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van’t Hof AE, Whiteford S, Yung CJ, Yoshido A, Zrzavá M, de Jong MA, Tan KL, Zhu D, Monteiro A, Brakefield PM, Marec F, Saccheri IJ. Zygosity-based sex determination in a butterfly drives hypervariability of Masculinizer. SCIENCE ADVANCES 2024; 10:eadj6979. [PMID: 38701204 PMCID: PMC11067997 DOI: 10.1126/sciadv.adj6979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 04/03/2024] [Indexed: 05/05/2024]
Abstract
Nature has devised many ways of producing males and females. Here, we report on a previously undescribed mechanism for Lepidoptera that functions without a female-specific gene. The number of alleles or allele heterozygosity in a single Z-linked gene (BaMasc) is the primary sex-determining switch in Bicyclus anynana butterflies. Embryos carrying a single BaMasc allele develop into WZ (or Z0) females, those carrying two distinct alleles develop into ZZ males, while (ZZ) homozygotes initiate female development, have mismatched dosage compensation, and die as embryos. Consequently, selection against homozygotes has favored the evolution of spectacular allelic diversity: 205 different coding sequences of BaMasc were detected in a sample of 246 females. The structural similarity of a hypervariable region (HVR) in BaMasc to the HVR in Apis mellifera csd suggests molecular convergence between deeply diverged insect lineages. Our discovery of this primary switch highlights the fascinating diversity of sex-determining mechanisms and underlying evolutionary drivers.
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Affiliation(s)
- Arjen E. van’t Hof
- Department of Evolution, Ecology and Behaviour, University of Liverpool, Liverpool L69 7ZB, UK
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, 370 05 České Budějovice, Czech Republic
| | - Sam Whiteford
- Department of Evolution, Ecology and Behaviour, University of Liverpool, Liverpool L69 7ZB, UK
| | - Carl J. Yung
- Department of Evolution, Ecology and Behaviour, University of Liverpool, Liverpool L69 7ZB, UK
| | - Atsuo Yoshido
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, 370 05 České Budějovice, Czech Republic
| | - Magda Zrzavá
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, 370 05 České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czech Republic
| | - Maaike A. de Jong
- Netherlands eScience Center, Science Park 402, 1098 XH Amsterdam, Netherlands
| | - Kian-Long Tan
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Dantong Zhu
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Antónia Monteiro
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | | | - František Marec
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, 370 05 České Budějovice, Czech Republic
| | - Ilik J. Saccheri
- Department of Evolution, Ecology and Behaviour, University of Liverpool, Liverpool L69 7ZB, UK
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2
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Chailertrit V, Panthum T, Kongkaew L, Chalermwong P, Singchat W, Ahmad SF, Kraichak E, Muangmai N, Duengkae P, Peyachoknagul S, Han K, Srikulnath K. Genome-wide SNP analysis provides insights into the XX/XY sex-determination system in silver barb (Barbonymus gonionotus). Genomics Inform 2023; 21:e47. [PMID: 38224714 PMCID: PMC10788355 DOI: 10.5808/gi.23075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 12/08/2023] [Accepted: 12/09/2023] [Indexed: 01/17/2024] Open
Abstract
Silver barb (Barbonymus gonionotus) is among the most economically important freshwater fish species in Thailand. It ranks fourth in economic value and third in production weight for fisheries and culture in Thailand. An XX/XY sex-determination system based on gynogenesis was previously reported for this fish. In this study, the molecular basis underlying the sex-determination system was further investigated. Genome-wide single-nucleotide polymorphism data were generated for 32 captive-bred silver barb individuals, previously scored by phenotypic sex, to identify sex-linked regions associated with sex determination. Sixty-three male-linked loci, indicating putative XY chromosomes, were identified. Male-specific loci were not observed, which indicates that the putative Y chromosome is young and the sex determination region is cryptic. A homology search revealed that most male-linked loci were homologous to the Mariner/Tc1 and Gypsy transposable elements and are probably the remnants of an initial accumulation of repeats on the Y chromosome from the early stages of sex chromosome differentiation. This research provides convincing insights into the mechanism of sex determination and reveals the potential sex determination regions in silver barb. The study provides the basic data necessary for increasing the commercial value of silver barbs through genetic improvements.
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Affiliation(s)
- Visarut Chailertrit
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Pathum Thani Aquatic Animal Genetics Research and Development Center, Aquatic Animal Genetics Research and Development Division, Department of Fisheries, Pathum Thani 12120, Thailand
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok 10900, Thailand
| | - Thitipong Panthum
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok 10900, Thailand
| | - Lalida Kongkaew
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok 10900, Thailand
| | - Piangjai Chalermwong
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Sciences for Industry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Worapong Singchat
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok 10900, Thailand
| | - Syed Farhan Ahmad
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Ekaphan Kraichak
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Department of Botany, Kasetsart University, Bangkok 10900, Thailand
| | - Narongrit Muangmai
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Department of Fishery Biology, Faculty of Fisheries, Kasetsart University, Bangkok 10900, Thailand
| | - Prateep Duengkae
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok 10900, Thailand
| | - Surin Peyachoknagul
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Kyudong Han
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Department of Microbiology, Dankook University, Cheonan 31116, Korea
- Bio-Medical Engineering Core Facility Research Center, Dankook University, Cheonan 31116, Korea
| | - Kornsorn Srikulnath
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok 10900, Thailand
- Sciences for Industry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Center for Advanced Studies in Tropical Natural Resources (CASTNAR), National Research University-Kasetsart University (NRU-KU), Kasetsart University, Bangkok 10900, Thailand
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3
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Cabral-de-Mello DC, Mora P, Rico-Porras JM, Ferretti ABSM, Palomeque T, Lorite P. The spread of satellite DNAs in euchromatin and insights into the multiple sex chromosome evolution in Hemiptera revealed by repeatome analysis of the bug Oxycarenus hyalinipennis. INSECT MOLECULAR BIOLOGY 2023; 32:725-737. [PMID: 37615351 DOI: 10.1111/imb.12868] [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: 05/15/2023] [Accepted: 08/07/2023] [Indexed: 08/25/2023]
Abstract
Satellite DNAs (satDNAs) are highly repeated tandem sequences primarily located in heterochromatin, although their occurrence in euchromatin has been reported. Here, our aim was to advance the understanding of satDNA and multiple sex chromosome evolution in heteropterans. We combined cytogenetic and genomic approaches to study, for the first time, the satDNA composition of the genome in an Oxycarenidae bug, Oxycarenus hyalinipennis. The species exhibits a male karyotype of 2n = 19 (14A + 2 m + X1 X2 Y), with a highly differentiated Y chromosome, as demonstrated by C-banding and comparative genomic hybridization, revealing an enrichment of repeats from the male genome. Additionally, comparative analysis between males and females revealed that the 26 identified satDNA families are significantly biased towards male genome, accumulating in discrete regions in the Y chromosome. Exceptionally, the OhyaSat04-125 family was found to be distributed virtually throughout the entire extension of the Y chromosome. This suggests an important role of satDNA in Y chromosome differentiation, in comparison of other repeats, which collectively shows similar abundance between sexes, about 50%. Furthermore, chromosomal mapping of all satDNA families revealed an unexpected high spread in euchromatic regions, covering the entire extension, irrespective of their abundance. Only discrete regions of heterochromatin on the Y chromosome and of the m-chromosomes (peculiar chromosomes commonly observed in heteropterans) were enriched with satDNAs. The putative causes of the intense enrichment of satDNAs in euchromatin are discussed, including the possible existence of burst cycles similar to transposable elements and as a result of holocentricity. These data challenge the classical notion that euchromatin is not enriched with satDNAs.
