1
|
Silva DSD, de Sousa RPC, Vallinoto M, Costa Lima MRD, Costa RAD, Furo IDO, Gomes AJB, Oliveira EHCD. Comparative molecular and conventional cytogenetic analyses of three species of Rhinella (Anura; Bufonidae). PLoS One 2024; 19:e0308785. [PMID: 39146271 PMCID: PMC11326569 DOI: 10.1371/journal.pone.0308785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 07/31/2024] [Indexed: 08/17/2024] Open
Abstract
The genus Rhinella corresponds to a group of anurans characterized by numerous taxonomic and systemic challenges, leading to their organization into species complexes. Cytogenetic data for this genus thus far are limited to the diploid number and chromosome morphology, which remain highly conserved among the species. In this study, we analyse the karyotypes of three species of the genus Rhinella (Rhinella granulosa, Rhinella margaritifera, and Rhinella marina) using both classical (conventional staining and C-banding) and molecular (FISH-fluorescence in situ hybridization with 18S rDNA, telomeric sequences, and microsatellite probes) cytogenetic approaches. The aim of this study is to provide data that can reveal variations in the distribution of repetitive sequences that can contribute to understanding karyotypic diversification in these species. The results revealed a conserved karyotype across the species, with 2n = 22 and FN = 44, with metacentric and submetacentric chromosomes. C-banding revealed heterochromatic blocks in the pericentromeric region for all species, with a proximal block on the long arms of pairs 3 and 6 in R. marina and on the short arms of pairs 4 and 6 in R. margaritifera. Additionally, 18S rDNA probes hybridized to pair 5 in R. granulosa, to pair 7 in R. marina, and to pair 10 in R. margaritifera. Telomeric sequence probes displayed signals exclusively in the distal region of the chromosomes, while microsatellite DNA probes showed species-specific patterns. These findings indicate that despite a conserved karyotypical macrostructure, chromosomal differences exist among the species due to the accumulation of repetitive sequences. This variation may be attributed to chromosome rearrangements or differential accumulation of these sequences, highlighting the dynamic role of repetitive sequences in the chromosomal evolution of Rhinella species. Ultimately, this study emphasizes the importance of the role of repetitive DNAs in chromosomal rearrangements to elucidate the evolutionary mechanisms leading to independent diversification in the distinct phylogenetic groups of Rhinella.
Collapse
Affiliation(s)
- David Santos da Silva
- Programa de Pós-Graduação em Genética e Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brazil
| | | | - Marcelo Vallinoto
- Laboratório de Evolução, Instituto de Estudos Costeiros, Universidade Federal do Pará, Bragança, Pará, Brazil
| | - Marlon Ramires da Costa Lima
- Laboratório de Biologia Molecular, Evolução e Microbiologia, Instituto Federal do Pará, Abaetetuba, Pará, Brazil
| | - Renato Araújo da Costa
- Laboratório de Biologia Molecular, Evolução e Microbiologia, Instituto Federal do Pará, Abaetetuba, Pará, Brazil
| | - Ivanete de Oliveira Furo
- Laboratório de Reprodução Animal, Universidade Federal Rural da Amazônia, Parauapebas, Pará, Brazil
| | - Anderson José Baia Gomes
- Laboratório de Biologia Molecular, Evolução e Microbiologia, Instituto Federal do Pará, Abaetetuba, Pará, Brazil
| | - Edivaldo Herculano Corrêa de Oliveira
- Faculdade de Ciências Naturais, Instituto de Ciências Exatas Naturais e Exatas, Universidade Federal do Pará, Belém, Pará, Brazil
- Laboratório de Citogenômica e Mutagênese Ambiental, Seção de Meio Ambiente, Instituto Evandro Chagas, Ananindeua, Pará, Brazil
| |
Collapse
|
2
|
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.
Collapse
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;
| |
Collapse
|
3
|
Sassi FDMC, Deon GA, Sember A, Liehr T, Oyakawa OT, Moreira Filho O, Bertollo LAC, Vicari MR, Cioffi MDB. Turnover of multiple sex chromosomes in Harttia catfish (Siluriformes, Loricariidae): a glimpse from whole chromosome painting. Front Genet 2023; 14:1226222. [PMID: 37576550 PMCID: PMC10421700 DOI: 10.3389/fgene.2023.1226222] [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: 05/20/2023] [Accepted: 07/17/2023] [Indexed: 08/15/2023] Open
Abstract
The remarkable fish biodiversity encompasses also great sex chromosome variability. Harttia catfish belong to Neotropical models for karyotype and sex chromosome research. Some species possess one of the three male-heterogametic sex chromosome systems, XY, X1X2Y or XY1Y2, while other members of the genus have yet uncharacterized modes of sex determination. Particularly the XY1Y2 multiple sex chromosome system shows a relatively low incidence among vertebrates, and it has not been yet thoroughly investigated. Previous research suggested two independent X-autosome fusions in Harttia which led to the emergence of XY1Y2 sex chromosome system in three of its species. In this study, we investigated evolutionary trajectories of synteny blocks involved in this XY1Y2 system by probing six Harttia species with whole chromosome painting (WCP) probes derived from the X (HCA-X) and the chromosome 9 (HCA-9) of H. carvalhoi. We found that both painting probes hybridize to two distinct chromosome pairs in Amazonian species, whereas the HCA-9 probe paints three chromosome pairs in H. guianensis, endemic to Guyanese drainages. These findings demonstrate distinct evolutionary fates of mapped synteny blocks and thereby elevated karyotype dynamics in Harttia among the three evolutionary clades.
Collapse
Affiliation(s)
| | - Geize Aparecida Deon
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Alexandr Sember
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czechia
| | - Thomas Liehr
- Institut für Humangenetik, Universitätsklinikum Jena, Jena, Germany
| | | | - Orlando Moreira Filho
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Luiz Antonio Carlos Bertollo
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Marcelo Ricardo Vicari
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa, Brazil
| | - Marcelo de Bello Cioffi
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| |
Collapse
|
4
|
Marajó L, Viana PF, Ferreira AMV, Py-Daniel LHR, Cioffi MDB, Sember A, Feldberg E. Chromosomal rearrangements and the first indication of an ♀X 1 X 1 X 2 X 2 /♂X 1 X 2 Y sex chromosome system in Rineloricaria fishes (Teleostei: Siluriformes). JOURNAL OF FISH BIOLOGY 2023; 102:443-454. [PMID: 36427042 DOI: 10.1111/jfb.15275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 11/15/2022] [Indexed: 06/16/2023]
Abstract
Rineloricaria is the most diverse genus within the freshwater fish subfamily Loricariinae, and it is widely distributed in the Neotropical region. Despite limited cytogenetic data, records from southern and south-eastern Brazil suggest a high rate of chromosomal rearrangements in this genus, mirrored in remarkable inter- and intraspecific karyotype variability. In the present work, we investigated the karyotype features of Rineloricaria teffeana, an endemic representative from northern Brazil, using both conventional and molecular cytogenetic techniques. We revealed different diploid chromosome numbers (2n) between sexes (33♂/34♀), which suggests the presence of an ♀X1 X1 X2 X2 /♂X1 X2 Y multiple sex chromosome system. The male-limited Y chromosome was the largest and the only biarmed element in the karyotype, implying Y-autosome fusion as the most probable mechanism behind its origination. C-banding revealed low amounts of constitutive heterochromatin, mostly confined to the (peri)centromeric regions of most chromosomes (including the X2 and the Y) but also occupying the distal regions of a few chromosomal pairs. The chromosomal localization of the 18S ribosomal DNA (rDNA) clusters revealed a single site on chromosome pair 4, which was adjacent to the 5S rDNA cluster. Additional 5S rDNA loci were present on the autosome pair 8, X1 chromosome, and in the presumed fusion point on the Y chromosome. The probe for telomeric repeat motif (TTAGGG)n revealed signals of variable intensities at the ends of all chromosomes except for the Y chromosome, where no detectable signals were evidenced. Male-to-female comparative genomic hybridization revealed no sex-specific or sex-biased repetitive DNA accumulations, suggesting a presumably low level of neo-Y chromosome differentiation. We provide evidence that rDNA sites might have played a role in the formation of this putative multiple sex chromosome system and that chromosome fusions originate through different mechanisms among different Rineloricaria species.
