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Nikitin P, Sidorov S, Liehr T, Klimina K, Al-Rikabi A, Korchagin V, Kolomiets O, Arakelyan M, Spangenberg V. Variants of a major DNA satellite discriminate parental subgenomes in a hybrid parthenogenetic lizard Darevskia unisexualis (Darevsky, 1966). JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2024; 342:368-379. [PMID: 38407543 DOI: 10.1002/jez.b.23244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 12/12/2023] [Accepted: 01/30/2024] [Indexed: 02/27/2024]
Abstract
Hybrid parthenogenetic animals are an exceptionally interesting model for studying the mechanisms and evolution of sexual and asexual reproduction. A diploid parthenogenetic lizard Darevskia unisexualis is a result of an ancestral cross between a maternal species Darevskia raddei nairensis and a paternal species Darevskia valentini and presents a unique opportunity for a cytogenetic and computational analysis of a hybrid karyotype. Our previous results demonstrated a significant divergence between the pericentromeric DNA sequences of the parental Darevskia species; however, an in-depth comparative study of their pericentromeres is still lacking. Here, using target sequencing of microdissected pericentromeric regions, we reveal and compare the repertoires of the pericentromeric tandem repeats of the parental Darevskia lizards. We found species-specific sequences of the major pericentromeric tandem repeat CLsat, which allowed computational prediction and experimental validation of fluorescent DNA probes discriminating parental chromosomes within the hybrid karyotype of D. unisexualis. Moreover, we have implemented a generalizable computational method, based on the optimization of the Levenshtein distance between tandem repeat monomers, for finding species-specific fluorescent probes for pericentromere staining. In total, we anticipate that our comparative analysis of Darevskia pericentromeric repeats, the species-specific fluorescent probes that we found and the pipeline that we developed will form a basis for the future detailed cytogenomic studies of a wide range of natural and laboratory hybrids.
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Affiliation(s)
- Pavel Nikitin
- Laboratory of Comparative Ethology and Biocommunication, Severtsov Institute of Ecology and Evolution RAS, Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Sviatoslav Sidorov
- Computational Regulatory Genomics, MRC Laboratory of Medical Sciences, Hammersmith Hospital Campus, London, UK
| | - Thomas Liehr
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Jena, Germany
| | - Ksenia Klimina
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Ahmed Al-Rikabi
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Jena, Germany
| | | | - Oxana Kolomiets
- Laboratory of Cytogenetics, Vavilov Institute of General Genetics RAS, Moscow, Russia
| | - Marine Arakelyan
- Department of Zoology, Yerevan State University, Yerevan, Armenia
| | - Victor Spangenberg
- Laboratory of Cytogenetics, Vavilov Institute of General Genetics RAS, Moscow, Russia
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Yurchenko A, Pšenička T, Mora P, Ortega JAM, Baca AS, Rovatsos M. Cytogenetic Analysis of Satellitome of Madagascar Leaf-Tailed Geckos. Genes (Basel) 2024; 15:429. [PMID: 38674364 PMCID: PMC11049218 DOI: 10.3390/genes15040429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 03/21/2024] [Accepted: 03/25/2024] [Indexed: 04/28/2024] Open
Abstract
Satellite DNA (satDNA) consists of sequences of DNA that form tandem repetitions across the genome, and it is notorious for its diversity and fast evolutionary rate. Despite its importance, satDNA has been only sporadically studied in reptile lineages. Here, we sequenced genomic DNA and PCR-amplified microdissected W chromosomes on the Illumina platform in order to characterize the monomers of satDNA from the Henkel's leaf-tailed gecko U. henkeli and to compare their topology by in situ hybridization in the karyotypes of the closely related Günther's flat-tail gecko U. guentheri and gold dust day gecko P. laticauda. We identified seventeen different satDNAs; twelve of them seem to accumulate in centromeres, telomeres and/or the W chromosome. Notably, centromeric and telomeric regions seem to share similar types of satDNAs, and we found two that seem to accumulate at both edges of all chromosomes in all three species. We speculate that the long-term stability of all-acrocentric karyotypes in geckos might be explained from the presence of specific satDNAs at the centromeric regions that are strong meiotic drivers, a hypothesis that should be further tested.
