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3. Dinosaurs: comparative cytogenomics of their reptile cousins and avian descendants

Author

Olmo, Ettore, Griffin, Darren K., Larkin, Denis M., O’Connor, Rebecca E., Romanov, Michael N., Olmo, Ettore, Griffin, Darren K., Larkin, Denis M., O’Connor, Rebecca E., and Romanov, Michael N.

Abstract

Simple Summary Dinosaurs have been in scientific and popular culture since early fossil discoveries, but increased interest, particularly in their genomes, is expanding. Birds are reptiles, specifically theropod dinosaurs, meaning that if we compare the genomes of related reptile relations, we can get an idea of what the extinct dinosaur genomes looked like. In all animals/plants/fungi, we think of genome organization in terms of chromosomes. Genes sit on chromosomes and each cell of each individual of each species has its own unique organization. Every gene is in exactly the same spot on each chromosome, organized like continents and islands, with the genes as the cities/ towns/villages. All reptiles apart from crocodilians have both big and small chromosomes in their genomes but birds particularly so, like the Philippines or Polynesia. Birds have ~80 chromosomes (far more than most organisms) and this is very consistent in most species. Recent studies suggest that this pattern was probably established ~255 million years ago as it is also mostly present in some turtles. In other words, most dinosaurs probably had chromosomes (genome organization) like chickens or emus. In this paper, we present ideas of how this may have contributed to dinosaurs being so diverse in appearance and function. Abstract Reptiles known as dinosaurs pervade scientific and popular culture, while interest in their genomics has increased since the 1990s. Birds (part of the crown group Reptilia) are living theropod dinosaurs. Chromosome‐level genome assemblies cannot be made from long‐extinct biological material, but dinosaur genome organization can be inferred through comparative genomics of related extant species. Most reptiles apart from crocodilians have both macro‐ and microchromosomes; comparative genomics involving molecular cytogenetics and bioinformatics has established chromosomal relationships between many species . The capacity of dinosaurs to survive multiple extinction events is

Published
2023

4. Reptile Evolution and Genetics: An Overview.

Author

Olmo, Ettore

Subjects
*KARYOTYPES, *GENETIC sex determination, *GENETICS, *SNAKE venom, *REPTILES, *COMPARATIVE biology, *CHROMOSOME analysis, *MOLECULAR biology
Abstract

In this species, several chromosome races differ in the number and morphology of chromosomes due to centric fission and pericentric inversions on various pairs of chromosomes. Despite the ancient divergence time, all crown reptiles' chromosomes and genome variability are low. As no intact DNA is available from fossil dinosaurs, information about extinct dinosaurs' karyotypes can be inferred via comparative analysis of chromosomes and genomes of several species of birds and non-avian reptiles. Analysis using FISH and BLAST methods shows that one DNA is mainly localized at the centromere of species belonging to both families, whereas the others form clusters specific on specific chromosomes or subsets of chromosomes. [Extracted from the article]

Published
2023
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11. Mitochondrial phylogeography of the killifish Aphanius fasciatus (Teleostei, Cyprinodontidae) reveals highly divergent mediterranean populations

Author

Ferrito, Venera, Pappalardo, Anna Maria, Canapa, Adriana, Barucca, Marco, Doadrio, Ignacio, Olmo, Ettore, and Tigano, Concetta

Subjects
Fish populations -- Genetic aspects, Cyprinodontidae -- Genetic aspects, Killifishes -- Genetic aspects, Biological sciences
Abstract

We studied the genetic structure of the Mediterranean killifish Aphanius fasciatus. analysis of the sequence variation in a 372-bp portion of the mitochondrial control region in 623 fish from 27 sampling sites along the species' distributional range (Tyrrhenian coast, Sardinia, Sicily, Adriatic coast, Malta, Tunisia, and Greece) yielded 120 distinct haplotypes. Most of the haplotypes are unique, and only 15 % are shared among different populations. The high FST value (=0.80) suggests a strong population genetic structuring. The phylogenetic analysis based on Bayesian inference, maximum likelihood and maximum parsimony, and the median-joining network show a sharp separation of the Southeastern Sicilian populations (belonging to the Hyblean region) and of the fluvial Tunisian population of Rio Melah from the others. The Adriatic, the Eastern Sicilian, and the Greek populations are well differentiated, while the group of populations from the Central-Western Mediterranean does not show a clear pattern of differentiation. Our findings indicate that the current genetic structuring of A. fasciatus reflects historical geographical patterns occurring within the Mediterranean basin from the Late Miocene to the Pleistocene. The presence of divergent evolutionary entities in the Hyblean region and the Tunisian Rio Melah supports their inclusion as target areas for the conservation of A. fasciatus., Introduction The phylogeographic approach--that is the fusion of phylogenetics and population genetics with biogeography--has been used to define patterns of population structure in geographic and chronological contexts. Beheregaray (2008), reviewing [...]

