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de Oliveira AM, Souza GM, Toma GA, Dos Santos N, Dos Santos RZ, Goes CAG, Deon GA, Setti PG, Porto-Foresti F, Utsunomia R, Gunski RJ, Del Valle Garnero A, Herculano Correa de Oliveira E, Kretschmer R, Cioffi MDB. Satellite DNAs, heterochromatin, and sex chromosomes of the wattled jacana (Charadriiformes; Jacanidae): a species with highly rearranged karyotype. Genome 2024; 67:109-118. [PMID: 38316150 DOI: 10.1139/gen-2023-0082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
Charadriiformes, which comprises shorebirds and their relatives, is one of the most diverse avian orders, with over 390 species showing a wide range of karyotypes. Here, we isolated and characterized the whole collection of satellite DNAs (satDNAs) at both molecular and cytogenetic levels of one of its representative species, named the wattled jacana (Jacana jacana), a species that contains a typical ZZ/ZW sex chromosome system and a highly rearranged karyotype. In addition, we also investigate the in situ location of telomeric and microsatellite repeats. A small catalog of 11 satDNAs was identified that typically accumulated on microchromosomes and on the W chromosome. The latter also showed a significant accumulation of telomeric signals, being (GA)10 the only microsatellite with positive hybridization signals among all the 16 tested ones. These current findings contribute to our understanding of the genomic organization of repetitive DNAs in a bird species with high degree of chromosomal reorganization contrary to the majority of bird species that have stable karyotypes.
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Affiliation(s)
- Alan Moura de Oliveira
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | - Guilherme Mota Souza
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | - Gustavo Akira Toma
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | | | | | | | - Geize Aparecida Deon
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | - Princia Grejo Setti
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | | | | | | | | | | | - Rafael Kretschmer
- Departamento de Ecologia, Zoologia e Genética, Instituto de Biologia, Universidade Federal de Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
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Louzada S, Lopes M, Ferreira D, Adega F, Escudeiro A, Gama-Carvalho M, Chaves R. Decoding the Role of Satellite DNA in Genome Architecture and Plasticity-An Evolutionary and Clinical Affair. Genes (Basel) 2020; 11:E72. [PMID: 31936645 PMCID: PMC7017282 DOI: 10.3390/genes11010072] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 12/29/2019] [Accepted: 01/08/2020] [Indexed: 12/11/2022] Open
Abstract
Repetitive DNA is a major organizational component of eukaryotic genomes, being intrinsically related with their architecture and evolution. Tandemly repeated satellite DNAs (satDNAs) can be found clustered in specific heterochromatin-rich chromosomal regions, building vital structures like functional centromeres and also dispersed within euchromatin. Interestingly, despite their association to critical chromosomal structures, satDNAs are widely variable among species due to their high turnover rates. This dynamic behavior has been associated with genome plasticity and chromosome rearrangements, leading to the reshaping of genomes. Here we present the current knowledge regarding satDNAs in the light of new genomic technologies, and the challenges in the study of these sequences. Furthermore, we discuss how these sequences, together with other repeats, influence genome architecture, impacting its evolution and association with disease.
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Affiliation(s)
- Sandra Louzada
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (S.L.); (M.L.); (D.F.); (F.A.); (A.E.)
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal;
| | - Mariana Lopes
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (S.L.); (M.L.); (D.F.); (F.A.); (A.E.)
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal;
| | - Daniela Ferreira
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (S.L.); (M.L.); (D.F.); (F.A.); (A.E.)
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal;
| | - Filomena Adega
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (S.L.); (M.L.); (D.F.); (F.A.); (A.E.)
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal;
| | - Ana Escudeiro
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (S.L.); (M.L.); (D.F.); (F.A.); (A.E.)
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal;
| | - Margarida Gama-Carvalho
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal;
| | - Raquel Chaves
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (S.L.); (M.L.); (D.F.); (F.A.); (A.E.)
