The Cytogenetic Map of the Nile Crocodile (Crocodylus niloticus, Crocodylidae, Reptilia) with Fluorescence In Situ Localization of Major Repetitive DNAs

Romanenko, Svetlana A.; Prokopov, Dmitry; Proskuryakova, Anastasia A.; Davletshina, G. I.; Tupikin, Alexey E.; Kasai, Fumie; Ferguson-Smith, Malcolm A.; Trifonov, Vladimir A.

doi:10.3390/ijms232113063

Cited by 4 publications

(2 citation statements)

References 78 publications

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“…SatDNAs are well known to be underrepresented in genome assemblies [ 4 ], particularly those genomes assembled using short-read sequencing technology, as is the case with alligators. In this context, knowledge about satDNAs in crocodilians was limited to just a few works [ 69 , 70 ]. Given that high-throughput satellitome analysis has been very enlightening for understanding the satDNA evolution in various organisms, we used a chromosome- and genomic-based approach to try to describe the satellitome from members of all current Alligatoridae genera for the first time.…”

Section: Discussionmentioning

confidence: 99%

Evolution of ancient satellite DNAs in extant alligators and caimans (Crocodylia, Reptilia)

Sales-Oliveira,

dos Santos,

Goes

et al. 2024

BMC Biol

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Background Crocodilians are one of the oldest extant vertebrate lineages, exhibiting a combination of evolutionary success and morphological resilience that has persisted throughout the history of life on Earth. This ability to endure over such a long geological time span is of great evolutionary importance. Here, we have utilized the combination of genomic and chromosomal data to identify and compare the full catalogs of satellite DNA families (satDNAs, i.e., the satellitomes) of 5 out of the 8 extant Alligatoridae species. As crocodilian genomes reveal ancestral patterns of evolution, by employing this multispecies data collection, we can investigate and assess how satDNA families evolve over time. Results Alligators and caimans displayed a small number of satDNA families, ranging from 3 to 13 satDNAs in A. sinensis and C. latirostris, respectively. Together with little variation both within and between species it highlighted long-term conservation of satDNA elements throughout evolution. Furthermore, we traced the origin of the ancestral forms of all satDNAs belonging to the common ancestor of Caimaninae and Alligatorinae. Fluorescence in situ experiments showed distinct hybridization patterns for identical orthologous satDNAs, indicating their dynamic genomic placement. Conclusions Alligators and caimans possess one of the smallest satDNA libraries ever reported, comprising only four sets of satDNAs that are shared by all species. Besides, our findings indicated limited intraspecific variation in satellite DNA, suggesting that the majority of new satellite sequences likely evolved from pre-existing ones.

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Section: Discussionmentioning

confidence: 99%

Evolution of ancient satellite DNAs in extant alligators and caimans (Crocodylia, Reptilia)

Sales-Oliveira,

dos Santos,

Goes

et al. 2024

BMC Biol

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“…To study the tropism of SARS-CoV-2 for the cells of some fish and reptile species, we used continuous cell cultures FHM and TH-1, primary fibroblasts CNI (4th passage), and diploid fibroblasts CGIB (22nd passage). The origin of CNI fibroblast culture was previously described by Romanenko et al [48], and the CGIB diploid fibroblasts culture was obtained at the IMCB, SB RAS. Vero E6 cell culture susceptible to SARS-CoV-2 was used as a reference culture.…”

Section: Cell Culturesmentioning

confidence: 99%

Features of SARS-CoV-2 Replication in Various Types of Reptilian and Fish Cell Cultures

Kononova,

Adamenko,

Kazachkova

et al. 2023

Viruses

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Background: SARS-CoV-2 can enter the environment from the feces of COVID-19 patients and virus carriers through untreated sewage. The virus has shown the ability to adapt to a wide range of hosts, so the question of the possible involvement of aquafauna and animals of coastal ecosystems in maintaining its circulation remains open. Methods: the aim of this work was to study the tropism of SARS-CoV-2 for cells of freshwater fish and reptiles, including those associated with aquatic and coastal ecosystems, and the effect of ambient temperature on this process. In a continuous cell culture FHM (fathead minnow) and diploid fibroblasts CGIB (silver carp), SARS-CoV-2 replication was not maintained at either 25 °C or 29 °C. At 29 °C, the continuous cell culture TH-1 (eastern box turtle) showed high susceptibility to SARS-CoV-2, comparable to Vero E6 (development of virus-induced cytopathic effect (CPE) and an infectious titer of 7.5 ± 0.17 log10 TCID50/mL on day 3 after infection), and primary fibroblasts CNI (Nile crocodile embryo) showed moderate susceptibility (no CPE, infectious titer 4.52 ± 0.14 log10 TCID50/mL on day 5 after infection). At 25 °C, SARS-CoV-2 infection did not develop in TH-1 and CNI. Conclusions: our results show the ability of SARS-CoV-2 to effectively replicate without adaptation in the cells of certain reptile species when the ambient temperature rises.

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Insights into avian molecular cytogenetics—with reptilian comparisons

Griffin,

Kretschmer,

Srikulnath

et al. 2024

Mol Cytogenet

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In last 100 years or so, much information has been accumulated on avian karyology, genetics, physiology, biochemistry and evolution. The chicken genome project generated genomic resources used in comparative studies, elucidating fundamental evolutionary processes, much of it funded by the economic importance of domestic fowl (which are also excellent model species in many areas). Studying karyotypes and whole genome sequences revealed population processes, evolutionary biology, and genome function, uncovering the role of repetitive sequences, transposable elements and gene family expansion. Knowledge of the function of many genes and non-expressed or identified regulatory components is however still lacking. Birds (Aves) are diverse, have striking adaptations for flight, migration and survival and inhabit all continents most islands. They also have a unique karyotype with ~ 10 macrochromosomes and ~ 30 microchromosomes that are smaller than other reptiles. Classified into Palaeognathae and Neognathae they are evolutionarily close, and a subset of reptiles. Here we overview avian molecular cytogenetics with reptilian comparisons, shedding light on their karyotypes and genome structure features. We consider avian evolution, then avian (followed by reptilian) karyotypes and genomic features. We consider synteny disruptions, centromere repositioning, and repetitive elements before turning to comparative avian and reptilian genomics. In this context, we review comparative cytogenetics and genome mapping in birds as well as Z- and W-chromosomes and sex determination. Finally, we give examples of pivotal research areas in avian and reptilian cytogenomics, particularly physical mapping and map integration of sex chromosomal genes, comparative genomics of chicken, turkey and zebra finch, California condor cytogenomics as well as some peculiar cytogenetic and evolutionary examples. We conclude that comparative molecular studies and improving resources continually contribute to new approaches in population biology, developmental biology, physiology, disease ecology, systematics, evolution and phylogenetic systematics orientation. This also produces genetic mapping information for chromosomes active in rearrangements during the course of evolution. Further insights into mutation, selection and adaptation of vertebrate genomes will benefit from these studies including physical and online resources for the further elaboration of comparative genomics approaches for many fundamental biological questions.

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The Cytogenetic Map of the Nile Crocodile (Crocodylus niloticus, Crocodylidae, Reptilia) with Fluorescence In Situ Localization of Major Repetitive DNAs

Cited by 4 publications

References 78 publications

Evolution of ancient satellite DNAs in extant alligators and caimans (Crocodylia, Reptilia)

Evolution of ancient satellite DNAs in extant alligators and caimans (Crocodylia, Reptilia)

Features of SARS-CoV-2 Replication in Various Types of Reptilian and Fish Cell Cultures

Insights into avian molecular cytogenetics—with reptilian comparisons

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