Published
2013
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27. The African coelacanth genome provides insights into tetrapod evolution

Author

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

Published
2013
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37. Preface

Author

Giovannotti, Massimo, primary, Olmo, Ettore, additional, and Caputo-Barucchi, Vincenzo, additional

Published
2019
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39. Cytogenetic Characterization of a Population of Acanthodactylus lineomaculatus Duméril and Bibron, 1839 (Reptilia, Lacertidae), from Southwestern Morocco and Insights into Sex Chromosome Evolution

Author

Giovannotti, Massimo, Nisi Cerioni, Paola, Slimani, Tahar, Splendiani, Andrea, Paoletti, Alessio, Fawzi, Adnane, Olmo, Ettore, and Caputo Barucchi, Vincenzo

Subjects
Interstitial telomeric sequences, Sex chromosomes, 18S + 28S rDNA, W chromosome
Abstract

Acanthodactylus lineomaculatus is now regarded as an ecotype of A. erythrurus with which it has been recently synonymized. Despite the wide range of A. erythrurus, karyological data for this species are scarce and limited to classical cytogenetic studies carried out in individuals from only 2 locations (central Spain and Spanish enclave of Melilla on the northwestern Mediterranean Moroccan coast). Here, for the first time, we cytogenetically characterized individuals of A. lineomaculatus from the southwestern Moroccan Atlantic coast with the aim to increase the karyological knowledge of this wide-ranging species and to assess if any chromosomal changes can be found in this ecotype in comparison to other populations of this species. The diploid number of the individuals investigated is 2n = 38 which is typical of most lacertids. Active NORs were located telomerically in a medium-small pair of chromosomes, and no inactive NORs were detected. C-banding revealed an intensely heterochromatic W chromosome composed of AT-rich (centromere and long arm telomeric region) and GC-rich (most of the long arm) regions, with extended interstitial telomeric sequences. These telomere-like repeats occupy the GC-rich heterochromatin of the W. The DNA composition of the W represents a trait distinguishing A. lineomaculatus (southwestern Morocco) from A. erythrurus from Spain that possess a DAPI-positive (AT-rich) W chromosome. In conclusion, these results add further evidence to the remarkable karyotype conservation in lacertid lizards, although differences in NOR location and in W chromosome structure among populations could suggest an incipient speciation mediated by chromosome changes in this wide-ranging lizard species.

Published
2017

41. Isolation and characterization of two satellite DNAs in Atlantolacerta andreanskyi (Werner, 1929) (Reptilia, Lacertidae).

Author

Giovannotti, Massimo, S'Khifa, Abderrahim, Nisi Cerioni, Paola, Splendiani, Andrea, Slimani, Tahar, Fioravanti, Tatiana, Olmo, Ettore, and Caputo Barucchi, Vincenzo

Subjects
SATELLITE DNA, LACERTIDAE, REPTILES, MICROSATELLITE repeats, BL Lacertae objects, FLUORESCENCE in situ hybridization
Abstract

Two satellite DNAs (satDNAs) have been isolated and characterized from three populations of Atlantolacerta andreanskyi. One satDNA (AAN‐TaqI) has been isolated here from the first time. It is characterized by a tendency to AT enrichment (AT = 54.2%) and monomer length ranging from 187 to 199 bp. FISH experiments showed that this element occurs in subterminal position on the short arms of all chromosomes of the complement. The analyses of genetic variability of AAN‐TaqI showed that the concerted evolution is acting effectively on these repeats that form separate clusters consistent with the geographic origin in the phylogenetic tree, thus supporting the hypothesis that A. andreanskyi would be a species complex. In addition, in the population from Jbel Aoulime this satDNA is already differentiated into two subfamilies. The other satDNA belongs to the family of IMO‐TaqI already isolated in other lacertids. Differently from AAN‐TaqI, concerted evolution does not seem to act effectively on this element that is not differentiated between populations. These results confirm that IMO‐TaqI (AT = 53.4%) is conserved in both chromosomal position and most of its sequence in the lacertids from which it has been characterized so far. Its remarkable evolutionary conservation for about 45 million years could indicate that this satDNA may have a functional role that future investigations could unveil. Once again, this study shows how satDNAs coexisting in the same genome may differ in their evolutionary pattern, even though the reasons underlying this phenomenon in the species here studied have still to be fully understood. Research Highlights: Two satDNAs have been described in Atlantolacerta andreanskyi. AAN‐TaqI has been described here for the first time, whereas IMO‐TaqI had been already described in other species of lacertids and it is evolutionary conserved in these lizards. [ABSTRACT FROM AUTHOR]

Published
2020
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43. Novel repeated DNAs in the antarctic polyplacophoran nuttallochiton mirandus (Thiele, 1906)

Author

Biscotti, Maria A, Canapa, Adriana, Forconi, Mariko, Olmo, Ettore, Petraccioli, Agnese, Barucca, Marco, CAPRIGLIONE, TERESA, ODIERNA, GAETANO, Biscotti, Maria A, Canapa, Adriana, Capriglione, Teresa, Forconi, Mariko, Odierna, Gaetano, Olmo, Ettore, Petraccioli, Agnese, and Barucca, Marco

Subjects
Polyplacophora, Tandem Repeat Sequence, Genetic, Animal, Medicine (all), Satellite DNA, DNA, Satellite, Biological Evolution, Molecular Biology, Phylogeny, Genetics (clinical), Nuttallochiton mirandu
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.