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal;
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Kalcounis-Rueppell MC, Pultorak JD, Marler CA. Ultrasonic Vocalizations of Mice in the Genus Peromyscus. HANDBOOK OF ULTRASONIC VOCALIZATION - A WINDOW INTO THE EMOTIONAL BRAIN 2018. [DOI: 10.1016/b978-0-12-809600-0.00022-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Paço A, Adega F, Meštrović N, Plohl M, Chaves R. The puzzling character of repetitive DNA in Phodopus genomes (Cricetidae, Rodentia). Chromosome Res 2016; 23:427-40. [PMID: 26281779 DOI: 10.1007/s10577-015-9481-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Three novel repetitive DNA sequences are described, presenting a similar heterochromatic chromosomal location in two hamster species: Phodopus roborovskii and Phodopus sungorus (Cricetidae, Rodentia). Namely, two species-specific repetitive sequences (PROsat from P. roborovskii and PSUchr1sat from P. sungorus) surrounding a third one (PsatDNA), that is shared by both hamster genomes. Fiber-FISH analyses revealed that PROsat intermingles with PsatDNA in P. roborovskii and PSUchr1sat intermingles with PsatDNA in P. sungorus. A model explaining the evolution of this intricate chromosomal distribution is proposed, which can explain better the evolution of these very derivative genomes (in comparison to the ancestral Muroidea). The most plausible evolutionary scenario seems to be the expansion of a number of repeats into other's domain, most probably resulting in its intermingling, followed by the subsequent spread of these complex repeats from a single chromosomal location to other chromosomes. Evidences of an association between repetitive sequences and the chromosome evolution process were observed, namely for PROsat. Most probably, the evolutionary breakpoints that shaped PRO and PSU chromosomes (pericentric inversions and fusions) occurred within the boundaries of PROsat blocks in the ancestor. The repeats high diversity at the heterochromatic regions of Phodopus chromosomes, together with its complex organization, suggests that these species are important models for evolutionary studies, namely in the investigation of a possible relationship between repetitive sequences and the occurrence of chromosomal rearrangements and consequently, in genome evolution.
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Affiliation(s)
- Ana Paço
- University of Trás-os-Montes and Alto Douro (UTAD), Department of Genetics and Biotechnology (DGB), Laboratory of Cytogenomics and Animal Genomics (CAG), Vila Real, Portugal
| | - Filomena Adega
- University of Trás-os-Montes and Alto Douro (UTAD), Department of Genetics and Biotechnology (DGB), Laboratory of Cytogenomics and Animal Genomics (CAG), Vila Real, Portugal.,University of Lisboa, Faculty of Sciences, BioISI-Biosystems & Integrative Sciences Institute, Campo Grande, Lisboa, Portugal
| | - Nevenka Meštrović
- Department of Molecular Biology, Ruđer Bošković Institute, Bijenička 54, HR-10002, Zagreb, Croatia
| | - Miroslav Plohl
- Department of Molecular Biology, Ruđer Bošković Institute, Bijenička 54, HR-10002, Zagreb, Croatia
| | - Raquel Chaves
- University of Trás-os-Montes and Alto Douro (UTAD), Department of Genetics and Biotechnology (DGB), Laboratory of Cytogenomics and Animal Genomics (CAG), Vila Real, Portugal. .,University of Lisboa, Faculty of Sciences, BioISI-Biosystems & Integrative Sciences Institute, Campo Grande, Lisboa, Portugal.