Collapse
Affiliation(s)
- Leandro Marajó
- Laboratório de Genética Animal, Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva, Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil
| | - Patrik Ferreira Viana
- Laboratório de Genética Animal, Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva, Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil
| | - Alex Matheus Viana Ferreira
- Laboratório de Genética Animal, Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva, Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil
| | - Lúcia Helena Rapp Py-Daniel
- Coleção de Peixes, Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil
| | - Marcelo de Bello Cioffi
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Alexandr Sember
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Libechov, Czech Republic
| | - Eliana Feldberg
- Laboratório de Genética Animal, Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva, Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil
| |
Collapse
|
5
|
Occurrence of Sex Chromosomes in Fish of the Genus Ancistrus with a New Description of Multiple Sex Chromosomes in the Ecuadorian Endemic Ancistrus clementinae (Loricariidae). Genes (Basel) 2023; 14:genes14020306. [PMID: 36833233 PMCID: PMC9956960 DOI: 10.3390/genes14020306] [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: 12/29/2022] [Revised: 01/16/2023] [Accepted: 01/20/2023] [Indexed: 01/26/2023] Open
Abstract
Ancistrus Kner, 1854, is the most diverse genus among the Ancistrini (Loricariidae) with 70 valid species showing a wide geographic distribution and great taxonomic and systematic complexity. To date, about 40 Ancistrus taxa have been karyotyped, all from Brazil and Argentina, but the statistic is uncertain because 30 of these reports deal with samples that have not yet been identified at the species level. This study provides the first cytogenetic description of the bristlenose catfish, Ancistrus clementinae Rendahl, 1937, a species endemic to Ecuador, aiming to verify whether a sex chromosome system is identifiable in the species and, if so, which, and if its differentiation is associated with the presence of repetitive sequences reported for other species of the family. We associated the karyotype analysis with the COI molecular identification of the specimens. Karyotype analysis suggested the presence of a ♂ZZ/♀ZW1W2 sex chromosome system, never detected before in Ancistrus, with both W1W2 chromosomes enriched with heterochromatic blocks and 18S rDNA, in addition to GC-rich repeats (W2). No differences were observed between males and females in the distribution of 5S rDNA or telomeric repeats. Cytogenetic data here obtained confirm the huge karyotype diversity of Ancistrus, both in chromosome number and sex-determination systems.
Collapse
|
6
|
de la Herrán R, Hermida M, Rubiolo JA, Gómez-Garrido J, Cruz F, Robles F, Navajas-Pérez R, Blanco A, Villamayor PR, Torres D, Sánchez-Quinteiro P, Ramirez D, Rodríguez ME, Arias-Pérez A, Cross I, Duncan N, Martínez-Peña T, Riaza A, Millán A, De Rosa MC, Pirolli D, Gut M, Bouza C, Robledo D, Rebordinos L, Alioto T, Ruíz-Rejón C, Martínez P. A chromosome-level genome assembly enables the identification of the follicule stimulating hormone receptor as the master sex-determining gene in the flatfish Solea senegalensis. Mol Ecol Resour 2023; 23:886-904. [PMID: 36587276 DOI: 10.1111/1755-0998.13750] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 12/23/2022] [Accepted: 12/28/2022] [Indexed: 01/02/2023]
Abstract
Sex determination (SD) shows huge variation among fish and a high evolutionary rate, as illustrated by the Pleuronectiformes (flatfishes). This order is characterized by its adaptation to demersal life, compact genomes and diversity of SD mechanisms. Here, we assembled the Solea senegalensis genome, a flatfish of great commercial value, into 82 contigs (614 Mb) combining long- and short-read sequencing, which were next scaffolded using a highly dense genetic map (28,838 markers, 21 linkage groups), representing 98.9% of the assembly. Further, we established the correspondence between the assembly and the 21 chromosomes by using BAC-FISH. Whole genome resequencing of six males and six females enabled the identification of 41 single nucleotide polymorphism variants in the follicle stimulating hormone receptor (fshr) consistent with an XX/XY SD system. The observed sex association was validated in a broader independent sample, providing a novel molecular sexing tool. The fshr gene displayed differential expression between male and female gonads from 86 days post-fertilization, when the gonad is still an undifferentiated primordium, concomitant with the activation of amh and cyp19a1a, testis and ovary marker genes, respectively, in males and females. The Y-linked fshr allele, which included 24 nonsynonymous variants and showed a highly divergent 3D protein structure, was overexpressed in males compared to the X-linked allele at all stages of gonadal differentiation. We hypothesize a mechanism hampering the action of the follicle stimulating hormone driving the undifferentiated gonad toward testis.
Collapse
Affiliation(s)
- Roberto de la Herrán
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | - Miguel Hermida
- Departamento de Zoología, Genética y Antropología Física; Facultad de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
| | - Juan Andres Rubiolo
- Departamento de Zoología, Genética y Antropología Física; Facultad de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
| | - Jèssica Gómez-Garrido
- Centre Nacional d'Anàlisi Genòmica (CNAG-CRG), Centre de Regulació Genómica, Parc Científic de Barcelona, Barcelona, Spain
| | - Fernando Cruz
- Centre Nacional d'Anàlisi Genòmica (CNAG-CRG), Centre de Regulació Genómica, Parc Científic de Barcelona, Barcelona, Spain
| | - Francisca Robles
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | - Rafael Navajas-Pérez
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | - Andres Blanco
- Departamento de Zoología, Genética y Antropología Física; Facultad de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
| | - Paula Rodriguez Villamayor
- Departamento de Zoología, Genética y Antropología Física; Facultad de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
| | - Dorinda Torres
- Departamento de Zoología, Genética y Antropología Física; Facultad de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
| | - Pablo Sánchez-Quinteiro
- Departamento de Anatomía, Producción Animal y Ciencias Clínicas Veterinarias Facultad de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
| | - Daniel Ramirez
- Departamento de Biomedicina, Biotecnología y Salud Pública CASEM - Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, Cádiz, Spain
| | - Maria Esther Rodríguez
- Departamento de Biomedicina, Biotecnología y Salud Pública CASEM - Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, Cádiz, Spain
| | - Alberto Arias-Pérez
- Departamento de Biomedicina, Biotecnología y Salud Pública CASEM - Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, Cádiz, Spain
| | - Ismael Cross
- Departamento de Biomedicina, Biotecnología y Salud Pública CASEM - Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, Cádiz, Spain
| | - Neil Duncan
- IRTA Sant Carles de la Rapita, Tarragona, Spain
| | | | - Ana Riaza
- Stolt Sea Farm SA, Departamento I+D, A Coruña, Spain
| | | | - M Cristina De Rosa
- Institute of Chemical Sciences and Technologies "Giulio Natta" (SCITEC) - CNR c/o Catholic University of Rome, Rome, Italy
| | - Davide Pirolli
- Institute of Chemical Sciences and Technologies "Giulio Natta" (SCITEC) - CNR c/o Catholic University of Rome, Rome, Italy
| | - Marta Gut
- Centre Nacional d'Anàlisi Genòmica (CNAG-CRG), Centre de Regulació Genómica, Parc Científic de Barcelona, Barcelona, Spain
| | - Carmen Bouza
- Departamento de Zoología, Genética y Antropología Física; Facultad de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
| | - Diego Robledo
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, UK
| | - Laureana Rebordinos
- Departamento de Biomedicina, Biotecnología y Salud Pública CASEM - Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, Cádiz, Spain
| | - Tyler Alioto
- Centre Nacional d'Anàlisi Genòmica (CNAG-CRG), Centre de Regulació Genómica, Parc Científic de Barcelona, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Carmelo Ruíz-Rejón
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | - Paulino Martínez
- Departamento de Zoología, Genética y Antropología Física; Facultad de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
| |
Collapse
|
7
|
Machado MDA, da Silva M, Feldberg E, O'Brien PCM, Ferguson-Smith MA, Pieczarka JC, Nagamachi CY. Chromosome Painting in Gymnotus carapo "Catalão" (Gymnotiformes, Teleostei): Dynamics of Chromosomal Rearrangements in Cryptic Species. Front Genet 2022; 13:832495. [PMID: 35401658 PMCID: PMC8992654 DOI: 10.3389/fgene.2022.832495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 02/10/2022] [Indexed: 11/13/2022] Open
Abstract
The genus Gymnotus is a large monophyletic group of freshwater weakly-electric fishes, with wide distribution in Central and South America. It has 46 valid species divided into six subgenera (Gymnotus, Tijax, Tigre, Lamontianus, Tigrinus and Pantherus) with large chromosome plasticity and diploid numbers (2n) ranging from 34 to 54. Within this rich diversity, there is controversy about whether Gymnotus (Gymnotus) carapo species is a single widespread species or a complex of cryptic species. Cytogenetic studies show different diploid numbers for G. carapo species, ranging from 40 to 54 chromosomes with varied karyotypes found even between populations sharing the same 2n. Whole chromosome painting has been used in studies on fish species and recently has been used for tracking the chromosomal evolution of Gymnotus and assisting in its cytotaxonomy. Comparative genomic mapping using chromosome painting has shown more complex rearrangements in Gymnotus carapo than shown in previous studies by classical cytogenetics. These studies demonstrate that multiple chromosome pairs are involved in its chromosomal reorganization, suggesting the presence of a complex of cryptic species due to a post zygotic barrier. In the present study, metaphase chromosomes of G. carapo occidentalis "catalão" (GCC, 2n = 40, 30m/sm+10st/a) from the Catalão Lake, Amazonas, Brazil, were hybridized with whole chromosome probes derived from the chromosomes of G. carapo (GCA, 2n = 42, 30m/sm+12st/a). The results reveal chromosome rearrangements and a high number of repetitive DNA sites. Of the 12 pairs of G. carapo chromosomes that could be individually identified (GCA 1-3, 6, 7, 9, 14, 16 and 18-21), 8 pairs (GCA 1, 2, 6, 7, 9, 14, 20, 21) had homeology conserved in GCC. Of the GCA pairs that are grouped (GCA [4, 8], [5, 17], [10, 11] and [12, 13, 15]), most kept the number of signals in GCC (GCA [5, 17], [10, 11] and [12, 13, 15]). The remaining chromosomes are rearranged in the GCC karyotype. Analysis of both populations of the G. carapo cytotypes shows extensive karyotype reorganization. Along with previous studies, this suggests that the different cytotypes analyzed here may represent different species and supports the hypothesis that G. carapo is not a single widespread species, but a group of cryptic species.
