1
|
Mallik R, Carlson KB, Wcisel DJ, Fisk M, Yoder JA, Dornburg A. A chromosome-level genome assembly of longnose gar, Lepisosteus osseus. G3 (BETHESDA, MD.) 2023; 13:jkad095. [PMID: 37119803 PMCID: PMC10320754 DOI: 10.1093/g3journal/jkad095] [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: 01/19/2023] [Revised: 04/18/2023] [Accepted: 04/19/2023] [Indexed: 05/01/2023]
Abstract
Holosteans (gars and bowfins) represent the sister lineage to teleost fishes, the latter being a clade that comprises over half of all living vertebrates and includes important models for comparative genomics and human health. A major distinction between the evolutionary history of teleosts and holosteans is that all teleosts experienced a genome duplication event in their early evolutionary history. As the teleost genome duplication occurred after teleosts diverged from holosteans, holosteans have been heralded as a means to bridge teleost models to other vertebrate genomes. However, only three species of holosteans have been genome-sequenced to date, and sequencing of more species is needed to fill sequence sampling gaps and provide a broader comparative basis for understanding holostean genome evolution. Here we report the first high quality reference genome assembly and annotation of the longnose gar (Lepisosteus osseus). Our final assembly consists of 22,709 scaffolds with a total length of 945 bp with contig N50 of 116.61 kb. Using BRAKER2, we annotated a total of 30,068 genes. Analysis of the repetitive regions of the genome reveals the genome to contain 29.12% transposable elements, and the longnose gar to be the only other known vertebrate outside of the spotted gar and bowfin to contain CR1, L2, Rex1, and Babar. These results highlight the potential utility of holostean genomes for understanding the evolution of vertebrate repetitive elements, and provide a critical reference for comparative genomic studies utilizing ray-finned fish models.
Collapse
Affiliation(s)
- Rittika Mallik
- Department of Bioinformatics and Genomics, UNC-Charlotte, Charlotte, NC 28223, USA
| | - Kara B Carlson
- Department of Molecular Biomedical Sciences, Genetics and Genomics Academy, and Comparative Medicine Institute, North Carolina State University, Raleigh, NC 27695, USA
| | - Dustin J Wcisel
- Department of Molecular Biomedical Sciences, Genetics and Genomics Academy, and Comparative Medicine Institute, North Carolina State University, Raleigh, NC 27695, USA
| | - Michael Fisk
- Aquatic Wildlife Diversity Group, North Carolina Wildlife Resources Commission, Raleigh, NC 27606, USA
| | - Jeffrey A Yoder
- Department of Molecular Biomedical Sciences, Genetics and Genomics Academy, and Comparative Medicine Institute, North Carolina State University, Raleigh, NC 27695, USA
| | - Alex Dornburg
- Department of Bioinformatics and Genomics, UNC-Charlotte, Charlotte, NC 28223, USA
| |
Collapse
|
2
|
Hatanaka T, de Oliveira EA, Ráb P, Yano CF, Bertollo LAC, Ezaz T, Jegede OOI, Liehr T, Olaleye VF, de Bello Cioffi M. First chromosomal analysis in Gymnarchus niloticus (Gymnarchidae: Osteoglossiformes): insights into the karyotype evolution of this ancient fish order. Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/bly098] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Terumi Hatanaka
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
| | - Ezequiel A de Oliveira
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
- Secretaria de Estado de Educação de Mato Grosso – SEDUC-MT, Cuiabá, MT, Brazil
| | - Petr Ráb
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
| | - Cassia F Yano
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
| | - Luiz A C Bertollo
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
| | - Tariq Ezaz
- Institute for Applied Ecology, University of Canberra, Bruce, Canberra, ACT, Australia
| | | | - Thomas Liehr
- Jena University Hospital, Institute of Human Genetics, Jena, Germany
| | - Victor F Olaleye
- Department of Zoology, Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
| |
Collapse
|
3
|
Sember A, Bohlen J, Šlechtová V, Altmanová M, Pelikánová Š, Ráb P. Dynamics of tandemly repeated DNA sequences during evolution of diploid and tetraploid botiid loaches (Teleostei: Cobitoidea: Botiidae). PLoS One 2018; 13:e0195054. [PMID: 29590207 PMCID: PMC5874072 DOI: 10.1371/journal.pone.0195054] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 03/15/2018] [Indexed: 12/16/2022] Open
Abstract
Polyploidization has played an important role in the evolution of vertebrates, particularly at the base of Teleostei-an enormously successful ray-finned fish group with additional genome doublings on lower taxonomic levels. The investigation of post-polyploid genome dynamics might provide important clues about the evolution and ecology of respective species and can help to decipher the role of polyploidy per se on speciation. Few studies have attempted to investigate the dynamics of repetitive DNA sequences in the post-polyploid genome using molecular cytogenetic tools in fishes, though recent efforts demonstrated their usefulness. The demonstrably monophyletic freshwater loach family Botiidae, branching to evolutionary diploid and tetraploid lineages separated >25 Mya, offers a suited model group for comparing the long-term repetitive DNA evolution. For this, we integrated phylogenetic analyses with cytogenetical survey involving Giemsa- and Chromomycin A3 (CMA3)/DAPI stainings and fluorescence in situ hybridization with 5S/45S rDNA, U2 snDNA and telomeric probes in representative sample of 12 botiid species. The karyotypes of all diploids were composed of 2n = 50 chromosomes, while majority of tetraploids had 2n = 4x = 100, with only subtle interspecific karyotype differences. The exceptional karyotype of Botia dario (2n = 4x = 96) suggested centric fusions behind the 2n reduction. Variable patterns of FISH signals revealed cases of intraspecific polymorphisms, rDNA amplification, variable degree of correspondence with CMA3+ sites and almost no phylogenetic signal. In tetraploids, either additivity or loci gain/loss was recorded. Despite absence of classical interstitial telomeric sites, large blocks of interspersed rDNA/telomeric regions were found in diploids only. We uncovered different molecular drives of studied repetitive DNA classes within botiid genomes as well as the advanced stage of the re-diploidization process in tetraploids. Our results may contribute to link genomic approach with molecular cytogenetic analyses in addressing the origin and mechanism of this polyploidization event.
