scholarly journals Linkage Groups of Protein-Coding Genes in Western Palearctic Water Frogs Reveal Extensive Evolutionary Conservation

Genetics ◽  
1997 ◽  
Vol 147 (1) ◽  
pp. 255-270
Author(s):  
Hansjürg Hotz ◽  
Thomas Uzzell ◽  
Leszek Berger
Keyword(s):  
Aspartate Aminotransferase ◽  
Published Data ◽  
Linkage Groups ◽  
Protein Coding ◽  
Aconitate Hydratase ◽  
Mitochondrial Superoxide ◽  
Water Frogs ◽  
Guanine Deaminase ◽  
Western Palearctic ◽  
Fructose Biphosphate

Abstract Among progeny of a hybrid (Rana shqiperica × R. lessonae) × R lessonae, 14 of 22 loci form four linkage groups (LGs): (1) mitochondrial aspartate aminotransferase, carbonate dehydratase-2, esterase 4, peptidase D; (2) mannosephosphate isomerase, lactate dehydrogenase-B, sex, hexokinase-1, peptidase B; (3) albumin, fructose-biphosphatase-1, guanine deaminase; (4) mitochondrial superoxide dismutase, cytosolic malic enzyme, xanthine oxidase. Fructose-biphosphate aldolase-2 and cytosolic aspartate aminotransferase possibly form a fifth LG. Mitochondrial aconitate hydratase, α-glucosidase, glyceraldehyde-3+hosphate dehydrogenase, phosphogluconate dehydrogenase, and phosphoglucomutase-2 are unlinked to other loci. All testable linkages (among eight loci of LGs 1, 2, 3, and 4) are shared with eastern Palearctic water frogs. Including published data, 44 protein loci can be assigned to 10 of the 13 chromosomes in Holarctic Rana. Of testable pairs among 18 protein loci, agreement between Palearctic and Nearctic Rana is complete (125 unlinked, 14 linked pairs among 14 loci of five syntenies), and Holarctic Rana and Xenopus laevis are highly concordant (125 shared nonlinkages, 13 shared linkages, three differences). Several Rana syntenies occur in mammals and fish. Many syntenies apparently have persisted for 60–140 × 106 years (frogs), some even for 350–400 × 106 years (mammals and teleosts).

scholarly journals Molecular investigations in western palearctic water frogs

2004 ◽  
Vol 71 (sup2) ◽  
pp. 17-23 ◽  
Author(s):  
Matilde Ragghianti ◽  
Stefania Bucci ◽  
Claudio Casola ◽  
Silvia Marracci ◽  
Giorgio Mancino
Keyword(s):  
Water Frogs ◽  
Western Palearctic

scholarly journals New records of the anomaly P syndrome in two water frog species (Pelophylax ridibundus and P. lessonae) in Russia

Herpetozoa ◽  
2019 ◽  
Vol 32 ◽  
pp. 277-281 ◽  
Author(s):  
Anton O. Svinin ◽  
Ivan V. Bashinskiy ◽  
Vitaly V. Osipov ◽  
Leonid A. Neymark ◽  
Alexander Yu. Ivanov ◽  
...  
Keyword(s):  
Hind Limb ◽  
New Records ◽  
Inguinal Region ◽  
Water Frog ◽  
Central Russia ◽  
Water Frogs ◽  
Western Palearctic ◽  
Frog Species ◽  
Jean Rostand ◽  
Anomalies Of Water

The “anomaly P” was described in Palearctic water frogs of the genus Pelophylax by Jean Rostand as complex morphological anomalies of water frogs, including polydactyly, brachymely, hind limb oedema, bone outgrowths, spikes, flexions and additional limbs in the inguinal region. In 2016, the anomaly P syndrome was rediscovered in central Russia, confirming the hypothesis concerning its wider distribution. Here, three new records of this syndrome in two species of western Palearctic water frog from Russia are described.

scholarly journals Recommendations for bacterial ribosome profiling experiments based on bioinformatic evaluation of published data

