this method did not match PCR and restriction fragment length polymorphism (PCR-RFLP) analysis in five samples. It took only three days to detect Ad and to identify the serotype, in contrast to culture isolation-NT, which took at least 2 weeks. These findings indicate that our newly developed PCR-sequence method is applicable for the detection and serotyping of human Ads.

scholarly journals The CpnClassiPhyR Is a Resource for cpn60 Universal Target-Based Classification of Phytoplasmas

Plant Disease ◽  
2019 ◽  
Vol 103 (10) ◽  
pp. 2494-2497 ◽  
Author(s):  
Kevin Muirhead ◽  
Edel Pérez-López ◽  
Brian W. Bahder ◽  
Janet E. Hill ◽  
Tim Dumonceaux
Keyword(s):  
Ribosomal Rna ◽  
Pathogenic Bacteria ◽  
Rflp Analysis ◽  
Single Copy ◽  
Web Interface ◽  
Phytoplasma Strain ◽  
Protein Encoding ◽  
Encoding Gene ◽  
Definition Of

Phytoplasmas are plant-pathogenic bacteria that are associated with yield losses in many crop plants worldwide. Phytoplasma strain differentiation is accomplished using in silico restriction fragment length polymorphism (RFLP) analysis of 16S ribosomal RNA-encoding gene sequences, which has resulted in the definition of ribosomal groups and subgroups of phytoplasmas. Due to limitations associated with this approach, a complementary classification scheme was recently developed based on RFLP analysis of the single-copy, protein-encoding gene chaperonin-60 (cpn60). We present the CpnClassiPhyR, software that facilitates phytoplasma strain classification using both RFLP and automated phylogenetic analysis of cpn60 sequences. This software is available through a web interface at http://cpnclassiphyr.ca .

scholarly journals Rapid differentiation of Staphylococcus aureus isolates harbouring egc loci with pseudogenes ψent1 and ψent2 and the selu or selu v gene using PCR-RFLP

2007 ◽  
Vol 56 (2) ◽  
pp. 208-216 ◽  
Author(s):  
Mark M. Collery ◽  
Cyril J. Smyth
Keyword(s):  
Dna Sequencing ◽  
Restriction Enzyme ◽  
Sequence Similarity ◽  
Rflp Analysis ◽  
Restriction Enzymes ◽  
Restriction Enzyme Digestion ◽  
Pcr Rflp ◽  
Intergenic Regions ◽  
Unique Restriction ◽  
Genomic Regions

The egc locus of Staphylococus aureus harbours two enterotoxin genes (seg and sei) and three enterotoxin-like genes (selm, seln and selo). Between the sei and seln genes are located two pseudogenes, ψent1 and ψent2, or the selu or selu v gene. While these two alternative sei–seln intergenic regions can be distinguished by PCR, to date, DNA sequencing has been the only confirmatory option because of the very high degree of sequence similarity between egc loci bearing the pseudogenes and the selu or selu v gene. In silico restriction enzyme digestion of genomic regions encompassing the egc locus from the 3′ end of the sei gene through the 5′ first quarter of the seln gene allowed pseudogene- and selu- or selu v-bearing egc loci to be distinguished by PCR-RFLP. Experimental application of these findings demonstrated that endonuclease HindIII cleaved PCR amplimers bearing pseudogenes but not those with a selu or selu v gene, while selu- or selu v-bearing amplimers were susceptible to cleavage by endonuclease HphI, but not by endonuclease HindIII. The restriction enzyme BccI cleaved selu- or selu v-harbouring amplimers at a unique restriction site created by their signature 15 bp insertion compared with pseudogene-bearing amplimers, thereby allowing distinction of these egc loci. PCR-RFLP analysis using these restriction enzymes provides a rapid, easy to interpret alternative to DNA sequencing for verification of PCR findings on the nature of an egc locus type, and can also be used for the primary identification of the intergenic sei–seln egc locus type.

