Maria Assunta BISCOTTI


Maria Assunta BISCOTTI


34 pubblicazioni classificate nel seguente modo:

Nr. doc. Classificazioni
33 1 Contributo su Rivista
1 8 Tesi di dottorato
Anno Risorsa
2019 The p53 gene family in vertebrates: Evolutionary considerations
Autore/i: Biscotti, Maria Assunta; Barucca, Marco; Carducci, Federica; Forconi, Mariko; Canapa, Adriana
Classificazione: 1 Contributo su Rivista
Abstract: The origin of the p53 gene family predates multicellular life since TP53 members of this gene family have been found in unicellular eukaryotes. In invertebrates one or two genes attributable to a TP53-like or TP63/73-like gene are present. The radiation into three genes, TP53, TP63, and TP73, has been reported as a vertebrate invention. TP53 is considered the "guardian of the genome" given its role in protecting cells against the DNA damage and cellular stressors. TP63 and TP73 play a role in epithelial development and neurogenesis, respectively. The evolution of the p53 gene family has been the subject of considerable analyses even if several questions remain still open. In this study we addressed the evolutionary history of the p53 gene family in vertebrates performing an extended microsyntenic investigation coupled with a phylogenetic analysis, together with protein domain organization and structure assessment. On the basis of our results we discussed a possible evolutionary scenario according to which a TP53/63/73 ancestor form gave rise to the current TP53 and a TP63/73 form, which in turn independently duplicated into two genes in agnathe and gnathostome lineages.
Scheda della pubblicazione: https://iris.univpm.it/handle/11566/267462 Collegamento a IRIS

2019 Vitellogenin gene family in vertebrates: evolution and functions
Autore/i: Carducci, F.; Biscotti, M. A.; Canapa, A.
Classificazione: 1 Contributo su Rivista
Abstract: Abstract The vitellogenin gene family is constituted of variable gene numbers encoding for polypeptides that are precursors of yolk proteins and derivatives in oviparous and ovoviviparous vertebrates. The comprehension of which mechanisms have shaped the evolution of vtg gene family represents an attractive field of research. The primary intent of this review is to summarize the evolutionary hypotheses that have been proposed over recent decades, highlighting the differences between the proposed models. Overall in vertebrates the evolutionary history of this gene family is the result of complex modifications deeply influenced by events such as Whole Genome Duplications (WGDs), lineage-specific gene losses and duplications. Interestingly the last hypothesis allowed to date the vitellogenin gene cluster origin in the common ancestor of gnathostomes. In addition, in the last decades, several works evidenced non-nutritional functions such as antibacterial, immunological and antioxidant activities overcoming its classical view as a simple source of nourishment for the developing embryos.
Scheda della pubblicazione: https://iris.univpm.it/handle/11566/267994 Collegamento a IRIS

2018 New insights into the genome repetitive fraction of the Antarctic bivalve Adamussium colbecki
Autore/i: Biscotti, Maria Assunta; Barucca, Marco; Canapa, Adriana
Classificazione: 1 Contributo su Rivista
Abstract: Repetitive 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.
Scheda della pubblicazione: https://iris.univpm.it/handle/11566/256509 Collegamento a IRIS

2018 New perspectives on the evolutionary history of vitellogenin gene family in vertebrates
Autore/i: Biscotti, Maria Assunta; Barucca, Marco; Carducci, Federica; Canapa, Adriana
Classificazione: 1 Contributo su Rivista
Abstract: Vitellogenin (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.
Scheda della pubblicazione: https://iris.univpm.it/handle/11566/261697 Collegamento a IRIS

2018 Phylogenetic relationships of Mediterranean black corals (Cnidaria: Anthozoa: Hexacorallia) and implications for classification within the order Antipatharia
Autore/i: Bo, M.; Barucca, M.; Biscotti, M. A.; Brugler, M. R.; Canapa, A.; Canese, S.; Lo Iacono, C.; Bavestrello, G.
Classificazione: 1 Contributo su Rivista
Abstract: Abstract. The Mediterranean black coral fauna includes type species of four antipatharian genera belonging to four different families, therefore phylogenetic studies hold great potential for enhancing systematics within the order. The analysis of six Mediterranean antipatharian species by means of nuclear sequence data of internal transcribed spacer (ITS1 and ITS2) rDNA confirms the separation into different families, as was previously noted on a morphological basis, with a clear distinction of the family Leiopathidae, whose position is supported by a unique number of mesenteries and lack of spines on thicker ramifications. The position of a newly recorded black coral species for the Mediterranean basin belonging to the genus Phanopathes is discussed. Antipathes dichotoma, the type species of the genus Antipathes, on which the order Antipatharia was based, does not group with other members of the family Antipathidae. Supporting a recent finding based on mitochondrial markers, this suggests a critical need for revision of the families that will be impacted by reassignment of this nomenclaturally important taxon.
Scheda della pubblicazione: https://iris.univpm.it/handle/11566/264104 Collegamento a IRIS

