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Höök L, Vila R, Wiklund C, Backström N. Temporal dynamics of faster neo-Z evolution in butterflies. Evolution 2024; 78:1554-1567. [PMID: 38813673 DOI: 10.1093/evolut/qpae082] [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: 01/10/2024] [Revised: 04/29/2024] [Accepted: 05/29/2024] [Indexed: 05/31/2024]
Abstract
The faster-Z/X hypothesis predicts that sex-linked genes should diverge faster than autosomal genes. However, studies across different lineages have shown mixed support for this effect. So far, most analyses have focused on old and well-differentiated sex chromosomes, but less is known about the divergence of more recently acquired neo-sex chromosomes. In Lepidoptera (moths and butterflies), Z-autosome fusions are frequent, but the evolutionary dynamics of neo-Z chromosomes have not been explored in detail. Here, we analyzed the faster-Z effect in Leptidea sinapis, a butterfly with three Z chromosomes. We show that the neo-Z chromosomes have been acquired stepwise, resulting in strata of differentiation and masculinization. While all Z chromosomes showed evidence of the faster-Z effect, selection for genes on the youngest neo-Z chromosome (Z3) appears to have been hampered by a largely intact, homologous neo-W chromosome. However, the intermediately aged neo-Z chromosome (Z2), which lacks W gametologs, showed fewer evolutionary constraints, resulting in particularly fast evolution. Our results therefore support that neo-sex chromosomes can constitute temporary hot-spots of adaptation and divergence. The underlying dynamics are likely causally linked to shifts in selective constraints, evolution of gene expression, and degeneration of W-linked gametologs which gradually expose Z-linked genes to selection.
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Affiliation(s)
- Lars Höök
- Evolutionary Biology Program, Department of Ecology and Genetics (IEG), Uppsala University, Uppsala, Sweden
| | - Roger Vila
- 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 (IEG), Uppsala University, Uppsala, Sweden
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2
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Gokhman VE, Kuznetsova VG. Structure and Evolution of Ribosomal Genes of Insect Chromosomes. INSECTS 2024; 15:593. [PMID: 39194798 DOI: 10.3390/insects15080593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Revised: 07/25/2024] [Accepted: 08/02/2024] [Indexed: 08/29/2024]
Abstract
Currently, clusters of 45S and 5S ribosomal DNA (rDNA) have been studied in about 1000 and 100 species of the class Insecta, respectively. Although the number of insect species with known 45S rDNA clusters (also referred to as nucleolus-organizing regions, or NORs) constitutes less than 0.1 percent of the described members of this enormous group, certain conclusions can already be drawn. Since haploid karyotypes with single 45S and 5S rDNA clusters predominate in both basal and derived insect groups, this character state is apparently ancestral for the class Insecta in general. Nevertheless, the number, chromosomal location, and other characteristics of both 45S and 5S rDNA sites substantially vary across different species, and sometimes even within the same species. There are several main factors and molecular mechanisms that either maintain these parameters or alter them on the short-term and/or long-term scale. Chromosome structure (i.e., monocentric vs. holokinetic chromosomes), excessive numbers of rRNA gene copies per cluster, interactions with transposable elements, pseudogenization, and meiotic recombination are perhaps the most important among them.
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Affiliation(s)
| | - Valentina G Kuznetsova
- Department of Karyosystematics, Zoological Institute, Russian Academy of Sciences, St. Petersburg 199034, Russia
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3
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Rueda-M N, Pardo-Diaz C, Montejo-Kovacevich G, McMillan WO, Kozak KM, Arias CF, Ready J, McCarthy S, Durbin R, Jiggins CD, Meier JI, Salazar C. Genomic evidence reveals three W-autosome fusions in Heliconius butterflies. PLoS Genet 2024; 20:e1011318. [PMID: 39024186 PMCID: PMC11257349 DOI: 10.1371/journal.pgen.1011318] [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: 03/27/2023] [Accepted: 05/24/2024] [Indexed: 07/20/2024] Open
Abstract
Sex chromosomes are evolutionarily labile in many animals and sometimes fuse with autosomes, creating so-called neo-sex chromosomes. Fusions between sex chromosomes and autosomes have been proposed to reduce sexual conflict and to promote adaptation and reproductive isolation among species. Recently, advances in genomics have fuelled the discovery of such fusions across the tree of life. Here, we discovered multiple fusions leading to neo-sex chromosomes in the sapho subclade of the classical adaptive radiation of Heliconius butterflies. Heliconius butterflies generally have 21 chromosomes with very high synteny. However, the five Heliconius species in the sapho subclade show large variation in chromosome number ranging from 21 to 60. We find that the W chromosome is fused with chromosome 4 in all of them. Two sister species pairs show subsequent fusions between the W and chromosomes 9 or 14, respectively. These fusions between autosomes and sex chromosomes make Heliconius butterflies an ideal system for studying the role of neo-sex chromosomes in adaptive radiations and the degeneration of sex chromosomes over time. Our findings emphasize the capability of short-read resequencing to detect genomic signatures of fusion events between sex chromosomes and autosomes even when sex chromosomes are not explicitly assembled.