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Affiliation(s)
- Diogo C Cabral-de-Mello
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências/IB, UNESP-Universidade Estadual Paulista, Rio Claro, Brazil
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Jaén, Spain
| | - Pablo Mora
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Jaén, Spain
| | - José M Rico-Porras
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Jaén, Spain
| | - Ana B S M Ferretti
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências/IB, UNESP-Universidade Estadual Paulista, Rio Claro, Brazil
| | - Teresa Palomeque
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Jaén, Spain
| | - Pedro Lorite
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Jaén, Spain
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4
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Orosová M, Marková A, Zrzavá M, Marec F, Oros M. Chromosome analysis and the occurrence of B chromosomes in fish parasite Acanthocephalus anguillae (Palaeacanthocephala: Echinorhynchida). Parasite 2023; 30:44. [PMID: 37870409 PMCID: PMC10592040 DOI: 10.1051/parasite/2023045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Accepted: 09/27/2023] [Indexed: 10/24/2023] Open
Abstract
The cytogenetics of Acanthocephala is a neglected area in the study of this group of endoparasites. Chromosome number and/or karyotypes are known for only 12 of the 1,270 described species, and molecular cytogenetic data are limited to rDNA mapping in two species. The standard karyological technique and mapping of 18S rRNA and H3 histone genes on the chromosomes of Acanthocephalus anguillae individuals from three populations, one of which originated from the unfavorable environmental conditions of the Zemplínska Šírava reservoir in eastern Slovakia, were applied for the first time. All specimens had 2n = 7/8 (male/female); n = 1m + 1m-sm + 1a + 1a (X). Fluorescence in situ hybridization (FISH) revealed three loci of 18S rDNA on two autosomes and dispersion of H3 histone genes on all autosomes and the X chromosome. In addition to the standard A chromosome set, 34% of specimens from Zemplínska Šírava possessed a small acrocentric B chromosome, which was always found to be univalent, with no pairing observed between the B chromosome and the A complement. The B chromosome had a small amount of heterochromatin in the centromeric and telomeric regions of the chromosomal arms and showed two clusters of H3 genes. It is well known that an environment permanently polluted with chemicals leads to an increased incidence of chromosomal rearrangements. As a possible scenario for the B chromosome origin, we propose chromosomal breaks due to the mutagenic effect of pollutants in the aquatic environment. The results are discussed in comparison with previous chromosome data from Echinorhynchida species.
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Affiliation(s)
- Martina Orosová
- Institute of Parasitology, Slovak Academy of Sciences Hlinkova 3 040 01 Košice Slovakia
| | - Anna Marková
- Institute of Parasitology, Slovak Academy of Sciences Hlinkova 3 040 01 Košice Slovakia
- Department of Zoology, Faculty of Natural Sciences, Comenius University Ilkovičova 6 842 15 Bratislava Slovakia
| | - Magda Zrzavá
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology Branišovská 31 370 05 České Budějovice Czech Republic
- Faculty of Science, University of South Bohemia Branišovská 1760 370 05 České Budějovice Czech Republic
| | - František Marec
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology Branišovská 31 370 05 České Budějovice Czech Republic
| | - Mikuláš Oros
- Institute of Parasitology, Slovak Academy of Sciences Hlinkova 3 040 01 Košice Slovakia
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5
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de Menezes Cavalcante Sassi F, Sember A, Deon GA, Liehr T, Padutsch N, Oyakawa OT, Vicari MR, Bertollo LAC, Moreira-Filho O, de Bello Cioffi M. Homeology of sex chromosomes in Amazonian Harttia armored catfishes supports the X-fission hypothesis for the X 1X 2Y sex chromosome system origin. Sci Rep 2023; 13:15756. [PMID: 37735233 PMCID: PMC10514344 DOI: 10.1038/s41598-023-42617-w] [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: 04/14/2023] [Accepted: 09/12/2023] [Indexed: 09/23/2023] Open
Abstract
The Neotropical monophyletic catfish genus Harttia represents an excellent model to study karyotype and sex chromosome evolution in teleosts. Its species split into three phylogenetic clades distributed along the Brazilian territory and they differ widely in karyotype traits, including the presence of standard or multiple sex chromosome systems in some members. Here, we investigate the chromosomal rearrangements and associated synteny blocks involved in the origin of a multiple X1X2Y sex chromosome system present in three out of six sampled Amazonian-clade species. Using 5S and 18S ribosomal DNA fluorescence in situ hybridization and whole chromosome painting with probes corresponding to X1 and X2 chromosomes of X1X2Y system from H. punctata, we confirm previous assumptions that X1X2Y sex chromosome systems of H. punctata, H. duriventris and H. villasboas represent the same linkage groups which also form the putative XY sex chromosomes of H. rondoni. The shared homeology between X1X2Y sex chromosomes suggests they might have originated once in the common ancestor of these closely related species. A joint arrangement of mapped H. punctata X1 and X2 sex chromosomes in early diverging species of different Harttia clades suggests that the X1X2Y sex chromosome system may have formed through an X chromosome fission rather than previously proposed Y-autosome fusion.
