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Zhao K, Bai Y, Zhang Q, Zhao Z, Cao Y, Yang L, Wang N, Xu J, Wang B, Wu L, Gong X, Lin T, Wang Y, Wang W, Cai X, Yin Y, Xiong Z. Karyotyping of aneuploid and polyploid plants from low coverage whole-genome resequencing. BMC PLANT BIOLOGY 2023; 23:630. [PMID: 38062348 PMCID: PMC10704825 DOI: 10.1186/s12870-023-04650-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 11/30/2023] [Indexed: 12/18/2023]
Abstract
BACKGROUND Karyotype, as a basic characteristic of species, provides valuable information for fundamental theoretical research and germplasm resource innovation. However, traditional karyotyping techniques, including fluorescence in situ hybridization (FISH), are challenging and low in efficiency, especially when karyotyping aneuploid and polyploid plants. The use of low coverage whole-genome resequencing (lcWGR) data for karyotyping was explored, but existing methods are complicated and require control samples. RESULTS In this study, a new protocol for molecular karyotype analysis was provided, which proved to be a simpler, faster, and more accurate method, requiring no control. Notably, our method not only provided the copy number of each chromosome of an individual but also an accurate evaluation of the genomic contribution from its parents. Moreover, we verified the method through FISH and published resequencing data. CONCLUSIONS This method is of great significance for species evolution analysis, chromosome engineering, crop improvement, and breeding.
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Affiliation(s)
- Kanglu Zhao
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Yanbo Bai
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Qingyu Zhang
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Zhen Zhao
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Yao Cao
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Lu Yang
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Ni Wang
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Junxiong Xu
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Bo Wang
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Lei Wu
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Xiufeng Gong
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Tuanrong Lin
- Institute of Ulanqab Agricultural and Forestry Sciences, Inner Mongolia, Ulanqab, 012000, China
| | - Yufeng Wang
- Institute of Ulanqab Agricultural and Forestry Sciences, Inner Mongolia, Ulanqab, 012000, China
| | - Wei Wang
- Institute of Ulanqab Agricultural and Forestry Sciences, Inner Mongolia, Ulanqab, 012000, China
| | - Xingkui Cai
- Key Laboratory of Horticultural Plant Biology, Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, College of Horticulture and Forestry Sciences, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuhe Yin
- Institute of Ulanqab Agricultural and Forestry Sciences, Inner Mongolia, Ulanqab, 012000, China
| | - Zhiyong Xiong
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China.
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2
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Lucek K, Giménez MD, Joron M, Rafajlović M, Searle JB, Walden N, Westram AM, Faria R. The Impact of Chromosomal Rearrangements in Speciation: From Micro- to Macroevolution. Cold Spring Harb Perspect Biol 2023; 15:a041447. [PMID: 37604585 PMCID: PMC10626258 DOI: 10.1101/cshperspect.a041447] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2023]
Abstract
Chromosomal rearrangements (CRs) have been known since almost the beginning of genetics. While an important role for CRs in speciation has been suggested, evidence primarily stems from theoretical and empirical studies focusing on the microevolutionary level (i.e., on taxon pairs where speciation is often incomplete). Although the role of CRs in eukaryotic speciation at a macroevolutionary level has been supported by associations between species diversity and rates of evolution of CRs across phylogenies, these findings are limited to a restricted range of CRs and taxa. Now that more broadly applicable and precise CR detection approaches have become available, we address the challenges in filling some of the conceptual and empirical gaps between micro- and macroevolutionary studies on the role of CRs in speciation. We synthesize what is known about the macroevolutionary impact of CRs and suggest new research avenues to overcome the pitfalls of previous studies to gain a more comprehensive understanding of the evolutionary significance of CRs in speciation across the tree of life.
