The molecular–cytogenetic analysis of grasses and its application to studying relationships among species of the Triticeae

Genome ◽  
1989 ◽  
Vol 31 (1) ◽  
pp. 122-133 ◽  
Author(s):  
R. Appels ◽  
P. Reddy ◽  
C. L. McIntyre ◽  
L. B. Moran ◽  
O. H. Frankel ◽  
...  
Keyword(s):  
Cytogenetic Analysis ◽  
Sequence Data ◽  
Evolutionary Relationship ◽  
Repeated Sequence ◽  
Time Span ◽  
Distribution Data ◽  
Molecular Cytogenetic ◽  
Dna Sequence Data ◽  
5S Dna ◽  
Close Relationship

An analysis of four species from the genus Secale, including the study of different accessions, has shown that the properties of DNA clones of monomer units from three repeated sequence loci, namely, Ter, Nor, and 5S DNA, proved to be representative of the entire loci from which they were isolated. This finding in Secale species, including the discovery of a new locus for 5S DNA on chromosome 5R, has been used to interpret information on the Ter, Nor, and 5S DNA loci from 15 species in the Triticeae complex. The evolutionary relationship among species suggested by the DNA sequence data has shown many consistencies with a number of other characters such as those used in classical systematics, as well as geographical distribution data and isozyme and chromosome-pairing studies. Apparent inconsistencies such as a close relationship between the R and P genomes at the Ter loci are interpreted in terms of amplification–deletion phenomena known to occur at repetitive sequence loci. In addition, this study included species endemic to Australia and thus provided a broad time span in which to consider some features of repeated sequence family evolution, such as the conservation of certain parts of 5S DNA spacer regions.Key words: Secale, Triticeae, molecular–cytogenetic analysis.

scholarly journals Characterization of an unusually conserved AluI highly reiterated DNA sequence family from the honeybee, Apis mellifera.

Genetics ◽  
1993 ◽  
Vol 134 (4) ◽  
pp. 1195-1204
Author(s):  
S Tarès ◽  
J M Cornuet ◽  
P Abad
Keyword(s):  
Apis Mellifera ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Sequence Data ◽  
Sequence Divergence ◽  
Repeated Sequence ◽  
Consensus Sequences ◽  
Dna Sequence Data ◽  
Repeat Class ◽  
Honeybee Subspecies

Abstract An AluI family of highly reiterated nontranscribed sequences has been found in the genome of the honeybee Apis mellifera. This repeated sequence is shown to be present at approximately 23,000 copies per haploid genome constituting about 2% of the total genomic DNA. The nucleotide sequence of 10 monomers was determined. The consensus sequences is 176 nucleotides long and has an A + T content of 58%. There are clusters of both direct and inverted repeats. Internal subrepeating units ranging from 11 to 17 nucleotides are observed, suggesting that it could have evolved from a shorter sequence. DNA sequence data reveal that this repeat class is unusually homogeneous compared to the other class of invertebrate highly reiterated DNA sequences. The average pairwise sequence divergence between the repeats is 2.5%. In spite of this unusual homogeneity, divergence has been found in the repeated sequence hybridization ladder between four different honeybee subspecies. Therefore, the AluI highly reiterated sequences provide a new probe for fingerprinting in A. m. mellifera.

A phylogenetic study of Pimelea and Thecanthes (Thymelaeaceae): evidence from plastid and nuclear ribosomal DNA sequence data

2010 ◽  
Vol 23 (4) ◽  
pp. 270 ◽  
Author(s):  
M. Cynthia Motsi ◽  
Annah N. Moteetee ◽  
Angela J. Beaumont ◽  
Barbara L. Rye ◽  
Martyn P. Powell ◽  
...  
Keyword(s):  
Sequence Data ◽  
Intergenic Spacer ◽  
Taxonomic Status ◽  
Molecular Study ◽  
Nuclear Ribosomal Dna ◽  
Phylogenetic Study ◽  
Rps16 Intron ◽  
Dna Sequence Data ◽  
Close Relationship ◽  
Nuclear Its