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Affiliation(s)
| | - Alexandr Sember
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská, 89, Liběchov, Czech Republic
| | - Geize Aparecida Deon
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, 13565-905, Brazil
| | - Thomas Liehr
- Institut für Humangenetik, Universitätsklinikum Jena, 07747, Jena, Germany.
| | - Niklas Padutsch
- Institut für Humangenetik, Universitätsklinikum Jena, 07747, Jena, Germany
| | | | - Marcelo Ricardo Vicari
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa, PR, Brazil
| | - Luiz Antonio Carlos Bertollo
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, 13565-905, 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
| | - Marcelo de Bello Cioffi
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, 13565-905, Brazil
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6
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Näsvall K, Boman J, Höök L, Vila R, Wiklund C, Backström N. Nascent evolution of recombination rate differences as a consequence of chromosomal rearrangements. PLoS Genet 2023; 19:e1010717. [PMID: 37549188 PMCID: PMC10434929 DOI: 10.1371/journal.pgen.1010717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 08/17/2023] [Accepted: 07/17/2023] [Indexed: 08/09/2023] Open
Abstract
Reshuffling of genetic variation occurs both by independent assortment of chromosomes and by homologous recombination. Such reshuffling can generate novel allele combinations and break linkage between advantageous and deleterious variants which increases both the potential and the efficacy of natural selection. Here we used high-density linkage maps to characterize global and regional recombination rate variation in two populations of the wood white butterfly (Leptidea sinapis) that differ considerably in their karyotype as a consequence of at least 27 chromosome fissions and fusions. The recombination data were compared to estimates of genetic diversity and measures of selection to assess the relationship between chromosomal rearrangements, crossing over, maintenance of genetic diversity and adaptation. Our data show that the recombination rate is influenced by both chromosome size and number, but that the difference in the number of crossovers between karyotypes is reduced as a consequence of a higher frequency of double crossovers in larger chromosomes. As expected from effects of selection on linked sites, we observed an overall positive association between recombination rate and genetic diversity in both populations. Our results also revealed a significant effect of chromosomal rearrangements on the rate of intergenic diversity change between populations, but limited effects on polymorphisms in coding sequence. We conclude that chromosomal rearrangements can have considerable effects on the recombination landscape and consequently influence both maintenance of genetic diversity and efficiency of selection in natural populations.
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Affiliation(s)
- Karin Näsvall
- Evolutionary Biology Program, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, Uppsala, Sweden
| | - Jesper Boman
- Evolutionary Biology Program, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, Uppsala, Sweden
| | - Lars Höök
- Evolutionary Biology Program, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, Uppsala, Sweden
| | - Roger Vila
- Butterfly Diversity and Evolution Lab, Institut de Biologia Evolutiva (CSIC-Univ. Pompeu Fabra), Barcelona, Spain
| | - Christer Wiklund
- Department of Zoology: Division of Ecology, Stockholm University, Stockholm, Sweden
| | - Niclas Backström
- Evolutionary Biology Program, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, Uppsala, Sweden
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7
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Pazhenkova EA, Lukhtanov VA. Chromosomal conservatism vs chromosomal megaevolution: enigma of karyotypic evolution in Lepidoptera. Chromosome Res 2023; 31:16. [PMID: 37300756 DOI: 10.1007/s10577-023-09725-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 05/21/2023] [Accepted: 05/23/2023] [Indexed: 06/12/2023]
Abstract
In the evolution of many organisms, periods of slow genome reorganization (= chromosomal conservatism) are interrupted by bursts of numerous chromosomal changes (= chromosomal megaevolution). Using comparative analysis of chromosome-level genome assemblies, we investigated these processes in blue butterflies (Lycaenidae). We demonstrate that the phase of chromosome number conservatism is characterized by the stability of most autosomes and dynamic evolution of the sex chromosome Z, resulting in multiple variants of NeoZ chromosomes due to autosome-sex chromosome fusions. In contrast during the phase of rapid chromosomal evolution, the explosive increase in chromosome number occurs mainly through simple chromosomal fissions. We show that chromosomal megaevolution is a highly non-random canalized process, and in two phylogenetically independent Lysandra lineages, the drastic parallel increase in number of fragmented chromosomes was achieved, at least partially, through reuse of the same ancestral chromosomal breakpoints. In species showing chromosome number doubling, we found no blocks of duplicated sequences or duplicated chromosomes, thus refuting the hypothesis of polyploidy. In the studied taxa, long blocks of interstitial telomere sequences (ITSs) consist of (TTAGG)n arrays interspersed with telomere-specific retrotransposons. ITSs are sporadically present in rapidly evolving Lysandra karyotypes, but not in the species with ancestral chromosome number. Therefore, we hypothesize that the transposition of telomeric sequences may be triggers of the rapid chromosome number increase. Finally, we discuss the hypothetical genomic and population mechanisms of chromosomal megaevolution and argue that the disproportionally high evolutionary role of the Z sex chromosome can be additionally reinforced by sex chromosome-autosome fusions and Z-chromosome inversions.
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Affiliation(s)
- Elena A Pazhenkova
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna Pot 111, 1000, Ljubljana, Slovenia.
| | - Vladimir A Lukhtanov
- Department of Karyosystematics, Zoological Institute of Russian Academy of Sciences, Universitetskaya Nab. 1, 199034, St. Petersburg, Russia.
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8
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Nazari V, Lukhtanov VA, Naderi A, Fric ZF, Dincă V, Vila R. More hidden diversity in a cryptic species complex: a new subspecies of Leptideasinapis (Lepidoptera, Pieridae) from Northern Iran. COMPARATIVE CYTOGENETICS 2023; 17:113-128. [PMID: 37304150 PMCID: PMC10252139 DOI: 10.3897/compcytogen.17.102830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 04/05/2023] [Indexed: 06/13/2023]
Abstract
A new subspecies of Leptideasinapis from Northern Iran, discovered by means of DNA barcoding, is described as Leptideasinapistabarestanassp. nov. The new subspecies is allopatric with respect to other populations of L.sinapis and is genetically distinct, appearing as a well-supported sister clade to all other populations in COI-based phylogenetic reconstructions. Details on karyotype, genitalia, ecology and behaviour for the new subspecies are given and a biogeographical speciation scenario is proposed.