2018 Rex Retroelements and Teleost Genomes: An Overview
Autore/i: Carducci, Federica; Barucca, Marco; Canapa, Adriana; Biscotti, MARIA ASSUNTA
Classificazione: 1 Contributo su Rivista
Abstract: Repetitive DNA is an intriguing portion of the genome still not completely discovered and shows a high variability in terms of sequence, genomic organization, and evolutionary mode. On the basis of the genomic organization, it includes satellite DNAs, which are organized as long arrays of head-to-tail linked repeats, and transposable elements, which are dispersed throughout the genome. These repeated elements represent a considerable fraction of vertebrate genomes contributing significantly in species evolution. In this review, we focus our attention on Rex1, Rex3 and Rex6, three elements specific of teleost genomes. We report an overview of data available on these retroelements highlighting their significative impact in chromatin and heterochromatin organization, in the differentiation of sex chromosomes, in the formation of supernumerary chromosomes, and in karyotype evolution in teleosts.
Scheda della pubblicazione: https://iris.univpm.it/handle/11566/264254 Collegamento a IRIS

2018 A comparative view on sex differentiation and gametogenesis genes in lungfish and coelacanths
Autore/i: Biscotti, MARIA ASSUNTA; Contar Adolfi, Mateus; Barucca, Marco; Forconi, Mariko'; Pallavicini, Alberto; Gerdol, Marco; Canapa, Adriana; Schartl, Manfred
Classificazione: 1 Contributo su Rivista
Abstract: Gonadal sex differentiation andreproductionare the keys totheperpetuationof favorable gene combinations andpositively selected traits. In vertebrates, several gonad development features that differentiate tetrapods and fishes are likely to be, at least in part, related to the water-to-land transition. The collection of information from basal sarcopterygians, coelacanths, and lungfishes, is crucial to improve our understanding of the molecular evolution of pathways involved in reproductive functions, since these organisms are generally regarded as “living fossils” and as the direct ancestors of tetrapods. Here, we report for the first time the characterization of >50 genes related to sex differentiation and gametogenesis in Latimeria menadoensis and Protopterus annectens. Although the expression profiles of most genes is consistent with the intermediate position of basal sarcopterygians between actinopterygian fish and tetrapods, their phylogenetic placement and presence/absence patterns often reveal a closer affinity to the tetrapod orthologs. On the other hand, particular genes, for example, the male gonad factor gsdf (Gonadal Soma-Derived Factor), provide examples of ancestral traits sharedwith actinopterygians,which disappeared in the tetrapod lineage.
Scheda della pubblicazione: https://iris.univpm.it/handle/11566/260684 Collegamento a IRIS

2017 The small non-coding RNA processing machinery of two living fossil species, lungfish and coelacanth, gives new insights into the evolution of the Argonaute protein family
Autore/i: Biscotti, MARIA ASSUNTA; Canapa, Adriana; Forconi, Mariko'; Marco, Gerdol; Alberto, Pallavicini; Manfred, Schartl; Barucca, Marco
Classificazione: 1 Contributo su Rivista
Abstract: Argonaute (AGO) family proteins play many roles in epigenetic programming, genome rearrangement, mRNA breakdown, inhibition of translation, and transposon silencing. Despite being a hotspot in current scientific research, their evolutionary history is still poorly understood and consequently the identification of evolutionary conserved structural features should also generate useful information for better understanding their functions.Wereport here for the first time the transcript sets of the two subfamilies, Ago and Piwi, in the West African lungfish Protopterus annectens and in the Indonesian coelacanth Latimeria menadoensis, two key species in the evolutionary lineage leading to tetrapods. The phylogenetic analysis of 142 inferred protein sequences in 22 fully sequenced species and the analysis of microsynteny performed in the major vertebrate lineages indicate an intricate pattern for the evolution of both subfamilies that has been shaped by whole genome duplications and lineage specific gains and losses. The argonaute subfamily was additionally expanded by local gene duplications at the base of the jawed vertebrate lineage. The subfamily of Piwi proteins is involved in several processes such as spermatogenesis, piRNA biogenesis, and transposon repression. Expression assessment of AGO genes and genes coding for proteins involved in small RNA biogenesis suggests a limited activity of the Piwi pathway in lungfish in agreement with the lungfish genome containing mainly old and inactive transposons
Scheda della pubblicazione: https://iris.univpm.it/handle/11566/246602 Collegamento a IRIS

