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Lichilín N, Salzburger W, Böhne A. No evidence for sex chromosomes in natural populations of the cichlid fish Astatotilapia burtoni. G3 (BETHESDA, MD.) 2023; 13:6989787. [PMID: 36649174 PMCID: PMC9997565 DOI: 10.1093/g3journal/jkad011] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 09/14/2022] [Accepted: 12/16/2022] [Indexed: 01/18/2023]
Abstract
Sex determination (SD) is not conserved among teleost fishes and can even differ between populations of the same species. Across the outstandingly species-rich fish family Cichlidae, more and more SD systems are being discovered. Still, the picture of SD evolution in this group is far from being complete. Lake Tanganyika and its affluent rivers are home to Astatotilapia burtoni, which belongs to the extremely successful East African cichlid lineage Haplochromini. Previously, in different families of an A. burtoni laboratory strain, an XYW system and an XY system have been described. The latter was also found in a second laboratory strain. In a laboratory-reared family descending from a population of the species' southern distribution, a second XY system was discovered. Yet, an analysis of sex chromosomes for the whole species distribution is missing. Here, we examined the genomes of 11 natural populations of A. burtoni, encompassing a wide range of its distribution, for sex-linked regions. We did not detect signs of differentiated sex chromosomes and also not the previously described sex chromosomal systems present in laboratory lines, suggesting different SD systems in the same species under natural and (long-term) artificial conditions. We suggest that SD in A. burtoni is more labile than previously assumed and consists of a combination of non-genetic, polygenic, or poorly differentiated sex chromosomes.
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Affiliation(s)
- Nicolás Lichilín
- Zoological Institute, Department of Environmental Sciences, University of Basel, Vesalgasse 1, 4051 Basel, Switzerland.,Department of Neuroscience and Developmental Biology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Walter Salzburger
- Zoological Institute, Department of Environmental Sciences, University of Basel, Vesalgasse 1, 4051 Basel, Switzerland
| | - Astrid Böhne
- Zoological Institute, Department of Environmental Sciences, University of Basel, Vesalgasse 1, 4051 Basel, Switzerland.,Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig Bonn, Adenauerallee 127, 53113 Bonn, Germany
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2
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Martins C, Jehangir M. A genomic glimpse of B chromosomes in cichlids. Genes Genomics 2021; 43:199-208. [PMID: 33547625 DOI: 10.1007/s13258-021-01049-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 01/11/2021] [Indexed: 01/25/2023]
Abstract
BACKGROUND B chromosomes (Bs) are extra karyotype elements in addition to A chromosomes and are found in all major eukaryotic taxa. Among hundreds of investigated species, cichlid fishes have emerged as an interesting group of model and have contributed to unravel the complex biology of B chromosome. OBJECTIVE We review the current state of knowledge on B chromosome investigation in cichlid fish and discuss the recent genomic advances over gene and sequences hunting on Bs and their impact on the current concept of B chromosomes. RESULTS The Bs of cichlids have been under the subject of classical cytogenetics and high scale DNA, RNA and epigenetics analysis and a list of B chromosome genes and functional sequences has been generated. B chromosomes of cichlids are restricted to females in some species and are enriched with genes, relics of genes, transposable elements and sequences transcribing for many significant biological functions. Diverse potentially functional sequences have been described in the B chromosome of cichlids and could influence important biological characteristics as well seems to affect transcription and epigenetic modifications of the whole genome. CONCLUSION One of the most enigmatic characteristics of Bs in cichlids is their genic content related to cell cycle and chromosome structure, and their influence over sex rates. The relationship of Bs with cell cycle and sex determination looks like to be connected with the drive of the Bs during cell divisions.
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Affiliation(s)
- Cesar Martins
- Department of Structural and Functional Biology, Institute of Biosciences at Botucatu, São Paulo State University (UNESP), Botucatu, SP, 18618-689, Brazil.
| | - Maryam Jehangir
- Department of Structural and Functional Biology, Institute of Biosciences at Botucatu, São Paulo State University (UNESP), Botucatu, SP, 18618-689, Brazil
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3
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Merlo MA, Portela-Bens S, Rodríguez ME, García-Angulo A, Cross I, Arias-Pérez A, García E, Rebordinos L. A Comprehensive Integrated Genetic Map of the Complete Karyotype of Solea senegalensis (Kaup 1858). Genes (Basel) 2020; 12:genes12010049. [PMID: 33396249 PMCID: PMC7824234 DOI: 10.3390/genes12010049] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/24/2020] [Accepted: 12/28/2020] [Indexed: 12/23/2022] Open
Abstract
Solea senegalensis aquaculture production has experienced a great increase in the last decade and, consequently, the genome knowledge of the species is gaining attention. In this sense, obtaining a high-density genome mapping of the species could offer clues to the aquaculture improvement in those aspects not resolved so far. In the present article, a review and new processed data have allowed to obtain a high-density BAC-based cytogenetic map of S. senegalensis beside the analysis of the sequences of such BAC clones to achieve integrative data. A total of 93 BAC clones were used to localize the chromosome complement of the species and 588 genes were annotated, thus almost reaching the 2.5% of the S. senegalensis genome sequences. As a result, important data about its genome organization and evolution were obtained, such as the lesser gene density of the large metacentric pair compared with the other metacentric chromosomes, which supports the theory of a sex proto-chromosome pair. In addition, chromosomes with a high number of linked genes that are conserved, even in distant species, were detected. This kind of result widens the knowledge of this species’ chromosome dynamics and evolution.