2020 ◽  
Vol 295 (27) ◽  
pp. 8999-9011 ◽  
Author(s):  
Alina Glaub ◽  
Christopher Huptas ◽  
Klaus Neuhaus ◽  
Zachary Ardern
Keyword(s):  
Ribosome Profiling ◽  
Published Data ◽  
Data Sets ◽  
Drug Induced ◽  
Data Set ◽  
Protein Coding ◽  
Bacterial Ribosome ◽  
Translation Start ◽  
Selection Step ◽  
Basic Characteristics

Ribosome profiling (RIBO-Seq) has improved our understanding of bacterial translation, including finding many unannotated genes. However, protocols for RIBO-Seq and corresponding data analysis are not yet standardized. Here, we analyzed 48 RIBO-Seq samples from nine studies of Escherichia coli K12 grown in lysogeny broth medium and particularly focused on the size-selection step. We show that for conventional expression analysis, a size range between 22 and 30 nucleotides is sufficient to obtain protein-coding fragments, which has the advantage of removing many unwanted rRNA and tRNA reads. More specific analyses may require longer reads and a corresponding improvement in rRNA/tRNA depletion. There is no consensus about the appropriate sequencing depth for RIBO-Seq experiments in prokaryotes, and studies vary significantly in total read number. Our analysis suggests that 20 million reads that are not mapping to rRNA/tRNA are required for global detection of translated annotated genes. We also highlight the influence of drug-induced ribosome stalling, which causes bias at translation start sites. The resulting accumulation of reads at the start site may be especially useful for detecting weakly expressed genes. As different methods suit different questions, it may not be possible to produce a “one-size-fits-all” ribosome profiling data set. Therefore, experiments should be carefully designed in light of the scientific questions of interest. We propose some basic characteristics that should be reported with any new RIBO-Seq data sets. Careful attention to the factors discussed should improve prokaryotic gene detection and the comparability of ribosome profiling data sets.

Some remarks on current research on western Palearctic water frogs

2001 ◽  
Vol 77 (1) ◽  
pp. 3-4
Author(s):  
Jörg Plötner ◽  
Dirk Scmeller
Keyword(s):  
Water Frogs ◽  
Western Palearctic

Rana/Pol III: A family of SINE-like sequences in the genomes of western Palearctic water frogs

Genome ◽  
1999 ◽  
Vol 42 (3) ◽  
pp. 504-511 ◽  
Author(s):  
S Bucci ◽  
M Ragghianti ◽  
G Mancino ◽  
G Petroni ◽  
F Guerrini ◽  
...  
Keyword(s):  
Repeat Unit ◽  
Rana Esculenta ◽  
Green Water ◽  
North African ◽  
Hybrid Form ◽  
Evolutionary Pattern ◽  
The North ◽  
Water Frogs ◽  
Western Palearctic ◽  
Pol Iii

The highly repetitive Rana/Pol III family consists of short, tandemly arrayed sequences, scattered throughout the genomes of Palearctic green water frogs. The repeat unit is about 250 bp in length and is a composite element: it contains a SINE-like retroposon with a tRNA structure, flanked by two short direct repeats, and the occurrence of two internal repeats gives evidence that an additional transposition event may have inserted a segment within the already transposed element. Rana/Pol III family is present in the genomes of Rana lessonae, R. ridibunda, and their hybrid form R. esculenta, as well as in R. shqiperica, R. epeirotica, R. cretensis, and the Italian taxon. These sequences are also present in the Iberian R. perezi, although less abundant, but appear to be lacking in the north African speciesR. saharica. The distribution of Rana/Pol III in the genomes of Palearctic green frogs is in agreement with the phyletic history based on genetic data. The evolutionary pattern proposed for the genus Rana enables us to suppose that the hybridogenetic mechanism is one of the factors accounting for the possible horizontal transfer of Rana/Pol III elements from the central-north Europe species to R. perezi.Key words: repetitive DNA, SINE-like retroposons, hybridogenesis, Rana esculenta group.

scholarly journals Linkage Relationships Reflecting Ancestral Tetraploidy in Salmonid Fish

Genetics ◽  
1987 ◽  
Vol 116 (4) ◽  
pp. 579-591
Author(s):  
K R Johnson ◽  
J E Wright ◽  
B May
Keyword(s):  
Salmo Trutta ◽  
Salvelinus Alpinus ◽  
Salvelinus Namaycush ◽  
Salmo Gairdneri ◽  
Linkage Groups ◽  
Protein Coding ◽  
Gynogenetic Offspring ◽  
Duplicate Loci ◽  
Salmo Clarki ◽  
Linkage Relationships