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Affiliation(s)
- Vazrick Nazari
- Department of Biology, University of Padova, Padova, ItalyUniversity of PadovaPadovaItaly
| | - Vladimir A. Lukhtanov
- Department of Karyosystematics, Zoological Institute of Russian Academy of Science, Universitetskaya nab. 1, 199034 St. Petersburg, RussiaZoological Institute of Russian Academy of ScienceSt. PetersburgRussia
| | - Alireza Naderi
- National Natural History Museum & Genetic Resources, Tehran, IranNational Natural History Museum & Genetic ResourcesTehranIran
| | - Zdenek Faltýnek Fric
- Department of Biodiversity and Conservation Biology, Institute of Entomology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech RepublicInstitute of Entomology, Biology Centre of the Czech Academy of SciencesČeské BudějoviceCzech Republic
| | - Vlad Dincă
- Ecology and Genetics Research Unit, University of Oulu, Oulu, FinlandUniversity of OuluOuluFinland
- Research Institute of the University of Bucharest (ICUB), University of Bucharest, Bucharest, RomaniaUniversity of BucharestBucharestRomania
| | - Roger Vila
- Institut de Biologia Evolutiva (CSIC – Universitat Pompeu Fabra), Barcelona, SpainUniversitat Pompeu FabraBarcelonaSpain
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9
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Mousavi SE, Grützner F, Patil JG. Enhanced mitotic arrest and chromosome resolution for cytogenetic analysis in the eastern mosquitofish, Gambusia holbrooki. Acta Histochem 2023; 125:152029. [PMID: 37062122 DOI: 10.1016/j.acthis.2023.152029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 04/11/2023] [Accepted: 04/13/2023] [Indexed: 04/18/2023]
Abstract
Maximising the number of cells arrested at metaphase and their resolution is fundamentally important for molecular cytogenetic investigations, particularly in fish, which typically yield low mitotic index and have highly condensed chromosomes. To overcome these limitations, fish were injected with a mitotic stimulator (the yeast, Saccharomyces cerevisiae) to improve the mitotic index, and the intercalating agent ethidium bromide to produce elongated chromosomes. Specifically, adults were injected with activated yeast and then Colcemid (0.025 µg/µl solution, 10 µl per 1 g of body weight) at 24-96 h post yeast injections, followed by chromosome preparations from multiple tissues. Results showed that gill tissue had the highest number of dividing cells at 72 h post yeast exposure with no significant (p > 0.05) differences between the sexes. Nonetheless, sex-specific differences in the mitotic index were observed in spleen, kidney, and liver, which may be attributed to sex-specific differences in immune responses. For elongation of mitotic chromosomes, individuals (both sexes) were first injected with activated yeast and after 48 h with ethidium bromide (2 or 4 µg/ml) and Colcemid (0.05 µg/µl solution, 10 µl per 1 g of body weight). Following which, animals were sampled at three time points (1, 4 and 8 h) for chromosome preparations. The results show that the optimum elongation of metaphase chromosomes of males and females was achieved by using 2 µg/ml and 4 µg/ml, respectively, for 1 h. Interestingly, the average mitotic chromosome length (μm) of males and females post-ethidium bromide exposure was significantly different (p < 0.05) for both concentrations, except at 1 h exposure for 2 µg/ml EtBr. Such differences can be attributed to overall chromosomal condensation differences between sexes. Regardless, the increased mitotic index and chromosome resolution could benefit cytogenetic studies in other fish species.
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Affiliation(s)
- Seyed Ehsan Mousavi
- Laboratory of Molecular Biology, Institute for Marine and Antarctic Studies, University of Tasmania, Taroona, TAS 7053, Australia; School of Medicine, University of Tasmania, Hobart, TAS 7000, Australia.
| | - Frank Grützner
- School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Jawahar G Patil
- Laboratory of Molecular Biology, Institute for Marine and Antarctic Studies, University of Tasmania, Taroona, TAS 7053, Australia
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10
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Höök L, Näsvall K, Vila R, Wiklund C, Backström N. High-density linkage maps and chromosome level genome assemblies unveil direction and frequency of extensive structural rearrangements in wood white butterflies (Leptidea spp.). Chromosome Res 2023; 31:2. [PMID: 36662301 PMCID: PMC9859909 DOI: 10.1007/s10577-023-09713-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/19/2022] [Accepted: 12/28/2022] [Indexed: 01/21/2023]
Abstract
Karyotypes are generally conserved between closely related species and large chromosome rearrangements typically have negative fitness consequences in heterozygotes, potentially driving speciation. In the order Lepidoptera, most investigated species have the ancestral karyotype and gene synteny is often conserved across deep divergence, although examples of extensive genome reshuffling have recently been demonstrated. The genus Leptidea has an unusual level of chromosome variation and rearranged sex chromosomes, but the extent of restructuring across the rest of the genome is so far unknown. To explore the genomes of the wood white (Leptidea) species complex, we generated eight genome assemblies using a combination of 10X linked reads and HiC data, and improved them using linkage maps for two populations of the common wood white (L. sinapis) with distinct karyotypes. Synteny analysis revealed an extensive amount of rearrangements, both compared to the ancestral karyotype and between the Leptidea species, where only one of the three Z chromosomes was conserved across all comparisons. Most restructuring was explained by fissions and fusions, while translocations appear relatively rare. We further detected several examples of segregating rearrangement polymorphisms supporting a highly dynamic genome evolution in this clade. Fusion breakpoints were enriched for LINEs and LTR elements, which suggests that ectopic recombination might be an important driver in the formation of new chromosomes. Our results show that chromosome count alone may conceal the extent of genome restructuring and we propose that the amount of genome evolution in Lepidoptera might still be underestimated due to lack of taxonomic sampling.