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4
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Gaffaroglu M, Majtánová Z, Symonová R, Pelikánová Š, Unal S, Lajbner Z, Ráb P. Present and Future Salmonid Cytogenetics. Genes (Basel) 2020; 11:E1462. [PMID: 33291343 PMCID: PMC7762217 DOI: 10.3390/genes11121462] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 11/30/2020] [Accepted: 12/02/2020] [Indexed: 01/04/2023] Open
Abstract
Salmonids are extremely important economically and scientifically; therefore, dynamic developments in their research have occurred and will continue occurring in the future. At the same time, their complex phylogeny and taxonomy are challenging for traditional approaches in research. Here, we first provide discoveries regarding the hitherto completely unknown cytogenetic characteristics of the Anatolian endemic flathead trout, Salmo platycephalus, and summarize the presently known, albeit highly complicated, situation in the genus Salmo. Secondly, by outlining future directions of salmonid cytogenomics, we have produced a prototypical virtual karyotype of Salmo trutta, the closest relative of S. platycephalus. This production is now possible thanks to the high-quality genome assembled to the chromosome level in S. trutta via soft-masking, including a direct labelling of repetitive sequences along the chromosome sequence. Repetitive sequences were crucial for traditional fish cytogenetics and hence should also be utilized in fish cytogenomics. As such virtual karyotypes become increasingly available in the very near future, it is necessary to integrate both present and future approaches to maximize their respective benefits. Finally, we show how the presumably repetitive sequences in salmonids can change the understanding of the overall relationship between genome size and G+C content, creating another outstanding question in salmonid cytogenomics waiting to be resolved.
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Affiliation(s)
- Muhammet Gaffaroglu
- Department of Molecular Biology and Genetics, Faculty of Science, University of Ahi Evran, Kirsehir 40200, Turkey;
| | - Zuzana Majtánová
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, 27721 Liběchov, Czech Republic; (Z.M.); (Š.P.); (P.R.)
| | - Radka Symonová
- Department of Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, 85354 Freising, Germany
| | - Šárka Pelikánová
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, 27721 Liběchov, Czech Republic; (Z.M.); (Š.P.); (P.R.)
| | - Sevgi Unal
- Department of Molecular Biology and Genetics, Faculty of Science, Bartin University, Bartin 74000, Turkey;
| | - Zdeněk Lajbner
- Physics and Biology Unit, Okinawa Institute of Science and Technology, Graduate University, Onna, Okinawa 904 0495, Japan;
| | - Petr Ráb
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, 27721 Liběchov, Czech Republic; (Z.M.); (Š.P.); (P.R.)
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5
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Tao W, Xu L, Zhao L, Zhu Z, Wu X, Min Q, Wang D, Zhou Q. High-quality chromosome-level genomes of two tilapia species reveal their evolution of repeat sequences and sex chromosomes. Mol Ecol Resour 2020; 21:543-560. [PMID: 33035394 DOI: 10.1111/1755-0998.13273] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 09/14/2020] [Accepted: 09/23/2020] [Indexed: 01/05/2023]
Abstract
Tilapias are one of the most farmed fishes that are coined as "aquatic chicken" by the food industry. Nile tilapia and blue tilapia exhibit very recent transition of sex chromosome systems since their divergence approximately five million years ago, making them a great model for elucidating the molecular and evolutionary mechanisms of sex chromosome turnovers. Studies of their sex-determining pathways are also critical for developing genetic sex control in aquaculture. We report here the newly produced genomes of Nile tilapia and blue tilapia that integrate long-read sequencing and chromatin conformation data. The two nearly complete genomes have anchored over 97% of the sequences into linkage groups (LGs), and assembled majorities of complex repetitive regions including telomeres, centromeres and rDNA clusters. In particular, we inferred two episodes of repeat expansion at LG3 respectively in the ancestor of cichlids and that of tilapias. The consequential large heterochromatic region concentrated at one end of LG3 comprises tandem arrays of mRNA and small RNA genes, among which we have identified a candidate female determining gene Paics in blue tilapia. Paics shows female-specific patterns of single-nucleotide variants, copy numbers and expression patterns in gonads during early gonadogenesis. Our work provides a very important genomic resource for functional studies of cichlids, and suggested that unequal distribution of repeat content that impacts the local recombination rate might make some chromosomes more likely to become sex chromosomes.
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Affiliation(s)
- Wenjing Tao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, China
| | - Luohao Xu
- MOE Laboratory of Biosystems Homeostasis & Protection, Life Sciences Institute, Zhejiang University, Hangzhou, China.,Department of Neuroscience and Developmental Biology, University of Vienna, Vienna, Austria
| | - Lin Zhao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, China
| | - Zexian Zhu
- MOE Laboratory of Biosystems Homeostasis & Protection, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Xin Wu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, China
| | - Qianwen Min
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, China
| | - Deshou Wang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, China
| | - Qi Zhou
- MOE Laboratory of Biosystems Homeostasis & Protection, Life Sciences Institute, Zhejiang University, Hangzhou, China.,Department of Neuroscience and Developmental Biology, University of Vienna, Vienna, Austria.,Center for Reproductive Medicine, The 2nd Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
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6
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Majtánová Z, Indermaur A, Nyom ARB, Ráb P, Musilova Z. Adaptive Radiation from a Chromosomal Perspective: Evidence of Chromosome Set Stability in Cichlid Fishes (Cichlidae: Teleostei) from the Barombi Mbo Lake, Cameroon. Int J Mol Sci 2019; 20:ijms20204994. [PMID: 31601021 PMCID: PMC6834198 DOI: 10.3390/ijms20204994] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 10/04/2019] [Accepted: 10/07/2019] [Indexed: 12/11/2022] Open
Abstract
Cichlid fishes are the subject of scientific interest because of their rapid adaptive radiation, resulting in extensive ecological and taxonomic diversity. In this study, we examined 11 morphologically distinct cichlid species endemic to Barombi Mbo, the largest crater lake in western Cameroon, namely Konia eisentrauti, Konia dikume, Myaka myaka, Pungu maclareni, Sarotherodon steinbachi, Sarotherodon lohbergeri, Sarotherodon linnellii, Sarotherodon caroli, Stomatepia mariae, Stomatepia pindu, and Stomatepia mongo. These species supposedly evolved via sympatric ecological speciation from a common ancestor, which colonized the lake no earlier than one million years ago. Here we present the first comparative cytogenetic analysis of cichlid species from Barombi Mbo Lake using both conventional (Giemsa staining, C-banding, and CMA3/DAPI staining) and molecular (fluorescence in situ hybridization with telomeric, 5S, and 28S rDNA probes) methods. We observed stability on both macro and micro-chromosomal levels. The diploid chromosome number was 2n = 44, and the karyotype was invariably composed of three pairs of meta/submetacentric and 19 pairs of subtelo/acrocentric chromosomes in all analysed species, with the same numbers of rDNA clusters and distribution of heterochromatin. The results suggest the evolutionary stability of chromosomal set; therefore, the large-scale chromosomal rearrangements seem to be unlikely associated with the sympatric speciation in Barombi Mbo.