2016 The lungfish transcriptome: A glimpse into molecular evolution events at the transition from water to land
Autore/i: Biscotti, Maria Assunta; Gerdol, Marco; Canapa, Adriana; Forconi, Mariko; Olmo, Ettore; Pallavicini, Alberto; Barucca, Marco; Schartl, Manfred
Classificazione: 1 Contributo su Rivista
Abstract: Lungfish and coelacanths are the only living sarcopterygian fish. The phylogenetic relationship of lungfish to the last common ancestor of tetrapods and their close morphological similarity to their fossil ancestors make this species uniquely interesting. However their genome size, the largest among vertebrates, is hampering the generation of a whole genome sequence. To provide a partial solution to the problem, a high-coverage lungfish reference transcriptome was generated and assembled. The present findings indicate that lungfish, not coelacanths, are the closest relatives to land-adapted vertebrates. Whereas protein-coding genes evolve at a very slow rate, possibly reflecting a "living fossil" status, transposable elements appear to be active and show high diversity, suggesting a role for them in the remarkable expansion of the lungfish genome. Analyses of single genes and gene families documented changes connected to the water to land transition and demonstrated the value of the lungfish reference transcriptome for comparative studies of vertebrate evolution.
Scheda della pubblicazione: https://iris.univpm.it/handle/11566/233749 Collegamento a IRIS

2016 Transposons, Genome Size, and Evolutionary Insights in Animals
Autore/i: Canapa, Adriana; Barucca, Marco; Biscotti, MARIA ASSUNTA; Forconi, Mariko'; Olmo, Ettore
Classificazione: 1 Contributo su Rivista
Abstract: The relationship between genome size and the percentage of transposons in 161 animal species evidenced that variations in genome size are linked to the amplification or the contraction of transposable elements. The activity of transposable elements could represent a response to environmental stressors. Indeed, although with different trends in protostomes and deuterostomes, comprehensive changes in genome size were recorded in concomitance with particular periods of evolutionary history or adaptations to specific environments. During evolution, genome size and the presence of transposable elements have influenced structural and functional parameters of genomes and cells. Changes of these parameters have had an impact on morphological and functional characteristics of the organism on which natural selection directly acts. Therefore, the current situation represents a balance between insertion and amplification of transposons and the mechanisms responsible for their deletion or for decreasing their activity. Among the latter, methylation and the silencing action of small RNAs likely represent the most frequent mechanisms.
Scheda della pubblicazione: https://iris.univpm.it/handle/11566/235580 Collegamento a IRIS

2016 An Overview of Hox Genes in Lophotrochozoa: Evolution and Functionality
Autore/i: Barucca, Marco; Canapa, Adriana; Biscotti, Maria
Classificazione: 1 Contributo su Rivista
Abstract: Hox 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.
Scheda della pubblicazione: https://iris.univpm.it/handle/11566/248502 Collegamento a IRIS

2015 Transcription of tandemly repetitive DNA: functional roles
Autore/i: Biscotti, Maria Assunta; Canapa, Adriana; Forconi, Mariko; Olmo, Ettore; Barucca, Marco
Classificazione: 1 Contributo su Rivista
Abstract: A considerable fraction of the eukaryotic genome is made up of satellite DNA constituted of tandemly repeated sequences. These elements are mainly located at centromeres, pericentromeres, and telomeres and are major components of constitutive heterochromatin. Although originally satellite DNA was thought silent and inert, an increasing number of studies are providing evidence on its transcriptional activity supporting, on the contrary, an unexpected dynamicity. This review summarizes the multiple structural roles of satellite noncoding RNAs at chromosome level. Indeed, satellite noncoding RNAs play a role in the establishment of a heterochromatic state at centromere and telomere. These highly condensed structures are indispensable to preserve chromosome integrity and genome stability, preventing recombination events, and ensuring the correct chromosome pairing and segregation. Moreover, these RNA molecules seem to be involved also in maintaining centromere identity and in elongation, capping, and replication of telomere. Finally, the abnormal variation of centromeric and pericentromeric DNA transcription across major eukaryotic lineages in stress condition and disease has evidenced the critical role that these transcripts may play and the potentially dire consequences for the organism.
Scheda della pubblicazione: https://iris.univpm.it/handle/11566/228000 Collegamento a IRIS

