1,721,012 research outputs found
Molecular and cytogenetic characterization of repetitive DNA in species belonging to Mollusca phylum
No full textMy thesis is focused on the identification and characterization of repetitive DNA sequences in two molluscan species, the bivalve Pecten maximus and the Antarctic polyplacophoran Nuttallochiton mirandus.
Two recombinant DNA libraries were constructed after partial digestion of genomic DNA from Pecten maximus with PstI and ApaI restriction enzymes. Colonies showing strong hybridisation were selected for analysis and sequencing. Six non-homologous tandemly repeated sequences were identified in the sequences, and southern hybridisation with all repeat families to genomic DNA of scallop digested with six different restriction enzymes showed characteristic ladders. Three families had monomer lengths around 40 bp while three had repeats characteristic of the length wrapping around one (170 bp), or two (326 bp) nucleosomes. In situ hybridisation to interphase nuclei showed each family had characteristic numbers of clusters indicating contrasting arrangements.
In Nuttallochiton mirandus clear bands indicating the presence of highly repeated DNA were detected in all three digestions carried out with HindIII, PstI, and EcoRV. Sequence analysis revealed four repeated DNAs (NmH, NmP, NmE250, and NmE700) showing no similarity between them with the exception of NmE700 and NmE250 families. In fact NmE700 family displayed an inserted sequence which might arise from a transposable element. Moreover subrepeat structures were identified in the monomers belonging to NmH and NmP families. Southern blotting analysis showed a ladder banding pattern in HindIII digest indicating a tandem organization of NmH family, while suggested a more complex arrangement for the other families identified. Finally, dot blot analyses carried out in several molluscan species revealed a different degree of conservation of the repeated DNAs isolated with EcoRV. Furthermore, fluorescent in situ hybridisation (FISH) on metaphase chromosomes revealed that NmE700 family is located mainly at centromeric regions on all chromosomes with the exception of the pair of macrochromosomes.
The study of the structure and organization of repetitive DNAs may contribute to understanding not only the genetic diversity but also mechanisms of DNA sequence evolution
New perspectives on the evolutionary history of vitellogenin gene family in vertebrates
No full textVitellogenin (Vtg) is a glycolipophosphoprotein produced by oviparous and ovoviviparous species and is the precursor protein of the yolk, an essential nutrient reserve for embryonic development and early larval stages. Vtg is encoded by a family of paralog genes whose number varies in the different vertebrate lineages. Its evolution has been the subject of considerable analyses but it remains still unclear. In this work, microsyntenic and phylogenetic analyses were performed in order to increase our knowledge on the evolutionary history of this gene family in vertebrates. Our results support the hypothesis that the vitellogenin gene family is expanded from two genes both present at the beginning of vertebrate radiation through multiple independent duplication events occurred in the diverse lineages
Transposable elements in vertebrates: species evolution and environmental adaptation.
No full textThe evolutionary success of species is strictly related to their genome in terms of composition and functionality. Transposable elements (TEs) represent a considerable fraction of the nuclear DNA content, and given to their ability to spread throughout the genome, they are able to create genetic diversity at sequence, gene structure, and chromosome level. Vertebrates represent a highly successful taxon and its lineages are characterized by a variable TE content suggesting a different impact on the genome. In this manuscript, we highlight the importance of TEs in creating new regulatory sequences and genetic innovations extremely useful for diversification of vertebrates. Moreover, an increasing number of evidence suggests a link between TEs and environment. Indeed, given the richness of species adapted to a wide range of habitats and conditions, vertebrates are exposed to several ecological pressures with consequent effects on evolutionary adaptation
Hox and ParaHox genes: A review on molluscs
No full textHox and ParaHox genes are involved in patterning the anterior-posterior body axis in metazoans during embryo development. Body plan evolution and diversification are affected by variations in the number and sequence of Hox and ParaHox genes, as well as by their expression patterns. For this reason Hox and ParaHox gene investigation in the phylum Mollusca is of great interest, as this is one of the most important taxa of protostomes, characterized by a high morphological diversity. The comparison of the works reviewed here indicates that species of molluscs, belonging to different classes, share a similar composition of Hox and ParaHox genes. Therefore evidence suggests that the wide morphological diversity of this taxon could be ascribed to differences in Hox gene interactions and expressions and changes in the Hox downstream genes rather than to Hox cluster composition. Moreover the data available on Hox and ParaHox genes in molluscs compared with those of other Lophotrochozoa shed light on the complex and controversial evolutionary histories that these genes have undergone within protostomes
Hox genes in the Antarctic polyplacophoran Nuttallochiton mirandus.
No full textABSTRACT Hox genes are conserved across all bilaterians and encode transcription factors
involved in the formation of the anteroposterior axis during embryo development. Differences in
homeotic gene evolution have been observed not only between deuterostomes and protostomes, but
also between the two large protostome clades, Ecdysozoa and Lophotrochozoa.