Collapse
Affiliation(s)
- Alexandr Sember
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, Liběchov, Czech Republic
| | - Jörg Bohlen
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, Liběchov, Czech Republic
| | - Vendula Šlechtová
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, Liběchov, Czech Republic
| | - Marie Altmanová
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, Liběchov, Czech Republic
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, Prague 2, Czech Republic
| | - Šárka Pelikánová
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, Liběchov, Czech Republic
| | - Petr Ráb
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, Liběchov, Czech Republic
| |
Collapse
|
4
|
Symonová R, Majtánová Z, Arias-Rodriguez L, Mořkovský L, Kořínková T, Cavin L, Pokorná MJ, Doležálková M, Flajšhans M, Normandeau E, Ráb P, Meyer A, Bernatchez L. Genome Compositional Organization in Gars Shows More Similarities to Mammals than to Other Ray-Finned Fish. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2016; 328:607-619. [DOI: 10.1002/jez.b.22719] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 11/13/2016] [Accepted: 11/22/2016] [Indexed: 12/12/2022]
Affiliation(s)
- Radka Symonová
- Laboratory of Fish Genetics; Institute of Animal Physiology and Genetics; The Czech Academy of Sciences; Liběchov Czech Republic
- Department of Zoology; Faculty of Science; Charles University; Prague 2 Czech Republic
- Research Institute for Limnology; University of Innsbruck; Mondsee Austria
| | - Zuzana Majtánová
- Laboratory of Fish Genetics; Institute of Animal Physiology and Genetics; The Czech Academy of Sciences; Liběchov Czech Republic
- Department of Zoology; Faculty of Science; Charles University; Prague 2 Czech Republic
| | - Lenin Arias-Rodriguez
- División Académica de Ciencias Biológicas; Universidad Juárez Autónoma de Tabasco (UJAT); Villahermosa Tabasco México
| | - Libor Mořkovský
- Department of Zoology; Faculty of Science; Charles University; Prague 2 Czech Republic
| | - Tereza Kořínková
- Laboratory of Fish Genetics; Institute of Animal Physiology and Genetics; The Czech Academy of Sciences; Liběchov Czech Republic
| | - Lionel Cavin
- Muséum d'Histoire Naturelle; Geneva 6 Switzerland
| | - Martina Johnson Pokorná
- Laboratory of Fish Genetics; Institute of Animal Physiology and Genetics; The Czech Academy of Sciences; Liběchov Czech Republic
- Department of Ecology; Faculty of Science; Charles University; Prague 2 Czech Republic
| | - Marie Doležálková
- Laboratory of Fish Genetics; Institute of Animal Physiology and Genetics; The Czech Academy of Sciences; Liběchov Czech Republic
- Department of Zoology; Faculty of Science; Charles University; Prague 2 Czech Republic
| | - Martin Flajšhans
- Faculty of Fisheries and Protection of Waters; South Bohemian Research Centre of Aquaculture and Biodiversity of Hydrocenoses; University of South Bohemia in České Budějovice; Vodňany Czech Republic
| | - Eric Normandeau
- IBIS, Department of Biology, University Laval, Pavillon Charles-Eugène-Marchand; Avenue de la Médecine Quebec City; Canada
| | - Petr Ráb
- Laboratory of Fish Genetics; Institute of Animal Physiology and Genetics; The Czech Academy of Sciences; Liběchov Czech Republic
| | - Axel Meyer
- Chair in Zoology and Evolutionary Biology; Department of Biology; University of Konstanz; Konstanz Germany
| | - Louis Bernatchez
- IBIS, Department of Biology, University Laval, Pavillon Charles-Eugène-Marchand; Avenue de la Médecine Quebec City; Canada
| |
Collapse
|
5
|
Ráb P, Yano CF, Lavoué S, Jegede OI, Bertollo LAC, Ezaz T, Majtánová Z, de Oliveira EA, Cioffi MB. Karyotype and Mapping of Repetitive DNAs in the African Butterfly Fish Pantodon buchholzi, the Sole Species of the Family Pantodontidae. Cytogenet Genome Res 2016; 149:312-320. [PMID: 27710958 DOI: 10.1159/000450534] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/09/2016] [Indexed: 11/19/2022] Open
Abstract
The monophyletic order Osteoglossiformes represents one of the most ancestral groups of teleosts and has at least 1 representative in all continents of the southern hemisphere, with the exception of Antarctica. However, despite its phylogenetic and biogeographical importance, cytogenetic data in Osteoglossiformes are scarce. Here, karyotype and chromosomal characteristics of the lower Niger River population of the African butterfly fish Pantodon buchholzi, the sole species of the family Pantodontidae (Osteoglossiformes), were examined using conventional and molecular cytogenetic approaches. All specimens examined had 2n = 46 chromosomes, with a karyotype composed of 5 pairs of metacentric, 5 pairs of submetacentric, and 13 pairs of acrocentric chromosomes in both sexes. No morphologically differentiated sex chromosomes were identified. C-bands were located in the centromeric/pericentromeric region of all chromosomes and were associated with the single AgNOR site. FISH with ribosomal DNA probes revealed that both 5S and 18S rDNA were present in only 1 pair of chromosomes each, but did not colocalize. CMA3+ bands were observed near the telomeres in several chromosome pairs and also at the 18S rDNA sites. The mapping of di- and trinucleotide repeat motifs, Rex6 transposable element, and U2 snRNA showed a scattered distribution over most of the chromosomes, but for some microsatellites and the U2 snRNA also a preferential accumulation at telomeric regions. This study presents the first detailed cytogenetic analysis in the African butterfly fish by both conventional and molecular cytogenetic protocols. This is the first of a series of further cytogenetic and cytogenomic studies on osteoglossiforms, aiming to comprehensively examine the chromosomal evolution in this phylogenetically important fish order.