2015 A novel satellite DNA isolated in Pecten jacobaeus shows high sequence similarity among molluscs
Autore/i: Petraccioli, Agnese; Odierna, Gaetano; Capriglione, Teresa; Barucca, Marco; Forconi, Mariko; Olmo, Ettore; Biscotti, Maria Assunta
Classificazione: 1 Contributo su Rivista
Abstract: The aim of this work is to investigate the sequence conservation and the evolution of repeated DNA in related species. Satellite DNA is a component of eukaryotic genomes and is made up of tandemly repeated sequences. These sequences are affected by high rates of mutation that lead to the occurrence of species-specific satellite DNAs, which are different in terms of both quantity and quality. In this work, a novel repetitive DNA family, named PjHhaI sat, is described in Pecten jacobaeus. The quantitative analyses revealed a different abundance of this element in the molluscan species investigated in agreement with the "library hypothesis" even if, in this case, at a high taxonomic level. In addition, the qualitative analysis demonstrated an astonishing sequence conservation not only among scallops but also in six other molluscan species belonging to three classes. These findings suggest that the PjHhaI sat may be considered as the most ancients of DNA described so far, which remained "frozen" during molluscan evolution. The widespread distribution of this sat DNA in molluscs as well as its long evolutionary preservation open up questions on the functional role of this element. A future challenge might be the identification of proteins or molecules which interact with the PjHhaI sat.
Scheda della pubblicazione: https://iris.univpm.it/handle/11566/224666 Collegamento a IRIS

2015 Repetitive DNA in eukaryotic genomes
Autore/i: Biscotti, Maria Assunta; Olmo, Ettore; Heslop-Harrison, J S Pat
Classificazione: 1 Contributo su Rivista
Abstract: Repetitive 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.
Scheda della pubblicazione: https://iris.univpm.it/handle/11566/229135 Collegamento a IRIS

2014 Transcriptional activity of transposable elements in coelacanth
Autore/i: Mariko Forconi; Domitille Chalopin; Marco Barucca; Maria Assunta Biscotti; Gianluca De Moro; Delphine Galiana; Marco Gerdol; Alberto Pallavicini; Adriana Canapa; Ettore Olmo; Jean-Nicolas Volff
Classificazione: 1 Contributo su Rivista
Abstract: The morphological stasis of coelacanths has long suggested a slow evolutionary rate. General genomic stasis might also imply a decrease of transposable elements activity. To evaluate the potential activity of transposable elements (TEs) in "living fossil" species, transcriptomic data of Latimeria chalumnae and its Indonesian congener Latimeria menadoensis were compared through the RNA-sequencing mapping procedures in three different organs (liver, testis, and muscle). The analysis of coelacanth transcriptomes highlights a significant percentage of transcribed TEs in both species. Major contributors are LINE retrotransposons, especially from the CR1 family. Furthermore, some particular elements such as a LF-SINE and a LINE2 sequences seem to be more expressed than other elements. The amount of TEs expressed in testis suggests possible transposition burst in incoming generations. Moreover, significant amount of TEs in liver and muscle transcriptomes were also observed. Analyses of elements displaying marked organ-specific expression gave us the opportunity to highlight exaptation cases, that is, the recruitment of TEs as new cellular genes, but also to identify a new Latimeria-specific family of Short Interspersed Nuclear Elements called CoeG-SINEs. Overall, transcriptome results do not seem to be in line with a slow-evolving genome with poor TE activity. © 2013 Wiley Periodicals, Inc.
Scheda della pubblicazione: https://iris.univpm.it/handle/11566/158919 Collegamento a IRIS

2014 Hox and ParaHox genes: A review on molluscs
Autore/i: Maria Assunta Biscotti; Adriana Canapa; Mariko Forconi; Marco Barucca
Classificazione: 1 Contributo su Rivista
Abstract: Hox 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.
Scheda della pubblicazione: https://iris.univpm.it/handle/11566/205732 Collegamento a IRIS

2014 Characterization of Purine Catabolic Pathway Genes in Coelacanths
Classificazione: 1 Contributo su Rivista
Abstract: Coelacanths are a critically valuable species to explore the gene changes that took place in the transition from aquatic to terrestrial life. One interesting and biologically relevant feature of the genus Latimeria is ureotelism. However not all urea is excreted from the body; in fact high concentrations are retained in plasma and seem to be involved in osmoregulation. The purine catabolic pathway, which leads to urea production in Latimeria, has progressively lost some steps, reflecting an enzyme loss during diversification of terrestrial species. We report the results of analyses of the liver and testis transcriptomes of the Indonesian coelacanth Latimeria menadoensis and of the genome of Latimeria chalumnae, which has recently been fully sequenced in the framework of the coelacanth genome project. We describe five genes, uricase, 5-hydroxyisourate hydrolase, parahox neighbor B, allantoinase, and allantoicase, each coding for one of the five enzymes involved in urate degradation to urea, and report the identification of a putative second form of 5-hydroxyisourate hydrolase that is characteristic of the genus Latimeria. The present data also highlight the activity of the complete purine pathway in the coelacanth liver and suggest its involvement in the maintenance of high plasma urea concentrations. J. Exp. Zool. © 2013 Wiley Periodicals, Inc.
Scheda della pubblicazione: https://iris.univpm.it/handle/11566/158921 Collegamento a IRIS

