As evolutionary relationships within the order Acipenseriformes are not well understood and some classifications are currently controversial, the study of evolutionary relationships, especially based on genetic data, has received much recent attention. In this reanalysis we present a nearly complete proposed phylogeny of the order, including 25 species, based on the maximum likelihood analysis of combined DNA sequence data (4406 base pairs) from five mitochondrial genes sequenced in our laboratories (cytochrome b, 12S rRNA, cytochrome c oxidase subunit II, tRNA Asp and tRNA Phe ) and three mitochondrial gene regions sequenced by Birstein et al. (2002) (16S rRNA, NADH5 and control region). Examination of the molecular phylogeny using either maximum likelihood, Bayesian analysis, maximum parsimony or neighbor-joining leads to the following conclusions: (i) the two species of paddlefish do form a clade; (ii) the most basal position within the Acipenseridae remains unresolved, held either by the genus Scaphirhynchus or by the clade containing Acipenser oxyrinchus and A. sturio; (iii) Huso is not monophyletic, with the two species of Huso found embedded separately within the genus Acipenser; (iv) A. sinensis and A. dabryanus are confirmed as closely related; (v) the previously described Atlantic-Pacific subdivision within the Acipenser ⁄ Huso complex is supported and (vi) the unexpected placement of Pseudoscaphirhynchus kaufmanni within Acipenser is supported by this analysis. These results offer further evidence that some revision of acipenseriform classification may be needed to accurately inform conservation efforts and that future phylogenetic studies of this group should focus on the analysis of nuclear genes.
Karyotype and other chromosomal characteristics of the Appenine endemic cyprinid fish, Toscana stream chub Squalius lucumonis, were analysed using conventional banding and FISH with 45S and 5S rDNA probes. The diploid chromosome number (2n = 50) and karyotype characteristics including pericentromeric heterochromatic blocks and GC-rich CMA(3)-positive sites corresponding to both positive Ag-NORs and 45S rDNA loci on the short arms of a single medium-sized submetacentric chromosome pair were consistent with those found in most European leuciscine cyprinids. On other hand, 5S rDNA FISH in the Toscana stream chub and three other Italian leuciscines, S. squalus, Rutilus rubilio and Telestes muticellus, revealed a species-specific hybridization pattern, i.e. signals on four (S. lucumonis), three (S. squalus and R. rubilio) and two (T. muticellus) chromosome pairs. Whereas all the species shared the 5S rDNA loci on the largest subtelocentric chromosome pair, a "leuciscine" cytotaxonomic marker, S. lucumonis showed both classes of rDNA loci tandem aligned on the short arms of chromosome pair No. 12. The present findings suggest that the observed high variability of 5S rDNA loci provides a powerful tool for investigation of karyotype differentiation in karyologically conservative leuciscine fishes.
The Sox-gene family represents an ancient group of transcription factors involved in numerous developmental processes and sex determination in vertebrates. SOX proteins are characterized by a conserved high mobility group (HMG)-box domain, which is responsible for DNA binding and bending. We studied Sox genes in sturgeon, one of the most primitive groups of fishes characterized by a high chromosome number. Male and female genomes were screened for Sox genes using highly degenerate primers that amplified a broad range of HMG boxes. A total of 102 clones, representing 22 different sequences coding for 8 Sox genes, was detected and classified according to their orthologues. Sox2, Sox3, Sox4, Sox9, Sox11, Sox17, Sox19, and Sox21 were found in sturgeon; these genes represent Sox groups B, C, E, and F. In a phylogenetic analysis (neighbor-joining, maximum likelihood, maximum parsimony), these genes clustered with their mouse orthologues. In the case of Sox4, Sox17, and Sox21, we found evidence of gene duplication.
Significant intraindividual variation in the sequence of the 18S rRNA gene is unusual in animal genomes. In a previous study, multiple 18S rRNA gene sequences were observed within individuals of eight species of sturgeon from North America but not in the North American paddlefish, Polyodon spathula, in two species of Polypterus (Polypterus delhezi and Polypterus senegalus), in other primitive fishes (Erpetoichthys calabaricus, Lepisosteus osseus, Amia calva) or in a lungfish (Protopterus sp.). These observations led to the hypothesis that this unusual genetic characteristic arose within the Acipenseriformes after the presumed divergence of the sturgeon and paddlefish families. In the present study, a survey of nearly all Eurasian acipenseriform species was conducted to examine 18S rDNA variation. Intraindividual variation was not found in the polyodontid species, the Chinese paddlefish, Psephurus gladius, but variation was detected in all Eurasian acipenserid species. The comparison of sequences from two major segments of the 18S rRNA gene and identification of sites where insertion/deletion events have occurred are placed in the context of evolutionary relationships within the Acipenseriformes and the evolution of rDNA variation in this group.