Collapse
Affiliation(s)
- Milla de Andrade Machado
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal Do Pará (UFPA), Belém, Brazil
| | - Maelin da Silva
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa, Brazil
| | - Eliana Feldberg
- Laboratório de Genética Animal, Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil
| | - Patricia Caroline Mary O'Brien
- Department of Veterinary Medicine, Cambridge Resource Centre for Comparative Genomics, University of Cambridge, Cambridge, United Kingdom
| | - Malcolm Andrew Ferguson-Smith
- Department of Veterinary Medicine, Cambridge Resource Centre for Comparative Genomics, University of Cambridge, Cambridge, United Kingdom
| | - Julio Cesar Pieczarka
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal Do Pará (UFPA), Belém, Brazil
| | - Cleusa Yoshiko Nagamachi
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal Do Pará (UFPA), Belém, Brazil
| |
Collapse
|
8
|
Santos da Silva K, Glugoski L, Vicari MR, de Souza ACP, Noronha RCR, Pieczarka JC, Nagamachi CY. Chromosomal Diversification in Ancistrus Species (Siluriformes: Loricariidae) Inferred From Repetitive Sequence Analysis. Front Genet 2022; 13:838462. [PMID: 35401670 PMCID: PMC8987504 DOI: 10.3389/fgene.2022.838462] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 02/25/2022] [Indexed: 11/25/2022] Open
Abstract
The Ancistrus genus has extensive chromosomal diversity among species, including heteromorphic sex chromosomes occurrence. However, studies have been shown that chromosomal diversity may still be underestimated. Repetitive sequences represent a large part of eukaryotic genomes, associated with mechanisms of karyotypic diversification, including sex chromosomes evolution. This study analyzed the karyotype diversification of two Ancistrus species (Ancistrus sp. 1 and Ancistrus sp. 2) from the Amazon region by classical and molecular chromosomal markers. Conventional chromosome bands and fluorescence in situ hybridization using probes 18S and 5S rDNA, besides (CA)n, (CG)n, (GA)n, (CAC)n, (CAG)n, (CAT)n, (GAA)n, (GAC)n, (TAA)n, and (TTAGGG)n in tandem repeats were determined on the karyotypes. Ancistrus sp. 1 and Ancistrus sp. 2 presented karyotypes with 2n = 38 (20 m + 14sm+4st, XX/XY) and 2n = 34 (20 m + 14sm, without heteromorphic sex chromosomes), respectively. Robertsonian rearrangements can explain the diploid number difference. C-bands occurred in pericentromeric regions in some chromosomes, and a single 18S rDNA locus occurred in both species. The 5S rDNA showed variation in the number of loci between species karyotypes, suggesting the occurrence of unstable sites and rearrangements associated with these sequences in Ancistrus. The microsatellite mapping evidenced distinct patterns of organization between the two analyzed species, occurring mainly in the sex chromosomes in Ancistrus sp. 1, and in the centromeric and pericentromeric regions of chromosomes m/sm in Ancistrus sp. 2. These data shows the extensive chromosomal diversity of repetitive sequences in Ancistrus, which were involved in Robertsonian rearrangements and sex chromosomes differentiation.
Collapse
Affiliation(s)
- Kevin Santos da Silva
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil
| | - Larissa Glugoski
- Laboratório de Citogenética de Peixes, Universidade Federal de São Carlos, São Carlos, Brazil
- Laboratório de Biologia Cromossômica: Estrutura e Função, Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa, Brazil
| | - Marcelo Ricardo Vicari
- Laboratório de Biologia Cromossômica: Estrutura e Função, Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa, Brazil
| | - Augusto César Paes de Souza
- Laboratório de Estudo da Ictiofauna Amazônica, Instituto Federal de Educação, Ciência e Tecnologia do Pará, Abaetetuba, Brazil
| | - Renata Coelho Rodrigues Noronha
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil
| | - Julio Cesar Pieczarka
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil
| | - Cleusa Yoshiko Nagamachi
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil
- *Correspondence: Cleusa Yoshiko Nagamachi, ,
| |
Collapse
|
9
|
Cayuela H, Lemaître JF, Léna JP, Ronget V, Martínez-Solano I, Muths E, Pilliod DS, Schmidt BR, Sánchez-Montes G, Gutiérrez-Rodríguez J, Pyke G, Grossenbacher K, Lenzi O, Bosch J, Beard KH, Woolbright LL, Lambert BA, Green DM, Jreidini N, Garwood JM, Fisher RN, Matthews K, Dudgeon D, Lau A, Speybroeck J, Homan R, Jehle R, Başkale E, Mori E, Arntzen JW, Joly P, Stiles RM, Lannoo MJ, Maerz JC, Lowe WH, Valenzuela-Sánchez A, Christiansen DG, Angelini C, Thirion JM, Merilä J, Colli GR, Vasconcellos MM, Boas TCV, Arantes ÍDC, Levionnois P, Reinke BA, Vieira C, Marais GAB, Gaillard JM, Miller DAW. Sex-related differences in aging rate are associated with sex chromosome system in amphibians. Evolution 2021; 76:346-356. [PMID: 34878663 PMCID: PMC9304222 DOI: 10.1111/evo.14410] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 11/11/2021] [Accepted: 11/16/2021] [Indexed: 12/03/2022]
Abstract
Sex‐related differences in mortality are widespread in the animal kingdom. Although studies have shown that sex determination systems might drive lifespan evolution, sex chromosome influence on aging rates have not been investigated so far, likely due to an apparent lack of demographic data from clades including both XY (with heterogametic males) and ZW (heterogametic females) systems. Taking advantage of a unique collection of capture–recapture datasets in amphibians, a vertebrate group where XY and ZW systems have repeatedly evolved over the past 200 million years, we examined whether sex heterogamy can predict sex differences in aging rates and lifespans. We showed that the strength and direction of sex differences in aging rates (and not lifespan) differ between XY and ZW systems. Sex‐specific variation in aging rates was moderate within each system, but aging rates tended to be consistently higher in the heterogametic sex. This led to small but detectable effects of sex chromosome system on sex differences in aging rates in our models. Although preliminary, our results suggest that exposed recessive deleterious mutations on the X/Z chromosome (the “unguarded X/Z effect”) or repeat‐rich Y/W chromosome (the “toxic Y/W effect”) could accelerate aging in the heterogametic sex in some vertebrate clades.
Collapse
Affiliation(s)
- Hugo Cayuela
- Department of Ecology and Evolution, University of Lausanne, Lausanne, 1015, Switzerland
| | - Jean-François Lemaître
- Université Lyon 1, CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, Villeurbanne, F-769622, France
| | - Jean-Paul Léna
- Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR5023 LEHNA, Villeurbanne, F-69622, France
| | - Victor Ronget
- Unité Eco-anthropologie (EA), Muséum National d'Histoire Naturelle, CNRS, Université Paris Diderot, Paris, F-75016, France
| | - Iñigo Martínez-Solano
- Museo Nacional de Ciencias Naturales, CSIC, c/ José Gutiérrez Abascal, 2, Madrid, 28006, Spain
| | - Erin Muths
- U.S. Geological Survey, Fort Collins Science Center, Fort Collins, CO, 80526, USA
| | - David S Pilliod
- U.S. Geological Survey, Forest and Rangeland Ecosystem Science Center, 970 Lusk Street, Boise, ID, 83706, USA
| | - Benedikt R Schmidt
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, 8057, Switzerland.,Info fauna karch, Neuchâtel, 2000, Switzerland
| | - Gregorio Sánchez-Montes
- Museo Nacional de Ciencias Naturales, CSIC, c/ José Gutiérrez Abascal, 2, Madrid, 28006, Spain
| | - Jorge Gutiérrez-Rodríguez
- Museo Nacional de Ciencias Naturales, CSIC, c/ José Gutiérrez Abascal, 2, Madrid, 28006, Spain.,Department of Integrative Ecology, Estación Biológica de Doñana (EBD-CSIC), Seville, Spain
| | - Graham Pyke
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, PR China.,Department of Biological Sciences, Macquarie University, Ryde, NSW, 2109, Australia
| | - Kurt Grossenbacher
- Abteilung Wirbeltiere, Naturhistorisches Museum, Bernastrasse 15, Bern, 3005, Switzerland
| | - Omar Lenzi
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, 8057, Switzerland
| | - Jaime Bosch
- Museo Nacional de Ciencias Naturales, CSIC, c/ José Gutiérrez Abascal, 2, Madrid, 28006, Spain.,UMIB-Research Unit of Biodiversity (CSIC, UO, PA), Universidad de Oviedo, Campus de Mieres, Mieres, 33600, Spain.,Centro de Investigación, Seguimiento y Evaluación, Sierra de Guadarrama National Park, Cta. M-604, Km 27.6, Rascafría, 28740, Spain
| | - Karen H Beard
- Department of Wildland Resources and the Ecology Center, Utah State University, Logan, Utah, 84322, USA
| | - Lawrence L Woolbright
- Biology Department, Siena College, 515 Loudon Road, Loudonville, New York, 12211, USA
| | - Brad A Lambert
- Colorado Natural Heritage Program, Colorado State University, Fort Collins, Colorado, 80523-1475, USA
| | - David M Green