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Affiliation(s)
- Kay Lucek
- Biodiversity Genomics Laboratory, Institute of Biology, University of Neuchâtel, 2000 Neuchâtel, Switzerland
| | - Mabel D Giménez
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Genética Humana de Misiones (IGeHM), Parque de la Salud de la Provincia de Misiones "Dr. Ramón Madariaga," N3300KAZ Posadas, Misiones, Argentina
- Facultad de Ciencias Exactas Químicas y Naturales, Universidad Nacional de Misiones, N3300LQH Posadas, Misiones, Argentina
| | - Mathieu Joron
- Centre d'Ecologie Fonctionnelle et Evolutive, Université de Montpellier, CNRS, EPHE, IRD, 34293 Montpellier, France
| | - Marina Rafajlović
- Department of Marine Sciences, University of Gothenburg, 405 30 Gothenburg, Sweden
- Centre for Marine Evolutionary Biology, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Jeremy B Searle
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York 14853, USA
| | - Nora Walden
- Centre for Organismal Studies, University of Heidelberg, 69117 Heidelberg, Germany
| | - Anja Marie Westram
- Institute of Science and Technology Austria (ISTA), 3400 Klosterneuburg, Austria
- Faculty of Biosciences and Aquaculture, Nord University, 8026 Bodø, Norway
| | - Rui Faria
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado;
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
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3
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Jacobina UP, Pontes AI, Costa L, Souza G. Macroevolutionary consequences of karyotypic changes in the neotropical Serrasalmidae fishes (Ostariophysi, Characiformes) diversification. Genetica 2023; 151:311-321. [PMID: 37566292 DOI: 10.1007/s10709-023-00191-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 07/11/2023] [Indexed: 08/12/2023]
Abstract
In the Neotropical region, one of the most diverse families of freshwater fishes is the monophyletic Serrasalmidae. Karyotypically, the family shows high diversity in chromosome numbers (2n = 54 to 64). However, little is discussed about whether the chromosomal changes are associated with cladogenetic events within this family. In the present study, we evaluated the role of chromosomal changes in the evolutionary diversification of Serrasalmidae. Our phylogenetic sampling included 36 species and revealed three main clades. The ancestral chromosome number reconstruction revealed the basic number 2n = 54 and a high frequency of ascending dysploid events in the most derived lineages. Our biogeographic reconstruction suggests an Amazonian origin of the family at 48-38 Mya, with independent colonization of other basins between 15 and 8 Mya. We did not find specific chromosomal changes or increased diversification rates correlated with the colonization of a new environment. On the other hand, an increase in the diversification rate was detected involving the genus Serrasalmus and Pygocentrus in the Miocene, correlated with the stasis of 2n = 60. Our data demonstrate that chromosomal rearrangements might have played an important evolutionary role in major cladogenetic events in Serrasalmidae, revealing them as a possible evolutionary driver in their diversification.
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Affiliation(s)
- Uedson Pereira Jacobina
- Laboratory of Molecular Integrative Systematics, Federal University of Alagoas, Campus Arapiraca, Arapiraca, 57076-100, Brazil.
| | - Alany Itala Pontes
- Laboratory of Molecular Integrative Systematics, Federal University of Alagoas, Campus Arapiraca, Arapiraca, 57076-100, Brazil
| | - Lucas Costa
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, 50670-420, Brazil
| | - Gustavo Souza
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, 50670-420, Brazil
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4
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Nirchio Tursellino M, de Bello Cioffi M, de Menezes Cavalcante Sassi F, Deon GA, Oliveira C, Kuranaka M, Valdiviezo-Rivera J, Gonzalez VH, Rossi AR. Integrating Genomic and Chromosomal Data: A Cytogenetic Study of Transancistrus santarosensis (Loricariidae: Hypostominae) with Characterization of a ZZ/ZW Sex Chromosome System. Genes (Basel) 2023; 14:1662. [PMID: 37761802 PMCID: PMC10531053 DOI: 10.3390/genes14091662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/14/2023] [Accepted: 08/19/2023] [Indexed: 09/29/2023] Open
Abstract
The plecos (Loricariidae) fish represent a great model for cytogenetic investigations due to their variety of karyotypes, including diploid and polyploid genomes, and different types of sex chromosomes. In this study we investigate Transancistrus santarosensis a rare loricariid endemic to Ecuador, integrating cytogenetic methods with specimens' molecular identification by mtDNA, to describe the the species karyotype. We aim to verify whether sex chromosomes are cytologically identifiable and if they are associated with the accumulation of repetitive sequences present in other species of the family. The analysis of the karyotype (2n = 54 chromosomes) excludes recent centric fusion and pericentromeric inversion and suggests the presence of a ZZ/ZW sex chromosome system at an early stage of differentiation: the W chromosome is degenerated but is not characterized by the presence of differential sex-specific repetitive DNAs. Data indicate that although T. santarosensis has retained the ancestral diploid number of Loricariidae, it accumulated heterochromatin and shows non-syntenic ribosomal genes localization, chromosomal traits considered apomorphic in the family.