A comprehensive molecular study, using sequence data from nuclear ITS rDNA and plastid rbcL and matK exons, rps16 intron, and the trnL-F intronic and intergenic spacer, was used to assess the taxonomic status of Thecanthes Wikstr., and to evaluate the relationships within Pimelea Banks & Sol. ex Gaertn. and Thecanthes (Thymelaeaceae). Both genera are Australasian and they constitute the subtribe Pimeleinae, which is characterised by a reduction to two stamens. Previous studies indicated a close relationship among Pimelea, Thecanthes and Gnidia L. species from tropical Africa. We conclude that Pimelea and Thecanthes form a strongly supported clade, with Thecanthes possibly included within Pimelea, although we await further data before formally proposing a series of new taxonomic combinations.

scholarly journals Verticillium Systematics and Evolution: How Confusion Impedes Verticillium Wilt Management and How to Resolve It

2014 ◽  
Vol 104 (6) ◽  
pp. 564-574 ◽  
Author(s):  
Patrik Inderbitzin ◽  
Krishna V. Subbarao
Keyword(s):  
Plant Pathogens ◽  
Sequence Data ◽  
Current System ◽  
Species Boundaries ◽  
Individual Species ◽  
Distribution Data ◽  
Dna Sequence Data ◽  
Taxonomic History ◽  
History Of ◽  
Taxonomic Changes

Verticillium wilts are important vascular wilt diseases that affect many crops and ornamentals in different regions of the world. Verticillium wilts are caused by members of the ascomycete genus Verticillium, a small group of 10 species that are related to the agents of anthracnose caused by Colletotrichum species. Verticillium has a long and complicated taxonomic history with controversies about species boundaries and long overlooked cryptic species, which confused and limited our knowledge of the biology of individual species. We first review the taxonomic history of Verticillium, provide an update and explanation of the current system of classification and compile host range and geographic distribution data for individual species from internal transcribed spacer (ITS) GenBank records. Using Verticillium as an example, we show that species names are a poor vehicle for archiving and retrieving information, and that species identifications should always be backed up by DNA sequence data and DNA extracts that are made publicly available. If such a system were made a prerequisite for publication, all species identifications could be evaluated retroactively, and our knowledge of the biology of individual species would be immune from taxonomic changes, controversy and misidentification. Adoption of this system would improve quarantine practices and the management of diseases caused by various plant pathogens.

Discovery of the second European Amalopis species: an integrative survey of the widespread Pedicia (Amalopis) occulta (Meigen, 1830) (Insecta, Diptera, Pediciidae)

Zootaxa ◽  
2012 ◽  
Vol 3189 (1) ◽  
pp. 1 ◽  
Author(s):  
LUJZA UJVÁROSI ◽  
MIKLÓS BÁLINT
Keyword(s):  
Sequence Data ◽  
Far East ◽  
Sequence Divergence ◽  
Integrative Taxonomy ◽  
Type Specimens ◽  
Species Discovery ◽  
Dna Sequence Data ◽  
Close Relationship ◽  
Male Genital ◽  
Comprehensive Study

Integrative taxonomy enhances species discovery and facilitates species delimitation by combining DNA sequence data,morphology, and distributional and ecological information. In this paper we use complementary methods of morphologyand DNA barcoding to delineate species boundaries in a widespread European spring-dwelling crane-fly, Pedicia (Amalo-pis) occulta (Meigen). We describe a previously overlooked large cryptic dipteran as Pedicia (Amalopis) fusca n. sp. Wealso designate the lectotype of P. occulta of the basis of a comprehensive study of relevant type specimens. Morphologicaldifferences between the two species are delicate but detectable, and comprise mostly male genital structures. However,the sequence divergence of 13.1% reflects an ancient divergence, which plausibly pre-dates the Pleistocene. The EuropeanAmalopis species differ significantly from all the rest of Amalopis species with Far East distributions, but share a numberof similarities with a species identified from the Himalayas, India and described as Pedicia (Tricyphona) ericarum Alexander, 1966. We also discuss a possible close relationship between P. ericarum and the European Amalopis species.