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Affiliation(s)
- Nicol Rueda-M
- Biology Program, Faculty of Natural Sciences, Universidad del Rosario, Bogotá, Colombia
- Tree of Life Programme, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Carolina Pardo-Diaz
- Biology Program, Faculty of Natural Sciences, Universidad del Rosario, Bogotá, Colombia
| | | | | | - Krzysztof M. Kozak
- Smithsonian Tropical Research Institute, Panama City, Panama
- Museum of Vertebrate Zoology, Berkeley, California, United States of America
| | - Carlos F. Arias
- Smithsonian Tropical Research Institute, Panama City, Panama
- Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, Washington DC, United States of America
| | - Jonathan Ready
- Institute for Biological Sciences, Federal University of Pará - UFPA, Belém, Brazil
- Centre for Advanced Studies of Biodiversity - CEABIO, Belém, Brazil
| | - Shane McCarthy
- Tree of Life Programme, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Richard Durbin
- Tree of Life Programme, Wellcome Sanger Institute, Hinxton, United Kingdom
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Chris D. Jiggins
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Joana I. Meier
- Tree of Life Programme, Wellcome Sanger Institute, Hinxton, United Kingdom
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Camilo Salazar
- Biology Program, Faculty of Natural Sciences, Universidad del Rosario, Bogotá, Colombia
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4
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Traut W, Sahara K, ffrench-Constant RH. Lepidopteran Synteny Units reveal deep chromosomal conservation in butterflies and moths. G3 (BETHESDA, MD.) 2023; 13:jkad134. [PMID: 37310934 PMCID: PMC10411566 DOI: 10.1093/g3journal/jkad134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 05/31/2023] [Accepted: 06/05/2023] [Indexed: 06/15/2023]
Abstract
DNA is compacted into individual particles or chromosomes that form the basic units of inheritance. However, different animals and plants have widely different numbers of chromosomes. This means that we cannot readily tell which chromosomes are related to which. Here, we describe a simple technique that looks at the similarity of genes on each chromosome and thus gives us a true picture of their homology or similarity through evolutionary time. We use this new system to look at the chromosomes of butterflies and moths or Lepidoptera. We term the associated synteny units, Lepidopteran Synteny Units (LSUs). Using a sample of butterfly and moth genomes from across evolutionary time, we show that LSUs form a simple and reliable method of tracing chromosomal homology back through time. Surprisingly, this technique reveals that butterfly and moth chromosomes show conserved blocks dating back to their sister group the Trichoptera. As Lepidoptera have holocentric chromosomes, it will be interesting to see if similar levels of synteny are shown in groups of animals with monocentric chromosomes. The ability to define homology via LSU analysis makes it considerably easier to approach many questions in chromosomal evolution.