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Affiliation(s)
- Alona Yurchenko
- Department of Ecology, Faculty of Science, Charles University, 128 44 Prague, Czech Republic; (A.Y.); (T.P.)
| | - Tomáš Pšenička
- Department of Ecology, Faculty of Science, Charles University, 128 44 Prague, Czech Republic; (A.Y.); (T.P.)
| | - Pablo Mora
- Department of Experimental Biology, Faculty of Experimental Sciences, University of Jaén, Campus Las Lagunillas s/n, E-23071 Jaen, Spain; (P.M.); (J.A.M.O.); (A.S.B.)
| | - Juan Alberto Marchal Ortega
- Department of Experimental Biology, Faculty of Experimental Sciences, University of Jaén, Campus Las Lagunillas s/n, E-23071 Jaen, Spain; (P.M.); (J.A.M.O.); (A.S.B.)
| | - Antonio Sánchez Baca
- Department of Experimental Biology, Faculty of Experimental Sciences, University of Jaén, Campus Las Lagunillas s/n, E-23071 Jaen, Spain; (P.M.); (J.A.M.O.); (A.S.B.)
| | - Michail Rovatsos
- Department of Ecology, Faculty of Science, Charles University, 128 44 Prague, Czech Republic; (A.Y.); (T.P.)
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Evolution of the parthenogenetic rock lizard hybrid karyotype: Robertsonian translocation between two maternal chromosomes in Darevskia rostombekowi. Chromosoma 2020; 129:275-283. [DOI: 10.1007/s00412-020-00744-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 06/26/2020] [Accepted: 10/26/2020] [Indexed: 02/08/2023]
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Ahmad SF, Singchat W, Jehangir M, Panthum T, Srikulnath K. Consequence of Paradigm Shift with Repeat Landscapes in Reptiles: Powerful Facilitators of Chromosomal Rearrangements for Diversity and Evolution. Genes (Basel) 2020; 11:E827. [PMID: 32708239 PMCID: PMC7397244 DOI: 10.3390/genes11070827] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 07/16/2020] [Accepted: 07/17/2020] [Indexed: 12/24/2022] Open
Abstract
Reptiles are notable for the extensive genomic diversity and species richness among amniote classes, but there is nevertheless a need for detailed genome-scale studies. Although the monophyletic amniotes have recently been a focus of attention through an increasing number of genome sequencing projects, the abundant repetitive portion of the genome, termed the "repeatome", remains poorly understood across different lineages. Consisting predominantly of transposable elements or mobile and satellite sequences, these repeat elements are considered crucial in causing chromosomal rearrangements that lead to genomic diversity and evolution. Here, we propose major repeat landscapes in representative reptilian species, highlighting their evolutionary dynamics and role in mediating chromosomal rearrangements. Distinct karyotype variability, which is typically a conspicuous feature of reptile genomes, is discussed, with a particular focus on rearrangements correlated with evolutionary reorganization of micro- and macrochromosomes and sex chromosomes. The exceptional karyotype variation and extreme genomic diversity of reptiles are used to test several hypotheses concerning genomic structure, function, and evolution.
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Affiliation(s)
- Syed Farhan Ahmad
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (M.J.); (T.P.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Worapong Singchat
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (M.J.); (T.P.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Maryam Jehangir
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (M.J.); (T.P.)