2014 Novel Repeated DNAs in the Antarctic Polyplacophoran Nuttallochiton mirandus (Thiele, 1906)
Autore/i: Biscotti, Maria A; Canapa, Adriana; Capriglione, Teresa; Forconi, Mariko; Odierna, Gaetano; Olmo, Ettore; Petraccioli, Agnese; Barucca, Marco
Classificazione: 1 Contributo su Rivista
Abstract: Within the scope of a project on the characterization of satellite DNAs in polar mollusks, the Antarctic chiton Nuttallochitonmirandus (Thiele, 1906) was analyzed. Two novel families of tandemly repeated DNAs, namely NmH and NmP, are described in their structure and chromosomal localization, and, furthermore, their presence was analyzed in related species. Data reported here display a particular variability in the structural organization of DNA satellites within this species. Processes driving satellite evolution, which are likely responsible for the intriguing variability of the identified satellite DNAs, are discussed. © 2015 S. Karger AG, Basel.
Scheda della pubblicazione: https://iris.univpm.it/handle/11566/224665 Collegamento a IRIS

2013 Characterization of Sex Determination and Sex Differentiation Genes in Latimeria
Autore/i: Mariko Forconi; Adriana Canapa; Marco Barucca; Maria A. Biscotti; Teresa Capriglione; Francesco Buonocore; Anna M. Fausto; Daisy M. Makapedua; Alberto Pallavicini; Marco Gerdol; Gianluca De Moro; Giuseppe Scapigliati; Ettore Olmo; Manfred Schartl
Classificazione: 1 Contributo su Rivista
Scheda della pubblicazione: https://iris.univpm.it/handle/11566/97068 Collegamento a IRIS

2013 The African coelacanth genome provides insights into tetrapod evolution
Autore/i: Chris T. Amemiya; Jessica Alföldi; Alison P. Lee; Shaohua Fan; Hervé Philippe; Iain MacCallum; Ingo Braasch; Tereza Manousaki; Igor Schneider; Nicolas Rohner; Chris Organ; Domitille Chalopin; Jeramiah J. Smith; Mark Robinson; Rosemary A. Dorrington; Marco Gerdol; Bronwen Aken; Maria Assunta Biscotti; Marco Barucca; Denis Baurain; Aaron M. Berlin; Gregory L. Blatch; Francesco Buonocore; Thorsten Burmester; Michael S. Campbell; Adriana Canapa; John P. Cannon; Alan Christoffels; Gianluca De Moro; Adrienne L. Edkins; Lin Fan; Anna Maria Fausto; Nathalie Feiner; Mariko Forconi; Junaid Gamieldien; Sante Gnerre; Andreas Gnirke; Jared V. Goldstone; Wilfried Haerty; Mark E. Hahn; Uljana Hesse; Steve Hoffmann; Jeremy Johnson; Sibel I. Karchner; Shigehiro Kuraku; Marcia Lara; Joshua Z. Levin; Gary W. Litman; Evan Mauceli; Tsutomu Miyake; M. Gail Mueller; David R. Nelson; Anne Nitsche; Ettore Olmo; Tatsuya Ota; Alberto Pallavicini; Sumir Panji; Barbara Picone; Chris P. Ponting; Sonja J. Prohaska; Dariusz Przybylski; Nil Ratan Saha; Vydianathan Ravi; Filipe J. Ribeiro; Tatjana Sauka-Spengler; Giuseppe Scapigliati; Stephen M. J. Searle; Ted Sharpe; Oleg Simakov; Peter F. Stadler; John J. Stegeman; Kenta Sumiyama; Diana Tabbaa; Hakim Tafer; Jason Turner-Maier; Peter van Heusden; Simon White; Louise Williams; Mark Yandell; Henner Brinkmann; Jean-Nicolas Volff; Clifford J. Tabin; Neil Shubin; Manfred Schartl; David B. Jaffe; John H. Postlethwait; Byrappa Venkatesh; Federica Di Palma; Eric S. Lander; Axel Meyer; Kerstin Lindblad-Toh
Classificazione: 1 Contributo su Rivista
Scheda della pubblicazione: https://iris.univpm.it/handle/11566/97069 Collegamento a IRIS