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Affiliation(s)
- L. Höök
- Evolutionary Biology Program, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden
| | - K. Näsvall
- Evolutionary Biology Program, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden
| | - R. Vila
- Butterfly Diversity and Evolution Lab, Institut de Biologia Evolutiva (CSIC-UPF), Barcelona, Spain
| | - C. Wiklund
- Department of Zoology, Division of Ecology, Stockholm University, Stockholm, Sweden
| | - N. Backström
- Evolutionary Biology Program, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden
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11
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Miller J, Zimin AV, Gordus A. Chromosome-level genome and the identification of sex chromosomes in Uloborus diversus. Gigascience 2022; 12:giad002. [PMID: 36762707 PMCID: PMC9912274 DOI: 10.1093/gigascience/giad002] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 11/18/2022] [Accepted: 01/03/2023] [Indexed: 02/11/2023] Open
Abstract
The orb web is a remarkable example of animal architecture that is observed in families of spiders that diverged over 200 million years ago. While several genomes exist for araneid orb-weavers, none exist for other orb-weaving families, hampering efforts to investigate the genetic basis of this complex behavior. Here we present a chromosome-level genome assembly for the cribellate orb-weaving spider Uloborus diversus. The assembly reinforces evidence of an ancient arachnid genome duplication and identifies complete open reading frames for every class of spidroin gene, which encode the proteins that are the key structural components of spider silks. We identified the 2 X chromosomes for U. diversus and identify candidate sex-determining loci. This chromosome-level assembly will be a valuable resource for evolutionary research into the origins of orb-weaving, spidroin evolution, chromosomal rearrangement, and chromosomal sex determination in spiders.
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Affiliation(s)
- Jeremiah Miller
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Aleksey V Zimin
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Andrew Gordus
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University, Baltimore, MD 21218, USA
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12
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Mola LM, Vrbová I, Tosto DS, Zrzavá M, Marec F. On the Origin of Neo-Sex Chromosomes in the Neotropical Dragonflies Rhionaeschna bonariensis and R. planaltica (Aeshnidae, Odonata). INSECTS 2022; 13:1159. [PMID: 36555069 PMCID: PMC9784284 DOI: 10.3390/insects13121159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/06/2022] [Accepted: 12/11/2022] [Indexed: 06/17/2023]
Abstract
Odonata have holokinetic chromosomes. About 95% of species have an XX/X0 sex chromosome system, with heterogametic males. There are species with neo-XX/neo-XY sex chromosomes resulting from an X chromosome/autosome fusion. The genus Rhionaeschna includes 42 species found in the Americas. We analyzed the distribution of the nucleolar organizer region (NOR) using FISH with rDNA probes in Rhionaeschna bonariensis (n = 12 + neo-XY), R. planaltica (n = 7 + neo-XY), and Aeshna cyanea (n = 13 + X0). In R. bonariensis and A. cyanea, the NOR is located on a large pair of autosomes, which have a secondary constriction in the latter species. In R. planaltica, the NOR is located on the ancestral part of the neo-X chromosome. Meiotic analysis and FISH results in R. planaltica led to the conclusion that the neo-XY system arose by insertion of the ancestral X chromosome into an autosome. Genomic in situ hybridization, performed for the first time in Odonata, highlighted the entire neo-Y chromosome in meiosis of R. bonariensis, suggesting that it consists mainly of repetitive DNA. This feature and the terminal chiasma localization suggest an ancient origin of the neo-XY system. Our study provides new information on the origin and evolution of neo-sex chromosomes in Odonata, including new types of chromosomal rearrangements, NOR transposition, and heterochromatin accumulation.
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Affiliation(s)
- Liliana M. Mola
- Laboratory of Cytogenetics and Evolution, Faculty of Exact and Natural Sciences, University of Buenos Aires, Buenos Aires C1428EGA, Argentina
- Institute of Ecology, Genetics and Evolution of Buenos Aires, National Council of Scientific and Technical Research, Buenos Aires C1428EGA, Argentina
| | - Iva Vrbová
- Biology Centre CAS, Institute of Entomology, Branišovská 31, 370 05 České Budějovice, Czech Republic
- Biology Centre CAS, Institute of Plant Molecular Biology, Branišovská 31, 370 05 České Budějovice, Czech Republic
| | - Daniela S. Tosto
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Hurlingham, Buenos Aires 1686, Argentina
| | - Magda Zrzavá
- Biology Centre CAS, Institute of Entomology, Branišovská 31, 370 05 České Budějovice, Czech Republic
- Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05 České Budějovice, Czech Republic
| | - František Marec
- Biology Centre CAS, Institute of Entomology, Branišovská 31, 370 05 České Budějovice, Czech Republic
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13
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Genome sequence and silkomics of the spindle ermine moth, Yponomeuta cagnagella, representing the early diverging lineage of the ditrysian Lepidoptera. Commun Biol 2022; 5:1281. [PMID: 36418465 PMCID: PMC9684489 DOI: 10.1038/s42003-022-04240-9] [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: 02/01/2022] [Accepted: 11/09/2022] [Indexed: 11/24/2022] Open
Abstract
Many lepidopteran species produce silk, cocoons, feeding tubes, or nests for protection from predators and parasites for caterpillars and pupae. Yet, the number of lepidopteran species whose silk composition has been studied in detail is very small, because the genes encoding the major structural silk proteins tend to be large and repetitive, making their assembly and sequence analysis difficult. Here we have analyzed the silk of Yponomeuta cagnagella, which represents one of the early diverging lineages of the ditrysian Lepidoptera thus improving the coverage of the order. To obtain a comprehensive list of the Y. cagnagella silk genes, we sequenced and assembled a draft genome using Oxford Nanopore and Illumina technologies. We used a silk-gland transcriptome and a silk proteome to identify major silk components and verified the tissue specificity of expression of individual genes. A detailed annotation of the major genes and their putative products, including their complete sequences and exon-intron structures is provided. The morphology of silk glands and fibers are also shown. This study fills an important gap in our growing understanding of the structure, evolution, and function of silk genes and provides genomic resources for future studies of the chemical ecology of Yponomeuta species.