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Affiliation(s)
- Zuzana Majtánová
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, 27721 Liběchov, Czech Republic.
| | - Adrian Indermaur
- Zoological Institute, University of Basel, 4051 Basel, Switzerland.
| | - Arnold Roger Bitja Nyom
- Department of Biological Sciences, University of Ngaoundéré, Ngaoundéré P.O Box 454, Cameroon.
- Department of Management of Fisheries and Aquatic Ecosystems, University of Douala, Douala P.O Box 2701, Cameroon.
| | - Petr Ráb
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, 27721 Liběchov, Czech Republic.
| | - Zuzana Musilova
- Department of Zoology, Faculty of Science, Charles University in Prague, 12844 Prague, Czech Republic.
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7
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Conte MA, Joshi R, Moore EC, Nandamuri SP, Gammerdinger WJ, Roberts RB, Carleton KL, Lien S, Kocher TD. Chromosome-scale assemblies reveal the structural evolution of African cichlid genomes. Gigascience 2019; 8:giz030. [PMID: 30942871 PMCID: PMC6447674 DOI: 10.1093/gigascience/giz030] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 01/11/2019] [Accepted: 03/07/2019] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND African cichlid fishes are well known for their rapid radiations and are a model system for studying evolutionary processes. Here we compare multiple, high-quality, chromosome-scale genome assemblies to elucidate the genetic mechanisms underlying cichlid diversification and study how genome structure evolves in rapidly radiating lineages. RESULTS We re-anchored our recent assembly of the Nile tilapia (Oreochromis niloticus) genome using a new high-density genetic map. We also developed a new de novo genome assembly of the Lake Malawi cichlid, Metriaclima zebra, using high-coverage Pacific Biosciences sequencing, and anchored contigs to linkage groups (LGs) using 4 different genetic maps. These new anchored assemblies allow the first chromosome-scale comparisons of African cichlid genomes. Large intra-chromosomal structural differences (∼2-28 megabase pairs) among species are common, while inter-chromosomal differences are rare (<10 megabase pairs total). Placement of the centromeres within the chromosome-scale assemblies identifies large structural differences that explain many of the karyotype differences among species. Structural differences are also associated with unique patterns of recombination on sex chromosomes. Structural differences on LG9, LG11, and LG20 are associated with reduced recombination, indicative of inversions between the rock- and sand-dwelling clades of Lake Malawi cichlids. M. zebra has a larger number of recent transposable element insertions compared with O. niloticus, suggesting that several transposable element families have a higher rate of insertion in the haplochromine cichlid lineage. CONCLUSION This study identifies novel structural variation among East African cichlid genomes and provides a new set of genomic resources to support research on the mechanisms driving cichlid adaptation and speciation.
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Affiliation(s)
- Matthew A Conte
- Department of Biology, University of Maryland, College Park, MD 20742, USA
| | - Rajesh Joshi
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, PO Box 5003, Ås, Norway
| | - Emily C Moore
- Department of Biological Sciences and W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC 27695, USA
| | | | | | - Reade B Roberts
- Department of Biological Sciences and W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC 27695, USA
| | - Karen L Carleton
- Department of Biology, University of Maryland, College Park, MD 20742, USA
| | - Sigbjørn Lien
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, PO Box 5003, Ås, Norway
| | - Thomas D Kocher
- Department of Biology, University of Maryland, College Park, MD 20742, USA
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8
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Barby FF, Bertollo LAC, de Oliveira EA, Yano CF, Hatanaka T, Ráb P, Sember A, Ezaz T, Artoni RF, Liehr T, Al-Rikabi ABH, Trifonov V, de Oliveira EHC, Molina WF, Jegede OI, Tanomtong A, de Bello Cioffi M. Emerging patterns of genome organization in Notopteridae species (Teleostei, Osteoglossiformes) as revealed by Zoo-FISH and Comparative Genomic Hybridization (CGH). Sci Rep 2019; 9:1112. [PMID: 30718776 PMCID: PMC6361938 DOI: 10.1038/s41598-019-38617-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 01/03/2019] [Indexed: 11/09/2022] Open
Abstract
Notopteridae (Teleostei, Osteoglossiformes) represents an old fish lineage with ten currently recognized species distributed in African and Southeastern Asian rivers. Their karyotype structures and diploid numbers remained conserved over long evolutionary periods, since African and Asian lineages diverged approximately 120 Mya. However, a significant genetic diversity was already identified for these species using molecular data. Thus, why the evolutionary relationships within Notopteridae are so diverse at the genomic level but so conserved in terms of their karyotypes? In an attempt to develop a more comprehensive picture of the karyotype and genome evolution in Notopteridae, we performed comparative genomic hybridization (CGH) and cross-species (Zoo-FISH) whole chromosome painting experiments to explore chromosome-scale intergenomic divergence among seven notopterid species, collected in different African and Southeast Asian river basins. CGH demonstrated an advanced stage of sequence divergence among the species and Zoo-FISH experiments showed diffuse and limited homology on inter-generic level, showing a temporal reduction of evolutionarily conserved syntenic regions. The sharing of a conserved chromosomal region revealed by Zoo-FISH in these species provides perspectives that several other homologous syntenic regions have remained conserved among their genomes despite long temporal isolation. In summary, Notopteridae is an interesting model for tracking the chromosome evolution as it is (i) ancestral vertebrate group with Gondwanan distribution and (ii) an example of animal group exhibiting karyotype stasis. The present study brings new insights into degree of genome divergence vs. conservation at chromosomal and sub-chromosomal level in representative sampling of this group.