scholarly journals Song and Molecular Data Identify Congruent but Novel Affinities of the Green Oropendola (Psarocolius Viridis)

The Auk ◽  
2004 ◽  
Vol 121 (1) ◽  
pp. 224-229
Author(s):  
J. Jordan Price ◽  
Scott M. Lanyon
Keyword(s):  
Sequence Data ◽  
Phylogenetic Reconstruction ◽  
Molecular Data ◽  
Phylogenetic Position ◽  
Data Sets ◽  
Dna Sequence Data ◽  
Close Relationship ◽  
Morphological Differences ◽  
Vocal Evolution ◽  
Avian Song

Abstract The accuracy with which avian song features indicate phylogenetic relationships has rarely been investigated. In a previous study of vocal evolution in oropendolas (Price and Lanyon 2002a), we estimated the phylogenetic position of the Green Oropendola (Psarocolius viridis) using characters derived from oropendolas' elaborate courtship songs. Here, we test that estimate using mitochondrial DNA sequence data. The position of the Green Oropendola determined from molecular data is remarkably close to that based solely on song characters; both data sets support a close relationship between P. viridis and members of the genus Gymnostinops. Numerous morphological differences yet low genetic divergence among the species in question suggest that rapid diversification has occurred in the group. The fact that this position has not been proposed previously for P. viridis underscores the effectiveness of song characters for phylogenetic reconstruction.

Is the horned pitviper Ceratrimeresurus shenlii Liang and Liu, 2003 from China a valid Protobothrops?

2011 ◽  
Vol 32 (1) ◽  
pp. 132-135
Author(s):  
Ellen Hitschfeld ◽  
Anna Hundsdörfer ◽  
Markus Auer ◽  
Fumin Wang ◽  
Lihua Zhou ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Maximum Likelihood ◽  
Sequence Data ◽  
Isolation By Distance ◽  
Guangdong Province ◽  
Distinct Species ◽  
Cyt B ◽  
Dna Sequence Data ◽  
Phylogenetic Placement ◽  
Close Relationship

AbstractPrevious records of horned pitvipers from Vietnam and China are reviewed and the phylogenetic placement of four snakes from two sites in Tianjingshan Forest, China (Ruyan County, Guangdong Province; 24°43′N, 113°03′E, 563 m a.s.l.; 24°43′N, 113°02′E, 585 m a.s.l.) is examined. Using mitochondrial DNA sequence data (12S, 16S, ND4, cyt b; 2306 bp) and Bayesian and Maximum Likelihood analyses, the Tianjingshan pitvipers are revealed as sister to Protobothrops cornutus with a differentiation resembling those of P. flavoviridis and P. tokarensis. This indicates a close relationship with P. cornutus and suggests that Ceratrimeresurus shenlii Liang and Liu, 2003, previously considered a junior synonym of P. cornutus (Smith, 1930), could be a valid subspecies of P. cornutus or a recently split distinct species. However, further studies and samples from intermediate localities are needed to decide whether the observed differentiation reflects a pattern of isolation-by-distance or a phylogeographic, and thus perhaps taxonomically relevant, break.

scholarly journals Phylogenetic Position Of The Monogenean Malayanodiscoides Bihamuli Lim Et Furtado, 1986 Inferred From Sequence And Secondary Structure Of 28S Rdna

2012 ◽  
Vol 57 (1-4) ◽  
pp. 47-64
Author(s):  
Anshu Chaudhary ◽  
Hridaya Shanker Singh
Keyword(s):  
Secondary Structure ◽  
Molecular Phylogeny ◽  
Structure Data ◽  
Sequence Data ◽  
Structural Parameters ◽  
28S Rdna ◽  
Phylogenetic Position ◽  
Phylogenetic Study ◽  
Dna Sequence Data ◽  
Close Relationship