- Integrative Genomics Lab-LGI, Department of Structural and Functional Biology, Institute of Bioscience at Botucatu, São Paulo State University (UNESP), Botucatu 18618-689, Brazil
| | - Thitipong Panthum
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (M.J.); (T.P.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Kornsorn Srikulnath
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (M.J.); (T.P.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University, Kasetsart University, Bangkok 10900, Thailand
- Center of Excellence on Agricultural Biotechnology (AG-BIO/PERDO-CHE), Bangkok 10900, Thailand
- Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand
- Amphibian Research Center, Hiroshima University, 1-3-1, Kagamiyama, Higashihiroshima 739-8526, Japan
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Murtskhvaladze M, Tarkhnishvili D, Anderson CL, Kotorashvili A. Phylogeny of caucasian rock lizards (Darevskia) and other true lizards based on mitogenome analysis: Optimisation of the algorithms and gene selection. PLoS One 2020; 15:e0233680. [PMID: 32511235 PMCID: PMC7279592 DOI: 10.1371/journal.pone.0233680] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 05/11/2020] [Indexed: 11/18/2022] Open
Abstract
We generated a phylogeny for Caucasian rock lizards (Darevskia), and included six other families of true lizards (Lacertini), based on complete mitochondrial genome analysis. Next-generation sequencing (NGS) of genomic DNA was used to obtain 16 new mitogenomes of Darevskia. These, along with 35 sequences downloaded from GenBank: genera Darevskia, Zootoca, Podarcis, Phoenicolacerta, Takydromus, Lacerta, and Eremias-were used in the analysis. All four analytical methods (Bayesian Inference, BI; Maximum Likelihood, ML; Maximum Parsimony, MP; and Neighbor-Joining, NJ) showed almost congruent intra-generic topologies for Darevskia and other lizard genera. However, ML and NJ methods on one side, and BI and MP methods on the other harvested conflicting phylogenies. The ML/NJ topology supports earlier published separation of Darevskia into three mitochondrial clades (Murphy, Fu, Macculloch, Darevsky, and Kupinova, 2000), but BI and MP topologies support that the basal branching occurred between D. parvula from the western Lesser Caucasus and the rest of Darevskia. All topologies altered the phylogenetic position of some individual species, including D. daghestanica, D. derjugini, and D. chlorogaster. Reanalysis after excluding four saturated genes from the data set, and excluding genus Eremias gives fully convergent topologies. The most basal branching for true lizards was between Far Eastern Takydromus and the Western Eurasian genera (BI). Comparing phylogenetic performance of individual genes relative to whole mitogenome data, concatenated 16S RNA (the least saturated gene in our analyses) and Cytochrome b genes generate a robust phylogeny that is fully congruent with that based on the complete mitogenome.
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Affiliation(s)
- Marine Murtskhvaladze
- School of Natural Sciences and Engineering, Ilia State University, Tbilisi, Georgia
- L. Sakvarelidze National Center for Disease Control and Public Health, Tbilisi, Georgia
| | - David Tarkhnishvili
- School of Natural Sciences and Engineering, Ilia State University, Tbilisi, Georgia
| | - Cort L. Anderson
- School of Natural Sciences and Engineering, Ilia State University, Tbilisi, Georgia
| | - Adam Kotorashvili
- L. Sakvarelidze National Center for Disease Control and Public Health, Tbilisi, Georgia
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Abstract
Darevskia rock lizards is a unique complex taxa, including more than thirty species, seven of which are parthenogenetic. In mixed populations of Darevskia lizards, tri- and tetraploid forms can be found. The most important issues in the theory of reticulate evolution of Darevskia lizards are the origin of parthenogenetic species and their taxonomic position. However, there is little data on how meiosis proceeds in these species. The present work reports the complex results of cytogenetics in a diploid parthenogenetic species – D. unisexualis. Here we detail the meiotic prophase I progression and the specific features оf mitotic chromosomes organization. The stages of meiosis prophase I were investigated by immunocytochemical analysis of preparations obtained from isolated primary oocytes of D. unisexualis in comparison with maternal species D. raddei nairensis. It has been shown that in D. unisexualis at the leptotene-zygotene stages the axial elements and the synaptonemal complex (SC) form typical “bouquets”. At the pachytene-diplotene stage, 18 autosomal SC-bivalents and thickened asynapted sex Z and w univalents were observed. The presence of SYCP1 protein between the lateral elements of autosomal chromosomes proved the formation of assembled SCs. Comparative genomic hybridization (CGH) on the mitotic metaphase chromosomes of D. unisexualis was carried out using the genomic DNA isolated from the parental species D. raddei nairensis and D. valentini. In the pericentromeric regions of half of the mitotic chromosomes of D. unisexualis, specific regions inherited from maternal species have been found. Following our results, we suggest a model for diploid germ cells formation from diploid oocytes without premeiotic duplication of chromosomes in the oogenesis of diploid parthenogenetic lizards D. unisexualis. Taken as a whole, our findings confirm the hybrid nature of D. unisexualis and shed light on heterozygosity and automixis in diploid parthenogenetic forms.
