scholarly journals Molecular and Chromosomal Markers for Evolutionary Considerations in Torpediniformes (Chondrichthyes, Batoidea)

ISRN Genetics ◽  
2013 ◽  
Vol 2013 ◽  
pp. 1-10 ◽  
Author(s):  
Lucia Rocco
Keyword(s):  
Genomic Organization ◽  
Cartilaginous Fish ◽  
Phylogenetic Position ◽  
Repeated Dna ◽  
Characteristic Distribution ◽  
Molecular Approaches ◽  
Chromosomal Markers ◽  
Taxonomic Groups ◽  
Basal Position ◽  
Specific Nucleotide

Due to their basal position in the vertebrate phylogenetic tree, the study on elasmobranch genetics and cytogenetics can provide remarkable information on the mechanisms underlying the evolution of all vertebrates. In recent years, different molecular approaches have been used to study the relationships between the different taxonomic groups of cartilaginous fish, among them are the physical mapping of specific nucleotide sequences on chromosomes. However, these are controversial, particularly in Torpediniformes in which the species have different karyological parameters. The purpose of this paper is to gather the molecular markers so far present in literature that were used to reconstruct the phylogenetic position of Torpediniformes with respect to the other Batoidea and to discriminate between the various chromosome pairs in the endemic species in the Mediterranean Sea, Torpedo torpedo, T. marmorata and T. nobiliana. The 5S and 18S ribosomal DNA, the HpaI and Alu SINE, the telomeric (TTAGGG)n and the spermatogenesis-related SPATA 16, SPATA 18, and UTY sequences were particularly useful. These last genomic segments were also able to differentiate between the male and the female karyotypes. Moreover, the torpedoes showed a particular genomic organization, especially Torpedo torpedo, in which large quantities of highly repeated DNA and a characteristic distribution of heterochromatin, which is never centromeric, were observed.

Phylogenetic approaches reveal a new sterile lichen in the genus Loxospora (Sarrameanales, Ascomycota) in Poland

Phytotaxa ◽  
2018 ◽  
Vol 348 (3) ◽  
pp. 211 ◽  
Author(s):  
BEATA GUZOW-KRZEMIŃSKA ◽  
ANNA ŁUBEK ◽  
DARIUSZ KUBIAK ◽  
EMILIA OSSOWSKA ◽  
MARTIN KUKWA
Keyword(s):  
New Species ◽  
Phylogenetic Position ◽  
Molecular Approaches

Loxospora cristinae sp. nov. is a sterile corticolous lichen characterized by sorediate, thin, smooth, folded, cracked-areolate and non-verruculose to partly verruculose thalli, soralia soon becoming confluent and the production of 2’-O-methylperlatolic acid. The new species is similar to the recently described L. assateaguensis and L. confusa, which are also sterile and contain 2’-O-methylperlatolic acid. Loxospora assateaguensis can be readily distinguished from the new species by the thallus, which is distinctly verruculose almost from the edge and pustular, and the circular soralia developing apically on the thalline verrucae, and from L. confusa by the presence of granular isidia. The distinction of all three species and their phylogenetic position are also corroborated by molecular approaches using mtSSU and ITS markers. The new species has been found so far only in well preserved forests in Poland.

scholarly journals Isolated clusters of paired tandemly repeated sequences in the Xenopus laevis genome.

1984 ◽  
Vol 4 (2) ◽  
pp. 254-259 ◽  
Author(s):  
D Carroll ◽  
J E Garrett ◽  
B S Lam
Keyword(s):  
Xenopus Laevis ◽  
Dna Sequences ◽  
Tandem Repeats ◽  
Genomic Organization ◽  
Evolutionary Conservation ◽  
Repeated Dna ◽  
Flanking Sequence ◽  
Base Pairs ◽  
Selection For ◽  
Tandemly Repeated Dna

There exist in the Xenopus laevis genome clusters of tandemly repeated DNA sequences, consisting of two types of 393-base-pair repeating unit. Each such cluster contains several units of one of these paired tandem repeats (PTR-1), followed by several units of the other repeat (PTR-2). The number of repeats of each type is variable from cluster to cluster and averages about seven of each type per cluster. Every cluster has ca. 1,000 base pairs of common left flanking sequence (adjacent to the PTR-1 repeats) and 1,000 base pairs of common right flanking sequence (adjacent to the PTR-2 repeats). Beyond these common flanks, the DNA sequences are different in the eight cloned genomic fragments we have studied. Thus, the hundreds of PTR clusters in the genome are dispersed at apparently unrelated sites. Nucleotide sequences of representative PTR-1 and PTR-2 repeats are 64% homologous. These sequences do not reveal an obvious function. However, the related species X. mulleri and X. borealis have sequences homologous to PTR-1 and PTR-2, which show the same repeat lengths and genomic organization. This evolutionary conservation suggests positive selection for the clusters. Maintenance of these sequences at dispersed sites imposes constraints on possible mechanisms of concerted evolution.