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Affiliation(s)
- Felipe Faix Barby
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos, SP, 13565-905, Brazil
| | - Luiz Antônio Carlos Bertollo
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos, SP, 13565-905, Brazil
| | - Ezequiel Aguiar de Oliveira
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos, SP, 13565-905, Brazil
| | - Cassia Fernanda Yano
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos, SP, 13565-905, Brazil
| | - Terumi Hatanaka
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos, SP, 13565-905, Brazil
| | - Petr Ráb
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, Liběchov, 277 21, Czech Republic
| | - Alexandr Sember
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, Liběchov, 277 21, Czech Republic
| | - Tariq Ezaz
- Institute for Applied Ecology, University of Canberra, Canberra, ACT 2617, Australia
| | - Roberto Ferreira Artoni
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa, PR, 84030-900, Brazil
| | - Thomas Liehr
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa, PR, 84030-900, Brazil
| | | | - Vladimir Trifonov
- Molecular and Cellular Biology, Russian Academy of Sciences, Novosibirsk, Russia
| | - Edivaldo H C de Oliveira
- Laboratório de Cultura de Tecidos e Citogenética, SAMAM, Instituto Evandro Chagas, Belém, Brazil
| | - Wagner Franco Molina
- Department of Cellular Biology and Genetics, Biosciences Center, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Oladele Ilesanmi Jegede
- Department of Fisheries and Aquaculture, Adamawa State University, P.M.B. 25, Mubi, Adamawa State, Nigeria
| | - Alongklod Tanomtong
- Toxic Substances in Livestock and Aquatic Animals Research Group, KhonKaen University, Muang, KhonKaen, 40002, Thailand
| | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos, SP, 13565-905, Brazil.
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9
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Cross I, Portela-Bens S, García-Angulo A, Merlo MA, Rodríguez ME, Liehr T, Rebordinos L. A preliminary integrated genetic map distinguishes every chromosome pair and locates essential genes related to abiotic adaptation of Crassostrea angulata/gigas. BMC Genet 2018; 19:104. [PMID: 30442092 PMCID: PMC6238303 DOI: 10.1186/s12863-018-0689-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 10/30/2018] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND The re-sequencing of C. angulata has revealed many polymorphisms in candidate genes related to adaptation to abiotic stress that are not present in C. gigas; these genes, therefore, are probably related to the ability of this oyster to retain high concentrations of toxic heavy metals. There is, in addition, an unresolved controversy as to whether or not C. angulata and C. gigas are the same species or subspecies. Both oysters have 20 metacentric chromosomes of similar size that are morphologically indistinguishable. From a genomic perspective, as a result of the great variation and selection for heterozygotes in C. gigas, the assembly of its draft genome was difficult: it is fragmented in more than seven thousand scaffolds. RESULTS In this work sixty BAC sequences of C. gigas downloaded from NCBI were assembled in BAC-contigs and assigned to BACs that were used as probes for mFISH in C. angulata and C. gigas. In addition, probes of H3, H4 histone, 18S and 5S rDNA genes were also used. Hence we obtained markers identifying 8 out the 10 chromosomes constituting the karyotype. Chromosomes 1 and 9 can be distinguished morphologically. The bioinformatic analysis carried out with the BAC-contigs annotated 88 genes. As a result, genes associated with abiotic adaptation, such as metallothioneins, have been positioned in the genome. The gene ontology analysis has also shown many molecular functions related to metal ion binding, a phenomenon associated with detoxification processes that are characteristic in oysters. Hence the provisional integrated map obtained in this study is a useful complementary tool for the study of oyster genomes. CONCLUSIONS In this study 8 out of 10 chromosome pairs of Crassostrea angulata/gigas were identified using BAC clones as probes. As a result all chromosomes can now be distinguished. Moreover, FISH showed that H3 and H4 co-localized in two pairs of chromosomes different that those previously escribed. 88 genes were annotated in the BAC-contigs most of them related with Molecular Functions of protein binding, related to the resistance of the species to abiotic stress. An integrated genetic map anchored to the genome has been obtained in which the BAC-contigs structure were not concordant with the gene structure of the C. gigas scaffolds displayed in the Genomicus database.
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Affiliation(s)
- Ismael Cross
- Area de Genética. Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz. Polígono Río San Pedro, 11510 Puerto Real, Cádiz, Spain
| | - Silvia Portela-Bens
- Area de Genética. Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz. Polígono Río San Pedro, 11510 Puerto Real, Cádiz, Spain
| | - Aglaya García-Angulo
- Area de Genética. Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz. Polígono Río San Pedro, 11510 Puerto Real, Cádiz, Spain
| | - Manuel A. Merlo
- Area de Genética. Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz. Polígono Río San Pedro, 11510 Puerto Real, Cádiz, Spain
| | - María E. Rodríguez
- Area de Genética. Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz. Polígono Río San Pedro, 11510 Puerto Real, Cádiz, Spain
| | - Thomas Liehr
- Institut für Humangenetik, Universitätsklinikum Jena, 07743 Jena, Germany
| | - Laureana Rebordinos
- Area de Genética. Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz. Polígono Río San Pedro, 11510 Puerto Real, Cádiz, Spain
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10
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Kasper C, Colombo M, Aubin-Horth N, Taborsky B. Brain activation patterns following a cooperation opportunity in a highly social cichlid fish. Physiol Behav 2018; 195:37-47. [DOI: 10.1016/j.physbeh.2018.07.025] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Revised: 07/21/2018] [Accepted: 07/25/2018] [Indexed: 11/24/2022]
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11
