Restriction fragment length polymorphism based phylogenetic analysis of Avena L.

Genome ◽  
1995 ◽  
Vol 38 (6) ◽  
pp. 1279-1284 ◽  
Author(s):  
Rita Alicchio ◽  
Lina Aranci ◽  
Lucia Conte
Keyword(s):  
Fragment Length Polymorphism ◽  
Phylogenetic Analyses ◽  
Diploid Species ◽  
The Other ◽  
Molecular Approach ◽  
Polyploid Species ◽  
Species Relationships ◽  
Biochemical Traits ◽  
A Genome ◽  
Restriction Fragment Length

We report a molecular approach to the study of the phylogenetic relationships of Avena diploid and polyploid species based on RFLP detected with three cDNA probes of nuclear genes belonging to multigenic families (low pI α-amylase, avenin, and globulin). All the probes were highly informative in the detection of polymorphism between oat species. Associations between species were determined from cluster (UPGMA) analysis based on distance values calculated from RFLP data separately for each of the two levels of ploidy. Results were in general agreement with morphology based phylogenetic analyses, confirming the large differentiation among A and C genomes in the evolution of diploid species and the genetic homogeneity among A. brevis, A. strigosa, and A. nuda and the recently discovered A. atlantica. A certain divergence was observed between two endemic species (A. canariensis and A. damascena) and the other diploid species with the A genome. The analysis of tetraploid species relationships confirms the differentiation of the barbata complex (A. wiestii, A. barbata, A. abyssinica, and A. vaviloviana) from the maroccana–murphyi–agadiriana group, which, despite some similarities in morphological and biochemical traits, seems to have accumulated deep genetic differences along its evolutionary pathway.Key words: Avena genomes, genetic distance, ploidy, RFLP, multigenic families.

scholarly journals Characterisation of avian Pasteurella multocida strains with PCR-RFLP analysis of the ompH gene

2013 ◽  
Vol 61 (1) ◽  
pp. 1-8 ◽  
Author(s):  
Boglárka Sellyei ◽  
Éva Ivanics ◽  
Tibor Magyar
Keyword(s):  
Restriction Fragment Length Polymorphism ◽  
Pasteurella Multocida ◽  
Fragment Length Polymorphism ◽  
Rflp Analysis ◽  
The Other ◽  
Pcr Rflp ◽  
H Gene ◽  
Geographic Regions ◽  
Type Strains ◽  
Restriction Fragment Length

The 16 somatic serotype type strains and 60 field isolates of Pasteurella multocida, representing various avian species and geographic regions in Hungary, were characterised by PCR-restriction fragment length polymorphism (PCR-RFLP) analysis of the ompH gene with DraI restriction endonuclease. The type strains yielded eight different (I-VIII) profiles. Strains whose PCR fragment was uncut by DraI (profile IV) could be differentiated with HindIII and PvuII restriction endonucleases. Five of the eight PCR-RFLP profiles (I, III, V, VI and VII) were detected among the field strains. Only a correlation of limited strength was found between the classical somatic serotypes and the PCR-RFLP profiles. However, the results confirmed that molecular methods could confidently distinguish serotype A:1 strains from the other serotypes. Moreover, the specific relationship between somatic serotypes and PCR-RFLP types among isolates from turkey raises the possibility of the existence of host-specific clones within the P. multocida population.

scholarly journals Genotyping of Mycobacterium avium subsp. avium isolates from domestic animals in Slovenia by IS901 RFLP

2009 ◽  
Vol 54 (No. 6) ◽  
pp. 270-279 ◽  
Author(s):  
M. Pate ◽  
M. Moravkova ◽  
B. Krt ◽  
I. Pavlik ◽  
M. Ocepek
Keyword(s):  
Czech Republic ◽  
Mycobacterium Avium ◽  
Fragment Length Polymorphism ◽  
Domestic Animals ◽  
The Other ◽  
Reference Laboratory ◽  
Rflp Type ◽  
Granulomatous Lesions ◽  
Pig Farms ◽  
Restriction Fragment Length