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Affiliation(s)
- Mauro Nirchio Tursellino
- Departamento de Acuicultura, Universidad Técnica de Machala, Av. Panamericana km 5.5, Vía Pasaje, Machala 070150, El Oro, Ecuador;
| | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos 13565-090, SP, Brazil; (M.d.B.C.); (F.d.M.C.S.); (G.A.D.)
| | | | - Geize Aparecida Deon
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos 13565-090, SP, Brazil; (M.d.B.C.); (F.d.M.C.S.); (G.A.D.)
| | - Claudio Oliveira
- Departamento de Biologia Estrutural e Funcional, Instituto de Biociências Universidade Estadual Paulista-UNESP, Botucatu 18618-689, SP, Brazil; (C.O.); (M.K.)
| | - Mariana Kuranaka
- Departamento de Biologia Estrutural e Funcional, Instituto de Biociências Universidade Estadual Paulista-UNESP, Botucatu 18618-689, SP, Brazil; (C.O.); (M.K.)
| | - Jonathan Valdiviezo-Rivera
- Instituto Nacional de Biodiversidad, Rumipamba No. 341 y Av. Shyris, Parque La Carolina, Quito 170135, Pichincha, Ecuador;
| | - Víctor Hugo Gonzalez
- Departamento de Acuicultura, Universidad Técnica de Machala, Av. Panamericana km 5.5, Vía Pasaje, Machala 070150, El Oro, Ecuador;
| | - Anna Rita Rossi
- Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza—Università di Roma, Via Alfonso Borelli 50, 00161 Rome, Italy;
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5
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Pazhenkova EA, Lukhtanov VA. Chromosomal conservatism vs chromosomal megaevolution: enigma of karyotypic evolution in Lepidoptera. Chromosome Res 2023; 31:16. [PMID: 37300756 DOI: 10.1007/s10577-023-09725-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 05/21/2023] [Accepted: 05/23/2023] [Indexed: 06/12/2023]
Abstract
In the evolution of many organisms, periods of slow genome reorganization (= chromosomal conservatism) are interrupted by bursts of numerous chromosomal changes (= chromosomal megaevolution). Using comparative analysis of chromosome-level genome assemblies, we investigated these processes in blue butterflies (Lycaenidae). We demonstrate that the phase of chromosome number conservatism is characterized by the stability of most autosomes and dynamic evolution of the sex chromosome Z, resulting in multiple variants of NeoZ chromosomes due to autosome-sex chromosome fusions. In contrast during the phase of rapid chromosomal evolution, the explosive increase in chromosome number occurs mainly through simple chromosomal fissions. We show that chromosomal megaevolution is a highly non-random canalized process, and in two phylogenetically independent Lysandra lineages, the drastic parallel increase in number of fragmented chromosomes was achieved, at least partially, through reuse of the same ancestral chromosomal breakpoints. In species showing chromosome number doubling, we found no blocks of duplicated sequences or duplicated chromosomes, thus refuting the hypothesis of polyploidy. In the studied taxa, long blocks of interstitial telomere sequences (ITSs) consist of (TTAGG)n arrays interspersed with telomere-specific retrotransposons. ITSs are sporadically present in rapidly evolving Lysandra karyotypes, but not in the species with ancestral chromosome number. Therefore, we hypothesize that the transposition of telomeric sequences may be triggers of the rapid chromosome number increase. Finally, we discuss the hypothetical genomic and population mechanisms of chromosomal megaevolution and argue that the disproportionally high evolutionary role of the Z sex chromosome can be additionally reinforced by sex chromosome-autosome fusions and Z-chromosome inversions.