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5
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Louzada S, Vieira-da-Silva A, Mendes-da-Silva A, Kubickova S, Rubes J, Adega F, Chaves R. A novel satellite DNA sequence in the Peromyscus genome (PMSat): Evolution via copy number fluctuation. Mol Phylogenet Evol 2015; 92:193-203. [PMID: 26103000 DOI: 10.1016/j.ympev.2015.06.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Revised: 06/11/2015] [Accepted: 06/12/2015] [Indexed: 12/16/2022]
Abstract
Satellite DNAs (satDNA) are tandemly arrayed repeated sequences largely present in eukaryotic genomes, which play important roles in genome evolution and function, and therefore, their analysis is vital. Here, we describe the isolation of a novel satellite DNA family (PMSat) from the rodent Peromyscus eremicus (Cricetidae, Rodentia), which is located in pericentromeric regions and exhibits a typical satellite DNA genome organization. Orthologous PMSat sequences were isolated and characterized from three species belonging to Cricetidae: Cricetus cricetus, Phodopus sungorus and Microtus arvalis. In these species, PMSat is highly conserved, with the absence of fixed species-specific mutations. Strikingly, different numbers of copies of this sequence were found among the species, suggesting evolution by copy number fluctuation. Repeat units of PMSat were also found in the Peromyscus maniculatus bairdii BioProject, but our results suggest that these repeat units are from genome regions outside the pericentromere. The remarkably high evolutionary sequence conservation along with the preservation of a few numbers of copies of this sequence in the analyzed genomes may suggest functional significance but a different sequence nature/organization. Our data highlight that repeats are difficult to analyze due to the limited tools available to dissect genomes and the fact that assemblies do not cover regions of constitutive heterochromatin.
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Affiliation(s)
- Sandra Louzada
- University of Trás-os-Montes and Alto Douro (UTAD), Department of Genetics and Biotechnology (DGB), Laboratory of Cytogenomics and Animal Genomics (CAG), Apdo 1013, 5001-801 Vila Real, Portugal
| | - Ana Vieira-da-Silva
- University of Trás-os-Montes and Alto Douro (UTAD), Department of Genetics and Biotechnology (DGB), Laboratory of Cytogenomics and Animal Genomics (CAG), Apdo 1013, 5001-801 Vila Real, Portugal; University of Lisboa, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, Lisboa, Portugal
| | - Ana Mendes-da-Silva
- University of Trás-os-Montes and Alto Douro (UTAD), Department of Genetics and Biotechnology (DGB), Laboratory of Cytogenomics and Animal Genomics (CAG), Apdo 1013, 5001-801 Vila Real, Portugal; University of Lisboa, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, Lisboa, Portugal
| | | | - Jiri Rubes
- Veterinary Research Institute, Brno, Czech Republic
| | - Filomena Adega
- University of Trás-os-Montes and Alto Douro (UTAD), Department of Genetics and Biotechnology (DGB), Laboratory of Cytogenomics and Animal Genomics (CAG), Apdo 1013, 5001-801 Vila Real, Portugal; University of Lisboa, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, Lisboa, Portugal
| | - Raquel Chaves
- University of Trás-os-Montes and Alto Douro (UTAD), Department of Genetics and Biotechnology (DGB), Laboratory of Cytogenomics and Animal Genomics (CAG), Apdo 1013, 5001-801 Vila Real, Portugal; University of Lisboa, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, Lisboa, Portugal.
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Vieira-da-Silva A, Louzada S, Adega F, Chaves R. A High-Resolution Comparative Chromosome Map of Cricetus cricetus and Peromyscus eremicus Reveals the Involvement of Constitutive Heterochromatin in Breakpoint Regions. Cytogenet Genome Res 2015; 145:59-67. [PMID: 25999143 DOI: 10.1159/000381840] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/02/2015] [Indexed: 11/19/2022] Open
Abstract
Compared to humans and other mammals, rodent genomes, specifically Muroidea species, underwent intense chromosome reshuffling in which many complex structural rearrangements occurred. This fact makes them preferential animal models for studying the process of karyotype evolution. Here, we present the first combined chromosome comparative maps between 2 Cricetidae species, Cricetus cricetus and Peromyscus eremicus, and the index species Mus musculus and Rattus norvegicus. Comparative chromosome painting was done using mouse and rat paint probes together with in silico analysis from the Ensembl genome browser database. Hereby, evolutionary events (inter- and intrachromosomal rearrangements) that occurred in C. cricetus and P. eremicus since the putative ancestral Muroidea genome could be inferred, and evolutionary breakpoint regions could be detected. A colocalization of constitutive heterochromatin and evolutionary breakpoint regions in each genome was observed. Our results suggest the involvement of constitutive heterochromatin in karyotype restructuring of these species, despite the different levels of conservation of the C. cricetus (derivative) and P. eremicus (conserved) genomes.