Isolated clusters of paired tandemly repeated sequences in the Xenopus laevis genome

1984 ◽  
Vol 4 (2) ◽  
pp. 254-259
Author(s):  
D Carroll ◽  
J E Garrett ◽  
B S Lam
Keyword(s):  
Xenopus Laevis ◽  
Dna Sequences ◽  
Tandem Repeats ◽  
Genomic Organization ◽  
Evolutionary Conservation ◽  
Repeated Dna ◽  
Flanking Sequence ◽  
Base Pairs ◽  
Selection For ◽  
Tandemly Repeated Dna

There exist in the Xenopus laevis genome clusters of tandemly repeated DNA sequences, consisting of two types of 393-base-pair repeating unit. Each such cluster contains several units of one of these paired tandem repeats (PTR-1), followed by several units of the other repeat (PTR-2). The number of repeats of each type is variable from cluster to cluster and averages about seven of each type per cluster. Every cluster has ca. 1,000 base pairs of common left flanking sequence (adjacent to the PTR-1 repeats) and 1,000 base pairs of common right flanking sequence (adjacent to the PTR-2 repeats). Beyond these common flanks, the DNA sequences are different in the eight cloned genomic fragments we have studied. Thus, the hundreds of PTR clusters in the genome are dispersed at apparently unrelated sites. Nucleotide sequences of representative PTR-1 and PTR-2 repeats are 64% homologous. These sequences do not reveal an obvious function. However, the related species X. mulleri and X. borealis have sequences homologous to PTR-1 and PTR-2, which show the same repeat lengths and genomic organization. This evolutionary conservation suggests positive selection for the clusters. Maintenance of these sequences at dispersed sites imposes constraints on possible mechanisms of concerted evolution.

Presence of various rye-specific repeated DNA sequences on the midget chromosome of rye

Genome ◽  
1994 ◽  
Vol 37 (4) ◽  
pp. 619-624 ◽  
Author(s):  
Rama S. Kota ◽  
Bikram S. Gill ◽  
Scot H. Hulbert
Keyword(s):  
Dna Sequences ◽  
Genomic Organization ◽  
Fertility Restoration ◽  
Repeated Dna ◽  
Alloplasmic Line ◽  
Pericentric Region ◽  
Repeated Dna Sequences ◽  
Physical Length ◽  
Banding Analysis ◽  
Chromosome 1R

The chromosome 1R of rye, or the midget chromosome, is necessary for plump, viable seed development and fertility restoration in the alloplasmic line with rye cytoplasm and a hexaploid wheat nucleus. The midget chromosome of rye represents 1/15th of the physical length of the chromosome 1R of rye. C-banding analysis indicated that the centromeric and pericentric region (approximately 30% physical length) of the midget chromosome is heterochromatic and the distant 70% physical length is euchromatic. These data suggest that the midget chromosome may represent the pericentric region of the long arm of chromosome 1R. In contrast with earlier reports, our results indicate that an array of rye-specific repeated sequences (both dispersed and tandem) are present on the midget chromosome. Various rye-specific repeated DNA sequences that are present on the midget chromosome will be useful in constructing a long-range map and studying the genomic organization of the midget chromosome. It is unclear if any of these repeated DNA sequences are involved in the origin of the midget chromosome.Key words: midget chromosome, pericentric region, repeated DNA sequences, rye telomere associated sequence.

scholarly journals Taxonomic position of several enigmatic Polyommatus (Agrodiaetus) species (Lepidoptera, Lycaenidae) from Central and Eastern Iran: insights from molecular and chromosomal data

2014 ◽  
Vol 8 (4) ◽  
pp. 313-322 ◽  
Author(s):  
Vladimir Lukhtanov ◽  
Nazar Shapoval ◽  
Alexander Dantchenko
Keyword(s):  
Chromosome Number ◽  
Species Group ◽  
Taxonomic Position ◽  
Phylogenetic Position ◽  
Rare Taxa ◽  
Eastern Iran ◽  
Chromosomal Markers ◽  
Chromosomal Data ◽  
Species Groups ◽  
Wing Coloration