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Affiliation(s)
- Elena A Pazhenkova
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna Pot 111, 1000, Ljubljana, Slovenia.
| | - Vladimir A Lukhtanov
- Department of Karyosystematics, Zoological Institute of Russian Academy of Sciences, Universitetskaya Nab. 1, 199034, St. Petersburg, Russia.
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6
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Long X, Charlesworth D, Qi J, Wu R, Chen M, Wang Z, Xu L, Fu H, Zhang X, Chen X, He L, Zheng L, Huang Z, Zhou Q. Independent Evolution of Sex Chromosomes and Male Pregnancy-Related Genes in Two Seahorse Species. Mol Biol Evol 2022; 40:6964685. [PMID: 36578180 PMCID: PMC9851323 DOI: 10.1093/molbev/msac279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 10/14/2022] [Accepted: 12/22/2022] [Indexed: 12/30/2022] Open
Abstract
Unlike birds and mammals, many teleosts have homomorphic sex chromosomes, and changes in the chromosome carrying the sex-determining locus, termed "turnovers", are common. Recent turnovers allow studies of several interesting questions. One question is whether the new sex-determining regions evolve to become completely non-recombining, and if so, how and why. Another is whether (as predicted) evolutionary changes that benefit one sex accumulate in the newly sex-linked region. To study these questions, we analyzed the genome sequences of two seahorse species of the Syngnathidae, a fish group in which many species evolved a unique structure, the male brood pouch. We find that both seahorse species have XY sex chromosome systems, but their sex chromosome pairs are not homologs, implying that at least one turnover event has occurred. The Y-linked regions occupy 63.9% and 95.1% of the entire sex chromosome of the two species and do not exhibit extensive sequence divergence with their X-linked homologs. We find evidence for occasional recombination between the extant sex chromosomes that may account for their homomorphism. We argue that these Y-linked regions did not evolve by recombination suppression after the turnover, but by the ancestral nature of the low crossover rates in these chromosome regions. With such an ancestral crossover landscape, a turnover can instantly create an extensive Y-linked region. Finally, we test for adaptive evolution of male pouch-related genes after they became Y-linked in the seahorse.
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Affiliation(s)
- Xin Long
- MOE Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China,Research Center for Intelligent Computing Platforms, Zhejiang Lab, Hangzhou 311100, China
| | - Deborah Charlesworth
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, West Mains Road, Edinburgh EH9 3LF, UK
| | - Jianfei Qi
- Department of Aquaculture, Fisheries Research Institute of Fujian, Xiamen 361013, China
| | - Ruiqiong Wu
- Fujian Key Laboratory of Developmental and Neural Biology & Southern Center for Biomedical Research, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian, China
| | - Meiling Chen
- Fujian Key Laboratory of Developmental and Neural Biology & Southern Center for Biomedical Research, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian, China
| | - Zongji Wang
- MOE Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Luohao Xu
- MOE Key Laboratory of Freshwater Fish Reproduction and Development, Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Honggao Fu
- Fujian Key Laboratory of Developmental and Neural Biology & Southern Center for Biomedical Research, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian, China
| | - Xueping Zhang
- Fujian Key Laboratory of Developmental and Neural Biology & Southern Center for Biomedical Research, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian, China
| | - Xinxin Chen
- Department of Aquaculture, Fisheries Research Institute of Fujian, Xiamen 361013, China
| | - Libin He
- Department of Aquaculture, Fisheries Research Institute of Fujian, Xiamen 361013, China
| | | | | | - Qi Zhou
- Corresponding authors: E-mails: ; ;
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7
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Nousias O, Oikonomou S, Manousaki T, Papadogiannis V, Angelova N, Tsaparis D, Tsakogiannis A, Duncan N, Estevez A, Tzokas K, Pavlidis M, Chatziplis D, Tsigenopoulos CS. Linkage mapping, comparative genome analysis, and QTL detection for growth in a non-model teleost, the meagre Argyrosomus regius, using ddRAD sequencing. Sci Rep 2022; 12:5301. [PMID: 35351938 PMCID: PMC8964699 DOI: 10.1038/s41598-022-09289-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 03/17/2022] [Indexed: 01/05/2023] Open