ABSTRACT: Apart from birds, <I>Mycobacterium avium</I> subsp. <I>avium (MAA) </I> is often isolated from granulomatous lesions in pigs and occasionally from cattle and other animals. The objectives of this study were the detection of IS<I>901</I> restriction fragment length polymorphism (RFLP) types of <I>MAA</I> isolates from different species of domestic animals between the years 1998 and 2004 and the comparison of the detected RFLP types with previously described RFLP types collected in the database of the OIE Reference Laboratory for Avian Tuberculosis (Brno, Czech Republic). Furthermore, the RFLP types of the isolates obtained from <I>MAA</I> outbreaks on one of the largest pig farms in Slovenia were also investigated. A total of 62 isolates (56 from pigs, five from poultry and one from cattle) were identified with IS<I>901</I> PCR and IS<I>901</I> RFLP typed using restriction endonucleases <I>Pvu</I>II and <I>Pst</I>I. Seven <I>Pvu</I>II RFLP and 11 <I>Pst</I>I RFLP types resulted in 12 combined <I>Pvu</I>II <I>Pst</I>I types; none of these matched the combined RFLP types described in previous studies. Our contributions to the database were two new <I>Pvu</I>II and eight new <I>Pst</I>I RFLP types. Identical RFLP types were found among isolates of animals originating from individual farms. Finding of identical RFLP types within a farm is not surprising because the animals were epidemiologically related and infected with one strain. A unique RFLP type F-A17 was detected in isolates from different pig herds and also in isolates from poultry. Detection of identical RFLP types on different farms may reflect one <I>MAA</I> source. The other combined <I>Pvu</I>II <I>Pst</I>I RFLP types were identified only once which indicates considerable variety of <I>MAA</I> RFLP types in Slovenia.

scholarly journals Chloroplast phylogenomics in Camelina (Brassicaceae) reveals multiple origins of polyploid species and the maternal lineage of C. sativa

2022 ◽  
Vol 9 ◽  
Author(s):  
Jordan R Brock ◽  
Terezie Mandáková ◽  
Michael McKain ◽  
Martin A Lysak ◽  
Kenneth M Olsen
Keyword(s):  
Phylogenetic Analyses ◽  
Divergence Time ◽  
Diploid Species ◽  
Time Estimation ◽  
Polyploid Species ◽  
Chromosome Counts ◽  
Diploid Parent ◽  
Divergence Time Estimation ◽  
Multiple Origins ◽  
Chloroplast Genomes

Abstract The genus Camelina (Brassicaceae) comprises 7–8 diploid, tetraploid, and hexaploid species. Of particular agricultural interest is the biofuel crop, C. sativa (gold-of-pleasure or false flax), an allohexaploid domesticated from the widespread weed, C. microcarpa. Recent cytogenetics and genomics work has uncovered the identity of the parental diploid species involved in ancient polyploidization events in Camelina. However, little is known about the maternal subgenome ancestry of contemporary polyploid species. To determine the diploid maternal contributors of polyploid Camelina lineages, we sequenced and assembled 84 Camelina chloroplast genomes for phylogenetic analysis. Divergence time estimation was used to infer the timing of polyploidization events. Chromosome counts were also determined for 82 individuals to assess ploidy and cytotypic variation. Chloroplast genomes showed minimal divergence across the genus, with no observed gene-loss or structural variation. Phylogenetic analyses revealed C. hispida as a maternal diploid parent to the allotetraploid Camelina rumelica, and C. neglecta as the closest extant diploid contributor to the allohexaploids C. microcarpa and C. sativa. The tetraploid C. rumelica appears to have evolved through multiple independent hybridization events. Divergence times for polyploid lineages closely related to C. sativa were all inferred to be very recent, at only ~65 thousand years ago. Chromosome counts confirm that there are two distinct cytotypes within C. microcarpa (2n = 38 and 2n = 40). Based on these findings and other recent research, we propose a model of Camelina subgenome relationships representing our current understanding of the hybridization and polyploidization history of this recently-diverged genus.

ANALYSIS OF SPECIES RELATIONSHIPS IN AVENAE BY THIN-LAYER CHROMATOGRAPHY AND DISC ELECTROPHORESIS

1972 ◽  
Vol 14 (2) ◽  
pp. 305-316 ◽  
Author(s):  
H. C. Dass
Keyword(s):  
Thin Layer ◽  
Diploid Species ◽  
Disc Electrophoresis ◽  
Tetraploid Species ◽  
Species Relationships ◽  
D Genome ◽  
Genome Donor ◽  
A Genome ◽  
Layer Chromatography ◽  
Esterase Patterns

Thin-layer chromatographic studies on flavonoids, and disc electrophoretic studies on proteins and esterase isoenzymes were conducted with Avena to determine species relationships and genome homologies. Distinctness of Avena ventricosa and A. pilosa was observed in comparison to other diploid species. Closeness of the diploid species of the A. strigosa group (including hirtula and wiestii) was evident from the similarity of their protein and esterase spectra. The tetraploid species, A. barbata and A. abyssinica, were found to be very close to A. hirtula and A. strigosa, respectively, by TLC studies. Proteins and esterases also showed that the tetraploid species are very close to the A. strigosa group of diploid species. The contribution of a genome by the A. strigosa group to the tetraploids and hexaploids was confirmed. The hexaploids showed different protein and esterase patterns. The involvement of A. ventricosa as the C genome donor to the hexaploids was shown by the protein and esterase spectra. A few extra protein bands observed may have been from the D genome.

scholarly journals Molecular and Symptom Analyses of Phytoplasma Strains from Lettuce Reveal a Diverse Population