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Affiliation(s)
- Walther Traut
- Institut für Biologie, Zentrum für Medizinische Struktur- und Zellbiologie, Universität zu Lübeck, Ratzeburger Allee 160, D-23562 Lübeck, Germany
| | - Ken Sahara
- Laboratory of Molecular Entomology, Faculty of Agriculture, Iwate University, 3-18-8, Ueda, Morioka 020-8550, Japan
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5
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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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6
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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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7
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Dalíková M, Provazníková I, Provazník J, Grof-Tisza P, Pepi A, Nguyen P. The Role of Repetitive Sequences in Repatterning of Major Ribosomal DNA Clusters in Lepidoptera. Genome Biol Evol 2023; 15:evad090. [PMID: 37226278 PMCID: PMC10257491 DOI: 10.1093/gbe/evad090] [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: 05/31/2022] [Revised: 04/27/2023] [Accepted: 05/09/2023] [Indexed: 05/26/2023] Open
Abstract
Genes for major ribosomal RNAs (rDNA) are present in multiple copies mainly organized in tandem arrays. The number and position of rDNA loci can change dynamically and their repatterning is presumably driven by other repetitive sequences. We explored a peculiar rDNA organization in several representatives of Lepidoptera with either extremely large or numerous rDNA clusters. We combined molecular cytogenetics with analyses of second- and third-generation sequencing data to show that rDNA spreads as a transcription unit and reveal association between rDNA and various repeats. Furthermore, we performed comparative long read analyses among the species with derived rDNA distribution and moths with a single rDNA locus, which is considered ancestral. Our results suggest that satellite arrays, rather than mobile elements, facilitate homology-mediated spread of rDNA via either integration of extrachromosomal rDNA circles or ectopic recombination. The latter arguably better explains preferential spread of rDNA into terminal regions of lepidopteran chromosomes as efficiency of ectopic recombination depends on the proximity of homologous sequences to telomeres.
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Affiliation(s)
- Martina Dalíková
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Institute of Entomology, Biology Centre CAS, České Budějovice, Czech Republic
| | - 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
| | - Jan Provazník
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Patrick Grof-Tisza
- Institute of Biology, Laboratory of Evolutionary Entomology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Adam Pepi
- Department of Biology, Tufts University
| | - 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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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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Pazhenkova EA, Lukhtanov VA. Whole-Genome Analysis Reveals the Dynamic Evolution of Holocentric Chromosomes in Satyrine Butterflies. Genes (Basel) 2023; 14:437. [PMID: 36833364 PMCID: PMC9956908 DOI: 10.3390/genes14020437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 02/01/2023] [Accepted: 02/07/2023] [Indexed: 02/11/2023] Open
Abstract
Butterfly chromosomes are holocentric, i.e., lacking a localized centromere. Potentially, this can lead to rapid karyotypic evolution through chromosome fissions and fusions, since fragmented chromosomes retain kinetic activity, while fused chromosomes are not dicentric. However, the actual mechanisms of butterfly genome evolution are poorly understood. Here, we analyzed chromosome-scale genome assemblies to identify structural rearrangements between karyotypes of satyrine butterfly species. For the species pair Erebia ligea-Maniola jurtina, sharing the ancestral diploid karyotype 2n = 56 + ZW, we demonstrate a high level of chromosomal macrosynteny and nine inversions separating these species. We show that the formation of a karyotype with a low number of chromosomes (2n = 36 + ZW) in Erebia aethiops was based on ten fusions, including one autosome-sex chromosome fusion, resulting in a neo-Z chromosome. We also detected inversions on the Z sex chromosome that were differentially fixed between the species. We conclude that chromosomal evolution is dynamic in the satyrines, even in the lineage that preserves the ancestral chromosome number. We hypothesize that the exceptional role of Z chromosomes in speciation may be further enhanced by inversions and sex chromosome-autosome fusions. We argue that not only fusions/fissions but also inversions are drivers of the holocentromere-mediated mode of chromosomal speciation.
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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, St. Petersburg 199034, Russia
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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: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [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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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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12
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Carey SB, Lovell JT, Jenkins J, Leebens-Mack J, Schmutz J, Wilson MA, Harkess A. Representing sex chromosomes in genome assemblies. CELL GENOMICS 2022; 2. [PMID: 35720975 PMCID: PMC9205529 DOI: 10.1016/j.xgen.2022.100132] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Sex chromosomes have evolved hundreds of independent times across eukaryotes. As genome sequencing, assembly, and scaffolding techniques rapidly improve, it is now feasible to build fully phased sex chromosome assemblies. Despite technological advances enabling phased assembly of whole chromosomes, there are currently no standards for representing sex chromosomes when publicly releasing a genome. Furthermore, most computational analysis tools are unable to efficiently investigate their unique biology relative to autosomes. We discuss a diversity of sex chromosome systems and consider the challenges of representing sex chromosome pairs in genome assemblies. By addressing these issues now as technologies for full phasing of chromosomal assemblies are maturing, we can collectively ensure that future genome analysis toolkits can be broadly applied to all eukaryotes with diverse types of sex chromosome systems. Here we provide best practice guidelines for presenting a genome assembly that contains sex chromosomes. These guidelines can also be applied to other non-recombining genomic regions, such as S-loci in plants and mating-type loci in fungi and algae.