2013 Analysis of the transcriptome of the Indonesian coelacanth Latimeria menadoensis
Autore/i: Alberto Pallavicini; Adriana Canapa; Marco Barucca; Jessica Alfőldi; Maria Biscotti; Francesco Buonocore; Gianluca De Moro; Federica Di Palma; Anna Fausto; Mariko Forconi; Marco Gerdol; Daisy Makapedua; Jason Turner-Meier; Ettore Olmo; Giuseppe Scapigliati
Classificazione: 1 Contributo su Rivista
Abstract: Latimeria menadoensis is a coelacanth species first identified in 1997 in Indonesia, at 10,000 Km of distance from its African congener. To date, only six specimens have been caught and just a very limited molecular data is available. In the present work we describe the de novo transcriptome assembly obtained from liver and testis samples collected from the fifth specimen ever caught of this species. The deep RNA sequencing performed with Illumina technologies generated 145,435,156 paired-end reads, accounting for ~14 GB of sequence data, which were de novo assembled using a Trinity/CLC combined strategy. The assembly output was processed and filtered producing a set of 66,308 contigs, whose quality was thoroughly assessed. The comparison with the recently sequenced genome of the African congener Latimeria chalumnae and with the available genomic resources of other vertebrates revealed a good reconstruction of full length transcripts and a high coverage of the predicted full coelacanth transcriptome. The RNA-seq analysis revealed remarkable differences in the expression profiles between the two tissues, allowing the identification of liver- and testis-specific transcripts which may play a fundamental role in important biological processes carried out by these two organs. Given the high genomic affinity between the two coelacanth species, the here described de novo transcriptome assembly can be considered a valuable support tool for the improvement of gene prediction within the genome of L. chalumnae and a valuable resource for investigation of many aspects of tetrapod evolution.
Scheda della pubblicazione: https://iris.univpm.it/handle/11566/113062 Collegamento a IRIS

2012 Composition and phylogenetic analysis of vitellogenin coding sequences in the Indonesian coelacanth Latimeria menadoensis
Classificazione: 1 Contributo su Rivista
Scheda della pubblicazione: https://iris.univpm.it/handle/11566/75175 Collegamento a IRIS

2010 Characterization and phylogenetic analysis of vitellogenin coding sequences in the Antarctic fish Trematomus bernacchii .
Classificazione: 1 Contributo su Rivista
Abstract: Vitellogenin is the yolk protein precursor. Multiple vitellogenins identified in several teleosts have been attributed different roles in the control of egg buoyancy and in early embryonic vs. late larval nutrition. In this study, the cDNA encoding VtgAa was characterized in the Antarctic fish Trematomus bernacchii (suborder Notothenioidei). The sequence contains 4,964 nucleotides and encodes 1,629 amino acids of the precursor molecule. To gain insights into the evolution of vitellogenin in Antarctic fishes, we identified the partial sequence of vtgAb, and vtgAa and vtgAb partial sequences of five other notothenioids. The phylogenetic analysis highlighted a close correlation between the Vtg amino acid sequences of the six Antarctic species and VtgAa and VtgAb of other perciforms. Finally, analysis of the ratio of vtgAa to vtgAb expression, evaluated in T. bernacchii by real-time PCR, showed a considerably greater expression of vtgAa in different periods of austral summer. J. Exp. Zool. (Mol. Dev. Evol.) 3148:645-652, 2010. (C) 2010 Wiley-Liss, Inc.
Scheda della pubblicazione: https://iris.univpm.it/handle/11566/36499 Collegamento a IRIS

2009 Description of Pseudocirrhipathes (Cnidaria: Anthozoa: Hexacorallia: Antipathidae), a new genus of whip black corals from the Indo-Pacific.
Classificazione: 1 Contributo su Rivista
Abstract: The new species, Pseudocirrhipathes mapia, is herein described from specimens coming from the coral reefs of the Bunaken Marine Park (North Sulawesi, Indonesia). The species is characterized by an unbranched thin corallum up to 1m high (maximum basal thickness 4mm), with large polyps arranged irregularly on one side of the stem, and by tentacles that are not completely contractile. The skeleton shows an array of spine morphologies along the stem, although most are typically verticillated in the apical section and highly tuberculated in the central portion. The study of its cnidome revealed the presence of an extremely long basitrich isorhiza. The morphological analysis has been coupled with a molecular study of the rDNA ITS sequences confirming the existence of the new genus Pseudocirrhipathes and its inclusion, together with the genus Allopathes, in a separate clade related to the Antipathidae.
Scheda della pubblicazione: https://iris.univpm.it/handle/11566/52723 Collegamento a IRIS