2004 ◽  
Vol 94 (8) ◽  
pp. 842-849 ◽  
Author(s):  
Jianhua Zhang ◽  
Saskia A. Hogenhout ◽  
Lowell R. Nault ◽  
Casey W. Hoy ◽  
Sally A. Miller
Keyword(s):  
Fragment Length Polymorphism ◽  
Phylogenetic Analyses ◽  
The Other ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Aster Yellows ◽  
Pcr Rflp ◽  
Horizontal Growth ◽  
Polymerase Chain ◽  
Leaf Distortion

Epidemics of aster yellows in lettuce in Ohio are caused by at least seven distinct phytoplasma strains in the aster yellows (AY) group. Five of the strains are newly reported: AY-BW, AY-WB, AY-BD3, AY-SS, and AY-SG. All seven strains were characterized based on symptoms in aster and lettuce, and by polymerase chain reaction (PCR). Strain AY-BD2 (formerly ‘Bolt’) causes yellowing and leaf distortion in lettuce and bolting in aster, whereas strain AY-S (formerly ‘Severe’) causes stunting, leaf clustering, and phyllody. Strain AY-WB causes yellowing and wilting in lettuce and witches'-broom in aster. Strain AY-SG induces horizontal growth in lettuce and aster plants. Strain AY-BW causes chlorosis of emerging leaves and abnormally upright growth of leaf petioles. AY-SS causes symptoms similar to those caused by AY-S but has a different PCR-restriction fragment length polymorphism (RFLP) banding pattern. Strains AY-BD2 and AY-BD-3 cause mild leaf and stem distortion in lettuce but are differentiated by PCR-RFLP. All phytoplasma strains collected from lettuce in Ohio belong to the 16SrI group. AY-WB belongs to the 16SrI-A subgroup and the other six belong to the 16SrI-B subgroup. Five of the seven strains were distinguished from each other by primer typing. The results of phylogenetic analyses of sequences of the 16S rRNA genes were basically consistent with the classification based on PCR-RFLP, in which AY-WB clustered with phytoplasmas of the 16rIA subgroup and the other Ohio lettuce strains clustered with phytoplasmas in the 16SrI-B subgroup.

scholarly journals Swordfish or Shark Slice? A Rapid Response by COIBar–RFLP

Foods ◽  
2019 ◽  
Vol 8 (11) ◽  
pp. 537 ◽  
Author(s):  
Ferrito ◽  
Raffa ◽  
Rossitto ◽  
Federico ◽  
Saccone ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Fragment Length Polymorphism ◽  
Phylogenetic Analyses ◽  
Enzymatic Digestion ◽  
Molecular Tools ◽  
Prionace Glauca ◽  
Market Transparency ◽  
Coi Barcoding ◽  
Species Substitution ◽  
Restriction Fragment Length

Market transparency is in strong demand by consumers, and the authentication of species is an important step for seafood traceability. In this study, a simple molecular strategy, COIBar–RFLP (cytochrome oxidase I barcode–restriction fragment length polymorphism), is proposed to unveil commercial fraud based on the practice of species substitution in the swordfish trade. In particular, COI barcoding allowed the identification of the species Prionace glauca, Mustelus mustelus, and Oxynotus centrina in slices labeled as Xiphias gladius. Furthermore, the enzymatic digestion of COI amplicons using the MboI restriction endonuclease allowed the simultaneous discrimination of the four species. Interestingly, an intraspecific differential MboI pattern was obtained for the swordfish samples. This pattern was useful to differentiate the two different clades revealed in this species by phylogenetic analyses using several molecular markers. These results indicate the need to strengthen regulations and define molecular tools for combating the occurrence of fraud along the seafood supply chain and show that COIBar–RFLP could become a standardized molecular tool to assess seafood authenticity.

Genomic in situ hybridization (GISH) discriminates between the A and the B genomes in diploid and tetraploid Setaria species

Genome ◽  
2001 ◽  
Vol 44 (4) ◽  
pp. 685-690 ◽  
Author(s):  
A Benabdelmouna ◽  
Y Shi ◽  
M Abirached-Darmency ◽  
H Darmency
Keyword(s):  
In Situ Hybridization ◽  
Foxtail Millet ◽  
Diploid Species ◽  
Genomic In Situ Hybridization ◽  
The Other ◽  
Polyploid Species ◽  
Nucleolar Organizing Regions ◽  
Genomic Relationships ◽  
Clear Differentiation

Genomic in situ hybridization (GISH) was used to investigate genomic relationships between different Setaria species of the foxtail millet gene pool (S. italica) and one interspecific F1 hybrid. The GISH patterns obtained on the two diploid species S. viridis (genome A) and S. adhaerans (genome B), and on their F1 hybrid showed clear differentiation between these two genomes except at the nucleolar organizing regions. Similar GISH patterns allowed differentiation of S. italica from S. adhaerans. However, GISH patterns did not distinguish between the genomes of S. italica and its putative wild ancestor S. viridis. GISH was also applied to polyploid Setaria species and enabled confirmation of the assumed allotetraploid nature of S. faberii and demonstration that both S. verticillata and S. verticillata var. ambigua were also allotetraploids. All these tetraploid species contained two sets of 18 chromosomes each, one from genome A and the other from genome B. Only one polyploid species, S. pumila, was shown to bear an unknown genomic composition that is not closely related either to genome A or to genome B.Key words: Setaria, genomic in situ hybridization, genome analysis.