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Kasper C, Hebert FO, Aubin-Horth N, Taborsky B. Divergent brain gene expression profiles between alternative behavioural helper types in a cooperative breeder. Mol Ecol 2018; 27:4136-4151. [DOI: 10.1111/mec.14837] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Revised: 07/21/2018] [Accepted: 08/07/2018] [Indexed: 01/17/2023]
Affiliation(s)
- Claudia Kasper
- Behavioural Ecology; University of Bern; Hinterkappelen Switzerland
| | - Francois Olivier Hebert
- Département de Biologie et Institut de Biologie Intégrative et des Systèmes; Université Laval; Québec Québec Canada
| | - Nadia Aubin-Horth
- Département de Biologie et Institut de Biologie Intégrative et des Systèmes; Université Laval; Québec Québec Canada
| | - Barbara Taborsky
- Behavioural Ecology; University of Bern; Hinterkappelen Switzerland
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12
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Pinhal D, Bovolenta LA, Moxon S, Oliveira AC, Nachtigall PG, Acencio ML, Patton JG, Hilsdorf AWS, Lemke N, Martins C. Genome-wide microRNA screening in Nile tilapia reveals pervasive isomiRs' transcription, sex-biased arm switching and increasing complexity of expression throughout development. Sci Rep 2018; 8:8248. [PMID: 29844338 PMCID: PMC5974277 DOI: 10.1038/s41598-018-26607-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 05/15/2018] [Indexed: 12/11/2022] Open
Abstract
MicroRNAs (miRNAs) are key regulators of gene expression in multicellular organisms. The elucidation of miRNA function and evolution depends on the identification and characterization of miRNA repertoire of strategic organisms, as the fast-evolving cichlid fishes. Using RNA-seq and comparative genomics we carried out an in-depth report of miRNAs in Nile tilapia (Oreochromis niloticus), an emergent model organism to investigate evo-devo mechanisms. Five hundred known miRNAs and almost one hundred putative novel vertebrate miRNAs have been identified, many of which seem to be teleost-specific, cichlid-specific or tilapia-specific. Abundant miRNA isoforms (isomiRs) were identified with modifications in both 5p and 3p miRNA transcripts. Changes in arm usage (arm switching) of nine miRNAs were detected in early development, adult stage and even between male and female samples. We found an increasing complexity of miRNA expression during ontogenetic development, revealing a remarkable synchronism between the rate of new miRNAs recruitment and morphological changes. Overall, our results enlarge vertebrate miRNA collection and reveal a notable differential ratio of miRNA arms and isoforms influenced by sex and developmental life stage, providing a better picture of the evolutionary and spatiotemporal dynamics of miRNAs.
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Affiliation(s)
- Danillo Pinhal
- Department of Genetics, Institute of Biosciences of Botucatu, Sao Paulo State University (UNESP), Botucatu, SP, Brazil.
| | - Luiz A Bovolenta
- Department of Physics and Biophysics, Institute of Biosciences of Botucatu, Sao Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Simon Moxon
- School of Biological Sciences, University of East Anglia (UEA), Norwich Research Park, Norwich, United Kingdom
| | - Arthur C Oliveira
- Department of Genetics, Institute of Biosciences of Botucatu, Sao Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Pedro G Nachtigall
- Department of Genetics, Institute of Biosciences of Botucatu, Sao Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Marcio L Acencio
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - James G Patton
- Stevenson Center, Vanderbilt University, Nashville, TN, USA
| | | | - Ney Lemke
- Department of Physics and Biophysics, Institute of Biosciences of Botucatu, Sao Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Cesar Martins
- Department of Morphology, Institute of Biosciences of Botucatu, Sao Paulo State University (UNESP), Botucatu, SP, Brazil
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13
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Taboada X, Rey M, Bouza C, Viñas A. Cytogenomic analysis of several repetitive DNA elements in turbot (Scophthalmus maximus). Gene 2018; 644:4-12. [PMID: 29246535 DOI: 10.1016/j.gene.2017.12.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 11/23/2017] [Accepted: 12/11/2017] [Indexed: 11/29/2022]
Abstract
Repetitive DNA plays a fundamental role in the organization, size and evolution of eukaryotic genomes. The sequencing of the turbot revealed a small and compact genome, as in all flatfish studied to date. The assembly of repetitive regions is still incomplete because it is difficult to correctly identify their position, number and array. The combination of classical cytogenetic techniques along with high quality sequencing is essential to increase the knowledge of the structure and composition of these sequences and, thus, of the structure and function of the whole genome. In this work, the in silico analysis of H1 histone, 5S rDNA, telomeric and Rex repetitive sequences, was compared to their chromosomal mapping by fluorescent in situ hybridization (FISH), providing a more comprehensive picture of these elements in the turbot genome. FISH assays confirmed the location of H1 in LG8; 5S rDNA in LG4 and LG6; telomeric sequences at the end of all chromosomes whereas Rex elements were dispersed along most chromosomes. The discrepancies found between both approaches could be related to the sequencing methodology applied in this species and also to the resolution limitations of the FISH technique. Turbot cytogenomic analyses have proven to add new chromosomal landmarks in the karyotype of this species, representing a powerful tool to investigate targeted genomic sequences or regions in the genetic and physical maps of this species.
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Affiliation(s)
- Xoana Taboada
- Departamento de Zoología, Genética y Antropología Física, Facultad de Biología, CIBUS, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Magalí Rey
- Departamento de Zoología, Genética y Antropología Física, Facultad de Biología, CIBUS, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Carmen Bouza
- Departamento de Zoología, Genética y Antropología Física, Facultad de Veterinaria, Universidade de Santiago de Compostela, 27002 Lugo, Spain
| | - Ana Viñas
- Departamento de Zoología, Genética y Antropología Física, Facultad de Biología, CIBUS, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain.