Sequencing and annotation of the chloroplast DNAs and identification of polymorphisms distinguishing normal male-fertile and male-sterile cytoplasms of onion

Genome ◽  
2013 ◽  
Vol 56 (12) ◽  
pp. 737-742 ◽  
Author(s):  
Christopher von Kohn ◽  
Agnieszka Kiełkowska ◽  
Michael J. Havey
Keyword(s):  
Single Copy ◽  
Size Difference ◽  
Normal Male ◽  
Hybrid Seed Production ◽  
Nucleotide Polymorphisms ◽  
Male Sterile ◽  
Close Phylogenetic Relationship ◽  
Alien Cytoplasm ◽  
Chloroplast Dnas ◽  
Small Single Copy

Male-sterile (S) cytoplasm of onion is an alien cytoplasm introgressed into onion in antiquity and is widely used for hybrid seed production. Owing to the biennial generation time of onion, classical crossing takes at least 4 years to classify cytoplasms as S or normal (N) male-fertile. Molecular markers in the organellar DNAs that distinguish N and S cytoplasms are useful to reduce the time required to classify onion cytoplasms. In this research, we completed next-generation sequencing of the chloroplast DNAs of N- and S-cytoplasmic onions; we assembled and annotated the genomes in addition to identifying polymorphisms that distinguish these cytoplasms. The sizes (153 538 and 153 355 base pairs) and GC contents (36.8%) were very similar for the chloroplast DNAs of N and S cytoplasms, respectively, as expected given their close phylogenetic relationship. The size difference was primarily due to small indels in intergenic regions and a deletion in the accD gene of N-cytoplasmic onion. The structures of the onion chloroplast DNAs were similar to those of most land plants with large and small single copy regions separated by inverted repeats. Twenty-eight single nucleotide polymorphisms, two polymorphic restriction-enzyme sites, and one indel distributed across 20 chloroplast genes in the large and small single copy regions were selected and validated using diverse onion populations previously classified as N or S cytoplasmic using restriction fragment length polymorphisms. Although cytoplasmic male sterility is likely associated with the mitochondrial DNA, maternal transmission of the mitochondrial and chloroplast DNAs allows for polymorphisms in either genome to be useful for classifying onion cytoplasms to aid the development of hybrid onion cultivars.

Mitochondrial DNA Heteroplasmy in Wheat, Aegilops and Their Nucleus-Cytoplasm Hybrids

Genetics ◽  
2002 ◽  
Vol 160 (4) ◽  
pp. 1619-1630
Author(s):  
Nobuaki Hattori ◽  
Kazuaki Kitagawa ◽  
Shigeo Takumi ◽  
Chiharu Nakamura
Keyword(s):  
Mitochondrial Dna ◽  
Tetraploid Wheat ◽  
Rflp Analysis ◽  
Transcriptional Unit ◽  
Aegilops Species ◽  
Paternal Contribution ◽  
Parental Lines ◽  
Mitochondrial Dna Heteroplasmy ◽  
Sequence Types ◽  
Wheat Parent

Abstract A mitochondrial (mt) transcriptional unit, nad3-orf156, was studied in the nucleus-cytoplasm hybrids of wheat with D/D2 plasmons from Aegilops species and their parental lines. A comparative RFLP analysis and sequencing of the random PCR clones revealed the presence of seven sequence types and their polymorphic sites were mapped. All the hybrids possessed the paternal copies besides the maternal copies. More paternal copies were present in the D2 plasmon hybrids, whereas more maternal copies were present in the D plasmon hybrids. Two major copies were present with different stoichiometries in the maternal Aegilops parents. However, only a major D plasmon copy was detected in the hybrids, irrespective of their plasmon types. The hexaploid wheat parent (AABBDD genome) possessed the major D plasmon copy in ~5% stoichiometry, while no D plasmon-homologous copies were detected in the tetraploid wheat parent (AABB genome). The results suggest that the observed mtDNA heteroplasmy is due to paternal contribution of mtDNA. The different copy stoichiometry suggests differential amplification of the heteroplasmic copies among the hybrids and the parental lines. All editing sites and their editing frequencies were conserved among the lines, and only the maternal pattern of editing occurred in the hybrids.

