Ribosomal DNA studies in poplars: Populus deltoides, P. nigra, P. trichocarpa, P. maximowiczii, and P. alba

Genome ◽  
1992 ◽  
Vol 35 (5) ◽  
pp. 733-740 ◽  
Author(s):  
P. Faivre-Rampant ◽  
S. Jeandroz ◽  
F. Lefevre ◽  
M. Lemoine ◽  
M. Villar ◽  
...  
Keyword(s):  
Populus Deltoides ◽  
Intergenic Spacer ◽  
Restriction Enzymes ◽  
Variable Length ◽  
Nuclear Rdna ◽  
Hindiii Site ◽  
Large Variability ◽  
Length Unit ◽  
Rdna Unit ◽  
Length Variant

The nuclear rDNA physical maps of Populus nigra, P. deltoides, P. trichocarpa, P. maximowiczii, and P. alba have been built up for the restriction enzymes EcoRI, EcoRV, BamHI, PstI, and SacI. There is no HindIII site. A large variability appeared between the species in the intergenic spacer mainly for EcoRI and PstI. For several clones of each species two to three major unit types coexist in the genome, while several minor units as well as length variant units or new unit types have been found. The variability between the species is due to different major unit types, while the variability between clones in one species is due to the minor unit types. Every species carries several rDNA unit types either different in size (variable length unit) or variable in restriction sites (variable unit types). Four thousands copies of rDNA units were found in P. nigra, P. deltoides, and P. maximowiczii. The clones belonging to the same species carry the same major unit types but are different in their minor variable length units or minor unit types. The hybrid clones carry the sum of the major unit types of the two parental species. These facts suggested the existence of three rDNA loci. The combination of one enzyme EcoRI and one probe (flax entire rDNA unit) allowed to easily recognize each of the five species. Conversely, we detected the presence of rDNA fragments characteristic to P. deltoides in some clones belonging to P. nigra. We conclude that these clones are likely to have a hybridization in their stands but without observable phenotypic consequences. This technique will be used to verify the purity of each P. nigra candidate clone before exploiting it in a breeding or propagation program.Key words: Populus, nuclear rDNA, intergenic spacer variation, introgression.

Variable-Length Unit Selection in TTS Using Structural Syntactic Cost

2007 ◽  
Vol 15 (4) ◽  
pp. 1227-1235 ◽  
Author(s):  
Chung-Hsien Wu ◽  
Chi-Chun Hsia ◽  
Jiun-Fu Chen ◽  
Jhing-Fa Wang
Keyword(s):  
Variable Length ◽  
Unit Selection ◽  
Length Unit

scholarly journals First Report of Meloidogyne haplanaria Infecting Mi-Resistant Tomato Plants in Florida and Its Molecular Diagnosis Based on Mitochondrial Haplotype

Plant Disease ◽  
2016 ◽  
Vol 100 (7) ◽  
pp. 1438-1445 ◽  
Author(s):  
Soumi Joseph ◽  
Tesfamariam Mekete ◽  
Wiseborn B. Danquah ◽  
Joseph Noling
Keyword(s):  
Large Subunit ◽  
Intergenic Spacer ◽  
Restriction Enzymes ◽  
Restriction Pattern ◽  
Mitochondrial Haplotype ◽  
Diagnostic Strategy ◽  
Root Knot Nematode ◽  
Unique Haplotype ◽  
Morphological Measurement ◽  
Morphological Differences

Meloidogyne haplanaria is a species originally found infesting peanut in Texas and, more recently, in Arkansas. In this study, we confirmed the presence of M. haplanaria in Florida based on morphological and molecular characterization. This species was identified from a sample submitted for diagnosis collected from Mi-resistant tomato rootstock grown in Naples, FL. The major diagnostic criteria to distinguish M. haplanaria from other closely related root-knot nematode (RKN) species are based on morphological differences and host range tests, which are time consuming and labor intensive and require living or well-preserved specimens. In our study, we provide an easy diagnostic strategy to distinguish M. haplanaria from other RKN species based on amplification of two mitochondrial DNA regions. These regions span the intergenic spacer and part of the adjacent large subunit ribosomal RNA gene (lrDNA) and sequence polymorphisms in lrDNA revealed by the restriction pattern following digestion with the restriction enzymes HinfI and MnlI. A unique haplotype pattern, which has not been observed in any of the RKN species described thus far, was observed in M. haplanaria. The outcome of molecular analysis of M. haplanaria aligned with morphological measurement and characteristics as well as perineal pattern originally described for M. haplanaria.