Collapse
Affiliation(s)
- Petr Ráb
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
| | | | | | | | | | | | | | | | | |
Collapse
|
6
|
Sember A, Bohlen J, Šlechtová V, Altmanová M, Symonová R, Ráb P. Karyotype differentiation in 19 species of river loach fishes (Nemacheilidae, Teleostei): extensive variability associated with rDNA and heterochromatin distribution and its phylogenetic and ecological interpretation. BMC Evol Biol 2015; 15:251. [PMID: 26573692 PMCID: PMC4647339 DOI: 10.1186/s12862-015-0532-9] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 11/04/2015] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Loaches of the family Nemacheilidae are one of the most speciose elements of Palearctic freshwater ichthyofauna and have undergone rapid ecological adaptations and colonizations. Their cytotaxonomy is largely unexplored; with the impact of cytogenetical changes on this evolutionary diversification still unknown. An extensive cytogenetical survey was performed in 19 nemacheilid species using both conventional (Giemsa staining, C- banding, Ag- and Chromomycin A3/DAPI stainings) and molecular (fluorescence in situ hybridization with 5S rDNA, 45S rDNA, and telomeric (TTAGGG)n probes) methods. A phylogenetic tree of the analysed specimens was constructed based on one mitochondrial (cytochrome b) and two nuclear (RAG1, IRBP) genes. RESULTS Seventeen species showed karyotypes composed of 2n = 50 chromosomes but differentiated by fundamental chromosome number (NF = 68-90). Nemachilichthys ruppelli (2n = 38) and Schistura notostigma (2n = 44-48) displayed reduced 2n with an elevated number of large metacentric chromosomes. Only Schistura fasciolata showed morphologically differentiated sex chromosomes with a multiple system of the XY1Y2 type. Chromomycin A3 (CMA3)- fluorescence revealed interspecific heterogeneity in the distribution of GC-rich heterochromatin including its otherwise very rare association with 5S rDNA sites. The 45S rDNA sites were mostly located on a single chromosome pair contrasting markedly with a pattern of two (Barbatula barbatula, Nemacheilus binotatus, N. ruppelli) to 20 sites (Physoschistura sp.) of 5S rDNA. The cytogenetic changes did not follow the phylogenetic relationships between the samples. A high number of 5S rDNA sites was present in species with small effective population sizes. CONCLUSION Despite a prevailing conservatism of 2n, Nemacheilidae exhibited a remarkable cytogenetic variability on microstructural level. We suggest an important role for pericentric inversions, tandem and centric fusions in nemacheilid karyotype differentiation. Short repetitive sequences, genetic drift, founder effect, as well as the involvement of transposable elements in the dispersion of ribosomal DNA sites, might also have played a role in evolutionary processes such as reproductive isolation. These remarkable dynamics of their genomes qualify river loaches as a model for the study of the cytogenetic background of major evolutionary processes such as radiation, endemism and colonization of a wide range of habitats.
Collapse
Affiliation(s)
- Alexandr Sember
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, Liběchov, 277 21, Czech Republic.
- Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Viničná 5, 128 44, Prague 2, Czech Republic.
| | - Jörg Bohlen
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, Liběchov, 277 21, Czech Republic.
| | - Vendula Šlechtová
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, Liběchov, 277 21, Czech Republic.
| | - Marie Altmanová
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, Liběchov, 277 21, Czech Republic.
- Department of Ecology, Faculty of Science, Charles University in Prague, Viničná 7, 128 44, Prague 2, Czech Republic.
| | - Radka Symonová
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, Liběchov, 277 21, Czech Republic.
- Research Institute for Limnology, University of Innsbruck, Mondseestraße 9, A-5310, Mondsee, Austria.
| | - Petr Ráb
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, Liběchov, 277 21, Czech Republic.
| |
Collapse
|
7
|
Śliwińska-Jewsiewicka A, Kuciński M, Kirtiklis L, Dobosz S, Ocalewicz K, Jankun M. Chromosomal characteristics and distribution of rDNA sequences in the brook trout Salvelinus fontinalis (Mitchill, 1814). Genetica 2015; 143:425-32. [PMID: 25958180 PMCID: PMC4486110 DOI: 10.1007/s10709-015-9841-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 05/04/2015] [Indexed: 11/09/2022]
Abstract
Brook trout Salvelinus fontinalis (Mitchill, 1814) chromosomes have been analyzed using conventional and molecular cytogenetic techniques enabling characteristics and chromosomal location of heterochromatin, nucleolus organizer regions (NORs), ribosomal RNA-encoding genes and telomeric DNA sequences. The C-banding and chromosome digestion with the restriction endonucleases demonstrated distribution and heterogeneity of the heterochromatin in the brook trout genome. DNA sequences of the ribosomal RNA genes, namely the nucleolus-forming 28S (major) and non-nucleolus-forming 5S (minor) rDNAs, were physically mapped using fluorescence in situ hybridization (FISH) and primed in situ labelling. The minor rDNA locus was located on the subtelo-acrocentric chromosome pair No. 9, whereas the major rDNA loci were dispersed on 14 chromosome pairs, showing a considerable inter-individual variation in the number and location. The major and minor rDNA loci were located at different chromosomes. Multichromosomal location (3-6 sites) of the NORs was demonstrated by silver nitrate (AgNO3) impregnation. All Ag-positive i.e. active NORs corresponded to the GC-rich blocks of heterochromatin. FISH with telomeric probe showed the presence of the interstitial telomeric site (ITS) adjacent to the NOR/28S rDNA site on the chromosome 11. This ITS was presumably remnant of the chromosome rearrangement(s) leading to the genomic redistribution of the rDNA sequences. Comparative analysis of the cytogenetic data among several related salmonid species confirmed huge variation in the number and the chromosomal location of rRNA gene clusters in the Salvelinus genome.