- Redpath Museum, McGill University, Montreal, QC, H3A 0C4, Canada
| | | | - Justin M Garwood
- California Department of Fish and Wildlife, 5341 Ericson Way, Arcata, CA, 95521, USA
| | - Robert N Fisher
- Western Ecological Research Center, U.S. Geological Survey, San Diego, CA, 92101, USA
| | - Kathleen Matthews
- USDA Forest Service, Pacific Southwest Research Station, Albany, California, USA
| | - David Dudgeon
- Division of Ecology and Biodiversity, School of Biological Sciences, The University of Hong Kong, Hong Kong SAR
| | - Anthony Lau
- Science Unit, Lingnan University, Hong Kong, China
| | - Jeroen Speybroeck
- Research Institute for Nature and Forest, Havenlaan 88 bus 73, Brussel, 1000, Belgium
| | - Rebecca Homan
- Biology Department, Denison University, Granville, Ohio, USA
| | - Robert Jehle
- School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Eyup Başkale
- Department of Biology, Faculty of Science and Arts, Pamukkale University, Denizli, Turkey
| | - Emiliano Mori
- Consiglio Nazionale delle Ricerche, Istituto di Ricerca sugli Ecosistemi Terrestri, Via Madonna del Piano 10, Sesto Fiorentino, 50019, Italy
| | - Jan W Arntzen
- Naturalis Biodiversity Center, Leiden, The Netherlands
| | - Pierre Joly
- Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR5023 LEHNA, Villeurbanne, F-69622, France
| | - Rochelle M Stiles
- San Francisco Zoological Society, 1 Zoo Road, San Francisco, California, 94132, USA
| | - Michael J Lannoo
- Indiana University School of Medicine-TH, 620 Chestnut Street, Terre Haute, Indiana, 47809, USA
| | - John C Maerz
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA, USA
| | - Winsor H Lowe
- Division of Biological Sciences, University of Montana, Missoula, Montana, 59812, USA
| | - Andrés Valenzuela-Sánchez
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, 5090000, Chile.,ONG Ranita de Darwin, Valdivia, 5112144, Chile
| | - Ditte G Christiansen
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, 8057, Switzerland
| | - Claudio Angelini
- Salamandrina Sezzese Search Society, via G. Marconi 30, Sezze, 04018, Italy
| | - Jean-Marc Thirion
- Objectifs Biodiversité, 22 rue du Dr. Gilbert, Pont-l'Abbé-d'Arnoult, 17250, France
| | - Juha Merilä
- Division of Ecology and Biodiversity, School of Biological Sciences, The University of Hong Kong, Hong Kong SAR.,Ecological Genetics Research Unit, Research Programme in Organismal and Evolutionary Biology, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, 00014, Finland
| | - Guarino R Colli
- Departamento de Zoologia, Universidade de Brasília, Brasília, Distrito Federal, 70910-900, Brazil
| | - Mariana M Vasconcellos
- Department of Biology, City College of New York, The City University of New York, New York, NY, 10031, USA
| | - Taissa C V Boas
- Departamento de Zoologia, Universidade de Brasília, Brasília, Distrito Federal, 70910-900, Brazil
| | - Ísis da C Arantes
- Department of Biology, University of Mississippi, Oxford, MS, 38677, USA
| | - Pauline Levionnois
- Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR5023 LEHNA, Villeurbanne, F-69622, France
| | - Beth A Reinke
- Department of Biology, Northeastern Illinois University, 5500 North St. Louis Avenue, Chicago, IL, 60625, USA
| | - Cristina Vieira
- Université Lyon 1, CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, Villeurbanne, F-769622, France
| | - Gabriel A B Marais
- Université Lyon 1, CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, Villeurbanne, F-769622, France.,LEAF- Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, Portugal
| | - Jean-Michel Gaillard
- Université Lyon 1, CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, Villeurbanne, F-769622, France
| | - David A W Miller
- Department of Ecosystem Sciences and Management, The Pennsylvania State University, University Park, Pennsylvania, USA
| |
Collapse
|
10
|
de Moraes RLR, Sassi FDMC, Bertollo LAC, Marinho MMF, Viana PF, Feldberg E, Oliveira VCS, Deon GA, Al-Rikabi ABH, Liehr T, Cioffi MDB. Tracking the Evolutionary Trends Among Small-Size Fishes of the Genus Pyrrhulina (Characiforme, Lebiasinidae): New Insights From a Molecular Cytogenetic Perspective. Front Genet 2021; 12:769984. [PMID: 34691160 PMCID: PMC8526856 DOI: 10.3389/fgene.2021.769984] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 09/22/2021] [Indexed: 11/13/2022] Open
Abstract
Miniature fishes have always been a challenge for cytogenetic studies due to the difficulty in obtaining chromosomal preparations, making them virtually unexplored. An example of this scenario relies on members of the family Lebiasinidae which include miniature to medium-sized, poorly known species, until very recently. The present study is part of undergoing major cytogenetic advances seeking to elucidate the evolutionary history of lebiasinids. Aiming to examine the karyotype diversification more deeply in Pyrrhulina, here we combined classical and molecular cytogenetic analyses, including Giemsa staining, C-banding, repetitive DNA mapping, comparative genomic hybridization (CGH), and whole chromosome painting (WCP) to perform the first analyses in five Pyrrhulina species (Pyrrhulina aff. marilynae, Pyrrhulina sp., P. obermulleri, P. marilynae and Pyrrhulina cf. laeta). The diploid number (2n) ranged from 40 to 42 chromosomes among all analyzed species, but P. marilynae is strikingly differentiated by having 2n = 32 chromosomes and a karyotype composed of large meta/submetacentric chromosomes, whose plesiomorphic status is discussed. The distribution of microsatellites does not markedly differ among species, but the number and position of the rDNA sites underwent significant changes among them. Interspecific comparative genome hybridization (CGH) found a moderate divergence in the repetitive DNA content among the species’ genomes. Noteworthy, the WCP reinforced our previous hypothesis on the origin of the X1X2Y multiple sex chromosome system in P. semifasciata. In summary, our data suggest that the karyotype differentiation in Pyrrhulina has been driven by major structural rearrangements, accompanied by high dynamics of repetitive DNAs.
Collapse
Affiliation(s)
- Renata Luiza Rosa de Moraes
- Laboratorio de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), São Carlos, Brazil
| | | | - Luiz Antonio Carlos Bertollo
- Laboratorio de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), São Carlos, Brazil
| | - Manoela Maria Ferreira Marinho
- Museu de Zoologia da Universidade de São Paulo (MZUSP), São Paulo, Brazil.,Laboratório de Sistemática e Morfologia de Peixes, Departamento de Sistemática e Ecologia (DSE), Universidade Federal da Paraíba (UFPB), João Pessoa, Brazil
| | - Patrik Ferreira Viana
- Laboratório de Gentética Animal, Instituto Nacional de Pesquisa da Amazônia, Coordenação de Biodiversidade, Manaus, Brazil
| | - Eliana Feldberg
- Laboratório de Gentética Animal, Instituto Nacional de Pesquisa da Amazônia, Coordenação de Biodiversidade, Manaus, Brazil
| | - Vanessa Cristina Sales Oliveira
- Laboratorio de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), São Carlos, Brazil
| | - Geize Aparecida Deon
- Laboratorio de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), São Carlos, Brazil.,Laboratório de Biologia Cromossômica, Estrutura e Função, Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa, Brazil
| | | | - Thomas Liehr
- Institute of Human Genetics, University Hospital Jena, Jena, Germany
| | - Marcelo de Bello Cioffi
- Laboratorio de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), São Carlos, Brazil
| |
Collapse
|
11
|
The Snakeskin Gourami (Trichopodus pectoralis) Tends to Exhibit XX/XY Sex Determination. FISHES 2021. [DOI: 10.3390/fishes6040043] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The snakeskin gourami (Trichopodus pectoralis) has a high meat yield and is one of the top five aquaculture freshwater fishes in Thailand. The species is not externally sexually dimorphic, and its sex determination system is unknown. Understanding the sex determination system of this species will contribute to its full-scale commercialization. In this study, a cytogenetic analysis did not reveal any between-sex differences in chromosomal patterns. However, we used genotyping-by-sequencing to identify 4 male-linked loci and 1 female-linked locus, indicating that the snakeskin gourami tends to exhibit an XX/XY sex determination system. However, we did not find any male-specific loci after filtering the loci for a ratio of 100:0 ratio of males:females. This suggests that the putative Y chromosome is young and that the sex determination region is cryptic. This approach provides solid information that can help identify the sex determination mechanism and potential sex determination regions in the snakeskin gourami, allowing further investigation of genetic improvements in the species.