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14
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Gasparotto AE, Milani D, Martí E, Ferretti ABSM, Bardella VB, Hickmann F, Zrzavá M, Marec F, Cabral-de-Mello DC. A step forward in the genome characterization of the sugarcane borer, Diatraea saccharalis: karyotype analysis, sex chromosome system and repetitive DNAs through a cytogenomic approach. Chromosoma 2022; 131:253-267. [PMID: 36219241 DOI: 10.1007/s00412-022-00781-4] [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: 06/22/2022] [Revised: 08/10/2022] [Accepted: 09/16/2022] [Indexed: 11/26/2022]
Abstract
Moths of the family Crambidae include a number of pests that cause economic losses to agricultural crops. Despite their economic importance, little is known about their genome architecture and chromosome evolution. Here, we characterized the chromosomes and repetitive DNA of the sugarcane borer Diatraea saccharalis using a combination of low-pass genome sequencing, bioinformatics, and cytogenetic methods, focusing on the sex chromosomes. Diploid chromosome numbers differed between the sexes, i.e., 2n = 33 in females and 2n = 34 in males. This difference was caused by the occurrence of a WZ1Z2 trivalent in female meiosis, indicating a multiple sex-chromosome system WZ1Z2/Z1Z1Z2Z2. A strong interstitial telomeric signal was observed on the W chromosome, indicating a fusion of the ancestral W chromosome with an autosome. Among repetitive DNAs, transposable elements (TEs) accounted for 39.18% (males) to 41.35% (females), while satDNAs accounted for only 0.214% (males) and 0.215% (females) of the genome. FISH mapping revealed different chromosomal organization of satDNAs, such as single localized clusters, spread repeats, and non-clustered repeats. Two TEs mapped by FISH were scattered. Although we found a slight enrichment of some satDNAs in the female genome, they were not differentially enriched on the W chromosome. However, we found enriched FISH signals for TEs on the W chromosome, suggesting their involvement in W chromosome degeneration and differentiation. These data shed light on karyotype and repetitive DNA dynamics due to multiple chromosome fusions in D. saccharalis, contribute to the understanding of genome structure in Lepidoptera and are important for future genomic studies.
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Affiliation(s)
- Ana E Gasparotto
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências/IB, UNESP - Universidade Estadual Paulista, Rio Claro, SP, 13506-900, Brazil
| | - Diogo Milani
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências/IB, UNESP - Universidade Estadual Paulista, Rio Claro, SP, 13506-900, Brazil
| | - Emiliano Martí
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências/IB, UNESP - Universidade Estadual Paulista, Rio Claro, SP, 13506-900, Brazil
| | - Ana Beatriz S M Ferretti
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências/IB, UNESP - Universidade Estadual Paulista, Rio Claro, SP, 13506-900, Brazil
| | - Vanessa B Bardella
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências/IB, UNESP - Universidade Estadual Paulista, Rio Claro, SP, 13506-900, Brazil
| | - Frederico Hickmann
- Department of Entomology and Acarology, Luiz de Queiroz College of Agriculture, (USP/ESALQ), University of São Paulo, Piracicaba, SP, Brazil
| | - Magda Zrzavá
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - František Marec
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czech Republic
| | - Diogo C Cabral-de-Mello
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências/IB, UNESP - Universidade Estadual Paulista, Rio Claro, SP, 13506-900, Brazil.
- Department of Experimental Biology, Genetics Area, University of Jaen, Paraje las Lagunillas s/n, 23071, Jaen, Spain.
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15
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Evolution of sexual systems, sex chromosomes and sex-linked gene transcription in flatworms and roundworms. Nat Commun 2022; 13:3239. [PMID: 35688815 PMCID: PMC9187692 DOI: 10.1038/s41467-022-30578-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 05/06/2022] [Indexed: 12/02/2022] Open
Abstract
Many species with separate male and female individuals (termed ‘gonochorism’ in animals) have sex-linked genome regions. Here, we investigate evolutionary changes when genome regions become completely sex-linked, by analyses of multiple species of flatworms (Platyhelminthes; among which schistosomes recently evolved gonochorism from ancestral hermaphroditism), and roundworms (Nematoda) which have undergone independent translocations of different autosomes. Although neither the evolution of gonochorism nor translocations fusing ancestrally autosomal regions to sex chromosomes causes inevitable loss of recombination, we document that formerly recombining regions show genomic signatures of recombination suppression in both taxa, and become strongly genetically degenerated, with a loss of most genes. Comparisons with hermaphroditic flatworm transcriptomes show masculinisation and some defeminisation in schistosome gonad gene expression. We also find evidence that evolution of sex-linkage in nematodes is accompanied by transcriptional changes and dosage compensation. Our analyses also identify sex-linked genes that could assist future research aimed at controlling some of these important parasites. Transitions between hermaphroditic and separate sexes are relatively understudied in animals compared to pants. Here, Wang et al. reconstruct the evolution of separate sexes in the flatworms and complex changes of sex chromosomes in the roundworms.
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16
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Yazdi HP. Digest: Neo-sex chromosome underlying the Faster-Z effect in a species of Lepidoptera . Evolution 2021; 76:357-358. [PMID: 34918358 DOI: 10.1111/evo.14418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Accepted: 11/26/2021] [Indexed: 11/29/2022]
Abstract
Do Z chromosomes evolve at a faster rate than autosomes in Lepidoptera? Mongue et al. show that Z-linked genes in two Lepidopteran species evolve faster than autosomal genes. However, the neo-sex chromosome differs from the ancestral chromosome and shows adaptive evolution for genes with a biased expression in the heterogametic sex. These findings indicate that studying molecular evolutionary patterns in sex-linked sequences at different evolutionary stages is essential to understand the dynamics of sex chromosome evolution.
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17
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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)'.