Relatedness of three species of Agaricus inferred from restriction fragment length polymorphism analysis of the ribosomal DNA repeat and mitochondrial DNA

Genome ◽  
1989 ◽  
Vol 32 (2) ◽  
pp. 173-178 ◽  
Author(s):  
William E. A. Hintz ◽  
James B. Anderson ◽  
Paul A. Horgen
Keyword(s):  
Mitochondrial Dna ◽  
Restriction Fragment Length Polymorphism ◽  
Restriction Site ◽  
Fragment Length Polymorphism ◽  
The Other ◽  
Rrna Genes ◽  
Polymorphism Analysis ◽  
Restriction Patterns ◽  
Dna Restriction ◽  
Restriction Fragment Length

The ribosomal DNA (rDNA) repeat of Agaricus brunnescens (= A. bisporus) was cloned and mapped for six restriction endonucleases. The map positions of the 26S, 18S, and 5.8S rRNA genes on the 9.2 kilo base pairs (kbp) repeat were determined by alignment of sites conserved in the rRNA genes of other fungi. The rDNA restriction site maps for six isolates of A. brunnescens, five isolates of A. bitorquis, and three isolates of A. campestris were compared using cloned A. brunnescens (Ag 50) rDNA as a hybridization probe. The rDNA restriction patterns for all six A. brunnescens isolates were identical. The A. bitorquis and A. campestris isolates were subdivided into two groups each, according to rDNA restriction-site polymorphisms. The A. brunnescens and A. bitorquis rDNAs were distinguished by a 0.7 kbp length difference in the noncoding spacer between the 18S and 26S rRNA genes. Despite the almost perfect conservation of the coding region between species, the noncoding spacers of A. campestris and the other two Agaricus species were too divergent to propose a simple series of mutational events to account for the differences. Interstrain and interspecies variation in the mitochondrial DNA was also surveyed. Strain-specific mitochondrial DNA restriction patterns were recognized and fewer differences were observed between the A. brunnescens and A. bitorquis isolates than between A. campestris and the other two species.Key words: Agaricus brunnescens (= A. bisporus), Agaricus, rDNA, mitochondrial DNA, restriction fragment length polymorphism analysis.

Evaluation of the taxonomic status of the genus Aliella (Compositae, Gnaphalieae): a recircumscription of the genus Phagnalon

Phytotaxa ◽  
2013 ◽  
Vol 148 (1) ◽  
pp. 1 ◽  
Author(s):  
NOEMÍ MONTES-MORENO ◽  
NÚRIA GARCIA-JACAS ◽  
CARLES BENEDÍ ◽  
LLORENÇ SÁEZ
Keyword(s):  
Phylogenetic Analyses ◽  
Taxonomic Status ◽  
The Other ◽  
New Combinations ◽  
Molecular Approach ◽  
Ecological Data ◽  
Diagnostic Characters ◽  
Distribution Maps ◽  
Atlas Mountains ◽  
Taxonomic Evaluation

A taxonomic evaluation of the genus Aliella, endemic to the Moroccan Atlas Mountains, is presented. We evaluate the taxonomic status of Aliella using a morphologic and molecular approach. Firstly, we discuss the variability and usefulness of its morphological diagnostic characters. Secondly, we analyse nuclear ETS and ITS, and chloroplast ycf3-trnS and trnT-trnL spacers. Phylogenetic analyses of the nrDNA and cpDNA spacers suggest the paraphyly of Aliella and Phagnalon. Two species of Aliella, A. ballii and A. embergeri, form a strongly supported clade. In contrast, relationships of A. platyphylla to A. ballii and A. embergeri are only weakly supported, and A. iminouakensis do not form a group with the other species and shows two different haplotypes. The morphological and diagnostic characters of Aliella are described and compared with an extensive sampling of the closely related genus Phagnalon. Our results strongly suggest that Aliella should be merged into Phagnalon. For each accepted taxon, taxonomical, chorological, and ecological data are provided. Six taxa are recognized, three species and three subspecies. Three lectotypifications of specific names and three new combinations are proposed. New descriptions and distribution maps of the recognized taxa are given.

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