Collapse
|
12
|
Sember A, Nguyen P, Perez MF, Altmanová M, Ráb P, Cioffi MDB. Multiple sex chromosomes in teleost fishes from a cytogenetic perspective: state of the art and future challenges. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200098. [PMID: 34304595 PMCID: PMC8310710 DOI: 10.1098/rstb.2020.0098] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/30/2020] [Indexed: 12/15/2022] Open
Abstract
Despite decades of cytogenetic and genomic research of dynamic sex chromosome evolution in teleost fishes, multiple sex chromosomes have been largely neglected. In this review, we compiled available data on teleost multiple sex chromosomes, identified major trends in their evolution and suggest further trajectories in their investigation. In a compiled dataset of 440 verified records of fish sex chromosomes, we counted 75 multiple sex chromosome systems with 60 estimated independent origins. We showed that male-heterogametic systems created by Y-autosome fusion predominate and that multiple sex chromosomes are over-represented in the order Perciformes. We documented a striking difference in patterns of differentiation of sex chromosomes between male and female heterogamety and hypothesize that faster W sex chromosome differentiation may constrain sex chromosome turnover in female-heterogametic systems. We also found no significant association between the mechanism of multiple sex chromosome formation and percentage of uni-armed chromosomes in teleost karyotypes. Last but not least, we hypothesized that interaction between fish populations, which differ in their sex chromosomes, can drive the evolution of multiple sex chromosomes in fishes. This underlines the importance of broader inter-population sampling in studies of fish sex chromosomes. This article is part of the theme issue 'Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part II)'.
Collapse
Affiliation(s)
- Alexandr Sember
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 277 21 Liběchov, Czech Republic
| | - Petr Nguyen
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 277 21 Liběchov, Czech Republic
- Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05 České Budějovice, Czech Republic
| | - Manolo F. Perez
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, Rod. Washington Luiz km 235 cep, 13565-905, São Carlos, Brazil
| | - Marie Altmanová
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 277 21 Liběchov, Czech Republic
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, 128 44 Prague, Czech Republic
| | - Petr Ráb
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 277 21 Liběchov, Czech Republic
| | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, Rod. Washington Luiz km 235 cep, 13565-905, São Carlos, Brazil
| |
Collapse
|
13
|
Martínez P, Robledo D, Taboada X, Blanco A, Moser M, Maroso F, Hermida M, Gómez-Tato A, Álvarez-Blázquez B, Cabaleiro S, Piferrer F, Bouza C, Lien S, Viñas AM. A genome-wide association study, supported by a new chromosome-level genome assembly, suggests sox2 as a main driver of the undifferentiatiated ZZ/ZW sex determination of turbot (Scophthalmus maximus). Genomics 2021; 113:1705-1718. [PMID: 33838278 DOI: 10.1016/j.ygeno.2021.04.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 03/20/2021] [Accepted: 04/05/2021] [Indexed: 01/10/2023]
Abstract
BACKGROUND Understanding sex determination (SD) across taxa is a major challenge for evolutionary biology. The new genomic tools are paving the way to identify genomic features underlying SD in fish, a group frequently showing limited sex chromosome differentiation and high SD evolutionary turnover. Turbot (Scophthalmus maximus) is a commercially important flatfish with an undifferentiated ZW/ZZ SD system and remarkable sexual dimorphism. Here we describe a new long-read turbot genome assembly used to disentangle the genetic architecture of turbot SD by combining genomics and classical genetics approaches. RESULTS The new turbot genome assembly consists of 145 contigs (N50 = 22.9 Mb), 27 of them representing >95% of its estimated genome size. A genome wide association study (GWAS) identified a ~ 6.8 Mb region on chromosome 12 associated with sex in 69.4% of the 36 families analyzed. The highest associated markers flanked sox2, the only gene in the region showing differential expression between sexes before gonad differentiation. A single SNP showed consistent differences between Z and W chromosomes. The analysis of a broad sample of families suggested the presence of additional genetic and/or environmental factors on turbot SD. CONCLUSIONS The new chromosome-level turbot genome assembly, one of the most contiguous fish assemblies to date, facilitated the identification of sox2 as a consistent candidate gene putatively driving SD in this species. This chromosome SD system barely showed any signs of differentiation, and other factors beyond the main QTL seem to control SD in a certain proportion of families.
Collapse
Affiliation(s)
- Paulino Martínez
- Departament of Zoology, Genetics and Physical Anthropology, Faculty of Veterinary, Universidade de Santiago de Compostela, Campus de Lugo, 27002 Lugo, Spain.
| | - Diego Robledo
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UK.
| | - Xoana Taboada
- Departament of Zoology, Genetics and Physical Anthropology, Faculty of Biology, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Andrés Blanco
- Departament of Zoology, Genetics and Physical Anthropology, Faculty of Veterinary, Universidade de Santiago de Compostela, Campus de Lugo, 27002 Lugo, Spain.
| | - Michel Moser
- Centre for Integrative Genetics, Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway.
| | - Francesco Maroso
- Department of Life Science and Biotechnology, University of Ferrara, 44121 Ferrara, Italy
| | - Miguel Hermida
- Departament of Zoology, Genetics and Physical Anthropology, Faculty of Veterinary, Universidade de Santiago de Compostela, Campus de Lugo, 27002 Lugo, Spain.
| | - Antonio Gómez-Tato
- Departament of Mathematics, Faculty of Mathematics, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain.
| | - Blanca Álvarez-Blázquez
- Instituto Español de Oceanografía (IEO), Centro Oceanográfico de Vigo, Cabo Estay-Canido, 36280 Vigo, Spain.
| | - Santiago Cabaleiro
- Cluster de Acuicultura de Galicia (Punta do Couso), Aguiño-Ribeira, 15695 A Coruña, Spain.
| | - Francesc Piferrer
- Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (CSIC), 08003 Barcelona, Spain.
| | - Carmen Bouza
- Departament of Zoology, Genetics and Physical Anthropology, Faculty of Veterinary, Universidade de Santiago de Compostela, Campus de Lugo, 27002 Lugo, Spain.
| | - Sigbjørn Lien
- Centre for Integrative Genetics, Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway.
| | - Ana M Viñas
- Departament of Zoology, Genetics and Physical Anthropology, Faculty of Biology, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain.
| |
Collapse
|
14
|
High Genetic Diversity despite Conserved Karyotype Organization in the Giant Trahiras from Genus Hoplias (Characiformes, Erythrinidae). Genes (Basel) 2021; 12:genes12020252. [PMID: 33578790 PMCID: PMC7916553 DOI: 10.3390/genes12020252] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 02/05/2021] [Accepted: 02/05/2021] [Indexed: 11/17/2022] Open
Abstract
In the fish genus Hoplias, two major general groups can be found, one of which is formed by the “common trahiras” (Hoplias malabaricus group) and the other by the “giant trahiras” (Hoplias lacerdae group, in addition to Hoplias aimara), which usually comprises specimens of larger body size. Previous investigations from the giant trahiras group recovered 2n = 50 meta/submetacentric chromosomes and no sex chromosome differentiation, indicating a probable conservative pattern for their karyotype organization. Here, we conducted comparative cytogenetic studies in six giant trahiras species, two of them for the first time. We employed standard and advanced molecular cytogenetics procedures, including comparative genomic hybridization (CGH), as well as genomic assessments of diversity levels and phylogenetic relationships among them. The results strongly suggest that the giant trahiras have a particular and differentiated evolutionary pathway inside the Hoplias genus. While these species share the same 2n and karyotypes, their congeneric species of the H. malabaricus group show a notable chromosomal diversity in number, morphology, and sex chromosome systems. However, at the same time, significant changes were characterized at their inner chromosomal level, as well as in their genetic diversity, highlighting their current relationships resulting from different evolutionary histories.
Collapse
|
15
|
Highly Rearranged Karyotypes and Multiple Sex Chromosome Systems in Armored Catfishes from the Genus Harttia (Teleostei, Siluriformes). Genes (Basel) 2020; 11:genes11111366. [PMID: 33218104 PMCID: PMC7698909 DOI: 10.3390/genes11111366] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/15/2020] [Accepted: 11/16/2020] [Indexed: 11/16/2022] Open
Abstract
Harttia comprises an armored catfish genus endemic to the Neotropical region, including 27 valid species with low dispersion rates that are restricted to small distribution areas. Cytogenetics data point to a wide chromosomal diversity in this genus due to changes that occurred in isolated populations, with chromosomal fusions and fissions explaining the 2n number variation. In addition, different multiple sex chromosome systems and rDNA loci location are also found in some species. However, several Harttia species and populations remain to be investigated. In this study, Harttia intermontana and two still undescribed species, morphologically identified as Harttia sp. 1 and Harttia sp. 2, were cytogenetically analyzed. Harttia intermontana has 2n = 52 and 2n = 53 chromosomes, while Harttia sp. 1 has 2n = 56 and 2n = 57 chromosomes in females and males, respectively, thus highlighting the occurrence of an XX/XY1Y2 multiple sex chromosome system in both species. Harttia sp. 2 presents 2n = 62 chromosomes for both females and males, with fission events explaining its karyotype diversification. Chromosomal locations of the rDNA sites were also quite different among species, reinforcing that extensive rearrangements had occurred in their karyotype evolution. Comparative genomic hybridization (CGH) experiments among some Harttia species evidenced a shared content of the XY1Y2 sex chromosomes in three of them, thus pointing towards their common origin. Therefore, the comparative analysis among all Harttia species cytogenetically studied thus far allowed us to provide an evolutionary scenario related to the speciation process of this fish group.