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Giovannotti M, S'Khifa A, Nisi Cerioni P, Splendiani A, Slimani T, Fioravanti T, Olmo E, Caputo Barucchi V. Isolation and characterization of two satellite DNAs in Atlantolacerta andreanskyi (Werner, 1929) (Reptilia, Lacertidae). JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2020; 334:178-191. [PMID: 32061054 DOI: 10.1002/jez.b.22937] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 11/29/2019] [Accepted: 01/30/2020] [Indexed: 11/07/2022]
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.
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Affiliation(s)
- Massimo Giovannotti
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona, Italy
| | - Abderrahim S'Khifa
- Laboratory Biodiversity and Ecosystem Dynamics, Faculty of Sciences Semlalia, Cadi Ayyad University, Boulevard Prince Moulay Abdellah, Marrakech, Morocco
| | - Paola Nisi Cerioni
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona, Italy
| | - Andrea Splendiani
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona, Italy
| | - Tahar Slimani
- Laboratory Biodiversity and Ecosystem Dynamics, Faculty of Sciences Semlalia, Cadi Ayyad University, Boulevard Prince Moulay Abdellah, Marrakech, Morocco
| | - Tatiana Fioravanti
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona, Italy
| | - Ettore Olmo
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona, Italy
| | - Vincenzo Caputo Barucchi
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona, Italy
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Spangenberg V, Arakelyan M, Galoyan E, Pankin M, Petrosyan R, Stepanyan I, Grishaeva T, Danielyan F, Kolomiets O. Extraordinary centromeres: differences in the meiotic chromosomes of two rock lizards species Darevskia portschinskii and Darevskia raddei. PeerJ 2019; 7:e6360. [PMID: 30723630 PMCID: PMC6359900 DOI: 10.7717/peerj.6360] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 12/28/2018] [Indexed: 01/27/2023] Open
Abstract
According to the synthesis of 30 years of multidisciplinary studies, parthenogenetic species of rock lizards of genus Darevskia were formed as a result of different combination patterns of interspecific hybridization of the four bisexual parental species: Darevskia raddei, D. mixta, D. valentini, and D. portschinskii. In particular, D. portschinskii and D. raddei are considered as the parental species for the parthenogenetic species D. rostombekowi. Here for the first time, we present the result of comparative immunocytochemical study of primary spermatocyte nuclei spreads from the leptotene to diplotene stages of meiotic prophase I in two species: D. portschinskii and D. raddei. We observed similar chromosome lengths for both synaptonemal complex (SC) karyotypes as well as a similar number of crossing over sites. However, unexpected differences in the number and distribution of anti-centromere antibody (ACA) foci were detected in the SC structure of bivalents of the two species. In all examined D. portschinskii spermatocyte nuclei, one immunostained centromere focus was detected per SC bivalent. In contrast, in almost every studied D. raddei nuclei we identified three to nine SCs with additional immunostained ACA foci per SC bivalent. Thus, the obtained results allow us to identify species-specific karyotype features, previously not been detected using conventional mitotic chromosome analysis. Presumably the additional centromere foci are result of epigenetic chromatin modifications. We assume that this characteristic of the D. raddei karyotype could represent useful marker for the future studies of parthenogenetic species hybrid karyotypes related to D. raddei.