Collapse
Affiliation(s)
- A. Śliwińska-Jewsiewicka
- />Department of Human Histology and Embryology, Faculty of Medical Sciences, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - M. Kuciński
- />Department of Ichthyology, Faculty of Environmental Sciences, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - L. Kirtiklis
- />Department of Zoology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - S. Dobosz
- />Department of Salmonid Research, Inland Fisheries Institute in Olsztyn, Olsztyn, Poland
| | - K. Ocalewicz
- />Department of Marine Biology and Ecology, Faculty of Oceanography and Geography, University of Gdansk, Gdańsk, Poland
| | - Malgorzata Jankun
- />Department of Ichthyology, Faculty of Environmental Sciences, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| |
Collapse
|
8
|
Merita K, Kattukunnel JJ, Yadav SR, Bhat KV, Rao SR. Comparative analysis of heterochromatin distribution in wild and cultivated Abelmoschus species based on fluorescent staining methods. PROTOPLASMA 2015; 252:657-664. [PMID: 25300590 DOI: 10.1007/s00709-014-0712-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 09/27/2014] [Indexed: 06/04/2023]
Abstract
A comparative analysis of fluorochrome-binding pattern in nine taxa of Abelmoschus had shown that the type, amount and distribution pattern of heterochromatin were characteristic for each taxa. The fluorescent chromosome-binding sites obtained by chromomycin A3 (CMA) and 4',6-diamidino-2-phenylindole (DAPI) staining in all the nine species showed constitutive heterochromatin CMA(+), DAPI(+) and CMA(+)/DAPI(+). Large amount of heterozygosity was observed with regard to heterochromatin distribution pattern in all the taxa studied. The CMA(+)-binding sites are comparatively less than DAPI(+)-binding sites which is clearly evident as AT-rich regions are more than GC-rich regions in all the nine taxa analysed in Abelmoschus. These CMA(+) and DAPI(+)-binding sites apparently rise with the increased in chromosome numbers of the different species. This pattern of heterochromatin heterogeneity seems to be a general characteristic feature. Therefore, the differential pattern of distribution of GC- and AT-rich sequences might have played an important role in diversification of the genus Abelmoschus. Polyploidy is an important factor in the evolution of Abelmoschus and the sole reason for range in chromosome numbers in this genus. It may be noted that, though often, but not always, the increase of DNA is caused by an increase in the amount of heterochromatin, i.e. increase of non-coding sections indicating restructuring of the heterochromatin. Thus, cumulative small and direct numerical changes might have played a role in the speciation of Abelmoschus.
Collapse
Affiliation(s)
- Keisham Merita
- Plant Biotechnology Laboratory, Department of Biotechnology and Bioinformatics, North-Eastern Hill University, Permanent Campus, Mawkynroh, Umnsing, Shillong, 793 022, Meghalaya, India
| | | | | | | | | |
Collapse
|
9
|
Hodaňová L, Kalous L, Musilová Z. Comparative cytogenetics of Neotropical cichlid fishes (Nannacara, Ivanacara and Cleithracara) indicates evolutionary reduction of diploid chromosome numbers. COMPARATIVE CYTOGENETICS 2014; 8:169-83. [PMID: 25349669 PMCID: PMC4205487 DOI: 10.3897/compcytogen.v8i3.7279] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 07/29/2014] [Indexed: 06/01/2023]
Abstract
A comparative cytogenetic analysis was carried out in five species of a monophyletic clade of neotropical Cichlasomatine cichlids, namely Cleithracara maronii Steindachner, 1881, Ivanacara adoketa (Kullander & Prada-Pedreros, 1993), Nannacara anomala Regan, 1905, N. aureocephalus Allgayer, 1983 and N. taenia Regan, 1912. Karyotypes and other chromosomal characteristics were revealed by CDD banding and mapped onto the phylogenetic hypothesis based on molecular analyses of four genes, namely cyt b, 16S rRNA, S7 and RAG1. The diploid numbers of chromosomes ranged from 44 to 50, karyotypes were composed predominantly of monoarmed chromosomes and one to three pairs of CMA3 signal were observed. The results showed evolutionary reduction in this monophyletic clade and the cytogenetic mechanisms (fissions/fusions) were hypothesized and discussed.
Collapse
Affiliation(s)
- Lucie Hodaňová
- Department of Zoology and Fisheries, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Lukáš Kalous
- Department of Zoology and Fisheries, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Zuzana Musilová
- Department of Zoology and Fisheries, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czech Republic
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics AV CR, Libechov, Czech Republic
- Zoological Institute, University of Basel, Switzerland
| |
Collapse
|
10
|
Gornung E. Twenty years of physical mapping of major ribosomal RNA genes across the teleosts: A review of research. Cytogenet Genome Res 2013; 141:90-102. [PMID: 24080951 DOI: 10.1159/000354832] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Molecular cytogenetic data on the number and position of 45S ribosomal RNA genes (rDNA; located in nucleolus organizing regions, NORs) detected by FISH in 330 species of 77 families and 22 orders of bony fishes (Teleostei) and, additionally, 11 species of basal ray-finned fishes are compiled and analyzed. The portion of species with single rDNA sites in the sample amounts to 72%. The percentage of species with multiple NORs decreases with increasing numbers of rDNA loci per genome, i.e. scarcely 3% of species carry 4 or more rDNA-bearing chromosome pairs. 43% of all rDNA sites analyzed occur terminally on the short arms of chromosomes or constitute them. In general, terminal rDNA sites account for 87% of all examined cases. Interspecific variation in the location of single rDNA sites among related taxa, polymorphisms of multiple NORs in some groups of teleosts and analytical outcomes on the subject are reviewed.
Collapse
Affiliation(s)
- E Gornung
- 'Charles Darwin' Department of Biology and Biotechnologies, University of Rome 'La Sapienza', Rome, Italy
| |
Collapse
|
11
|
Symonová R, Flajšhans M, Sember A, Havelka M, Gela D, Kořínková T, Rodina M, Rábová M, Ráb P. Molecular cytogenetics in artificial hybrid and highly polyploid sturgeons: An evolutionary story narrated by repetitive sequences. Cytogenet Genome Res 2013; 141:153-62. [PMID: 24051427 DOI: 10.1159/000354882] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We applied comparative genomic hybridization (CGH) and genomic in situ hybridization (GISH) to examine genomes of artificially produced sturgeon hybrids between sterlet, Acipenser ruthenus female (∼120 chromosomes) or Russian sturgeon, A. gueldenstaedtii female (∼240 chromosomes) and a spontaneous triploid Siberian sturgeon A. baerii male (∼360 chromosomes), respectively. The ploidy levels of progenies were analyzed by karyotyping and flow cytometry. We found that the species-specific regions were surprisingly identifiable only on some micro- and small(er) macrochromosomes in hybrid metaphases. We hypothesize that these distinguishable regions are represented by species-specific repetitive sequences driven by more dynamic molecular evolutionary mechanisms. On larger chromosomes, GISH faintly visualized only blocks of pericentromeric and telomeric repetitive sequences, remaining regions were equally shared by both parental species. We concluded that the interspecies hybridization producing viable and even fertile progeny is enabled by the fact that genomes of the species involved are likely divergent at the level of the repetitive sequences only and probably highly conserved in the coding sequences. These small differences of coding sequences are in concordance with previous estimations of relatedness of examined species producing artificial as well as natural hybrids. CGH and GISH represent a challenge in sturgeon cytogenetics as a valuable though technically not simple tool to discriminate chromosomes of parental species in hybrids. The potentials and drawbacks of CGH and GISH application in sturgeons are discussed and further experimental possibilities are proposed.