Collapse
|
16
|
Sassi FDMC, Deon GA, Moreira-Filho O, Vicari MR, Bertollo LAC, Liehr T, de Oliveira EA, Cioffi MB. Multiple Sex Chromosomes and Evolutionary Relationships in Amazonian Catfishes: The Outstanding Model of the Genus Harttia (Siluriformes: Loricariidae). Genes (Basel) 2020; 11:genes11101179. [PMID: 33050411 PMCID: PMC7600804 DOI: 10.3390/genes11101179] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 10/06/2020] [Accepted: 10/08/2020] [Indexed: 02/06/2023] Open
Abstract
The armored Harttia catfishes present great species diversity and remarkable cytogenetic variation, including different sex chromosome systems. Here we analyzed three new species, H. duriventris, H. villasboas and H. rondoni, using both conventional and molecular cytogenetic techniques (Giemsa-staining and C-banding), including the mapping of repetitive DNAs using fluorescence in situ hybridization (FISH) and comparative genomic hybridization (CGH) experiments. Both H. duriventris and H. villasboas have 2n = ♀56/♂55 chromosomes, and an X1X1X2X2 /X1X2Y sex chromosome system, while a proto or neo-XY system is proposed for H. rondoni (2n = 54♀♂). Single motifs of 5S and 18S rDNA occur in all three species, with the latter being also mapped in the sex chromosomes. The results confirm the general evolutionary trend that has been noticed for the genus: an extensive variation on their chromosome number, single sites of rDNA sequences and the occurrence of multiple sex chromosomes. Comparative genomic analyses with another congeneric species, H. punctata, reveal that the X1X2Y sex chromosomes of these species share the genomic contents, indicating a probable common origin. The remarkable karyotypic variation, including sex chromosomes systems, makes Harttia a suitable model for evolutionary studies focusing on karyotype differentiation and sex chromosome evolution among lower vertebrates.
Collapse
Affiliation(s)
- Francisco de M. C. Sassi
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São, Carlos, São Carlos, SP 13565-905, Brazil; (F.d.M.C.S.); (G.A.D.); (O.M.-F.); (L.A.C.B.); (M.B.C.)
| | - Geize A. Deon
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São, Carlos, São Carlos, SP 13565-905, Brazil; (F.d.M.C.S.); (G.A.D.); (O.M.-F.); (L.A.C.B.); (M.B.C.)
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa, PR 84010-330, Brazil;
| | - Orlando Moreira-Filho
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São, Carlos, São Carlos, SP 13565-905, Brazil; (F.d.M.C.S.); (G.A.D.); (O.M.-F.); (L.A.C.B.); (M.B.C.)
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa, PR 84010-330, Brazil;
| | - Marcelo R. Vicari
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa, PR 84010-330, Brazil;
| | - Luiz A. C. Bertollo
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São, Carlos, São Carlos, SP 13565-905, Brazil; (F.d.M.C.S.); (G.A.D.); (O.M.-F.); (L.A.C.B.); (M.B.C.)
| | - Thomas Liehr
- Institute of Human Genetics, University Hospital Jena, Jena 07747, Germany
- Correspondence: ; Tel.: +49-3641-9396850; Fax: +49-3641-9396852
| | | | - Marcelo B. Cioffi
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São, Carlos, São Carlos, SP 13565-905, Brazil; (F.d.M.C.S.); (G.A.D.); (O.M.-F.); (L.A.C.B.); (M.B.C.)
| |
Collapse
|
17
|
Dulz TA, Azambuja M, Nascimento VD, Lorscheider CA, Noleto RB, Moreira-Filho O, Nogaroto V, Diniz D, Affonso PRADM, Vicari MR. Karyotypic Diversification in Two Megaleporinus Species (Characiformes, Anostomidae) Inferred from In Situ Localization of Repetitive DNA Sequences. Zebrafish 2020; 17:333-341. [PMID: 32990531 DOI: 10.1089/zeb.2020.1918] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Anostomidae species have conserved diploid numbers (2n = 54), although comparative cytogenetic studies have demonstrated chromosomal rearrangements occurrence among them, especially in repetitive DNA rich regions. The location and distribution of ribosomal DNA (rDNA) and small nuclear RNAs (snRNAs) multigene families are highly dynamic in the genomes of several organisms. In this study, we in situ located the rDNA and snRNA sites in two populations of Megaleporinus obtusidens and a sample of Megaleporinus reinhardti to infer their chromosomal changes in the evolutionary lineages. Both species of Megaleporinus shared 2n = 54 chromosomes with the presence of ZZ/ZW sex chromosome system, but they diverged in relationship to the location of 5S and 45S rDNAs as well as the distribution of snRNAs sites. The characterization of the analyzed sequences revealed the presence of complete rDNA and snRNAs sequences as well as snRNAs containing transposable elements (TEs) and microsatellite repeats. After chromosomal mapping, the sequences encompassing TEs proved to be dispersed through autosomes and accumulated on sex chromosomes. The data demonstrate that intra- and interspecific chromosomal changes occurred involving the multigene family's sites in Megaleporinus karyotypes. Furthermore, we detected TE-like sequences in the differentiation of sex chromosome systems in M. obtusidens and M. reinhardti.
Collapse
Affiliation(s)
- Thais Aparecida Dulz
- Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Curitiba, Brazil.,Departamento de Ciências Biológicas, Universidade Estadual do Paraná, União da Vitória, Brazil
| | - Matheus Azambuja
- Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Curitiba, Brazil
| | | | | | - Rafael Bueno Noleto
- Departamento de Ciências Biológicas, Universidade Estadual do Paraná, União da Vitória, Brazil
| | - Orlando Moreira-Filho
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Viviane Nogaroto
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa, Brazil
| | - Débora Diniz
- Departamento de Ciências Biológicas, Universidade Estadual do Sudoeste da Bahia, Jequié, Brazil
| | | | - Marcelo Ricardo Vicari
- Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Curitiba, Brazil.,Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa, Brazil
| |
Collapse
|
18
|
Sex Chromosomes and Internal Telomeric Sequences in Dormitator latifrons (Richardson 1844) (Eleotridae: Eleotrinae): An Insight into their Origin in the Genus. Genes (Basel) 2020; 11:genes11060659. [PMID: 32560434 PMCID: PMC7349016 DOI: 10.3390/genes11060659] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 06/11/2020] [Accepted: 06/15/2020] [Indexed: 12/16/2022] Open
Abstract
The freshwater fish species Dormitator latifrons, commonly named the Pacific fat sleeper, is an important food resource in CentralSouth America, yet almost no genetic information on it is available. A cytogenetic analysis of this species was undertaken by standard and molecular techniques (chromosomal mapping of 18S rDNA, 5S rDNA, and telomeric repeats), aiming to describe the karyotype features, verify the presence of sex chromosomes described in congeneric species, and make inferences on chromosome evolution in the genus. The karyotype (2n = 46) is mainly composed of metacentric and submetacentic chromosomes, with nucleolar organizer regions (NORs) localized on the short arms of submetacentric pair 10. The presence of XX/XY sex chromosomes was observed, with the X chromosome carrying the 5S rDNA sequences. These heterochromosomes likely appeared before 1 million years ago, since they are shared with another derived Dormitator species (Dormitator maculatus) distributed in the Western Atlantic. Telomeric repeats hybridize to the terminal portions of almost all chromosomes; additional interstitial sites are present in the centromeric region, suggesting pericentromeric inversions as the main rearrangement mechanisms that has driven karyotypic evolution in the genus. The data provided here contribute to improving the cytogenetics knowledge of D. latifrons, offering basic information that could be useful in aquaculture farming of this neotropical fish.
Collapse
|
19
|
Nirchio M, Paim FG, Britzke R, Rossi AR, Milana V, Oliveira C. Molecular Analysis and Chromosome Mapping of Repetitive DNAs in the Green Terror Andinoacara rivulatus (Cichlidae: Cichlasomatini). Zebrafish 2020; 17:38-47. [PMID: 31994993 DOI: 10.1089/zeb.2019.1811] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Neotropical cichlids include hundreds of species whose taxonomy has benefited of molecular phylogeny and whose karyotype evolution has been related to the amount and distribution of different classes of repetitive sequences. This study provides the first integrative molecular (cytochrome c oxidase subunit 1 and 16S sequences) and cytogenetic analyses of wild samples of the green terror Andinoacara rivulatus, a cichlid naturally distributed in Ecuador and spread throughout the world as an aquarium pet. Molecular data revealed that sequences of green terror constitute a single monophyletic clade within the genus and allowed species attribution of uncertain samples previously cytogenetically analyzed. Chromosome number (2n = 48) conforms to the general trend observed within neotropical cichlids. However, mapping of different classes of repeated sequences (18S rDNA, 5S rDNA, U1 snDNA and telomeric) revealed the presence of features uncommon among representatives of these fishes, like multiple major rDNA sites, and suggested a recent occurrence of rearrangements (fusion/inversion) in two chromosome pairs.