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14
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Symonová R, Howell WM. Vertebrate Genome Evolution in the Light of Fish Cytogenomics and rDNAomics. Genes (Basel) 2018; 9:genes9020096. [PMID: 29443947 PMCID: PMC5852592 DOI: 10.3390/genes9020096] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 01/25/2018] [Accepted: 01/29/2018] [Indexed: 12/19/2022] Open
Abstract
To understand the cytogenomic evolution of vertebrates, we must first unravel the complex genomes of fishes, which were the first vertebrates to evolve and were ancestors to all other vertebrates. We must not forget the immense time span during which the fish genomes had to evolve. Fish cytogenomics is endowed with unique features which offer irreplaceable insights into the evolution of the vertebrate genome. Due to the general DNA base compositional homogeneity of fish genomes, fish cytogenomics is largely based on mapping DNA repeats that still represent serious obstacles in genome sequencing and assembling, even in model species. Localization of repeats on chromosomes of hundreds of fish species and populations originating from diversified environments have revealed the biological importance of this genomic fraction. Ribosomal genes (rDNA) belong to the most informative repeats and in fish, they are subject to a more relaxed regulation than in higher vertebrates. This can result in formation of a literal 'rDNAome' consisting of more than 20,000 copies with their high proportion employed in extra-coding functions. Because rDNA has high rates of transcription and recombination, it contributes to genome diversification and can form reproductive barrier. Our overall knowledge of fish cytogenomics grows rapidly by a continuously increasing number of fish genomes sequenced and by use of novel sequencing methods improving genome assembly. The recently revealed exceptional compositional heterogeneity in an ancient fish lineage (gars) sheds new light on the compositional genome evolution in vertebrates generally. We highlight the power of synergy of cytogenetics and genomics in fish cytogenomics, its potential to understand the complexity of genome evolution in vertebrates, which is also linked to clinical applications and the chromosomal backgrounds of speciation. We also summarize the current knowledge on fish cytogenomics and outline its main future avenues.
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Affiliation(s)
- Radka Symonová
- Faculty of Science, Department of Biology, University of Hradec Králové, 500 03 Hradec Králové, Czech Republic.
| | - W Mike Howell
- Department of Biological and Environmental Sciences, Samford University, Birmingham, AL 35229, USA.
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15
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Egger B, Roesti M, Böhne A, Roth O, Salzburger W. Demography and genome divergence of lake and stream populations of an East African cichlid fish. Mol Ecol 2017; 26:5016-5030. [DOI: 10.1111/mec.14248] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 06/22/2017] [Indexed: 12/17/2022]
Affiliation(s)
- Bernd Egger
- Zoological Institute; University of Basel; Basel Switzerland
| | - Marius Roesti
- Zoological Institute; University of Basel; Basel Switzerland
- Department of Zoology; Biodiversity Research Centre; University of British Columbia; Vancouver BC Canada
| | - Astrid Böhne
- Zoological Institute; University of Basel; Basel Switzerland
| | - Olivia Roth
- Evolutionary Ecology of Marine Fishes; Helmholtz Zentrum für Ozeanforschung Kiel (GEOMAR); Kiel Germany
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16
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Böhne A, Wilson CA, Postlethwait JH, Salzburger W. Variations on a theme: Genomics of sex determination in the cichlid fish Astatotilapia burtoni. BMC Genomics 2016; 17:883. [PMID: 27821061 PMCID: PMC5100337 DOI: 10.1186/s12864-016-3178-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 10/18/2016] [Indexed: 12/17/2022] Open
Abstract
Background Sex chromosomes change more frequently in fish than in mammals or birds. However, certain chromosomes or genes are repeatedly used as sex determinants in different members of the teleostean lineage. East African cichlids are an enigmatic model system in evolutionary biology representing some of the most diverse extant vertebrate adaptive radiations. How sex is determined and if different sex-determining mechanisms contribute to speciation is unknown for almost all of the over 1,500 cichlid species of the Great Lakes. Here, we investigated the genetic basis of sex determination in a cichlid from Lake Tanganyika, Astatotilapia burtoni, a member of the most species-rich cichlid lineage, the haplochromines. Results We used RAD-sequencing of crosses for two populations of A. burtoni, a lab strain and fish caught at the south of Lake Tanganyika. Using association mapping and comparative genomics, we confirmed male heterogamety in A. burtoni and identified different sex chromosomes (LG5 and LG18) in the two populations of the same species. LG5, the sex chromosome of the lab strain, is a fusion chromosome in A. burtoni. Wnt4 is located on this chromosome, representing the best candidate identified so far for the master sex-determining gene in our lab strain of A. burtoni. Conclusions Cichlids exemplify the high turnover rate of sex chromosomes in fish with two different chromosomes, LG5 and LG18, containing major sex-determining loci in the two populations of A. burtoni examined here. However, they also illustrate that particular chromosomes are more likely to be used as sex chromosomes. Chromosome 5 is such a chromosome, which has evolved several times as a sex chromosome, both in haplochromine cichlids from all Great Lakes and also in other teleost fishes. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3178-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Astrid Böhne
- Zoological Institute, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland.
| | | | | | - Walter Salzburger
- Zoological Institute, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland
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17
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Gante HF, Matschiner M, Malmstrøm M, Jakobsen KS, Jentoft S, Salzburger W. Genomics of speciation and introgression in Princess cichlid fishes from Lake Tanganyika. Mol Ecol 2016; 25:6143-6161. [DOI: 10.1111/mec.13767] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 05/30/2016] [Accepted: 07/11/2016] [Indexed: 01/02/2023]
Affiliation(s)
- Hugo F. Gante
- Zoological Institute University of Basel Vesalgasse 1 4051 Basel Switzerland
| | - Michael Matschiner
- Department of Biosciences CEES (Centre for Ecological and Evolutionary Synthesis) University of Oslo 0316 Oslo Norway
| | - Martin Malmstrøm
- Department of Biosciences CEES (Centre for Ecological and Evolutionary Synthesis) University of Oslo 0316 Oslo Norway
| | - Kjetill S. Jakobsen
- Department of Biosciences CEES (Centre for Ecological and Evolutionary Synthesis) University of Oslo 0316 Oslo Norway
| | - Sissel Jentoft
- Department of Biosciences CEES (Centre for Ecological and Evolutionary Synthesis) University of Oslo 0316 Oslo Norway
- Department of Natural Sciences University of Agder 4604 Kristiansand Norway
| | - Walter Salzburger
- Zoological Institute University of Basel Vesalgasse 1 4051 Basel Switzerland
- Department of Biosciences CEES (Centre for Ecological and Evolutionary Synthesis) University of Oslo 0316 Oslo Norway
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18
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Böhne A, Sengstag T, Salzburger W. Comparative transcriptomics in East African cichlids reveals sex- and species-specific expression and new candidates for sex differentiation in fishes. Genome Biol Evol 2015; 6:2567-85. [PMID: 25364805 PMCID: PMC4202336 DOI: 10.1093/gbe/evu200] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Males and females of the same species differ largely in gene expression, which accounts for most of the morphological and physiological differences and sex-specific phenotypes. Here, we analyzed sex-specific gene expression in the brain and the gonads of cichlid fishes from Lake Tanganyika belonging to four different lineages, so-called tribes (Eretmodini, Ectodini, Haplochromini, and Lamprologini), using the outgroup Nile tilapia (Oreochromis niloticus) as reference. The comparison between male and female brains revealed few differences between the sexes, consistent in all investigated species. The gonads, on the other hand, showed a large fraction of differentially expressed transcripts with the majority of them showing the same direction of expression in all four species. All here-studied cichlids, especially the three investigated mouth-breeding species, showed a trend toward more male- than female biased transcripts. Transcripts, which were female-biased in expression in all four species, were overrepresented on linkage group (LG)1 in the reference genome and common male-biased transcripts showed accumulation on LG23, the presumable sex chromosomes of the Nile tilapia. Sex-specific transcripts contained candidate genes for sex determination and differentiation in fishes,especially members of the transforming growth factor-b-superfamily and the Wnt-pathway and also prominent members of the sox-, dm-domain-, and high mobility group-box families. We further confirmed our previous finding on species/lineage-specific gene expression shifts in the sex steroid pathway, including synthesizing enzymes as the aromatase cyp19a1 and estrogen and androgen receptors.