Abstract
Meagre (Argyrosomus regius), is a benthopelagic species rapidly emerging in aquaculture, due to its low food to biomass conversion rate, good fillet yield and ease of production. Tracing a species genomic background along with describing the genetic basis of important traits can greatly influence both conservation strategies and production perspectives. In this study, we employed ddRAD sequencing of 266 fish from six F1 meagre families, to construct a high-density genetic map comprising 4529 polymorphic SNP markers. The QTL mapping analysis provided a genomic appreciation for the weight trait identifying a statistically significant QTL on linkage group 15 (LG15). The comparative genomics analysis with six teleost species revealed an evolutionarily conserved karyotype structure. The synteny observed, verified the already well-known fusion events of the three-spine stickleback genome, reinforced the evidence of reduced evolutionary distance of Sciaenids with the Sparidae family, reflected the evolutionary proximity with Dicentrarchus labrax, traced several putative chromosomal rearrangements and a prominent putative fusion event in meagre’s LG17. This study presents novel elements concerning the genome evolutionary history of a non-model teleost species recently adopted in aquaculture, starts to unravel the genetic basis of the species growth-related traits, and provides a high-density genetic map as a tool that can help to further establish meagre as a valuable resource for research and production.
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Affiliation(s)
- O Nousias
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Heraklion, Greece.,Department of Biology, University of Crete, Heraklion, Greece
| | - S Oikonomou
- Department of Agriculture, International Hellenic University (IHU), Thessaloniki, Greece
| | - T Manousaki
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Heraklion, Greece
| | - V Papadogiannis
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Heraklion, Greece
| | - N Angelova
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Heraklion, Greece
| | - D Tsaparis
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Heraklion, Greece
| | - A Tsakogiannis
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Heraklion, Greece
| | - N Duncan
- IRTA Institute of Agrifood Research and Technology, Barcelona, Spain
| | - A Estevez
- IRTA Institute of Agrifood Research and Technology, Barcelona, Spain
| | - K Tzokas
- Andromeda S.A., Agios Vasilios, Rion, Greece
| | - M Pavlidis
- Department of Biology, University of Crete, Heraklion, Greece
| | - D Chatziplis
- Department of Agriculture, International Hellenic University (IHU), Thessaloniki, Greece
| | - C S Tsigenopoulos
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Heraklion, Greece.
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8
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Pedroso RN, Santos MTT, Lourenço LB. Rapid karyotypic evolution with high diploid number variation in a rare genus of bromeligenous frogs. Genome 2022; 65:255-264. [PMID: 35275781 DOI: 10.1139/gen-2021-0090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Bromeligenous Crossodactylodes is a leptodactylid genus closely related to Paratelmatobius and Scythrophrys. The diploid number in all karyotyped species of these two latter genera is 24, which diverges from the modal diploid number (2n = 22) in the family. Here, we analyzed three species of Crossodactylodes and found karyotypes with 2n = 30, 2n = 32, and 2n = 36, diploid numbers that have not been reported in any other diploid leptodactylid species to date. Reconstruction of the ancestral chromosome number indicated that the diploid number changed from 22 to 24 in the common ancestor of Crossodactylodes, Paratelmatobius, and Scythrophrys, and that progressive increases in diploid number have occurred in Crossodactylodes. The large number of telocentric/subtelocentric chromosomes in karyotypes with higher diploid numbers raises the possibility that centric fissions may have occurred during the evolution of Paratelmatobiinae. Three metacentric chromosomes, probably involved in fission events, were inferred to be present in the common ancestor of all species of Crossodactylodes, but in C. bokermanni. Chromosome mapping of the satellite DNA PcP190 suggests homology between one arm of metacentric chromosome 1 of Crossodactylodes sp. 3 and telocentric chromosome 2 of C. itambe, supporting one of the presumed centric fission events.