The species-rich subgenus Polyommatus (Agrodiaetus) has become one of the best studied groups of Palearctic blue butterflies (Lepidoptera, Lycaenidae). However, the identity and phylogenetic position of some rare taxa from Iran have remained unclear. An enigmatic, recently described Central Iranian species Polyommatus (Agrodiaetus) shirkuhensis ten Hagen et Eckweiler, 2001 has been considered as a taxon closely related either to Polyommatus (Agrodiaetus) eckweileri ten Hagen, 1998 or to Polyommatus (Agrodiaetus) baltazardi (de Lesse, 1962). Polyommatus (Agrodiaetus) baltazardi, in its turn, was treated as a taxon close to Iranian-Pakistani Polyommatus (Agrodiaetus) bogra Evans, 1932. Here we used a combination of molecular and chromosomal markers to show that none of these hypotheses was true. Instead, Polyommatus (Agrodiaetus) shirkuhensis was recovered as a member of a species group close to Polyommatus (Agrodiaetus) cyaneus (Staudinger, 1899). From genetically closest species, Polyommatus (Agrodiaetus) kermansis (de Lesse, 1962), Polyommatus (Agrodiaetus) cyaneus and Polyommatus (Agrodiaetus) sennanensis (de Lesse, 1959), it differs by the wing coloration. From morphologically similar Polyommatus (Agrodiaetus) mofidii (de Lesse, 1963) and Polyommatus (Agrodiaetus) sorkhensis Eckweiler, 2003, it differs by its chromosome number, n=21. Polyommatus (Agrodiaetus) bogra and Polyommatus (Agrodiaetus) baltazardi were found to be members of two different species groups and, thus, are not closely related.

The Spermatozoon of Capilloventer Australis and the Systematic Position of the Capilloventridae (Annelida: Oligochaeta)

1996 ◽  
Vol 44 (5) ◽  
pp. 469 ◽  
Author(s):  
M Ferraguti ◽  
C Erseus ◽  
A Pinder
Keyword(s):  
Basal Body ◽  
Systematic Position ◽  
Acute Angle ◽  
Phylogenetic Position ◽  
Middle Piece ◽  
The Family ◽  
Oligochaete Annelid ◽  
Radial Arrangement ◽  
Basal Position

The spermatozoon and spermiogenesis of Capilloventer australis, an oligochaete annelid belonging to the family Capilloventridae, were examined with the aim of supplying further elements for the discussion of the phylogenetic position of the family. Capilloventer australis has a typical oligochaete spermatozoon, with an acrosome tube, mitochondria between the nucleus and flagellum, and a basal cylinder inside the basal body. The acrosome is plesiomorphic, with many characters in common with the Enchytraeidae. The nucleus is twisted, as that of most microdriles, but the middle piece is highly apomorphic in being formed by 11 mitochondria that are not in the usual radial arrangement. The basal cylinder is long and similar to that of the Enchytraeidae. Some features of spermiogenesis, including the acute angle between the nuclear and flagellar axes, are probably plesiomorphic. The spermatological study here presented supports a basal position for the Capilloventridae among the oligochaetes.

scholarly journals Orthology-Based Estimate of the Contribution of Horizontal Gene Transfer from Distantly Related Bacteria to the Intraspecific Diversity and Differentiation of Xylella fastidiosa

Pathogens ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 46
Author(s):  
Giuseppe Firrao ◽  
Marco Scortichini ◽  
Laura Pagliari
Keyword(s):  
Xylella Fastidiosa ◽  
Large Fraction ◽  
Environmental Dna ◽  
Intraspecific Diversity ◽  
Phylogenetic Position ◽  
Pan Genome ◽  
Genome Analyses ◽  
Taxonomic Groups ◽  
Xanthomonas Albilineans ◽  
Relevant Component

Xylella fastidiosa is a xylem-limited bacterium phylogenetically related to the xanthomonads, with an unusually large and diversified range of plant hosts. To ascertain the origin of its peculiarities, its pan-genome was scanned to identify the genes that are not coherent with its phylogenetic position within the order Xanthomonadales. The results of the analysis revealed that a large fraction of the genes of the Xylella pan-genome have no ortholog or close paralog in the order Xanthomonadales. For a significant part of the genes, the closest homologue was found in bacteria belonging to distantly related taxonomic groups, most frequently in the Betaproteobacteria. Other species, such as Xanthomonas vasicola and Xanthomonas albilineans which were investigated for comparison, did not show a similar genetic contribution from distant branches of the prokaryotic tree of life. This finding indicates that the process of acquisition of DNA from the environment is still a relevant component of Xylella fastidiosa evolution. Although the ability of Xylella fastidiosa strains to recombine among themselves is well known, the results of the pan-genome analyses stressed the additional relevance of environmental DNA in shaping their genomes, with potential consequences on their phytopathological features.

Sign in / Sign up

Export Citation Format

Share Document