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Affiliation(s)
- Ana Vieira-da-Silva
- Center of Agricultural and Genomics Biotechnology (CGBA), University of Trás-os-Montes and Alto Douro, Vila Real, Portugal
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7
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Nanger, Eudorcas, Gazella, and Antilope form a well-supported chromosomal clade within Antilopini (Bovidae, Cetartiodactyla). Chromosoma 2014; 124:235-47. [PMID: 25416455 DOI: 10.1007/s00412-014-0494-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 11/05/2014] [Accepted: 11/05/2014] [Indexed: 10/24/2022]
Abstract
The evolutionary clade comprising Nanger, Eudorcas, Gazella, and Antilope, defined by an X;BTA5 translocation, is noteworthy for the many autosomal Robertsonian fusions that have driven the chromosome number variation from 2n = 30 observed in Antilope cervicapra, to the 2n = 58 in present Eudorcas thomsoni and Eudorcas rufifrons. This work reports the phylogenetic relationships within the Antilopini using comprehensive cytogenetic data from A. cervicapra, Gazella leptoceros, Nanger dama ruficollis, and E. thomsoni together with corrected karyotypic data from an additional nine species previously reported in the literature. Fluorescence in situ hybridization using BAC and microdissected cattle painting probes, in conjunction with differential staining techniques, provide the following: (i) a detailed analysis of the E. thomsoni chromosomes, (ii) the identification and fine-scale analysis the BTA3 orthologue in species of Antilopini, and (iii) the location of the pseudoautosomal regions on sex chromosomes of the four species. Our phylogenetic analysis of the chromosomal data supports monophyly of Nanger and Eudorcas and suggests an affiliation between A. cervicapra and some of the Gazella species. This renders Gazella paraphyletic and emphasizes a closer relationship between Antilope and Gazella than what has previously been considered.
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LINE-1 retrotransposons: from 'parasite' sequences to functional elements. J Appl Genet 2014; 56:133-45. [PMID: 25106509 DOI: 10.1007/s13353-014-0241-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 07/24/2014] [Accepted: 07/25/2014] [Indexed: 10/24/2022]
Abstract
Long interspersed nuclear elements-1 (LINE-1) are the most abundant and active retrotransposons in the mammalian genomes. Traditionally, the occurrence of LINE-1 sequences in the genome of mammals has been explained by the selfish DNA hypothesis. Nevertheless, recently, it has also been argued that these sequences could play important roles in these genomes, as in the regulation of gene expression, genome modelling and X-chromosome inactivation. The non-random chromosomal distribution is a striking feature of these retroelements that somehow reflects its functionality. In the present study, we have isolated and analysed a fraction of the open reading frame 2 (ORF2) LINE-1 sequence from three rodent species, Cricetus cricetus, Peromyscus eremicus and Praomys tullbergi. Physical mapping of the isolated sequences revealed an interspersed longitudinal AT pattern of distribution along all the chromosomes of the complement in the three genomes. A detailed analysis shows that these sequences are preferentially located in the euchromatic regions, although some signals could be detected in the heterochromatin. In addition, a coincidence between the location of imprinted gene regions (as Xist and Tsix gene regions) and the LINE-1 retroelements was also observed. According to these results, we propose an involvement of LINE-1 sequences in different genomic events as gene imprinting, X-chromosome inactivation and evolution of repetitive sequences located at the heterochromatic regions (e.g. satellite DNA sequences) of the rodents' genomes analysed.