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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
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18
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Hejníčková M, Dalíková M, Potocký P, Tammaru T, Trehubenko M, Kubíčková S, Marec F, Zrzavá M. Degenerated, Undifferentiated, Rearranged, Lost: High Variability of Sex Chromosomes in Geometridae (Lepidoptera) Identified by Sex Chromatin. Cells 2021; 10:cells10092230. [PMID: 34571879 PMCID: PMC8468057 DOI: 10.3390/cells10092230] [Citation(s) in RCA: 7] [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: 07/28/2021] [Revised: 08/19/2021] [Accepted: 08/23/2021] [Indexed: 02/04/2023] Open
Abstract
Sex chromatin is a conspicuous body that occurs in polyploid nuclei of most lepidopteran females and consists of numerous copies of the W sex chromosome. It is also a cytogenetic tool used to rapidly assess the W chromosome presence in Lepidoptera. However, certain chromosomal features could disrupt the formation of sex chromatin and lead to the false conclusion that the W chromosome is absent in the respective species. Here we tested the sex chromatin presence in 50 species of Geometridae. In eight selected species with either missing, atypical, or normal sex chromatin patterns, we performed a detailed karyotype analysis by means of comparative genomic hybridization (CGH) and fluorescence in situ hybridization (FISH). The results showed a high diversity of W chromosomes and clarified the reasons for atypical sex chromatin, including the absence or poor differentiation of W, rearrangements leading to the neo-W emergence, possible association with the nucleolus, and the existence of multiple W chromosomes. In two species, we detected intraspecific variability in the sex chromatin status and sex chromosome constitution. We show that the sex chromatin is not a sufficient marker of the W chromosome presence, but it may be an excellent tool to pinpoint species with atypical sex chromosomes.
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Affiliation(s)
- Martina Hejníčková
- Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05 České Budějovice, Czech Republic; (M.H.); (M.D.); (M.T.)
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 370 05 České Budějovice, Czech Republic; (P.P.); (F.M.)
| | - Martina Dalíková
- Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05 České Budějovice, Czech Republic; (M.H.); (M.D.); (M.T.)
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 370 05 České Budějovice, Czech Republic; (P.P.); (F.M.)
| | - Pavel Potocký
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 370 05 České Budějovice, Czech Republic; (P.P.); (F.M.)
| | - Toomas Tammaru
- Institute of Ecology and Earth Sciences, University of Tartu, Vanemuise 46, 51014 Tartu, Estonia;
| | - Marharyta Trehubenko
- Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05 České Budějovice, Czech Republic; (M.H.); (M.D.); (M.T.)
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 370 05 České Budějovice, Czech Republic; (P.P.); (F.M.)
| | - Svatava Kubíčková
- Veterinary Research Institute, Hudcova 70, 621 00 Brno, Czech Republic;
| | - František Marec
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 370 05 České Budějovice, Czech Republic; (P.P.); (F.M.)
| | - Magda Zrzavá
- Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05 České Budějovice, Czech Republic; (M.H.); (M.D.); (M.T.)
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 370 05 České Budějovice, Czech Republic; (P.P.); (F.M.)
- Correspondence:
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19
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Lewis JJ, Cicconardi F, Martin SH, Reed RD, Danko CG, Montgomery SH. The Dryas iulia Genome Supports Multiple Gains of a W Chromosome from a B Chromosome in Butterflies. Genome Biol Evol 2021; 13:evab128. [PMID: 34117762 PMCID: PMC8290107 DOI: 10.1093/gbe/evab128] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/29/2021] [Indexed: 12/17/2022] Open
Abstract
In butterflies and moths, which exhibit highly variable sex determination mechanisms, the homogametic Z chromosome is deeply conserved and is featured in many genome assemblies. The evolution and origin of the female W sex chromosome, however, remains mostly unknown. Previous studies have proposed that a ZZ/Z0 sex determination system is ancestral to Lepidoptera, and that W chromosomes may originate from sex-linked B chromosomes. Here, we sequence and assemble the female Dryas iulia genome into 32 highly contiguous ordered and oriented chromosomes, including the Z and W sex chromosomes. We then use sex-specific Hi-C, ATAC-seq, PRO-seq, and whole-genome DNA sequence data sets to test if features of the D. iulia W chromosome are consistent with a hypothesized B chromosome origin. We show that the putative W chromosome displays female-associated DNA sequence, gene expression, and chromatin accessibility to confirm the sex-linked function of the W sequence. In contrast with expectations from studies of homologous sex chromosomes, highly repetitive DNA content on the W chromosome, the sole presence of domesticated repetitive elements in functional DNA, and lack of sequence homology with the Z chromosome or autosomes is most consistent with a B chromosome origin for the W, although it remains challenging to rule out extensive sequence divergence. Synteny analysis of the D. iulia W chromosome with other female lepidopteran genome assemblies shows no homology between W chromosomes and suggests multiple, independent origins of the W chromosome from a B chromosome likely occurred in butterflies.
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Affiliation(s)
- James J Lewis
- Baker Institute for Animal Health, Cornell University, Ithaca, New York, USA
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Francesco Cicconardi
- School of Biological Sciences, University of Bristol, United Kingdom
- Department of Zoology, University of Cambridge, United Kingdom
| | - Simon H Martin
- Institute of Evolutionary Biology, University of Edinburgh, United Kingdom
| | - Robert D Reed
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Charles G Danko
- Baker Institute for Animal Health, Cornell University, Ithaca, New York, USA
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20
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Provazníková I, Hejníčková M, Visser S, Dalíková M, Carabajal Paladino LZ, Zrzavá M, Voleníková A, Marec F, Nguyen P. Large-scale comparative analysis of cytogenetic markers across Lepidoptera. Sci Rep 2021; 11:12214. [PMID: 34108567 PMCID: PMC8190105 DOI: 10.1038/s41598-021-91665-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 05/24/2021] [Indexed: 11/25/2022] Open
Abstract
Fluorescence in situ hybridization (FISH) allows identification of particular chromosomes and their rearrangements. Using FISH with signal enhancement via antibody amplification and enzymatically catalysed reporter deposition, we evaluated applicability of universal cytogenetic markers, namely 18S and 5S rDNA genes, U1 and U2 snRNA genes, and histone H3 genes, in the study of the karyotype evolution in moths and butterflies. Major rDNA underwent rather erratic evolution, which does not always reflect chromosomal changes. In contrast, the hybridization pattern of histone H3 genes was well conserved, reflecting the stable organisation of lepidopteran genomes. Unlike 5S rDNA and U1 and U2 snRNA genes which we failed to detect, except for 5S rDNA in a few representatives of early diverging lepidopteran lineages. To explain the negative FISH results, we used quantitative PCR and Southern hybridization to estimate the copy number and organization of the studied genes in selected species. The results suggested that their detection was hampered by long spacers between the genes and/or their scattered distribution. Our results question homology of 5S rDNA and U1 and U2 snRNA loci in comparative studies. We recommend the use of histone H3 in studies of karyotype evolution.