Among lophotrochozoans, the phylum Mollusca displays high diversity of body plans, ranging from
the wormlike appearance of aplacophorans to the complex body plan of cephalopods. Using a PCRbased
method, we were able to identify eight Hox genes in the polyplacophoran Nuttallochiton
mirandus, two orthologous to the anterior class (lab, pb), four to the central class (Scr, Lox5, Antp,
Lox2) and two to the posterior class (Post-1, Post-2). Comparison with the results obtained in other
molluscs seems to confirm the conservation of Hox genes in this phylum in terms of both presence
and characteristics
Repetitive DNA in eukaryotic genomes
No full textRepetitive DNA-sequence motifs repeated hundreds or thousands of times in the genome-makes up the major proportion of all the nuclear DNA in most eukaryotic genomes. However, the significance of repetitive DNA in the genome is not completely understood, and it has been considered to have both structural and functional roles, or perhaps even no essential role. High-throughput DNA sequencing reveals huge numbers of repetitive sequences. Most bioinformatic studies focus on low-copy DNA including genes, and hence, the analyses collapse repeats in assemblies presenting only one or a few copies, often masking out and ignoring them in both DNA and RNA read data. Chromosomal studies are proving vital to examine the distribution and evolution of sequences because of the challenges of analysis of sequence data. Many questions are open about the origin, evolutionary mode and functions that repetitive sequences might have in the genome. Some, the satellite DNAs, are present in long arrays of similar motifs at a small number of sites, while others, particularly the transposable elements (DNA transposons and retrotranposons), are dispersed over regions of the genome; in both cases, sequence motifs may be located at relatively specific chromosome domains such as centromeres or subtelomeric regions. Here, we overview a range of works involving detailed characterization of the nature of all types of repetitive sequences, in particular their organization, abundance, chromosome localization, variation in sequence within and between chromosomes, and, importantly, the investigation of their transcription or expression activity. Comparison of the nature and locations of sequences between more, and less, related species is providing extensive information about their evolution and amplification. Some repetitive sequences are extremely well conserved between species, while others are among the most variable, defining differences between even closely relative species. These data suggest contrasting modes of evolution of repetitive DNA of different types, including selfish sequences that propagate themselves and may even be transferred horizontally between species rather than by descent, through to sequences that have a tendency to amplification because of their sequence motifs, to those that have structural significance because of their bulk rather than precise sequence. Functional consequences of repeats include generation of variability by movement and insertion in the genome (giving useful genetic markers), the definition of centromeres, expression under stress conditions and regulation of gene expression via RNA moieties. Molecular cytogenetics and bioinformatic studies in a comparative context are now enabling understanding of the nature and behaviour of this major genomic component
Isolation of Hox and ParaHox genes in bivalve Pecten maximus.
No full textThe Hox cluster genes encode a set of transcription factors that have been shown to control spatial patterning mechanisms in bilaterian organism development. The ParaHox cluster is the evolutionary sister of the Hox cluster. The two are believed to descend from an ancestral ProtoHox cluster of four genes from which the three ParaHox genes (Gsx, Xlox, and Cdx) and the four Hox gene classes are believed to have originated. Although molluscs are among the most successful lophotrochozoan groups, very little work has been devoted to the characteristics of their homeotic genes. Using polymerase chain reaction-based approaches, we isolated 13 different Pecten maximus (Bivalvia: Pteriomorphia) sequences corresponding to all the genes of the four Hox cluster classes and to genes Xlox and Cdx of the ParaHox cluster. Comparison of results with those obtained in other lophotrochozoans seems to confirm the considerable homogeneity of the Hox and ParaHox genes in these taxa both as regards the presence of nearly all the genes of the two clusters and the marked sequence resemblance among orthologous genes. © 2005 Elsevier B.V. All rights reserved
New insights into the genome repetitive fraction of the Antarctic bivalve Adamussium colbecki.
Full text linkRepetitive DNA represents the major component of the genome in both plant and animal species. It includes transposable elements (TEs), which are dispersed throughout the genome, and satellite DNAs (satDNAs), which are tandemly organized in long arrays. The study of the structure and organization of repetitive DNA contributes to our understanding of genome architecture and the mechanisms leading to its evolution. Molluscs represent one of the largest groups of invertebrates and include organisms with a wide variety of morphologies and lifestyles. To increase our knowledge of bivalves at the genome level, we analysed the Antarctic scallop Adamussium colbecki. The screening of the genomic library evidenced the presence of two novel satDNA elements and the CvA transposon. The interspecific investigation performed in this study demonstrated that one of the two satDNAs isolated in A. colbecki is widespread in polar molluscan species, indicating a possible link between repetitive DNA and abiotic factors. Moreover, the transcriptional activity of CvA and its presence in long-diverged bivalves suggests a possible role for this ancient element in shaping the genome architecture of this clade
An Overview of Hox Genes in Lophotrochozoa: Evolution and Functionality
No full textHox genes are regulators of animal embryonic development. Changes in the number and sequence of Hox genes as well as in their expression patterns have been related to the evolution of the body plan. Lophotrochozoa is a clade of Protostomia characterized by several phyla which show a wide morphological diversity. Despite that the works summarized in this review emphasize the fragmentary nature of the data available regarding the presence and expression of Hox genes, they also offer interesting insight into the evolution of the Hox cluster and the role played by Hox genes in several phyla. However, the number of genes involved in the cluster of the lophotrochozoan ancestor is still a question of debate. The data presented here suggest that at least nine genes were present while two other genes, Lox4 and Post-2, may either have been present in the ancestor or may have arisen as a result of duplication in the Brachiopoda-Mollusca-Annelida lineage. Spatial and temporal collinearity is a feature of Hox gene expression which was probably present in the ancestor of deuterostomes and protostomes. However, in Lophotrochozoa, it has been detected in only a few species belonging to Annelida and Mollusca
All the three ParaHox genes are present in Nuttallochiton mirandus (Mollusca: Polyplacophora): evolutionary considerations.
No full textABSTRACT The ParaHox gene cluster contains three homeobox genes, Gsx, Xlox and Cdx and
has been demonstrated to be an evolutionary sister of the Hox gene cluster. Among deuterostomes
the three genes are found in the majority of taxa, whereas among protostomes they have so far been
isolated only in the phylum Sipuncula.
We report the partial sequences of all three ParaHox genes in the polyplacophoran Nuttallochiton
mirandus, the first species of the phylum Mollusca where all ParaHox genes have been isolated. This
finding has phylogenetic implications for the phylum Mollusca and for its relationships with the
other lophotrochozoan taxa
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