Published
2014

44. Biologia della Cellula e dei Tessuti

Author

VENTURINI, Giorgio, OLMO ETTORE, COLOMBO ROBERTO, ANGELINI FRANCESCO, BOTTI DARIO, GORNATI ROSALBA, MONACO GIANNI, ODIERNA GAETENO, OTTAVIANI ENZO, PANZICA GIAN CARLO, ROSATI FLORIANA, SOTTILE LORENZO, STINGO VINCENZO, Olmo Ettore e Roberto Colombo, Venturini, Giorgio, Olmo, Ettore, Colombo, Roberto, Angelini, Francesco, Botti, Dario, Gornati, Rosalba, Monaco, Gianni, Odierna, Gaeteno, Ottaviani, Enzo, PANZICA GIAN, Carlo, Rosati, Floriana, Sottile, Lorenzo, and Stingo, Vincenzo

Published
2008

45. Cytogenetic Characterization of a Population of Acanthodactylus lineomaculatus Duméril and Bibron, 1839 (Reptilia, Lacertidae), from Southwestern Morocco and Insights into Sex Chromosome Evolution

Author

Giovannotti, Massimo, primary, Nisi Cerioni, Paola, additional, Slimani, Tahar, additional, Splendiani, Andrea, additional, Paoletti, Alessio, additional, Fawzi, Adnane, additional, Olmo, Ettore, additional, and Caputo Barucchi, Vincenzo, additional

Published
2017
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47. Citogenetica dei rettili

Author

ODIERNA, GAETANO, Mancino Giorgio, Olmo Ettore, Corti C., Capula M., Luiselli L., Razzetti E., Sindaco R., Odierna, Gaetano, Mancino, Giorgio, and Olmo, Ettore

Subjects
rettili, cariotipo, cromosomi
Published
2011

49. Karyological Characterization of the Endemic Iberian Rock Lizard, Iberolacerta Monticola (Squamata, Lacertidae): Insights into Sex Chromosome Evolution

Author

Rojo Oróns, Verónica, Giovannotti, Massimo, Naveira, Horacio, Nisi Cerioni, Paola, González-Tizón, Ana M., Caputo Barucchi, Vincenzo, Galán, Pedro, Olmo, Ettore, and Martínez-Lage, Andrés

Subjects
FISH, Comparative cytogenetics, Chromosome banding, Rock lizards, Sex chromosomes
Abstract

[Abstract] Rock lizards of the genus Iberolacerta constitute a promising model to examine the process of sex chromosome evolution, as these closely related taxa exhibit remarkable diversity in the degree of sex chromosome differentiation with no clear phylogenetic segregation, ranging from cryptic to highly heteromorphic ZW chromosomes and even multiple chromosome systems (Z1Z1Z2Z2/Z1Z2W). To gain a deeper insight into the patterns of karyotype and sex chromosome evolution, we performed a cytogenetic analysis based on conventional staining, banding techniques and fluorescence in situ hybridization in the species I. monticola, for which previous cytogenetic investigations did not detect differentiated sex chromosomes. The karyotype is composed of 2n = 36 acrocentric chromosomes. NORs and the major ribosomal genes were located in the subtelomeric region of chromosome pair 6. Hybridization signals of the telomeric sequences (TTAGGG)n were visualized at the telomeres of all chromosomes and interstitially in 5 chromosome pairs. C-banding showed constitutive heterochromatin at the centromeres of all chromosomes, as well as clear pericentromeric and light telomeric C-bands in several chromosome pairs. These results highlight some chromosomal markers which can be useful to identify species specific diagnostic characters, although they may not accurately reflect the phylogenetic relationships among the taxa. In addition, C-banding revealed the presence of a heteromorphic ZW sex chromosome pair, where W is smaller than Z and almost completely heterochromatic. This finding sheds light on sex chromosome evolution in the genus Iberolacerta and suggests that further comparative cytogenetic analyses are needed to understand the processes underlying the origin, differentiation and plasticity of sex chromosome systems in lacertid lizards. Xunta de Galicia; PGIDIT03RFO10301PR Xunta de Galicia; PGIDIT06RFO10301PR Italia. Ministero dell'istruzione, dell'università e della ricerca; PRIN 2009

Published
2013

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