scholarly journals The Phytoplasma Associated with Ramu Stunt Disease of Sugarcane Is Closely Related to the White Leaf Phytoplasma Group

Plant Disease ◽  
1999 ◽  
Vol 83 (6) ◽  
pp. 588-588 ◽  
Author(s):  
C. P. R. Cronjé ◽  
R. A. Bailey ◽  
P. Jones ◽  
S. Suma
Keyword(s):  
Intergenic Spacer ◽  
Restriction Enzymes ◽  
Nested Polymerase Chain Reaction ◽  
Viral Pathogen ◽  
Intergenic Spacer Region ◽  
Severe Stunting ◽  
Sugarcane Varieties ◽  
Large Yield ◽  
White Leaf ◽  
Pot Trials

Ramu stunt disease of sugarcane (ScRS) was responsible for large yield losses in commercial sugarcane varieties (interspecific hybrids of Saccharum spp.) in the Ramu Valley in northeast Papua New Guinea during the late 1980s. Losses were total in the cultivar Ragnar; Q90 and Yasawa were also affected but Cadmus and Q107 were resistant. Since that time, replanting with resistant cultivars has kept the disease under control. The disease spreads rapidly in susceptible cultivars, where it results in severe stunting of the cane and a yellow mottled striping of the leaves. Although several attempts have been made to detect a viral pathogen, no evidence for viral etiology exists and the causal agent remains unknown. With a nested polymerase chain reaction (PCR) of general phytoplasma primers from the 16S rDNA (1), phytoplasma-specific products were consistently amplified from the leaves of field-grown sugarcane, from sugarcane with ScRS symptoms grown in the glasshouse at IACR-Rothamsted, UK, and from samples of the putative vector collected at Ramu, the delphacid plant hopper Eumetopina flavipes Muir, which had been found to transmit symptoms of Ramu stunt in pot trials (2). Digestion of the amplimers with restriction enzymes RsaI and HaeIII gave profiles that matched those of members of the sugarcane white leaf (SCWL) phytoplasma group. The DNA sequence of the intergenic spacer region of the phytoplasma associated with ScRS showed a 95.98% homology with that of SCWL, suggesting that this newly discovered phytoplasma can provisionally be placed in this group. The 16S-23S intergenic spacer sequence has been submitted to GenBank (accession no. AF 106061). References: (1) C. P. R. Cronjé et al. Ann. Appl. Biol. 133:177, 1998; (2) L. S. Kuniata et al. J. Aust. Entomol. Soc. 33:185, 1994.

scholarly journals Intergenic Transcribed Spacer PCR Ribotyping for Differentiation of Saccharomyces Species and Interspecific Hybrids

1998 ◽  
Vol 36 (4) ◽  
pp. 1035-1038 ◽  
Author(s):  
Michael J. McCullough ◽  
Karl V. Clemons ◽  
John H. McCusker ◽  
David A. Stevens
Keyword(s):  
Interspecific Hybrids ◽  
Intergenic Spacer ◽  
Restriction Enzymes ◽  
Species Level ◽  
Rrna Genes ◽  
Ecological Niches ◽  
Intergenic Spacer Region ◽  
Pcr Ribotyping ◽  
Type Strains ◽  
Its Pcr