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Affiliation(s)
- Ricardo Neves Pedroso
- LabEsC (Laboratório de Estudos Cromossômicos), Departamento de Biologia Estrutural e Funcional, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), 13083-863, Campinas, SP, Brazil
| | - Marcus Thadeu Teixeira Santos
- Laboratório de Herpetologia, Departamento de Biodiversidade e Centro de Aquicultura (CAUNESP), Instituto de Biociências, Universidade Estadual Paulista (UNESP), 13506-900, Rio Claro, SP, Brazil.,Laboratório de Herpetologia, Departamento de Zoologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), 31270-901, Belo Horizonte, MG, Brazil
| | - Luciana Bolsoni Lourenço
- LabEsC (Laboratório de Estudos Cromossômicos), Departamento de Biologia Estrutural e Funcional, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), 13083-863, Campinas, SP, Brazil
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9
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Ibiapino A, García MA, Amorim B, Baez M, Costea M, Stefanović S, Pedrosa-Harand A. The Evolution of Cytogenetic Traits in Cuscuta (Convolvulaceae), the Genus With the Most Diverse Chromosomes in Angiosperms. FRONTIERS IN PLANT SCIENCE 2022; 13:842260. [PMID: 35432411 PMCID: PMC9011109 DOI: 10.3389/fpls.2022.842260] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 03/03/2022] [Indexed: 05/17/2023]
Abstract
Karyotypes are characterized by traits such as chromosome number, which can change through whole-genome duplication and dysploidy. In the parasitic plant genus Cuscuta (Convolvulaceae), chromosome numbers vary more than 18-fold. In addition, species of this group show the highest diversity in terms of genome size among angiosperms, as well as a wide variation in the number and distribution of 5S and 35S ribosomal DNA (rDNA) sites. To understand its karyotypic evolution, ancestral character state reconstructions were performed for chromosome number, genome size, and position of 5S and 35S rDNA sites. Previous cytogenetic data were reviewed and complemented with original chromosome counts, genome size estimates, and rDNA distribution assessed via fluorescence in situ hybridization (FISH), for two, seven, and 10 species, respectively. Starting from an ancestral chromosome number of x = 15, duplications were inferred as the prevalent evolutionary process. However, in holocentric clade (subgenus Cuscuta), dysploidy was identified as the main evolutionary mechanism, typical of holocentric karyotypes. The ancestral genome size of Cuscuta was inferred as approximately 1C = 12 Gbp, with an average genome size of 1C = 2.8 Gbp. This indicates an expansion of the genome size relative to other Convolvulaceae, which may be linked to the parasitic lifestyle of Cuscuta. Finally, the position of rDNA sites varied mostly in species with multiple sites in the same karyotype. This feature may be related to the amplification of rDNA sites in association to other repeats present in the heterochromatin. The data suggest that different mechanisms acted in different subgenera, generating the exceptional diversity of karyotypes in Cuscuta.