Collapse
Affiliation(s)
- R Symonová
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic, Liběchov, Czech Republic
| | | | | | | | | | | | | | | | | |
Collapse
|
12
|
Rubert M, da Rosa R, Jerep FC, Bertollo LAC, Giuliano-Caetano L. Cytogenetic characterization of four species of the genus Hypostomus Lacépède, 1803 (Siluriformes, Loricariidae) with comments on its chromosomal diversity. COMPARATIVE CYTOGENETICS 2011; 5:397-410. [PMID: 24260644 PMCID: PMC3833761 DOI: 10.3897/compcytogen.v5i5.1589] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2011] [Accepted: 08/08/2011] [Indexed: 06/01/2023]
Abstract
Cytogenetic analyses were performed on fishes of the genus Hypostomus (Hypostomus ancistroides (Ihering, 1911), Hypostomus strigaticeps (Regan, 1908), Hypostomus regani (Ihering, 1905), and Hypostomus paulinus (Ihering, 1905)) from the seven tributaries of the Paranapanema River Basin (Brazil) by means of different staining techniques (C-, Ag-, CMA3- and DAPI-banding) and fluorescence in situ hybridization (FISH) to detect 18S rDNA sites. All species showed different diploid numbers: 2n=68 (10m+26sm+32st-a) in Hypostomus ancistroides, 2n=72 (10m+16sm+46st-a) in Hypostomus strigaticeps, 2n=72 (10m+18sm+44st-a) in Hypostomus regani and 2n=76 (6m+16sm+54st-a) in Hypostomus paulinus. Ag-staining and FISH revealed various numbers and locations of NORs in the group. NORs were usually located terminally on the subtelocentric/acrocentric chromosomes: on the long arm in Hypostomus strigaticeps (2 to 4) and Hypostomus paulinus (2); and on the short arm in Hypostomus ancistroides (2 to 8) and Hypostomus regani (2 to 4). Conspicuous differences in heterochromatin distribution and composition were found among the species, terminally located in some st-a chromosomes in Hypostomus ancistroides, Hypostomus strigaticeps, and Hypostomus paulinus, and interstitially dispersed in most st-a chromosomes, in Hypostomus regani. The fluorochrome staining indicated that different classes of GC and/or AT-rich repetitive DNA evolved in this group. Our results indicate that chromosomal rearrangements and heterochromatin base-pair composition were significant events during the course of differentiation of this group. These features emerge as an excellent cytotaxonomic marker, providing a better understanding of the evolutionary mechanisms underlying the chromosomal diversity in Hypostomus species.
Collapse
Affiliation(s)
- Marceléia Rubert
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, Rodovia Washington Luís, km 235 - SP-310, P.O. Box 676, CEP 13565-905, São Carlos, São Paulo, Brazil
| | - Renata da Rosa
- Departamento de Biologia Geral, Universidade Estadual de Londrina, Rodovia Celso Garcia Cid, Pr 445 Km 380, Campus Universitário, P.O. Box 6001, CEP 86051-970, Londrina, Paraná, Brazil
| | - Fernando Camargo Jerep
- Museu de Ciências e Tecnologia, Pontifícia Universidade Católica, Av. Ipiranga, 6681, P.O. Box 1429, CEP 90619-900, Porto Alegre, Rio Grande do Sul, Brazil
| | - Luiz Antônio Carlos Bertollo
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, Rodovia Washington Luís, km 235 - SP-310, P.O. Box 676, CEP 13565-905, São Carlos, São Paulo, Brazil
| | - Lucia Giuliano-Caetano
- Departamento de Biologia Geral, Universidade Estadual de Londrina, Rodovia Celso Garcia Cid, Pr 445 Km 380, Campus Universitário, P.O. Box 6001, CEP 86051-970, Londrina, Paraná, Brazil
| |
Collapse
|
13
|
Genome evolution and meiotic maps by massively parallel DNA sequencing: spotted gar, an outgroup for the teleost genome duplication. Genetics 2011; 188:799-808. [PMID: 21828280 PMCID: PMC3176089 DOI: 10.1534/genetics.111.127324] [Citation(s) in RCA: 276] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Genomic resources for hundreds of species of evolutionary, agricultural, economic, and medical importance are unavailable due to the expense of well-assembled genome sequences and difficulties with multigenerational studies. Teleost fish provide many models for human disease but possess anciently duplicated genomes that sometimes obfuscate connectivity. Genomic information representing a fish lineage that diverged before the teleost genome duplication (TGD) would provide an outgroup for exploring the mechanisms of evolution after whole-genome duplication. We exploited massively parallel DNA sequencing to develop meiotic maps with thrift and speed by genotyping F(1) offspring of a single female and a single male spotted gar (Lepisosteus oculatus) collected directly from nature utilizing only polymorphisms existing in these two wild individuals. Using Stacks, software that automates the calling of genotypes from polymorphisms assayed by Illumina sequencing, we constructed a map containing 8406 markers. RNA-seq on two map-cross larvae provided a reference transcriptome that identified nearly 1000 mapped protein-coding markers and allowed genome-wide analysis of conserved synteny. Results showed that the gar lineage diverged from teleosts before the TGD and its genome is organized more similarly to that of humans than teleosts. Thus, spotted gar provides a critical link between medical models in teleost fish, to which gar is biologically similar, and humans, to which gar is genomically similar. Application of our F(1) dense mapping strategy to species with no prior genome information promises to facilitate comparative genomics and provide a scaffold for ordering the numerous contigs arising from next generation genome sequencing.