The taxonomy of the genus Saccharomyces has undergone significant changes recently with the use of genotypic rather than phenotypic methods for the identification of strains to the species level. The sequence of rRNA genes has been utilized for the identification of a variety of fungi to the species level. This methodology, applied to species of Saccharomyces, allows unknown Saccharomyces isolates to be assigned to the type strains. It was the aim of the present study to assess whether typing of the intergenic spacer region by using restriction fragment length polymorphisms of PCR products (intergenic transcribed spacer PCR [ITS-PCR] ribotyping) could distinguish among type strains of the 10 accepted species of Saccharomyces and further to assess if this method could distinguish strains that were interspecific hybrids. Cellular DNA, isolated after the lysis of protoplasts, was amplified by PCR using ITS1 and ITS4 primers, purified by liquid chromatography, and digested with restriction endonucleases. Ribotyping patterns using the restriction enzymes MaeI and HaeIII could distinguish all species of Saccharomyces from each other, as well as from Candida glabrata, Candida albicans, and Blastomyces dermatitidis. The only exception to this was the inability to distinguish betweenSaccharomyces bayanus and S. pastorianus(S. carlsbergensis). Furthermore, interspecific hybrids resulting from the mating of sibling species ofSaccharomyces were shown to share the ITS-PCR ribotyping patterns of both parental species. It should now be possible, by this simple PCR-based technique, to accurately identify these strains to the species level, thereby allowing an increase in our understanding of the characteristics required by these interspecific hybrids for their particular ecological niches.

scholarly journals Characterization of California Isolates of Fusarium oxysporum f. sp. vasinfectum

Plant Disease ◽  
2005 ◽  
Vol 89 (4) ◽  
pp. 366-372 ◽  
Author(s):  
Y. Kim ◽  
R. B. Hutmacher ◽  
R. M. Davis
Keyword(s):  
Fusarium Oxysporum ◽  
Elongation Factor ◽  
Intergenic Spacer ◽  
Culture Collection ◽  
Nuclear Rdna ◽  
Bt Genes ◽  
Pathogenicity Tests ◽  
Race 4 ◽  
Lineage Iv

Thirty isolates of Fusarium oxysporum f. sp. vasinfectum from California, Australia, China, and the American Type Culture Collection were characterized by partial sequences of translational elongation factor (EF-1α), phosphate permase (PHO), and beta-tubulin (BT) genes, restriction digests of the intergenic spacer (IGS) region of nuclear rDNA, and pathogenicity tests. Based on phylogenetic analysis of combined sequences of EF-1α, PHO, and BT genes, California isolates represented four lineages. Lineage I contained race 3, lineage II contained races 1, 2, and 6, lineage III contained race 8, and lineage IV contained race 4. The Australian isolates formed a strongly supported independent clade. There were nine haplotypes based on restriction digests of the IGS region. In greenhouse pathogenicity tests with California isolates, those from the race 4 lineage were highly aggressive on certain Pima cotton (Gossypium barbadense) cultivars and less aggressive on Upland cotton (Gossypium hirsutum) cultivars. All isolates belonging to the other lineages caused relatively mild symptoms on both Pima and Upland cultivars. This is the first report of the occurrence of races 3, 4, and 8 in California.

Phylogenetic positions of Actites megalocarpa and Sonchus hydrophilus (Sonchinae: Asteraceae) based on ITS and chloroplast non-coding DNA sequences

2004 ◽  
Vol 17 (1) ◽  
pp. 73 ◽  
Author(s):  
Seung-Chul Kim ◽  
Christina T. Lu ◽  
Brendan J. Lepschi
Keyword(s):  
New Zealand ◽  
Chloroplast Dna ◽  
Dna Sequences ◽  
Intergenic Spacer ◽  
Its Sequences ◽  
Monotypic Genus ◽  
Nuclear Rdna

Phylogenetic positions of the Australian endemic taxa Actites megalocarpa and Sonchus hydrophilus within the subtribe Sonchinae were determined on the basis of ITS sequences of nuclear rDNA and the psbA–trnH(GUG) intergenic spacer of chloroplast DNA. Both ITS and cpDNA phylogenies suggest that the monotypic genus Actites is not closely related to the members of Sonchus section Asperi, as previously suggested. Rather, this study indicates that it is more closely related to the members of Sonchus sections Maritimi (S.�maritimus) and Arvenses (S. arvensis). It also suggests that S. maritimus from section Maritimi is one of the closest relatives of Actites in Australia, although an alternative origin from section Arvenses is possible. Actites and Embergeria, once treated as congeneric taxa, appear to have originated independently in Australia and New Zealand, respectively. Sonchus hydrophilus is closely related to the S. asper complex, S. oleraceus and S. kirkii. This study suggests that S. kirkii may be involved in the origin of S. hydrophilus in Australia.

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