Collapse
Affiliation(s)
- Mauro Nirchio
- Departamento de Acuicultura, Escuela de Ciencias Aplicadas del Mar, Núcleo de Nueva Esparta, Universidad de Oriente, Porlamar, Venezuela.,Departamento de Acuicultura, Facultad de Ciencias Agropecuarias, Universidad Técnica de Machala, Machala, Ecuador
| | - Fabilene Gomes Paim
- Departamento de Morfologia, Instituto de Biociências Universidade Estadual Paulista, UNESP, Botucatu, Brazil
| | - Ricardo Britzke
- Departamento de Acuicultura, Facultad de Ciencias Agropecuarias, Universidad Técnica de Machala, Machala, Ecuador.,Departamento de Morfologia, Instituto de Biociências Universidade Estadual Paulista, UNESP, Botucatu, Brazil
| | - Anna Rita Rossi
- Dipartimento di Biologia e Biotecnologie "C. Darwin," Sapienza-Università di Roma, Rome, Italy
| | - Valentina Milana
- Dipartimento di Biologia e Biotecnologie "C. Darwin," Sapienza-Università di Roma, Rome, Italy
| | - Claudio Oliveira
- Departamento de Morfologia, Instituto de Biociências Universidade Estadual Paulista, UNESP, Botucatu, Brazil
| |
Collapse
|
20
|
Pinheiro Figliuolo VS, Goll L, Ferreira Viana P, Feldberg E, Gross MC. First Record on Sex Chromosomes in a Species of the Family Cynodontidae: Cynodon gibbus (Agassiz, 1829). Cytogenet Genome Res 2020; 160:29-37. [PMID: 32092757 DOI: 10.1159/000505889] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/06/2019] [Indexed: 01/09/2023] Open
Abstract
The fish family Cynodontidae belongs to the superfamily Curimatoidea, together with the Hemiodontidae, Serrasalmidae, Parodontidae, Prochilodontidae, Chilodontidae, Curimatidae, and Anostomidae. The majority of the species of this superfamily that have been analyzed to date have a diploid chromosome number of 2n = 54. Differentiated sex chromosomes (with female heterogamety) have been observed only in the Prochilodontidae, Parodontidae, and Anostomidae. The present study provides the first description of differentiated sex chromosomes in the cynodontid species Cynodon gibbus, which has a ZZ/ZW system, and shows that repetitive DNA has played a fundamental role in the differentiation of these sex chromosomes.
Collapse
|
21
|
Sember A, de Oliveira EA, Ráb P, Bertollo LAC, de Freitas NL, Viana PF, Yano CF, Hatanaka T, Marinho MMF, de Moraes RLR, Feldberg E, Cioffi MDB. Centric Fusions behind the Karyotype Evolution of Neotropical Nannostomus Pencilfishes (Characiforme, Lebiasinidae): First Insights from a Molecular Cytogenetic Perspective. Genes (Basel) 2020; 11:genes11010091. [PMID: 31941136 PMCID: PMC7017317 DOI: 10.3390/genes11010091] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 01/07/2020] [Accepted: 01/08/2020] [Indexed: 02/07/2023] Open
Abstract
Lebiasinidae is a Neotropical freshwater family widely distributed throughout South and Central America. Due to their often very small body size, Lebiasinidae species are cytogenetically challenging and hence largely underexplored. However, the available but limited karyotype data already suggested a high interspecific variability in the diploid chromosome number (2n), which is pronounced in the speciose genus Nannostomus, a popular taxon in ornamental fish trade due to its remarkable body coloration. Aiming to more deeply examine the karyotype diversification in Nannostomus, we combined conventional cytogenetics (Giemsa-staining and C-banding) with the chromosomal mapping of tandemly repeated 5S and 18S rDNA clusters and with interspecific comparative genomic hybridization (CGH) to investigate genomes of four representative Nannostomus species: N. beckfordi, N. eques, N. marginatus, and N. unifasciatus. Our data showed a remarkable variability in 2n, ranging from 2n = 22 in N. unifasciatus (karyotype composed exclusively of metacentrics/submetacentrics) to 2n = 44 in N. beckfordi (karyotype composed entirely of acrocentrics). On the other hand, patterns of 18S and 5S rDNA distribution in the analyzed karyotypes remained rather conservative, with only two 18S and two to four 5S rDNA sites. In view of the mostly unchanged number of chromosome arms (FN = 44) in all but one species (N. eques; FN = 36), and with respect to the current phylogenetic hypothesis, we propose Robertsonian translocations to be a significant contributor to the karyotype differentiation in (at least herein studied) Nannostomus species. Interspecific comparative genome hybridization (CGH) using whole genomic DNAs mapped against the chromosome background of N. beckfordi found a moderate divergence in the repetitive DNA content among the species’ genomes. Collectively, our data suggest that the karyotype differentiation in Nannostomus has been largely driven by major structural rearrangements, accompanied by only low to moderate dynamics of repetitive DNA at the sub-chromosomal level. Possible mechanisms and factors behind the elevated tolerance to such a rate of karyotype change in Nannostomus are discussed.
Collapse
Affiliation(s)
- Alexandr Sember
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 277 21 Liběchov, Czech Republic; (A.S.); (P.R.)
| | - Ezequiel Aguiar de Oliveira
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo 13565-905, Brazil; (E.A.d.O.); (L.A.C.B.); (N.L.d.F.); (C.F.Y.); (T.H.); (R.L.R.d.M.)
- Secretaria de Estado de Educação de Mato Grosso–SEDUC-MT, Cuiabá 78049-909, Brazil
| | - Petr Ráb
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 277 21 Liběchov, Czech Republic; (A.S.); (P.R.)
| | - Luiz Antonio Carlos Bertollo
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo 13565-905, Brazil; (E.A.d.O.); (L.A.C.B.); (N.L.d.F.); (C.F.Y.); (T.H.); (R.L.R.d.M.)
| | - Natália Lourenço de Freitas
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo 13565-905, Brazil; (E.A.d.O.); (L.A.C.B.); (N.L.d.F.); (C.F.Y.); (T.H.); (R.L.R.d.M.)
| | - Patrik Ferreira Viana
- Instituto Nacional de Pesquisas da Amazônia, Coordenação de Biodiversidade, Av. André Araújo 2936, Petrópolis, Manaus 69067-375, Brazil; (P.F.V.); (E.F.)
| | - Cassia Fernanda Yano
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo 13565-905, Brazil; (E.A.d.O.); (L.A.C.B.); (N.L.d.F.); (C.F.Y.); (T.H.); (R.L.R.d.M.)
| | - Terumi Hatanaka
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo 13565-905, Brazil; (E.A.d.O.); (L.A.C.B.); (N.L.d.F.); (C.F.Y.); (T.H.); (R.L.R.d.M.)
| | - Manoela Maria Ferreira Marinho
- Universidade Federal da Paraíba (UFPB), Departamento de Sistemática e Ecologia (DSE), Laboratório de Sistemática e Morfologia de Peixes, João Pessoa 58051-090, Brazil;
| | - Renata Luiza Rosa de Moraes
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo 13565-905, Brazil; (E.A.d.O.); (L.A.C.B.); (N.L.d.F.); (C.F.Y.); (T.H.); (R.L.R.d.M.)
| | - Eliana Feldberg
- Instituto Nacional de Pesquisas da Amazônia, Coordenação de Biodiversidade, Av. André Araújo 2936, Petrópolis, Manaus 69067-375, Brazil; (P.F.V.); (E.F.)
| | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo 13565-905, Brazil; (E.A.d.O.); (L.A.C.B.); (N.L.d.F.); (C.F.Y.); (T.H.); (R.L.R.d.M.)
- Correspondence: ; Tel.: +55-16-3351-8431; Fax: +55-16-3351-8377
| |
Collapse
|
22
|
Kowalski S, Paiz LM, da Silva M, Machado ADS, Feldberg E, Traldi JB, Margarido VP, Lui RL. Chromosomal analysis of Centromochlus heckelii (Siluriformes: Auchenipteridae), with a contribution to Centromochlus definition. NEOTROPICAL ICHTHYOLOGY 2020. [DOI: 10.1590/1982-0224-2020-0009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
ABSTRACT Historically, there are divergences in the species allocation between Centromochlus and Tatia. This study aimed to generate the first cytogenetic data about Centromochlus and, by analyzing a population of Centromochlus heckelii from the Amazon River basin, to contribute as evidence to a historical taxonomic dilemma. Diploid number of 46 chromosomes and a heteromorphic pair was found in the female karyotypes, thus characterizing a ZZ/ZW sex chromosome system. Pale blocks of heterochromatin were located in centromeric regions of some chromosomes; however, the exclusive female chromosome (W) is almost entirely heterochromatic. AgNORs were detected in terminal position on the short arms of one acrocentric pair in males and two chromosome pairs in females, the acrocentric plus the sex chromosome pair. Notable differences between Centromochlus heckelii and previous data about species of Tatia are: lower diploid number, presence of a sex chromosome system and multiple AgNORs in Centromochlus, while species of Tatia have simple AgNORs and the absence of acrocentric chromosomes. Results in this study show that chromosomal markers could contribute as evidence to taxonomic delimitation studies.