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Affiliation(s)
- Astrid Böhne
- Zoological Institute, University of Basel, Switzerland
- *Corresponding author: E-mail:
| | - Thierry Sengstag
- SIB Swiss Institute of Bioinformatics and sciCORE Computing Center, University of Basel, Switzerland
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19
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Nirchio M, Rossi AR, Foresti F, Oliveira C. Chromosome evolution in fishes: a new challenging proposal from Neotropical species. NEOTROPICAL ICHTHYOLOGY 2014. [DOI: 10.1590/1982-0224-20130008] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
We present a database containing cytogenetic data of Neotropical actinopterygian fishes from Venezuela obtained in a single laboratory for the first time. The results of this study include 103 species belonging to 74 genera assigned to 45 families and 17 out of the 40 teleost orders. In the group of marine fishes, the modal diploid number was 2n=48 represented in 60% of the studied species, while in the freshwater fish group the modal diploid complement was 2n=54, represented in 21.21 % of the studied species. The average number of chromosomes and the mean FN were statistically higher in freshwater fish than in marine fish. The degree of diversification and karyotype variation was also higher in freshwater fish in contrast to a more conserved cytogenetic pattern in marine fish. In contrast to the assumption according to which 48 acrocentric chromosomes was basal chromosome number in fish, data here presented show that there is an obvious trend towards the reduction of the diploid number of chromosomes from values near 2n=60 with high number of biarmed chromosomes in more basal species to 2n=48 acrocentric elements in more derived Actinopterygii.
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Affiliation(s)
| | | | - Fausto Foresti
- Universidade Estadual Paulista Júlio de Mesquita Filho, Brazil
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20
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Henning F, Lee HJ, Franchini P, Meyer A. Genetic mapping of horizontal stripes in Lake Victoria cichlid fishes: benefits and pitfalls of using RAD markers for dense linkage mapping. Mol Ecol 2014; 23:5224-40. [PMID: 25039588 DOI: 10.1111/mec.12860] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 07/02/2014] [Accepted: 07/12/2014] [Indexed: 01/25/2023]
Abstract
The genetic dissection of naturally occurring phenotypes sheds light on many fundamental and longstanding questions in speciation and adaptation and is a central research topic in evolutionary biology. Until recently, forward-genetic approaches were virtually impossible to apply to nonmodel organisms, but the development of next-generation sequencing techniques eases this difficulty. Here, we use the ddRAD-seq method to map a colour trait with a known adaptive function in cichlid fishes, well-known textbook examples for rapid rates of speciation and astonishing phenotypic diversification. A suite of phenotypic key innovations is related to speciation and adaptation in cichlids, among which body coloration features prominently. The focal trait of this study, horizontal stripes, evolved in parallel in several cichlid radiations and is associated with piscivorous foraging behaviour. We conducted interspecific crosses between Haplochromis sauvagei and H. nyererei and constructed a linkage map with 867 SNP markers distributed on 22 linkage groups and total size of 1130.63 cM. Lateral stripes are inherited as a Mendelian trait and map to a single genomic interval that harbours a paralog of a gene with known function in stripe patterning. Dorsolateral and mid-lateral stripes were always coinherited and are thus under the same genetic control. Additionally, we directly quantify the genotyping error rates in RAD markers and offer guidelines for identifying and dealing with errors. Uncritical marker selection was found to severely impact linkage map construction. Fortunately, by applying appropriate quality control steps, a genotyping accuracy of >99.9% can be reached, thus allowing for efficient linkage mapping of evolutionarily relevant traits.
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Affiliation(s)
- Frederico Henning
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstraße 10, Konstanz, 78457, Germany
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21
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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.
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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
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22
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Yan B, Wang ZH, Zhu CD, Guo JT, Zhao JL. MicroRNA repertoire for functional genome research in tilapia identified by deep sequencing. Mol Biol Rep 2014; 41:4953-63. [PMID: 24752404 DOI: 10.1007/s11033-014-3361-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Accepted: 03/31/2014] [Indexed: 12/17/2022]
Abstract
The Nile tilapia (Oreochromis niloticus; Cichlidae) is an economically important species in aquaculture and occupies a prominent position in the aquaculture industry. MicroRNAs (miRNAs) are a class of noncoding RNAs that post-transcriptionally regulate gene expression involved in diverse biological and metabolic processes. To increase the repertoire of miRNAs characterized in tilapia, we used the Illumina/Solexa sequencing technology to sequence a small RNA library using pooled RNA sample isolated from the different developmental stages of tilapia. Bioinformatic analyses suggest that 197 conserved and 27 novel miRNAs are expressed in tilapia. Sequence alignments indicate that all tested miRNAs and miRNAs* are highly conserved across many species. In addition, we characterized the tissue expression patterns of five miRNAs using real-time quantitative PCR. We found that miR-1/206, miR-7/9, and miR-122 is abundantly expressed in muscle, brain, and liver, respectively, implying a potential role in the regulation of tissue differentiation or the maintenance of tissue identity. Overall, our results expand the number of tilapia miRNAs, and the discovery of miRNAs in tilapia genome contributes to a better understanding the role of miRNAs in regulating diverse biological processes.