Collapse
|
14
|
Morescalchi MA, Stingo V, Capriglione T. Cytogenetic analysis in Polypterus ornatipinnis (Actinopterygii, Cladistia, Polypteridae) and 5S rDNA. Mar Genomics 2011; 4:25-31. [PMID: 21429462 DOI: 10.1016/j.margen.2010.12.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2010] [Revised: 12/05/2010] [Accepted: 12/09/2010] [Indexed: 11/17/2022]
Abstract
Polypteridae is a family of archaic freshwater African fish that constitute an interesting subject for the study of the karyological evolution in vertebrates, on account of their primitive morphological characters and peculiar relationships with lower Osteichthyans. In this paper, a cytogenetic analysis on twenty specimens of both sexes of Polypterus ornatipinnis the ornate "bichir", coming from the Congo River basin, was performed by using both classical and molecular techniques. The karyotypic formula (2n=36; FN=72) was composed of 26 M+10 SM. The Alu I banding, performed to characterize heterochromatin in this species, was mainly centromeric. Both the chromosome location of the ribosomal 5S and 18S rRNA genes were examined by using Ag-NOR, classical C-banding, CMA(3) staining and FISH. CMA(3) marked all centromerical regions and showed the presence of two GC rich regions on the p arm of the chromosome pair n°1 and on the q arm of the pair n°14. Staining with Ag-NOR marked the only telomeric region of the chromosome n°1 p arm. After PCR, the 5S rDNA in this species was cloned, sequenced and analyzed. In the 665bp 5S rDNA sequence of P.ornatipinnis, a conserved 120bp gene region for the 5S rDNA was identified, followed by a non-transcribed variable spacer (NTS) which included simple repeats, microsatellites and a fragment of a non-LTR retrotransposon R-TEX. FISH with 5S rDNA marked the subtelomeric region of the q arm of the chromosome pair n°14, previously marked by CMA(3). FISH with 18S rDNA marked the telomeric region of the p arm of the pair n°1, previously marked both by Ag-NOR and CMA(3). The (GATA)(7) repeats marked the telomeric regions of all chromosome pairs, with the exclusion of the n°1, n°3 and n°14; hybridization with telomeric probes (TTAGGG)(n) showed signals at the end of all chromosomes. Karyotype evolution in Polypterus genus was finally discussed, including the new data obtained.
Collapse
Affiliation(s)
- Maria Alessandra Morescalchi
- Dipartimento di Scienze della Vita, Seconda Università degli Studi di Napoli, via Vivaldi 43, 81100 Caserta, Italy.
| | | | | |
Collapse
|
15
|
Valić D, Kapetanović D, Zanella D, Mrakovčić M, Teskeredžić E, Besendorfer V, Rábová M, Ráb P. The karyotype and NOR phenotype ofTelestes ukliva(Cyprinidae). FOLIA ZOOLOGICA 2010. [DOI: 10.25225/fozo.v59.i2.a1.2010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Damir Valić
- Laboratory for Research and Development of Aquaculture, Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54, HR-10000 Zagreb, Croatia
| | - Damir Kapetanović
- Laboratory for Research and Development of Aquaculture, Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54, HR-10000 Zagreb, Croatia
| | - Davor Zanella
- Department of Zoology, Division of Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, HR-10000 Zagreb, Croatia
| | - Milorad Mrakovčić
- Department of Zoology, Division of Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, HR-10000 Zagreb, Croatia
| | - Emin Teskeredžić
- Laboratory for Research and Development of Aquaculture, Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54, HR-10000 Zagreb, Croatia
| | - Višnja Besendorfer
- Department of Molecular Biology, Division of Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, HR-10000 Zagreb, Croatia
| | - Marie Rábová
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic, 277 21 Liběchov, Czech Republic
| | - Petr Ráb
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic, 277 21 Liběchov, Czech Republic
| |
Collapse
|
16
|
de Araújo WC, Martínez PA, Molina WF. Mapping of Ribosomal DNA by FISH, EcoRI Digestion and Replication Bands in the Cardinalfish Apogon americanus (Perciformes). CYTOLOGIA 2010. [DOI: 10.1508/cytologia.75.109] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Washington Candeia de Araújo
- Departamento de Biologia Celular e Genética, Universidade Federal do Rio Grande do Norte, Laboratório de Genética de Recursos Marinhos, Campus Universitário
| | - Pablo Ariel Martínez
- Departamento de Biologia Celular e Genética, Universidade Federal do Rio Grande do Norte, Laboratório de Genética de Recursos Marinhos, Campus Universitário
| | - Wagner Franco Molina
- Departamento de Biologia Celular e Genética, Universidade Federal do Rio Grande do Norte, Laboratório de Genética de Recursos Marinhos, Campus Universitário
| |
Collapse
|
17
|
Morescalchi MA, Liguori I, Rocco L, Archimandritis A, Stingo V. Karyotypic characterization and genomic organization of the 5S rDNA in Polypterus senegalus (Osteichthyes, Polypteridae). Genetica 2007; 132:179-86. [PMID: 17587184 DOI: 10.1007/s10709-007-9160-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2006] [Accepted: 05/29/2007] [Indexed: 10/23/2022]
Abstract
Polypteridae (Cladistia) is a family of archaic fishes, confined to African freshwaters. On account of their primitiveness in anatomical and morphological characters and mosaic relationships among lower Osteichthyans fishes, they constitute an important subject for the study of evolution in vertebrates. Very little is known about the karyological structure of these species. In this article, a cytogenetic analysis on twenty specimens of Polypterus senegalus (Cuvier, 1829) was performed using both classical and molecular techniques. Karyotype (2n=36; FN=72), chromosome location of telomeric sequences (TTAGGG)(n), (GATA)(7) repeats and ribosomal 5S and 18S rRNA genes were examined by using Ag-NOR, classical C-banding, CMA(3) staining and FISH. Staining with Ag-NOR showed the presence of two GC rich NORs on the p arm of the chromosome pair no. 1. CMA(3) marked all centromerical and some (no. 1 and no. 14) telomeric regions. FISH with 5S rDNA marked the subtelomeric region of the q arm of the chromosome pair no. 14. FISH with 18S rDNA marked the telomeric region of the p arm of the chromosome pair no. 1, previously marked by Ag-NOR. (GATA)(7) repeats marked the subtelomeric regions of all chromosome pairs, with the exclusion of the no. 1, 3 and 14. Hybridization with telomeric probes (TTAGGG)(n) showed bright signals at the end of all chromosomes. After cloning, the 5SrDNA alignment revealed an organization of sequences made up of two different classes of tandem arrays (5S type I and 5S type II) of different lengths.