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Kopecna O, Kubickova S, Cernohorska H, Cabelova K, Vahala J, Martinkova N, Rubes J. Tribe-specific satellite DNA in non-domestic Bovidae. Chromosome Res 2014; 22:277-91. [PMID: 24452783 DOI: 10.1007/s10577-014-9401-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Revised: 01/02/2014] [Accepted: 01/10/2014] [Indexed: 01/08/2023]
Abstract
Satellite sequences present in the centromeric and pericentric regions of chromosomes represent useful source of information. Changes in satellite DNA composition may coincide with the speciation and serve as valuable markers of phylogenetic relationships. Here, we examined satellite DNA clones isolated by laser microdissection of centromeric regions of 38 bovid species and categorized them into three types. Sat I sequences from members of Bovini/Tragelaphini/Boselaphini are similar to the well-documented 1.715 sat I DNA family. Sat I DNA from Caprini/Alcelaphini/Hippotragini/Reduncini/Aepycerotini/Cephalophini/Antilopini/Neotragini/Oreotragini form the second group homologous to the common 1.714 sat I DNA. The analysis of sat II DNAs isolated in our study confirmed conservativeness of these sequences within Bovidae. Newly described centromeric clones from Madoqua kirkii and Strepsiceros strepsiceros were similar in length and repetitive tandem arrangement but showed no similarity to any other satellite DNA in the GenBank database. Phylogenetic analysis of sat I sequences isolated in our study from 38 bovid species enabled the description of relationships at the subfamily and tribal levels. The maximum likelihood and Bayesian inference analyses showed a basal position of sequences from Oreotragini in the subfamily Antilopinae. According to the Bayesian inference analysis based on the indels in a partitioned mixed model, Antilopinae satellite DNA split into two groups with those from Neotragini as a basal tribe, followed by a stepwise, successive branching of Cephalophini, Aepycerotini and Antilopini sequences. In the second group, Reduncini sequences were basal followed by Caprini, Alcelaphini and Hippotragini.
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Affiliation(s)
- Olga Kopecna
- Department of Genetics and Reproduction, Veterinary Research Institute, Hudcova 70, 621 00, Brno, Czech Republic,
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Kopecna O, Kubickova S, Cernohorska H, Cabelova K, Vahala J, Rubes J. Isolation and comparison of tribe-specific centromeric repeats within Bovidae. J Appl Genet 2012; 53:193-202. [PMID: 22249998 DOI: 10.1007/s13353-011-0080-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2011] [Revised: 12/08/2011] [Accepted: 12/09/2011] [Indexed: 12/23/2022]
Abstract
A taxonomic division of the family Bovidae (Artiodactyla) is difficult and the evolutionary relationships among most bovid subfamilies remain uncertain. In this study, we isolated the cattle satellite I clone BTREP15 (1.715 satellite DNA family) and autosomal centromeric DNAs of members of ten bovid tribes. We wished to determine whether the analysis of fluorescence in situ hybridization patterns of the cattle satellite I clone (BTREP15) and tribe-specific centromeric repeats isolated by laser microdissection would help to reveal some of the ambiguities occurring in the systematic classification of the family Bovidae. The FISH study of the presence and distribution of the cattle satellite I clone BTREP15 (1.715 satellite DNA family) within members of ten bovid tribes was not informative. FISH analysis of autosomal centromeric DNA probes in several species within one tribe revealed similar hybridization patterns in autosomes confirming tribal homogeneity of these probes. Sex chromosomes showed considerable variation in sequence composition and arrangement not only between tribes but also between species of one tribe. According to our findings it seems that Oreotragus oreotragus developed its own specific satellite DNA which does not hybridize to any other bovid species analysed. Our results suggest O. oreotragus as well as Aepyceros melampus may be unique species not particularly closely related to any of the recognized bovid tribes. This study indicates the isolation of tribe-specific centromeric DNAs by laser microdissection and cloning the sequence representing the main motif of these repetitive DNAs could offer the perspectives for comparative phylogenetic studies.