scholarly journals Molecular Characterization of IS1541Insertions in the Genome of Yersinia pestis

1998 ◽  
Vol 180 (1) ◽  
pp. 178-181 ◽  
Author(s):  
Monique Odaert ◽  
Annie Devalckenaere ◽  
Patrick Trieu-Cuot ◽  
Michel Simonet
Keyword(s):  
Yersinia Pestis ◽  
Hot Spots ◽  
Insertion Sequence ◽  
Single Copy ◽  
Open Reading Frames ◽  
Stem Loop ◽  
Insertion Sites ◽  
Flanking Regions ◽  
Reading Frames

ABSTRACT The genome of Yersinia pestis, the causative agent of plague, contains at least 30 copies of an element, designated IS1541, which is structurally related to IS200(85% identity). One such element is inserted within the chromosomalinv gene (M. Simonet, B. Riot, N. Fortineau, and P. Berche, Infect. Immun. 64:375–379, 1996). We characterized other IS1541 insertions by cloning 14 different Y. pestis 6/69M loci carrying a single copy of this insertion sequence (IS) into Escherichia coli and, for each element, sequencing 250 bp of both flanking regions. In no case was this IS element inserted into large open reading frames; however, in eight cases, it was detected downstream (17 to 139 bp) of genes thought to be transcribed monocistronically or which constituted the last gene of an operon, and in only one case was it detected upstream (37 bp) of the first gene of an operon. Sequence analysis revealed stem-loop structures (ΔG, <−10 kcal) resembling rho-independent transcription terminators in 8 of the 14 insertion sites. These motifs might constitute hot spots for insertion of this IS1541element within the Y. pestis genome.

scholarly journals Comparative chloroplast genomics of Fritillaria (Liliaceae), inferences for phylogenetic relationships between Fritillaria and Lilium and genome evolution

2019 ◽  
Author(s):  
Jiao Huang ◽  
Yan Yu ◽  
Yan-Mei Liu ◽  
Deng-Feng Xie ◽  
Xing-Jin He ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
New World ◽  
Genome Structure ◽  
Single Copy ◽  
Phylogenomic Analysis ◽  
Structural Variations ◽  
Weak Support ◽  
Hypervariable Regions ◽  
Chloroplast Genomes ◽  
Gene Data

Abstract Background Fritillaria is a genus consisting of about 140 species that has important medicinal and horticultural values. The monophyly of Fritillaria and phylogenetic relationships with Lilium were previously not fully resolved. The study involved the most comprehensive chloroplast genomes samples to date referring to Old and New World clades of Fritillaria as identified in earlier studies.Results We reported and compared eleven newly sequenced whole-plastome sequences of Fritillaria as well as characterization of SSRs and repeat sequence. These 11 plastomes proved highly similar in overall size (151,652-152,434bp), genome structure, gene content and order; Comparing them with other species of Liliales (6 out of 10 families) indicated the same similarity but showed some structural variations due to the contraction or expansion of the IR regions out or into of adjacent single-copy regions. A/T mononucleotides, palindromic and forward repeats were the most common types. Six hypervariable regions ( rps16 - trnQ, rbcL - accD, accD - psaI, psaJ - rpl33, petD - rpoA and rpl32 - trnL ) were discovered based on 26 Fritillaria whole-plastomes to be potential molecular markers. 26 species of Fritillaria plastomes and 21 species of Lilium plastomes were combined in a phylogenomic study with 3 Cardiocrinum species as out groups. Fritillaria was monophyly with moderate support as sister to Lilium based on 64 protein-coding genes (CDS) and the interspecific relationship within subgenus Fritillaria has strong resolution. The topology recovered from the whole plastome and single-copy gene data sets was the same as for coding gene data, but weak support for monophyly of Fritillaria .Conclusions The phylogenomic analysis reconstructed a topology that had some incongruences with previous studies. The six hypervariable regions can be used as candidate DNA barcodes for global genetic diversity detection of Fritillaria . The phylogenomic framework from this study can guide extensive genomic sampling to further discern the relationships among the Old and New World clades of Fritillaria and Lilium .

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