2008 Karyology of the Antarctic chiton Nuttallochiton mirandus (Thiele, 1906) (Mollusca: Polyplacophora) with some considerations on chromosome evolution in chitons
Classificazione: 1 Contributo su Rivista
Abstract: We describe the karyotype, location of nucleolus-organizing regions (NORs) and heterochromatin distribution and composition in the Antarctic chiton Nuttallochiton mirandus. Specimens had a karyotype of 2n=32 chromosomes, of which two were microchromosomes. Among macrochromosomes, the elements of the first and fourth pair were bi-armed, the others were telocentric. At least six NOR sites were detected with NOR-FISH, but only four were Ag-NOR-banding-positive. The two microchromosomes were essentially euchromatic, while all macrochromosomes exhibited clear pericentromeric C bands that were found to be AT-rich (being quinacrine- and DAPI-positive) and resistant to digestion with AluI and HaeIII. N. mirandus has the largest number of chromosomes (2n=32) and telocentric elements (26) of all the chiton species studied to date. The karyological results of our study agree with previous molecular data indicating N. mirandus as a sister taxon of Acanthochitona crinita. The karyotypes of the two species could be related as a result of Robertsonian rearrangements. According to the more parsimonious hypothesis, the former would be the primitive karyotype, although other evolutionary events cannot be ruled out.
Scheda della pubblicazione: https://iris.univpm.it/handle/11566/51192 Collegamento a IRIS

2008 Molecular and cytogenetic characterization of repetitive DNA in the Antarctic polyplacophoran Nuttallochiton mirandus
Classificazione: 1 Contributo su Rivista
Abstract: Two highly repeated DNAs, designated NmE1/NmE2 and NmE5, were identified by EcoRV digestion in the chiton Nuttallochiton mirandus (Mollusca: Polyplacophora). The comparison of the sequences obtained showed high similarity in 5' and 3' regions and the NmE5 sequence displayed an inserted sequence that might arise from a transposable element. Southern blotting analyses suggested a tandem organization of both satellite DNA families identified. Moreover, dot blot analyses, performed on several molluscan species, revealed a different degree of conservation of the repeated DNAs. Fluorescence in-situ hybridizations (FISH) on metaphase chromosomes showed that both satellite DNAs are located at centromeric regions.
Scheda della pubblicazione: https://iris.univpm.it/handle/11566/51961 Collegamento a IRIS

2008 Molecular and cytogenetic characterization of repetitive DNA in species belonging to Mollusca phylum
Autore/i: Biscotti, Maria Assunta
Editore: Università Politecnica delle Marche
Classificazione: 8 Tesi di dottorato
Abstract: My 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.
Scheda della pubblicazione: https://iris.univpm.it/handle/11566/242967 Collegamento a IRIS

2007 A Systematic study of Black Corals species (Antipatharia, Hexacorallia) based on rDNA internal transcribed spacers sequences.
Classificazione: 1 Contributo su Rivista
Abstract: Abstract A phylogenetic analysis based on rDNA internal transcribed spacers (ITS) sequences was performed on 15 species of black corals assigned to the genera Antipathes, Stichopathes, Cirrhipathes, Rhipidipathes, Antipathella, Myriopathes and Cupressopathes recorded from the Messina Strait (Mediterranean Sea) and the Bunaken Marine Park (Celebes Sea, Indonesia). The phylogenetic analysis shows that the examined species are grouped in two main branches corresponding to the families Antipathidae-Aphanipathidae and Myriopathidae. While among the Myriopathidae species there is a very small genetic distance, the Antipathidae-Aphanipathidae clade shows a high degree of divergence between diVerent genera. According to this study, the taxon Antipathes? sp. 3 characterised by a bush-like corallum without a welldeWned axis, probably belongs to a new undescribed genus of the family Antipathidae.
Scheda della pubblicazione: https://iris.univpm.it/handle/11566/52790 Collegamento a IRIS