Collapse
Affiliation(s)
- Maria Alessandra Morescalchi
- Dipartimento di Scienze della Vita, Seconda Università degli Studi di Napoli, Via Vivaldi 43, 81100 Caserta, Italy.
| | | | | | | | | |
Collapse
|
18
|
Volker M, Sonnenberg R, Ráb P, Kullmann H. Karyotype differentiation in Chromaphyosemion killifishes (Cyprinodontiformes, Nothobranchiidae). III: extensive karyotypic variability associated with low mitochondrial haplotype differentiation in C. bivittatum. Cytogenet Genome Res 2007; 116:116-26. [PMID: 17268189 DOI: 10.1159/000097429] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2006] [Accepted: 05/22/2006] [Indexed: 11/19/2022] Open
Abstract
We investigated chromosomal evolution in the African killifish species Chromaphyosemion bivittatum using a combination of cytogenetic and phylogenetic methods. Specimens from five populations were examined by conventional Giemsa staining as well as sequential chromosome banding with 4',6-diamidino-2-phenylindole (DAPI), chromomycin A(3) (CMA(3)), AgNO(3)-staining and C-banding. The cytogenetic analysis revealed variability in 2n ranging from 2n = 29 to 2n = 36 and in NF ranging from NF = 38 to NF = 44. Two populations showed an extensive chromosomal polymorphism (2n = 29-34, NF = 44 and 2n = 32-34, NF = 38-42, respectively). Karyotypic variability within and among populations was mainly due to Robertsonian translocations and heterochromatin additions, and chromosome banding patterns suggested that both types of chromosomal rearrangements were related to the presence of AT-rich heterochromatin. A phylogenetic analysis of the partial mitochondrial (mt) cytochrome b gene, using specimens from eleven populations, revealed a low degree of haplotype differentiation, which suggested a relatively recent divergence of the populations examined. This finding conformed to the low degree of morphological differentiation observed among C. bivittatum populations and might indicate fast chromosomal evolution. The high karyotypic variability may be caused by an elevated chromosomal mutation rate as well as certain aspects of the mating system and population dynamics of C. bivittatum facilitating the fixation of new chromosomal variants.
Collapse
Affiliation(s)
- M Volker
- Institut fur Evolutionsbiologie und Okologie, Rheinische Friedrich-Wilhelms-Universitat Bonn, Germany.
| | | | | | | |
Collapse
|
19
|
Nirchio M, Oliveira C, Ferreira IA, Granado A, Ron E. Extensive polymorphism and chromosomal characteristics of ribosomal DNA in the characid fish Triportheus venezuelensis (Characiformes, Characidae). Genet Mol Biol 2007. [DOI: 10.1590/s1415-47572007000100007] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
|
20
|
Morescalchi MA, Liguori I, Rocco L, Stingo V. Karyotypic characterization and genomic organization of the 5S rDNA in Erpetoichthys calabaricus (Osteichthyes, Polypteridae). Genetica 2006; 131:209-16. [PMID: 17136578 DOI: 10.1007/s10709-006-9119-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2006] [Accepted: 10/20/2006] [Indexed: 10/23/2022]
Abstract
Polypterids are a group of Osteichthyan fish whose evolutionary relationships with closer basal ray-finned and lobe-finned fish have been disputed since their discovery. Very little is known about the evolutive karyology in the whole Polypteriformes group. In order to fill this gap, a cytogenetic analysis of Erpetoichthys calabaricus species was performed, using both classical and molecular techniques. Karyotype structure (2n = 36; FN = 72), chromosome location of telomeric sequences (TTAGGG)n and ribosomal 5S and 18S rRNA genes were examined in twenty specimens of E. calabaricus by using Ag-NOR, classical C-banding, sequential CMA3/4',6-diaminidino-2-phenylindole (DAPI) staining and fluorescent in situ hybridization (FISH). CMA3 marked all centromerical and some (no. 1 and no. 15) telomeric regions. Staining with Ag-NOR and CMA3 showed the presence of two NORs on the p arm of the chromosome pair no. 1. Hybridization with telomeric probes (TTAGGG)n showed signals at the end of all chromosomes. 5S rDNA was cloned and sequenced. After the alignment, the 5S rRNA sequences revealed an organization made up of two different classes of tandem arrays (type I and type II). FISH with 5S rDNA marked the telomeric regions of the small chromosome pair no. 15, while FISH with 18S rDNA marked the telomeric region of the pair no. 1. The results obtained were compared with cariological data on closer species now available in literature.
Collapse
Affiliation(s)
- Maria Alessandra Morescalchi
- Dipartimento di Scienze della Vita, Seconda Università degli Studi di Napoli, Via Vivaldi 43, 81100, Caserta, Italy.
| | | | | | | |
Collapse
|
21
|
Völker M, Sonnenberg R, Ráb P, Kullmann H. Karyotype differentiation in Chromaphyosemion killifishes (Cyprinodontiformes, Nothobranchiidae). II: cytogenetic and mitochondrial DNA analyses demonstrate karyotype differentiation and its evolutionary direction in C. riggenbachi. Cytogenet Genome Res 2006; 115:70-83. [PMID: 16974086 DOI: 10.1159/000094803] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2005] [Accepted: 02/21/2006] [Indexed: 11/19/2022] Open
Abstract
African killifishes of the genus Chromaphyosemion show a high degree of phenotypic and karyotypic diversity. The latter is especially pronounced in C. riggenbachi, a morphologically defined species restricted to a small distribution area in Cameroon. This study presents a detailed reconstruction of karyotype differentiation within C. riggenbachi using conventional Giemsa staining and sequential chromosome banding as well as a phylogenetic analysis based on part of the mitochondrial (mt) cytochrome b gene from eleven populations. The cytogenetic analysis revealed differences in chromosome morphology, banding patterns and/or diploid chromosome number (2n) among all populations examined. Diploid number ranged from 2n = 20 to 2n = 36 and varied mainly among populations, while C-banding patterns and NOR phenotypes showed fixed differences among populations as well as some variability within populations. The mtDNA analysis disclosed five clearly differentiated haplotype groups. Mapping the karyotype data onto the mtDNA dendrogram revealed a decrease in 2n from the most basal to the most derived groups, thus demonstrating a reduction of 2n during their evolutionary history. Our results indicate that karyotype differentiation involved Robertsonian fusions as well as non-Robertsonian processes. Causes of the high karyotypic variability may include an elevated chromosomal mutation rate as well as certain features of the ecology and mating system that could facilitate the fixation of chromosomal rearrangements. The pattern of karyotype and haplotype differentiation and the results of previous crossing experiments suggest incipient speciation in C. riggenbachi.