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Affiliation(s)
| | - Marine Arakelyan
- Department of Zoology, Yerevan State University, Yerevan, Armenia
| | - Eduard Galoyan
- Zoological Museum, Moscow State University, Moscow, Russia
| | - Mark Pankin
- Vavilov Institute of General Genetics, Moscow, Russian Federation
| | | | - Ilona Stepanyan
- Scientific Center of Zoology and Hydroecology, Yerevan, Armenia
| | | | - Felix Danielyan
- Department of Zoology, Yerevan State University, Yerevan, Armenia
| | - Oxana Kolomiets
- Vavilov Institute of General Genetics, Moscow, Russian Federation
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Giovannotti M, Nisi Cerioni P, Rojo V, Olmo E, Slimani T, Splendiani A, Caputo Barucchi V. Characterization of a satellite DNA in the genera Lacerta andTimon(Reptilia, Lacertidae) and its role in the differentiation of the W chromosome. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2018; 330:83-95. [DOI: 10.1002/jez.b.22790] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 12/04/2017] [Accepted: 01/09/2018] [Indexed: 12/24/2022]
Affiliation(s)
- Massimo Giovannotti
- Dipartimento di Scienze della Vita e dell'Ambiente; Università Politecnica delle Marche; via Brecce Bianche Ancona Italy
| | - Paola Nisi Cerioni
- Dipartimento di Scienze della Vita e dell'Ambiente; Università Politecnica delle Marche; via Brecce Bianche Ancona Italy
| | - Verónica Rojo
- AllGenetics & Biology SL; Edificio CICA; Campus de Elviña s/n, A Coruña Spain
- Department of Molecular and Cell Biology; Evolutionary Biology Group (GIBE); Universidade da Coruña; A Fraga 10, A Coruña Spain
| | - Ettore Olmo
- Dipartimento di Scienze della Vita e dell'Ambiente; Università Politecnica delle Marche; via Brecce Bianche Ancona Italy
| | - Tahar Slimani
- Cadi Ayyad University; Faculty of Sciences Semlalia; Laboratory Biodiversity and Ecosystem Dynamics; Marrakech Morocco
| | - Andrea Splendiani
- Dipartimento di Scienze della Vita e dell'Ambiente; Università Politecnica delle Marche; via Brecce Bianche Ancona Italy
| | - Vincenzo Caputo Barucchi
- Dipartimento di Scienze della Vita e dell'Ambiente; Università Politecnica delle Marche; via Brecce Bianche Ancona Italy
- Consiglio Nazionale delle Ricerche; Istituto di Scienze Marine Sezione Pesca Marittima; Largo Fiera della Pesca; Ancona Italy
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Evolutionary dynamics of two satellite DNA families in rock lizards of the genus Iberolacerta (Squamata, Lacertidae): different histories but common traits. Chromosome Res 2016; 23:441-61. [PMID: 26384818 DOI: 10.1007/s10577-015-9489-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Satellite DNAs compose a large portion of all higher eukaryotic genomes. The turnover of these highly repetitive sequences is an important element in genome organization and evolution. However, information about the structure and dynamics of reptilian satellite DNA is still scarce. Two satellite DNA families, HindIII and TaqI, have been previously characterized in four species of the genus Iberolacerta. These families showed different chromosomal locations, abundances, and evolutionary rates. Here, we extend the study of both satellite DNAs (satDNAs) to the remaining Iberolacerta species, with the aim to investigate the patterns of variability and factors influencing the evolution of these repetitive sequences. Our results revealed disparate patterns but also common traits in the evolutionary histories of these satellite families: (i) each satellite DNA is made up of a library of monomer variants or subfamilies shared by related species; (ii) species-specific profiles of satellite repeats are shaped by expansions and/or contractions of different variants from the library; (iii) different turnover rates, even among closely related species, result in great differences in overall sequence homogeneity and in concerted or non-concerted evolution patterns, which may not reflect the phylogenetic relationships among taxa. Contrasting turnover rates are possibly related to genomic constraints such as karyotype architecture and the interspersed organization of diverging repeat variants in satellite arrays. Moreover, rapid changes in copy number, especially in the centromeric HindIII satDNA, may have been associated with chromosomal rearrangements and even contributed to speciation within Iberolacerta.