2007 The systematic position of some boring sponges (Demospongiae, Hadromerida) studied by molecular analysis
Editore: Springer Verlag Germany:Tiergartenstrasse 17, D 69121 Heidelberg Germany:011 49 6221 3450, EMAIL: g.braun@springer.de, INTERNET: http://www.springer.de, Fax: 011 49 6221 345229
Classificazione: 1 Contributo su Rivista
Abstract: A phylogenetic analysis of some bioeroding sponges of the family Clionaidae (Order Hadromerida) was performed to resolve some taxonomic problems both at the specific and the supraspecific level using the D2 and D3 regions of 28S rDNA. Species belonging to the genera Cliona, Cliothosa, Spheciospongia (fam. Clionaidae) and Diplastrella (fam. Spirastrellidae) from the Mediterranean Sea and Celebes Sea (Indonesia) were analysed. In the phylogenetic tree, the species clustered on two main branches, one comprising Cliona celata, C. rhodensis, C. utricularis, and Cliothosa hancocki, and the other made up of C. viridis, C. nigricans, C. schmidti, C. jullieni, Spheciospongia solida and S. vagabunda. Above the species level, data do not support the separation of the genus Cliothosa from Cliona, while they do support the inclusion of some massive boring species, previously assigned to the genus Spirastrella, in the family Clionaidae. At the species level, data demonstrated the genetic identity of taxa C. viridis and C. nigricans, in spite of their considerable morphological differences. In contrast, the yellow species commonly attributed to C. celata are probably to be considered as a complex of sibling species with a number of distinct taxa present in the Mediterranean. Data also showed the identity of the Mediterranean and Pacific populations of C. schmidti, suggesting the status of a Tethyan relict for this species.
Scheda della pubblicazione: https://iris.univpm.it/handle/11566/65734 Collegamento a IRIS

2007 Hox genes in the Antarctic polyplacophoran Nuttallochiton mirandus.
Classificazione: 1 Contributo su Rivista
Abstract: ABSTRACT 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.
Scheda della pubblicazione: https://iris.univpm.it/handle/11566/50706 Collegamento a IRIS

2007 Ripetitive DNA, molecular cytogenetics and genome organization in the King scallop (Pecten maximus)
Classificazione: 1 Contributo su Rivista
Abstract: We studied the structure, organization and relationship of repetitive DNA sequences in the genome of the scallop, Pecten Maximus, a bivalve that is important both commercially and in marine ecology. Recombinant DNA libraries were constructed after partial digestion of genomic DNA from scallop with PstI and ApaI restriction enzymes. Clones containing repetitive DNA were selected by hybridisation to labelled DNA from scallop, oyster and mussel; colonies showing strong hybridisation only to scallop 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 digests showed characteristic ladders of hybridised bands. 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. Two of the repeats had unusual repetitions of bases within their sequence, which may relate to the nature of microsatellites reported in bivalves. The study of these rapidly evolving sequences is valuable to understand an important source of genomic diversity, has the potential to provide useful markers for population studies and gives a route to identify mechanisms of DNA sequence evolution. (C) 2007 Elsevier B.V. All rights reserved.
Scheda della pubblicazione: https://iris.univpm.it/handle/11566/52971 Collegamento a IRIS

2007 Vitellogenin gene expression in males of the Antarctic fish Trematomus bernacchii from Terra Nova Bay (Ross Sea). A role of environmental cadmium?
Classificazione: 1 Contributo su Rivista
Abstract: Synthesis of vitellogenin (VTG) in male fish is a widely recognized effect for estrogenic pollutants in temperate environments, while similar investigations are still lacking for Antarctic organisms. In this study, a preliminary characterization of vitellogenin gene expression was performed by RT-PCR in the key species Trematomus bernacchii sampled in different phases of reproductive cycle and food availability. Females exhibited the highest gene expression during the spawning period, but VTG mRNA was always detected also in males; a significant increase of gene expression was observed both in males and females at the end of the feeding season. These results were not fully supported by a differential exposure to phyto- or anthropogenic estrogens during the planctonic cycle; on the other side, the endocrine properties of cadmium, naturally elevated in Terra Nova Bay and increasing during algal bloom, would explain both the presence of VTG mRNA in males and the seasonal changes of gene induction. Laboratory exposures did not reveal short-term estrogenic effects of cadmium while an elevated responsiveness of T. bernacchii was observed toward a classical estrogenic receptor agonist (17β-estradiol). Different hypotheses were considered to suggest delayed endocrine effects of cadmium, including the early interaction with other cellular detoxification systems or alterations at multiple levels of the hypothalamus-pituitary-gonad-liver axis. Although molecular mechanisms of VTG gene expression in males of T. bernacchii remain unclear, obtained results provide interesting insights on this species which should stimulate future research activities.
Scheda della pubblicazione: https://iris.univpm.it/handle/11566/51365 Collegamento a IRIS

2006 All the three ParaHox genes are present in Nuttallochiton mirandus (Mollusca: Polyplacophora): evolutionary considerations.
Classificazione: 1 Contributo su Rivista
Abstract: ABSTRACT 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.
Scheda della pubblicazione: https://iris.univpm.it/handle/11566/51694 Collegamento a IRIS

2005 Isolation of Hox and ParaHox genes in bivalve Pecten maximus.
Classificazione: 1 Contributo su Rivista
Abstract: The 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.
Scheda della pubblicazione: https://iris.univpm.it/handle/11566/53446 Collegamento a IRIS

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