Collapse
Affiliation(s)
- M Völker
- Institut für Evolutionsbiologie und Okologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Germany.
| | | | | | | |
Collapse
|
22
|
Völker M, Ráb P, Kullmann H. Karyotype Differentiation in Chromaphyosemion Killifishes (Cyprinodontiformes, Nothobranchiidae). I: Chromosome Banding Patterns of C. Alpha, C. Kouamense and C. Lugens. Genetica 2005; 125:33-41. [PMID: 16175453 DOI: 10.1007/s10709-005-4267-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2004] [Accepted: 03/18/2005] [Indexed: 10/25/2022]
Abstract
The karyotypes of three recently described species of Chromaphyosemion, namely C. lugens, C. alpha and C. kouamense, were analysed using conventional Giemsa staining, C-banding and sequential banding (fluorescence banding with 4', 6-diamidino-2-phenylindole (DAPI) and Chromomycin A(3) (CMA(3)), C-banding, AgNO(3)-staining). Diploid chromosome numbers ranged from 2n = 36 in C. lugens to 2n = 38 in C. alpha and C. kouamense. The karyotype of C. lugens consisted of one pair of metacentric (m) and 17 pairs of telocentric (t) chromosomes, that of C. alpha was composed of one pair of submetacentric (sm), six pairs of subtelocentric (st) and 12 pairs of t chromosomes, and that of C. kouamense comprised five pairs of st and 14 pairs of t chromosomes. In addition to the differences in karyotype structures and/or chromosome numbers, the karyotypes of the examined species differed with respect to NOR phenotype and distribution and base composition of heterochromatin. No heteromorphic sex chromosomes were detected in any of the species. Our findings provide cytotaxonomic evidence for the species distinctness of C. alpha, C. kouamense and C. lugens whose descriptions were based primarily on external morphology.
Collapse
Affiliation(s)
- Martin Völker
- Institut für Evolutionsbiologie und Okologie, Rheinishce Friedrich-Wilhelms-Universität Bonn, An der Immenburg 1, 53121 Bonn, Germany.
| | | | | |
Collapse
|
23
|
Ráb P, Crossman EJ, Reed KM, Rábová M. Chromosomal characteristics of ribosomal DNA in two extant species of North American mudminnows Umbra pygmaea and U. limi (Euteleostei: Umbridae). Cytogenet Genome Res 2003; 98:194-8. [PMID: 12698003 DOI: 10.1159/000069800] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2003] [Accepted: 01/07/2003] [Indexed: 11/19/2022] Open
Abstract
The locations and chromosomal characteristics of ribosomal DNA (rDNA) sites in the karyotypes of two extant North American species of mudminnows, Umbra pygmaea and U. limi (2n = 22, NF = 44), were analyzed sequentially by conventional Giemsa staining, Ag staining, CMA(3) fluorescence and fluorescence in situ hybridization (FISH). The nucleolar organizer regions (NORs) were located in the fourth chromosomal pair in both species (pericentromeric region in U. pygmaea and subtelomeric in U. LIMI). These sites were strongly CMA(3)-positive suggesting that the rDNA sites in these species are associated with GC-rich DNA. FISH with a rDNA probe gave consistently positive signals in the same regions detected by Ag-staining and CMA(3)-fluorescence. However, both species also had additional CMA(3)-positive/Ag-negative heterochromatic blocks at pericentrometric regions of several chromosomal pairs (three in U. pygmaea and five in U. limi). FISH revealed additional rDNA clusters in both species. It is hypothesized that a paracentric inversion of the chromosome arm carrying the NORs might be one of the rearrangements differentiating the karyotypes of two North American species. The presence of additional rDNA sites is indicative of more complex rearrangements. The pericentromeric NOR phenotype of Umbra pygmaea is similar to that seen in U. krameri and in the distantly related genus Esox.
Collapse
Affiliation(s)
- P Ráb
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Libechov, Czech Republic.
| | | | | | | |
Collapse
|
24
|
Rábová M, Ráb P, Ozouf-Costaz C. Extensive polymorphism and chromosomal characteristics of ribosomal DNA in a loach fish, Cobitis vardarensis (Ostariophysi, Cobitidae) detected by different banding techniques and fluorescence in situ hybridization (FISH). Genetica 2002; 111:413-22. [PMID: 11841184 DOI: 10.1023/a:1013763903513] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
When surveying the karyotype diversity of European loaches of the genus Cobitis to identify species involved in hybrid polyploid complexes, an extensive polymorphism in number and location of NORs was discovered in C. vardarensis using Ag-staining, C-banding, CMA3-fluorescence and fluorescence in situ hybridization (FISH). This species had 2n = 50, the karyotype contained 13 pairs of metacentric, 10 pairs of submetacentric and two pairs of subtelocentric chromosomes. The NOR-bearing chromosomes included one medium-sized metacentric pair with a large CMA3-positive heterochromatic pericentromeric block, one small metacentric as well as one large submetacentric pairs. Ribosomal sites were always located in telomeres of these chromosomes. Each of the pair of NOR-bearing chromosomes occurred in three variants - (1) presence and/or (2) absence of NORs on both homologues and (3) heterozygous combination where only one of the homologues bears NORs. Altogether, 10 different NOR cytotypes from 27 theoretically possible ones were discovered among 20 indviduals examined. The number of NORs ranged from two to five per specimen. The results regarding the number and locations of NORs as revealed by banding techniques were confirmed using FISH with rDNA probe. NOR sites were of CMA3-positive, suggesting that ribosomal sites are associated with GC-rich DNA. Very similar structural polymorphism with multiple NORs is expressed in the Danubian loach C. elongatoides indicating a close relationship between both species.
Collapse
Affiliation(s)
- M Rábová
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Libechov, Czech Republic
| | | | | |
Collapse
|