Leuciscine fishes represent an important component of freshwater ichthyofauna endemic to northern Mediterranean areas. This lineage shows high intra-specific morphological variability and exhibits high levels of hybridization, two characteristics that contribute to systematic uncertainties, misclassification of taxa and, potentially, the mismanagement of biodiversity. This study focused on brook chub, Squalius lucumonis, an endemic taxon of Central Italy. The taxonomic status of this species has long been questioned, and a hybrid origin from sympatric leusciscines (S. squalus x Rutilus rubilio, or S. squalus x Telestes muticellus) has been hypothesised. A phenotypic (evaluating shape and meristic counts) and genetic (using mitochondrial and nuclear markers) investigation of these four taxa was conducted to test species delimitation in sympatric areas and to evaluate the taxonomic status of S. lucumonis. One hundred and forty-five individuals of all four taxa were collected within streams of the lowest portion of the Tiber River basin and analysed; this region encompasses a large portion of the S. lucumonis distribution. The different morphological and genetic approaches were individually examined, compared, and then combined in a quantitative model to both investigate the limits of each approach and to identify cases of misclassification. The results obtained confirm the cladogenetic non-hybrid origin of S. lucumonis, highlight the need for immediate conservation actions and emphasise the value of an integrated approach in the study of leuciscines evolution.
Most human pre-mRNAs contain introns that are removed by splicing. Such a complex process needs strict control and regulation in order to prevent the expression of aberrant or unprocessed transcripts. To analyse the fate of pre-mRNAs that cannot be spliced, we inhibited splicing using an anti-sense morpholino (AMO) against U4 snRNA. As a consequence, splicing of several selected transcripts was strongly inhibited. This was accompanied by the formation of enlarged nuclear speckles containing polyadenylated RNA, splicing factors and the nuclear poly(A) binding protein. Consistently, more polyadenylated pre-mRNA could be isolated from nucleoplasmic as well as chromatin-associated RNA fractions following U4 inhibition. Further analysis demonstrated that accumulated pre-mRNAs were stable in the nucleus and that nuclear RNA degradation factors did not re-localise to nuclear speckles following splicing inhibition. The accumulation of pre-mRNA and the formation of enlarged speckles were sensitive to depletion of the 3′ end processing factor, CPSF73, suggesting a requirement for poly(A) site processing in this mechanism. Finally, we provide evidence that the pre-mRNAs produced following U4 snRNA inhibition remain competent for splicing, perhaps providing a biological explanation for their stability. These data further characterise processes ensuring the nuclear retention of pre-mRNA that cannot be spliced and suggest that, in some cases, unspliced transcripts can complete splicing sometime after their initial synthesis.
The Sox9 gene of Acipenser sturio, one of the most primitive vertebrates, was analyzed. No sex-specific differences were observed. Sturgeon Sox9 consists of three exons and two introns with completely conserved exon-intron boundaries showing high levels of homology to other vertebrate Sox9 sequences, especially in the N-terminus region containing the HMG box. We found strong evidence for negative (purifying) selection. In contrast to previous studies of other fishes, we observed no evidence for gene duplication in sturgeon. Phylogenetic analyses of Sox9 evolution revealed a basal position for sturgeon Sox9.
Lutjanidae, commonly known as snappers, includes 105 species, grouped in four subfamilies. In spite of the high number of species and of its worldwide distribution, the family has been little investigated and the phylogenetic relationships among some of its genera and species are still cause for debate. Only a small number of the species has been cytogenetically analysed. This study reports the first description of the karyotype of Rhomboplites aurorubens as well as data concerning the distribution of the constitutive heterochromatin and the location of the 18S rRNA and the 5S rRNA genes. Specimens of Ocyurus chrysurus from Venezuela were also investigated for the same cytogenetic features. Both species have a 48 uniarmed karyotype, but R. aurorubens has a single subtelocentric chromosome pair, the smallest of the chromosome complement, among the other acrocentric chromosomes. The C-positive heterochromatin is limited to the pericentromeric regions of all chromosomes. Both species show a single chromosome pair bearing the Nucleolus Organizer Regions, but NORs are differently located, in a terminal position on the short arms of the smallest chromosomes in R. aurorubens and in a paracentromeric position in a chromosome pair of large size in O. chrysurus. In O. chrysurus, the 5S rDNA gene cluster is located on a medium-sized chromosome pair, whereas in R. aurorubens it is syntenic with the 18S rDNA gene cluster on chromosome pair number 24. The obtained cytogenetic data, along with previous cytogenetic, morphological and molecular data for the family, reinforce the proposal to synonymize genus Ocyurus with Lutjanus. A review of Lutjanidae cytogenetics is also included.Lutjanidae, comumente conhecidos como snappers, inclui 105 espécies, reunidas em quatro subfamílias. A despeito do grande número de espécies e de sua distribuição mundial, a família tem sido pouco estudada e as relações filogenéticas entre alguns de seus gêneros e espécies ainda é motivo de debates. Apenas um pequeno número de espécies foi citogeneticamente analisada. Esse estudo apresenta a primeira descrição do cariótipo de Rhomboplites aurorubens assim como dados relativos à distribuição de heterocromatina constitutiva e localização dos genes 18S rRNA e 5S rRNA. Espécimes de Ocyurus chrysurus da Venezuela foram também analisados quanto às mesmas características citogenéticas. Ambas as espécies têm cariótipos compostos de 48 cromossomos com um único braço, entretanto R. aurorubens tem um único par de cromossomos subtelocêntrico, o menor do complemento cromossômico, entre os outros cromossomos acrocêntricos. A heterocromatina C-positiva é limitada à região pericentromérica de todos os cromossomos. Ambas as species apresentam um único par com Regiões Organizadoras de Nucléolo, mas as RONs são localizadas em posições diferentes, em posição terminal no braço curto dos menores cromossomos de R. aurorubens e em posição paracentromérica no braço longo de um par de cromossomos grandes de O. chrysurus. Em O. chrysurus, os genes 5S rDNA estão localizados em u...
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