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11
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Giovannotti M, Rojo V, Nisi Cerioni P, González-Tizón A, Martínez-Lage A, Splendiani A, Naveira H, Ruggeri P, Arribas Ó, Olmo E, Caputo Barucchi V. Isolation and characterization of two satellite DNAs in some Iberian rock lizards (Squamata, Lacertidae). JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2013; 322:13-26. [PMID: 24014193 DOI: 10.1002/jez.b.22530] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Revised: 07/29/2013] [Accepted: 07/31/2013] [Indexed: 01/15/2023]
Abstract
Satellite DNAs represent a large portion of all high eukaryotic genomes. They consist of numerous very similar repeated sequences, tandemly arranged in large clusters up to 100 million base pairs in length, usually located in the heterochromatic parts of chromosomes. The biological significance of satDNAs is still under discussion, but most of their proposed functions are related to heterochromatin and/or centromere formation and function. Because information about the structure of reptilian satDNA is far from exhaustive, we present a molecular and cytogenetic characterization of two satDNA families in four lacertid species. Two families of tandemly repeated DNAs, namely TaqI and HindIII satDNAs, have been cloned and sequenced from four species belonging to the genus Iberolacerta. These satDNAs are characterized by a monomer length of 171-188 and 170-172 bp, and by an AT content of 60.5% and 58.1%, respectively. FISH experiments with TaqI satDNA probe produced bright signals in pericentromeric regions of a subset of chromosomes whereas all the centromeres were marked by HindIII probe. The results obtained in this study suggest that chromosome location and abundance of satDNAs influence the evolution of these elements, with centromeric families evolving tenfold faster than interstitial/pericentromeric ones. Such different rates render different satellites useful for phylogenetic investigation at different taxonomic ranks.
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Affiliation(s)
- Massimo Giovannotti
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona, Italy
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Kosushkin SA, Grechko VV. Molecular genetic relationships and some issues of systematics of rock lizards of the genus Darevskia (Squamata: Lacertidae) based on locus analysis of SINE-type repeats (Squam1). RUSS J GENET+ 2013. [DOI: 10.1134/s1022795413070089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Martinsen L, Venanzetti F, Johnsen A, Sbordoni V, Bachmann L. Molecular evolution of the pDo500 satellite DNA family in Dolichopoda cave crickets (Rhaphidophoridae). BMC Evol Biol 2009; 9:301. [PMID: 20038292 PMCID: PMC2808323 DOI: 10.1186/1471-2148-9-301] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2009] [Accepted: 12/28/2009] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Non-coding satellite DNA (satDNA) usually has a high turn-over rate frequently leading to species specific patterns. However, some satDNA families evolve more slowly and can be found in several related species. Here, we analyzed the mode of evolution of the pDo500 satDNA family of Dolichopoda cave crickets. In addition, we discuss the potential of slowly evolving satDNAs as phylogenetic markers. RESULTS We sequenced 199 genomic or PCR amplified satDNA repeats of the pDo500 family from 12 Dolichopoda species. For the 38 populations under study, 39 pDo500 consensus sequences were deduced. Phylogenetic analyses using Bayesian, Maximum Parsimony, and Maximum Likelihood approaches yielded largely congruent tree topologies. The vast majority of pDo500 sequences grouped according to species designation. Scatter plots and statistical tests revealed a significant correlation between genetic distances for satDNA and mitochondrial DNA. Sliding window analyses showed species specific patterns of variable and conserved regions. The evolutionary rate of the pDo500 satDNA was estimated to be 1.63-1.78% per lineage per million years. CONCLUSIONS The pDo500 satDNA evolves gradually at a rate that is only slightly faster than previously published rates of insect mitochondrial COI sequences. The pDo500 phylogeny was basically congruent with the previously published mtDNA phylogenies. Accordingly, the slowly evolving pDo500 satDNA family is indeed informative as a phylogenetic marker.
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Affiliation(s)
- Lene Martinsen
- National Centre of Biosystematics, Natural History Museum, University of Oslo, 0318 Oslo, Norway
| | | | - Arild Johnsen
- National Centre of Biosystematics, Natural History Museum, University of Oslo, 0318 Oslo, Norway
| | - Valerio Sbordoni
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133 Rome, Italy
| | - Lutz Bachmann
- National Centre of Biosystematics, Natural History Museum, University of Oslo, 0318 Oslo, Norway
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Kosushkin SA, Borodulina OR, Solovyeva EN, Grechko VV. A family of short retroposons (Squam1) from squamate reptiles (Reptilia: Squamata): Structure, evolution, and correlation with phylogeny. Mol Biol 2008. [DOI: 10.1134/s002689330806006x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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16
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Grechko VV, Bannikova AA, Kosushkin SA, Ryabinina NL, Milto KD, Darevsky IS, Kramerov DA. Molecular genetic diversification of the lizard complex Darevskia raddei (Sauria: Lacertidae): Early stages of speciation. Mol Biol 2007. [DOI: 10.1134/s0026893307050093] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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