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Affiliation(s)
- Irena Provazníková
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Institute of Entomology, Biology Centre CAS, České Budějovice, Czech Republic
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Martina Hejníčková
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Institute of Entomology, Biology Centre CAS, České Budějovice, Czech Republic
| | - Sander Visser
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Institute of Entomology, Biology Centre CAS, České Budějovice, Czech Republic
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Martina Dalíková
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Institute of Entomology, Biology Centre CAS, České Budějovice, Czech Republic
| | | | - Magda Zrzavá
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Institute of Entomology, Biology Centre CAS, České Budějovice, Czech Republic
| | - Anna Voleníková
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Institute of Entomology, Biology Centre CAS, České Budějovice, Czech Republic
| | - František Marec
- Institute of Entomology, Biology Centre CAS, České Budějovice, Czech Republic
| | - Petr Nguyen
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic.
- Institute of Entomology, Biology Centre CAS, České Budějovice, Czech Republic.
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21
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Cabral-de-Mello DC, Zrzavá M, Kubíčková S, Rendón P, Marec F. The Role of Satellite DNAs in Genome Architecture and Sex Chromosome Evolution in Crambidae Moths. Front Genet 2021; 12:661417. [PMID: 33859676 PMCID: PMC8042265 DOI: 10.3389/fgene.2021.661417] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 03/04/2021] [Indexed: 12/21/2022] Open
Abstract
Tandem repeats are important parts of eukaryotic genomes being crucial e.g., for centromere and telomere function and chromatin modulation. In Lepidoptera, knowledge of tandem repeats is very limited despite the growing number of sequenced genomes. Here we introduce seven new satellite DNAs (satDNAs), which more than doubles the number of currently known lepidopteran satDNAs. The satDNAs were identified in genomes of three species of Crambidae moths, namely Ostrinia nubilalis, Cydalima perspectalis, and Diatraea postlineella, using graph-based computational pipeline RepeatExplorer. These repeats varied in their abundance and showed high variability within and between species, although some degree of conservation was noted. The satDNAs showed a scattered distribution, often on both autosomes and sex chromosomes, with the exception of both satellites in D. postlineella, in which the satDNAs were located at a single autosomal locus. Three satDNAs were abundant on the W chromosomes of O. nubilalis and C. perspectalis, thus contributing to their differentiation from the Z chromosomes. To provide background for the in situ localization of the satDNAs, we performed a detailed cytogenetic analysis of the karyotypes of all three species. This comparative analysis revealed differences in chromosome number, number and location of rDNA clusters, and molecular differentiation of sex chromosomes.
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Affiliation(s)
- Diogo C Cabral-de-Mello
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências/IB, UNESP-Univ Estadual Paulista, Rio Claro, Brazil.,Biology Centre, Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czechia
| | - Magda Zrzavá
- Biology Centre, Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czechia.,Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | | | - Pedro Rendón
- IAEA-TCLA-Consultant-USDA-APHIS-Moscamed Program Guatemala, Guatemala City, Guatemala
| | - František Marec
- Biology Centre, Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czechia
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22
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Nguyen DHM, Panthum T, Ponjarat J, Laopichienpong N, Kraichak E, Singchat W, Ahmad SF, Muangmai N, Peyachoknagul S, Na-Nakorn U, Srikulnath K. An Investigation of ZZ/ZW and XX/XY Sex Determination Systems in North African Catfish ( Clarias gariepinus, ). Front Genet 2021; 11:562856. [PMID: 33584785 PMCID: PMC7874028 DOI: 10.3389/fgene.2020.562856] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 12/07/2020] [Indexed: 12/30/2022] Open
Abstract
An investigation of sex-specific loci may provide important insights into fish sex determination strategies. This may be useful for biotechnological purposes, for example, to produce all-male or all-female fish for commercial breeding. The North African catfish species, Clarias gariepinus, has been widely adopted for aquaculture because its superior growth and disease resistance render the species suitable for hybridization with other catfish to improve the productivity and quality of fish meat. This species has either a ZZ/ZW or XX/XY sex determination system. Here, we investigate and characterize these systems using high-throughput genome complexity reduction sequencing as Diversity Arrays Technology. This approach was effective in identifying moderately sex-linked loci with both single-nucleotide polymorphisms (SNPs) and restriction fragment presence/absence (PA) markers in 30 perfectly sexed individuals of C. gariepinus. However, SNPs based markers were not found in this study. In total, 41 loci met the criteria for being moderately male-linked (with male vs. female ratios 80:20 and 70:30), while 25 loci were found to be moderately linked to female sex. No strictly male- or female-linked loci were detected. Seven moderately male-linked loci were partially homologous to some classes of transposable elements and three moderately male-linked loci were partially homologous to functional genes. Our data showed that the male heterogametic XX/XY sex determination system should co-exist with the ZZ/ZW system in C. gariepinus. Our finding of the co-existence of XX/XY and ZZ/ZW systems can be applied to benefit commercial breeding of this species in Thailand. This approach using moderately sex-linked loci provides a solid baseline for revealing sex determination mechanisms and identify potential sex determination regions in catfish, allowing further investigation of genetic improvements in breeding programs.
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Affiliation(s)
- Dung Ho My Nguyen
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand.,Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok, Thailand
| | - Thitipong Panthum
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand.,Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok, Thailand
| | - Jatupong Ponjarat
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Nararat Laopichienpong
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand.,Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok, Thailand
| | | | - Worapong Singchat
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand.,Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok, Thailand
| | - Syed Farhan Ahmad
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand.,Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok, Thailand
| | - Narongrit Muangmai
- Department of Fishery Biology, Faculty of Fisheries, Kasetsart University, Bangkok, Thailand
| | - Surin Peyachoknagul
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Uthairat Na-Nakorn
- Department of Aquaculture, Faculty of Fisheries, Kasetsart University, Bangkok, Thailand
| | - Kornsorn Srikulnath
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand.,Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok, Thailand.,Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University, Kasetsart University, Bangkok, Thailand.,Center of Excellence on Agricultural Biotechnology (AG-BIO/PERDO-CHE), Bangkok, Thailand.,Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok, Thailand.,Amphibian Research Center, Hiroshima University, Higashihiroshima, Japan
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