Collapse
|
23
|
de Moraes RLR, Sember A, Bertollo LAC, de Oliveira EA, Ráb P, Hatanaka T, Marinho MMF, Liehr T, Al-Rikabi ABH, Feldberg E, Viana PF, Cioffi MDB. Comparative Cytogenetics and Neo-Y Formation in Small-Sized Fish Species of the Genus Pyrrhulina (Characiformes, Lebiasinidae). Front Genet 2019; 10:678. [PMID: 31428127 PMCID: PMC6689988 DOI: 10.3389/fgene.2019.00678] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 06/27/2019] [Indexed: 12/20/2022] Open
Abstract
Although fishes have traditionally been the subject of comparative evolutionary studies, few reports have concentrated on the application of multipronged modern molecular cytogenetic techniques (such as comparative genomic hybridization = CGH and whole chromosome painting = WCP) to analyze deeper the karyotype evolution of specific groups, especially the historically neglected small-sized ones. Representatives of the family Lebiasinidae (Characiformes) are a notable example, where only a few cytogenetic investigations have been conducted thus far. Here, we aim to elucidate the evolutionary processes behind the karyotype differentiation of Pyrrhulina species on a finer-scale cytogenetic level. To achieve this, we applied C-banding, repetitive DNA mapping, CGH and WCP in Pyrrhulina semifasciata and P. brevis. Our results showed 2n = 42 in both sexes of P. brevis, while the difference in 2n between male and female in P. semifasciata (♂41/♀42) stands out due to the presence of a multiple X1X2Y sex chromosome system, until now undetected in this family. As a remarkable common feature, multiple 18S and 5S rDNA sites are present, with an occasional synteny or tandem-repeat amplification. Male-vs.-female CGH experiments in P. semifasciata highlighted the accumulation of male-enriched repetitive sequences in the pericentromeric region of the Y chromosome. Inter-specific CGH experiments evidenced a divergence between both species’ genomes based on the presence of several species-specific signals, highlighting their inner genomic diversity. WCP with the P. semifasciata-derived Y (PSEMI-Y) probe painted not only the entire metacentric Y chromosome in males but also the X1 and X2 chromosomes in both male and female chromosomes of P. semifasciata. In the cross-species experiments, the PSEMI-Y probe painted four acrocentric chromosomes in both males and females of the other tested Pyrrhulina species. In summary, our results show that both intra- and interchromosomal rearrangements together with the dynamics of repetitive DNA significantly contributed to the karyotype divergence among Pyrrhulina species, possibly promoted by specific populational and ecological traits and accompanied in one species by the origin of neo-sex chromosomes. The present results suggest how particular evolutionary scenarios found in fish species can help to clarify several issues related to genome organization and the karyotype evolution of vertebrates in general.
Collapse
Affiliation(s)
- Renata Luiza Rosa de Moraes
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), São Carlos, Brazil
| | - Alexandr Sember
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czechia
| | - Luiz Antônio Carlos Bertollo
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), São Carlos, Brazil
| | - Ezequiel Aguiar de Oliveira
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), São Carlos, Brazil.,Secretaria de Estado de Educação de Mato Grosso - SEDUC-MT, Cuiabá, Brazil
| | - Petr Ráb
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czechia
| | - Terumi Hatanaka
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), São Carlos, Brazil
| | | | - Thomas Liehr
- Institute of Human Genetics, University Hospital Jena, Jena, Germany
| | | | - Eliana Feldberg
- Laboratório de Genética Animal, Instituto Nacional de Pesquisas da Amazônia, Coordenação de Biodiversidade, Manaus, Brazil
| | - Patrik F Viana
- Laboratório de Genética Animal, Instituto Nacional de Pesquisas da Amazônia, Coordenação de Biodiversidade, Manaus, Brazil
| | - Marcelo de Bello Cioffi
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), São Carlos, Brazil.,Institute of Human Genetics, University Hospital Jena, Jena, Germany
| |
Collapse
|
24
|
García-Angulo A, Merlo MA, Portela-Bens S, Rodríguez ME, García E, Al-Rikabi A, Liehr T, Rebordinos L. Evidence for a Robertsonian fusion in Solea senegalensis (Kaup, 1858) revealed by zoo-FISH and comparative genome analysis. BMC Genomics 2018; 19:818. [PMID: 30428854 PMCID: PMC6236887 DOI: 10.1186/s12864-018-5216-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 10/31/2018] [Indexed: 11/16/2022] Open
Abstract
Background Solea senegalensis (Kaup, 1858) is a commercially important flatfish species, belonging to the Pleuronectiformes order. The taxonomy of this group has long been controversial, and the karyotype of the order presents a high degree of variability in diploid number, derived from chromosomal rearrangements such as Robertsonian fusions. Previously it has been proposed that the large metacentric chromosome of S. senegalensis arises from this kind of chromosome rearrangement and that this is a proto-sex chromosome. Results In this work, the Robertsonian origin of the large metacentric chromosome of S. senegalensis has been tested by the Zoo-FISH technique applied to two species of the Soleidae family (Dicologlossa cuneata and Dagetichthys lusitanica), and by comparative genome analysis with Cynoglossus semilaevis. From the karyotypic analysis we were able to determine a chromosome complement comprising 2n = 50 (FN = 54) in D. cuneata and 2n = 42 (FN = 50) in D. lusitanica. The large metacentric painting probe gave consistent signals in four acrocentric chromosomes of the two Soleidae species; and the genome analysis proved a common origin with four chromosome pairs of C. semilaevis. As a result of the genomic analysis, up to 61 genes were annotated within the thirteen Bacterial Artificial Chromosome clones analysed. Conclusions These results confirm that the large metacentric chromosome of S. senegalensis originated from a Robertsonian fusion and provide new data about the chromosome evolution of S. senegalensis in particular, and of Pleuronectiformes in general. Electronic supplementary material The online version of this article (10.1186/s12864-018-5216-6) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Aglaya García-Angulo
- Área de Genética, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, 11510, Cádiz, Spain
| | - Manuel A Merlo
- Área de Genética, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, 11510, Cádiz, Spain
| | - Silvia Portela-Bens
- Área de Genética, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, 11510, Cádiz, Spain
| | - María E Rodríguez
- Área de Genética, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, 11510, Cádiz, Spain
| | - Emilio García
- Área de Genética, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, 11510, Cádiz, Spain
| | - Ahmed Al-Rikabi
- Institut für Humangenetik, Universitätsklinikum Jena, 07743, Jena, Germany
| | - Thomas Liehr
- Institut für Humangenetik, Universitätsklinikum Jena, 07743, Jena, Germany
| | - Laureana Rebordinos
- Área de Genética, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, 11510, Cádiz, Spain.
| |
Collapse
|
25
|
Conventional Cytogenetic Approaches—Useful and Indispensable Tools in Discovering Fish Biodiversity. CURRENT GENETIC MEDICINE REPORTS 2018. [DOI: 10.1007/s40142-018-0148-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
26
|
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: 20] [Impact Index Per Article: 3.3] [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.
Collapse
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.
| |
Collapse
|
27
|
Jetybayev IY, Bugrov AG, Buleu OG, Bogomolov AG, Rubtsov NB. Origin and Evolution of the Neo-Sex Chromosomes in Pamphagidae Grasshoppers through Chromosome Fusion and Following Heteromorphization. Genes (Basel) 2017; 8:genes8110323. [PMID: 29137168 PMCID: PMC5704236 DOI: 10.3390/genes8110323] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 11/06/2017] [Accepted: 11/07/2017] [Indexed: 11/16/2022] Open
Abstract
In most phylogenetic lineages, the evolution of sex chromosomes is accompanied by their heteromorphization and degradation of one of them. The neo-sex chromosomes are useful model for studying early stages of these processes. Recently two lineages of the neo-sex chromosomes on different stages of heteromorphization was discovered in Pamphagidae family. The neo-sex chromosome heteromorphization was analyzed by generation of DNA probes derived from the neo-Xs and neo-Ys followed with chromosome painting in nineteen species of Pamphagidae family. The homologous regions of the neo-sex chromosomes were determined in closely related species with the painting procedure and image analysis with application of the Visualization of the Specific Signal in Silico software package. Results of these analyses and distribution of C-positive regions in the neo-sex chromosomes revealed details of the heteromorphization of the neo-sex chromosomes in species from both phylogenetic lineages of Pamphagidae grasshoppers. The hypothetical mechanism of the neo-Y degradation was suggested. It includes expansion of different repeats from the proximal neo-Y chromosome region by inversions, spreading them towards distal region. Amplification of these repeats leads to formation of C-positive regions and elimination of the C-negative regions located between them.
Collapse
Affiliation(s)
- Ilyas Yerkinovich Jetybayev
- The Federal Research Center, Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, Lavrentjev Ave., 10, 630090 Novosibirsk, Russia.
- Institute of Systematics and Ecology of Animals, Russian Academy of Sciences, Siberian Branch, Frunze str. 11, 630091 Novosibirsk, Russia.
| | - Alexander Gennadievich Bugrov
- Institute of Systematics and Ecology of Animals, Russian Academy of Sciences, Siberian Branch, Frunze str. 11, 630091 Novosibirsk, Russia.
- Novosibirsk State University, Department of Natural Sciences, Pirogov str., 2, 630090 Novosibirsk, Russia.
| | - Olesya Georgievna Buleu
- Institute of Systematics and Ecology of Animals, Russian Academy of Sciences, Siberian Branch, Frunze str. 11, 630091 Novosibirsk, Russia.
- Novosibirsk State University, Department of Natural Sciences, Pirogov str., 2, 630090 Novosibirsk, Russia.
| | - Anton Gennadievich Bogomolov
- The Federal Research Center, Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, Lavrentjev Ave., 10, 630090 Novosibirsk, Russia.
- Novosibirsk State University, Department of Natural Sciences, Pirogov str., 2, 630090 Novosibirsk, Russia.
| | - Nikolay Borisovich Rubtsov
- The Federal Research Center, Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, Lavrentjev Ave., 10, 630090 Novosibirsk, Russia.
- Novosibirsk State University, Department of Natural Sciences, Pirogov str., 2, 630090 Novosibirsk, Russia.
| |
Collapse
|