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Affiliation(s)
- Amalia Ibiapino
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, Brazil
| | | | - Bruno Amorim
- Postgraduate Program of Biotechnology and Natural Resources of the Amazonia (PPGMBT), State University of Amazonas, Manaus, Brazil
| | - Mariana Baez
- Plant Breeding Department, University of Bonn, Bonn, Germany
| | - Mihai Costea
- Department of Biology, University of Wilfrid Laurier, Waterloo, ON, Canada
| | - Saša Stefanović
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada
| | - Andrea Pedrosa-Harand
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, Brazil
- *Correspondence: Miguel A. García,
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Adding New Pieces to the Puzzle of Karyotype Evolution in Harttia (Siluriformes, Loricariidae): Investigation of Amazonian Species. BIOLOGY 2021; 10:biology10090922. [PMID: 34571799 PMCID: PMC8472603 DOI: 10.3390/biology10090922] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/10/2021] [Accepted: 09/13/2021] [Indexed: 12/21/2022]
Abstract
A remarkable morphological diversity and karyotype variability can be observed in the Neotropical armored catfish genus Harttia. These fishes offer a useful model to explore both the evolution of karyotypes and sex chromosomes, since many species possess male-heterogametic sex chromosome systems and a high rate of karyotype repatterning. Based on the karyotype organization, the chromosomal distribution of several repetitive DNA classes, and the rough estimates of genomic divergences at the intraspecific and interspecific levels via Comparative Genomic Hybridization, we identified shared diploid chromosome numbers (2n = 54) but different karyotype compositions in H. dissidens (20m + 26sm + 8a) and Harttia sp. 3 (16m + 18sm + 14st + 6a), and different 2n in H. guianensis (2n = 58; 20m + 26sm + 2st + 10a). All species further displayed similar patterns of chromosomal distribution concerning constitutive heterochromatin, 18S ribosomal DNA (rDNA) sites, and most of the surveyed microsatellite motifs. Furthermore, differences in the distribution of 5S rDNA sites and a subset of microsatellite sequences were identified. Heteromorphic sex chromosomes were lacking in H. dissidens and H. guianensis at the scale of our analysis. However, one single chromosome pair in Harttia sp. 3 males presented a remarkable accumulation of male genome-derived probe after CGH, pointing to a tentative region of early sex chromosome differentiation. Thus, our data support already previously outlined evidence that Harttia is a vital model for the investigation of teleost karyotype and sex chromosome dynamics.
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Yoshida K, Kitano J. Tempo and mode in karyotype evolution revealed by a probabilistic model incorporating both chromosome number and morphology. PLoS Genet 2021; 17:e1009502. [PMID: 33861748 PMCID: PMC8081341 DOI: 10.1371/journal.pgen.1009502] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 04/28/2021] [Accepted: 03/22/2021] [Indexed: 12/12/2022] Open
Abstract
Karyotype, including the chromosome and arm numbers, is a fundamental genetic characteristic of all organisms and has long been used as a species-diagnostic character. Additionally, karyotype evolution plays an important role in divergent adaptation and speciation. Centric fusion and fission change chromosome numbers, whereas the intra-chromosomal movement of the centromere, such as pericentric inversion, changes arm numbers. A probabilistic model simultaneously incorporating both chromosome and arm numbers has not been established. Here, we built a probabilistic model of karyotype evolution based on the "karyograph", which treats karyotype evolution as a walk on the two-dimensional space representing the chromosome and arm numbers. This model enables analysis of the stationary distribution with a stable karyotype for any given parameter. After evaluating their performance using simulated data, we applied our model to two large taxonomic groups of fish, Eurypterygii and series Otophysi, to perform maximum likelihood estimation of the transition rates and reconstruct the evolutionary history of karyotypes. The two taxa significantly differed in the evolution of arm number. The inclusion of speciation and extinction rates demonstrated possibly high extinction rates in species with karyotypes other than the most typical karyotype in both groups. Finally, we made a model including polyploidization rates and applied it to a small plant group. Thus, the use of this probabilistic model can contribute to a better understanding of tempo and mode in karyotype evolution and its possible role in speciation and extinction.
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Affiliation(s)
- Kohta Yoshida
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima, Japan
| | - Jun Kitano
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima, Japan
- * E-mail:
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