Abstract The present study is a brief description of the morphology and molecular phylogeny of Malayanodiscoides bihamuli Lim and Furtado, 1986 infecting gill filaments of fish Notopterus chitala (Hamilton). The phylogenetic study was made of M. bihamuli and closely related taxa using DNA sequence data obtained from 28S rDNA region. Morphology as well as molecular phylogeny strongly supports the establishment of genus Malayanodiscoides and also demonstrates its close relationship with other genera of class Monogenea. In addition, the 28S secondary structure model was predicted and found to serve as a useful tool for reconstruction of optimal alignment and can be used as an additional source of data incorporating structural parameters of molecules for the study of phylogeny. Application of the secondary 28S structure data allows a more resolved and realistic picture of relationships. Results also demonstrate the phylogenetic utility of the 28S sequence secondary structure data for inferences at higher taxonomic levels.

Thismia inconspicua (Thismiaceae), a new mycoheterotrophic species from Borneo

Phytotaxa ◽  
2017 ◽  
Vol 295 (3) ◽  
pp. 263 ◽  
Author(s):  
MICHAL SOCHOR ◽  
RAHAYU SUKMARIA SUKRI ◽  
FAIZAH METALI ◽  
MARTIN DANČÁK
Keyword(s):  
Phylogenetic Analysis ◽  
National Park ◽  
Sequence Data ◽  
Dipterocarp Forest ◽  
Dna Sequence Data ◽  
Brunei Darussalam ◽  
Close Relationship ◽  
Perianth Tube ◽  
A New Species ◽  
Mixed Dipterocarp Forest

A new species belonging to the mycoheterotrophic genus Thismia is described and illustrated. Thismia inconspicua was found in a lowland mixed dipterocarp forest in Ulu Temburong National Park, Brunei Darussalam. It is characterized by its sepia-brown perianth with free equal lobes with very short terminal appendages, two pairs of appendages on connective apices, perianth tube displaced from the ovary axis and short stem. DNA sequence data from commonly studied nuclear and mitochondrial loci are provided. Phylogenetic analysis confirmed the close relationship with other members of section Thismia, subsection Odoardoa. An updated determination key of Thismia species of Borneo is included.

Phylogenetic Position and Morphological Observation of the Ctenocladus circinnatus Borzi, a rare green alga from Changtang Plateau, China

Phytotaxa ◽  
2016 ◽  
Vol 260 (1) ◽  
pp. 75 ◽  
Author(s):  
BENWEN LIU ◽  
XUDONG LIU ◽  
ZHENGYU HU ◽  
HUAN ZHU ◽  
GUOXIANG LIU
Keyword(s):  
Sequence Data ◽  
Elongation Factor ◽  
Morphological Observation ◽  
Phylogenetic Position ◽  
Dna Sequence Data ◽  
Large Samples ◽  
Incertae Sedis ◽  
Green Algal ◽  
Marine Habitats ◽  
Close Relationship

Two microfilamentous green algal specimens from Tibet were identified as Ctenocladus circinnatus Borzi, due to their unique morphology and saline habitat. The phylogenetic evidence based on DNA sequence data from the nucleus (SSU) and chloroplast elongation factor TU (tufA) sequences clearly revealed that the genus Ctenocladus, which has been classified in the Chaetophorales (Chlorophyceae) or Trebouxiophyceae incertae sedis by most phycologists, should be included in the Ulvales (Ulvophyceae) instead, and has a close relationship with the genera Pseudendoclonium and Phaeophila. We speculate that there may be undescribed or cryptic species especially in freshwater and other non-marine habitats. A phylogenetic re-evaluation based on large samples of microfilamentous ulvophycean algae especially freshwater specimens is needed.

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