ABSTRACT Fifteen classical linkage groups were identified in two salmonid species (Salmo trutta and Salmo gairdneri) and three fertile, interspecific hybrids (S. gairdneri × Salmo clarki, Salvelinus fontinalis × Salvelinus namaycush and S. fontinalisx Salvelinus alpinus) by backcrossing multiply heterozygous individuals. These linkage relationships of electrophoretically detected, protein coding loci were highly conserved among species. The loci encoding the enzymes appeared to be randomly distributed among the salmonid chromosomes. Recombination frequencies were generally greater in females than in males. In males, certain linkage groups were pseudolinked with other linkage groups, presumably because of facultative multivalent pairing and directed disjunction of chromosomes. Five such pseudolinkage groups were identified and they also appeared to be common among species and hybrids. Duplicate loci were never classically linked with each other, although some exhibited pseudolinkage and some showed evidence of exchanging alleles. Gene-centromere recombination frequencies estimated from genotypic distributions of gynogenetic offspring were consistent with map locations inferred from female intergenic recombination frequencies. These linkage relationships support the contention that all extant salmonids arose from a common tetraploid progenitor and that this progenitor may have been a segmental allotetraploid.

scholarly journals Revisiting the phylogeny of phylum Ctenophora: a molecular perspective

F1000Research ◽  
2017 ◽  
Vol 5 ◽  
pp. 2881
Author(s):  
Luis A. Arteaga-Figueroa ◽  
Valentina Sánchez-Bermúdez ◽  
Nicolás D. Franco-Sierra
Keyword(s):  
Phylogenetic Analysis ◽  
Ribosomal Rna ◽  
Fluorescent Protein ◽  
Phylogenetic Analyses ◽  
Meta Analysis ◽  
Tyrosine Aminotransferase ◽  
The Other ◽  
Published Data ◽  
Undescribed Species ◽  
Protein Coding

The phylogenetic relationships of deep metazoans, specifically in the phylum Ctenophora (inside and outside the phylum), are not totally understood. Several loci (protein coding and ribosomal RNA) from organisms belonging to this phylum are currently available on public databases (e.g. GenBank). Previous studies take into account the ribosomal data and the protein data separately. In this study, we perform a meta-analysis of previously published data together. The published data of this phylum have been used in previous phylogenetic analyses inside the phylum and consist in nuclear ribosomal data, such as 18S, 5.8S, ITS1, ITS2, and protein-coding markers such as NFP (non-fluorescent protein). Previous studies concentrate their efforts toward the analyses of ribosomal data or the protein-coding marker separately. Now we take into account these markers together for an upgrade of the phylogenetic analysis of this phylum. We also test several markers such as 28S, IPNS, Tyrosine aminotransferase and HLH domaincontaining protein for the improvement of the study. This markers were analyzed by Bayesian Inference (MrBayes) and Maximum Likelihood (Garli and RAxML), individually and concatenated, showing improvement in the orders placement and presenting new interesting relationship between the paraphyletic order Cydippida and the other ctenophores. These analyses also include sequences from undescribed species that have been reported in GenBank which improved the alignment matrices and support values of some nodes. Adding the undescribed species suggests interesting and well supported clades, the posterior identification of this species would led to an improvement on the ctenophore’s taxonomy.

Microsatellites: A tool for evolutionary genetic studies of western Palearctic water frogs

2001 ◽  
Vol 77 (1) ◽  
pp. 43-50 ◽  
Author(s):  
Hansjürg Hotz ◽  
Thomas Uzzell ◽  
Gaston-Denis Guex ◽  
Deryn Alpers ◽  
Raymond D. Semlitsch ◽  
...  
Keyword(s):  
Genetic Studies ◽  
Water Frogs ◽  
Western Palearctic ◽  
Evolutionary Genetic

Some remarks on current research on western Palearctic water frogs

2008 ◽  
Vol 77 (1) ◽  
pp. 3-4
Author(s):  
Jörg Plötner ◽  
Dirk Scmeller
Keyword(s):  
Water Frogs ◽  
Western Palearctic
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