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Affiliation(s)
- Olga Kopecna
- Department of Genetics and Reproduction, Veterinary Research Institute, Hudcova 70, 621 00 Brno, Czech Republic.
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11
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Chromosomal evolution in Rattini (Muridae, Rodentia). Chromosome Res 2011; 19:709-27. [PMID: 21850459 DOI: 10.1007/s10577-011-9227-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Revised: 07/28/2011] [Accepted: 07/29/2011] [Indexed: 10/17/2022]
Abstract
The Rattini (Muridae, Murinae) includes the biologically important model species Rattus norvegicus (RNO) and represents a group of rodents that are of clinical, agricultural and epidemiological importance. We present a comparative molecular cytogenetic investigation of ten Rattini species representative of the genera Maxomys, Leopoldamys, Niviventer, Berylmys, Bandicota and Rattus using chromosome banding, cross-species painting (Zoo-fluorescent in situ hybridization or FISH) and BAC-FISH mapping. Our results show that these taxa are characterised by slow to moderate rates of chromosome evolution that contrasts with the extensive chromosome restructuring identified in most other murid rodents, particularly the mouse lineage. This extends to genomic features such as NOR location (for example, NORs on RNO 3 are present on the corresponding chromosomes in all species except Bandicota savilei and Niviventer fulvescens, and the NORs on RNO 10 are conserved in all Rattini with the exception of Rattus). The satellite I DNA family detected and characterised herein appears to be taxon (Rattus) specific, and of recent origin (consistent with a feedback model of satellite evolution). BAC-mapping using clones that span regions responsible for the morphological variability exhibited by RNO 1, 12 and 13 (acrocentric/submetacentric) and their orthologues in Rattus species, demonstrated that the differences are most likely due to pericentric inversions as exemplified by data on Rattus tanezumi. Chromosomal characters detected using R. norvegicus and Maxomys surifer whole chromosome painting probes were mapped to a consensus sequence-based phylogenetic tree thus allowing an objective assessment of ancestral states for the reconstruction of the putative Rattini ancestral karyotype. This is thought to have comprised 46 chromosomes that, with the exception of a single pair of metacentric autosomes, were acrocentric in morphology.
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12
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Divergent patterns of breakpoint reuse in Muroid rodents. Mamm Genome 2009; 21:77-87. [PMID: 20033182 DOI: 10.1007/s00335-009-9242-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2009] [Accepted: 11/09/2009] [Indexed: 01/09/2023]
Abstract
Multiple Genome Rearrangement (MGR) analysis was used to define the trajectory and pattern of chromosome rearrangement within muroid rodents. MGR was applied using 107 chromosome homologies between Mus, Rattus, Peromyscus, the muroid sister taxon Cricetulus griseus, and Sciurus carolinensis as a non-Muroidea outgroup, with specific attention paid to breakpoint reuse and centromere evolution. This analysis revealed a high level of chromosome breakpoint conservation between Rattus and Peromyscus and indicated that the chromosomes of Mus are highly derived. This analysis identified several conserved evolutionary breakpoints that have been reused multiple times during karyotypic evolution in rodents. Our data demonstrate a high level of reuse of breakpoints among muroid rodents, further supporting the "Fragile Breakage Model" of chromosome evolution. We provide the first analysis of rodent centromeres with respect to evolutionary breakpoints. By analyzing closely related rodent species we were able to clarify muroid rodent karyotypic evolution. We were also able to derive several high-resolution ancestral karyotypes and identify rearrangements specific to various stages of Muroidea evolution. These data were useful in further characterizing lineage-specific modes of chromosome evolution.
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