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Affiliation(s)
- Biao Yan
- Key Laboratory of Freshwater Fisheries Germplasm Resource, Ministry of Agriculture, SHOU, Shanghai, 201306, China,
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23
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Consolidation of the genetic and cytogenetic maps of turbot (Scophthalmus maximus) using FISH with BAC clones. Chromosoma 2014; 123:281-91. [PMID: 24473579 DOI: 10.1007/s00412-014-0452-2] [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: 01/09/2014] [Accepted: 01/10/2014] [Indexed: 10/25/2022]
Abstract
Bacterial artificial chromosomes (BAC) have been widely used for fluorescence in situ hybridization (FISH) mapping of chromosome landmarks in different organisms, including a few in teleosts. In this study, we used BAC-FISH to consolidate the previous genetic and cytogenetic maps of the turbot (Scophthalmus maximus), a commercially important pleuronectiform. The maps consisted of 24 linkage groups (LGs) but only 22 chromosomes. All turbot LGs were assigned to specific chromosomes using BAC probes obtained from a turbot 5× genomic BAC library. It consisted of 46,080 clones with inserts of at least 100 kb and <5 % empty vectors. These BAC probes contained gene-derived or anonymous markers, most of them linked to quantitative trait loci (QTL) related to productive traits. BAC clones were mapped by FISH to unique marker-specific chromosomal positions, which showed a notable concordance with previous genetic mapping data. The two metacentric pairs were cytogenetically assigned to LG2 and LG16, and the nucleolar organizer region (NOR)-bearing pair was assigned to LG15. Double-color FISH assays enabled the consolidation of the turbot genetic map into 22 linkage groups by merging LG8 with LG18 and LG21 with LG24. In this work, a first-generation probe panel of BAC clones anchored to the turbot linkage and cytogenetical map was developed. It is a useful tool for chromosome traceability in turbot, but also relevant in the context of pleuronectiform karyotypes, which often show small hardly identifiable chromosomes. This panel will also be valuable for further integrative genomics of turbot within Pleuronectiformes and teleosts, especially for fine QTL mapping for aquaculture traits, comparative genomics, and whole-genome assembly.
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24
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Kuroiwa A, Terai Y, Kobayashi N, Yoshida K, Suzuki M, Nakanishi A, Matsuda Y, Watanabe M, Okada N. Construction of chromosome markers from the Lake Victoria cichlid Paralabidochromis chilotes and their application to comparative mapping. Cytogenet Genome Res 2013; 142:112-20. [PMID: 24217467 DOI: 10.1159/000356128] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/11/2013] [Indexed: 11/19/2022] Open
Abstract
Cichlid fishes in the African Great Lakes are known as a spectacular example of adaptive radiation in vertebrates. Four linkage maps have been constructed to identify the genes responsible for adaptation and speciation, and the genetic linkages of those genes are assumed to play an important role during adaptive evolution. However, it is difficult to analyze such linkages because the linkage groups of one species do not match well with those of the other species. Chromosome markers are a powerful tool for the direct identification of linkage homology between different species. We used information about the linkage map of the Lake Malawi cichlid (Labeotropheus fuelleborni/Metriaclima zebra) to isolate bacterial artificial chromosome (BAC) clones from the BAC library of Paralabidochromis chilotes, Lake Victoria. We identified 18 of 22 P. chilotes chromosomes by single- and multi-color BAC fluorescence in situ hybridization using 19 BAC clones. Comparative mapping with the chromosome markers of P. chilotes in Astatotilapia burtoni (2n = 40) from Lake Tanganyika revealed the chromosome rearrangements that have occurred in this lineage. These chromosome markers will be useful for delineating the process of genome and chromosome evolution in African species.
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Affiliation(s)
- A Kuroiwa
- Laboratory of Animal Cytogenetics, Faculty of Science, Hokkaido University, Sapporo, Japan
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25
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García-Cegarra A, Merlo MA, Ponce M, Portela-Bens S, Cross I, Manchado M, Rebordinos L. A preliminary genetic map in Solea senegalensis (Pleuronectiformes, Soleidae) using BAC-FISH and next-generation sequencing. Cytogenet Genome Res 2013; 141:227-40. [PMID: 24107490 DOI: 10.1159/000355001] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
This article presents the first physical mapping carried out in the Senegalese sole (Solea senegalensis), an important marine fish species of Southern Europe. Eight probes were designated to pick up genes of interest in aquaculture (candidate genes) from a bacterial artificial chromosome (BAC) library using a method of rapid screening based on a 4-dimension PCR. Seven known and 3 unknown clones were isolated and labeled. The 10 BAC clones were used as probes to map the karyotype of the species by fluorescence in situ hybridization (FISH). Nine out of the 10 clones were localized in only 1 chromosome pair, whereas the remaining one hybridized on 2 chromosome pairs. The 2-color FISH experiments showed colocation of 4 probes in 2 chromosome pairs. In addition, 2-color FISH was carried out both with 5S rDNA and the BAC containing the lysozyme gene published previously. This first genetic map of the Senegalese sole represents a starting point for future studies of the sole genome. In addition, 7 out of the 10 BAC clones were sequenced using next-generation sequencing, and bioinformatic characterization of the sequences was carried out. Hence the anchoring of the sequences to specific chromosomes or chromosome arms is now possible, leading to an initial scaffold of the Senegalese sole genome.
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Affiliation(s)
- A García-Cegarra
- Laboratorio de Genética, Facultad de Ciencias del Mar y Ambientales - CACYTMAR, Puerto Real, Spain
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