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Affiliation(s)
- Sarah B Carey
- Department of Crop, Soil, and Environmental Sciences, Auburn University, Auburn, AL 36849, USA.,HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - John T Lovell
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Jerry Jenkins
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Jim Leebens-Mack
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA.,US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Melissa A Wilson
- School of Life Sciences, Center for Evolution and Medicine, The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Alex Harkess
- Department of Crop, Soil, and Environmental Sciences, Auburn University, Auburn, AL 36849, USA.,HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
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13
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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: 42] [Impact Index Per Article: 14.0] [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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14
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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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15
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Pajpach F, Wu T, Shearwin-Whyatt L, Jones K, Grützner F. Flavors of Non-Random Meiotic Segregation of Autosomes and Sex Chromosomes. Genes (Basel) 2021; 12:genes12091338. [PMID: 34573322 PMCID: PMC8471020 DOI: 10.3390/genes12091338] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/26/2021] [Accepted: 08/26/2021] [Indexed: 12/14/2022] Open
Abstract
Segregation of chromosomes is a multistep process occurring both at mitosis and meiosis to ensure that daughter cells receive a complete set of genetic information. Critical components in the chromosome segregation include centromeres, kinetochores, components of sister chromatid and homologous chromosomes cohesion, microtubule organizing centres, and spindles. Based on the cytological work in the grasshopper Brachystola, it has been accepted for decades that segregation of homologs at meiosis is fundamentally random. This ensures that alleles on chromosomes have equal chance to be transmitted to progeny. At the same time mechanisms of meiotic drive and an increasing number of other examples of non-random segregation of autosomes and sex chromosomes provide insights into the underlying mechanisms of chromosome segregation but also question the textbook dogma of random chromosome segregation. Recent advances provide a better understanding of meiotic drive as a prominent force where cellular and chromosomal changes allow autosomes to bias their segregation. Less understood are mechanisms explaining observations that autosomal heteromorphism may cause biased segregation and regulate alternating segregation of multiple sex chromosome systems or translocation heterozygotes as an extreme case of non-random segregation. We speculate that molecular and cytological mechanisms of non-random segregation might be common in these cases and that there might be a continuous transition between random and non-random segregation which may play a role in the evolution of sexually antagonistic genes and sex chromosome evolution.
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Affiliation(s)
- Filip Pajpach
- School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia; (F.P.); (L.S.-W.)
| | - Tianyu Wu
- Department of Central Laboratory, Clinical Laboratory, Jing’an District Centre Hospital of Shanghai and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China;
| | - Linda Shearwin-Whyatt
- School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia; (F.P.); (L.S.-W.)
| | - Keith Jones
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton BN1 9RH, UK;
| | - Frank Grützner
- School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia; (F.P.); (L.S.-W.)
- Correspondence:
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16
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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: 6] [Impact Index Per Article: 2.0] [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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17
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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: 20] [Impact Index Per Article: 6.7] [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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18
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Meiotic analyses show adaptations to maintenance of fertility in X1Y1X2Y2X3Y3X4Y4X5Y5 system of amazon frog Leptodactylus pentadactylus (Laurenti, 1768). Sci Rep 2020; 10:16327. [PMID: 33004883 PMCID: PMC7529792 DOI: 10.1038/s41598-020-72867-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 08/28/2020] [Indexed: 02/06/2023] Open
Abstract
Heterozygous chromosomal rearrangements can result in failures during the meiotic cycle and the apoptosis of germline, making carrier individuals infertile. The Amazon frog Leptodactylus pentadactylus has a meiotic multivalent, composed of 12 sex chromosomes. The mechanisms by which this multi-chromosome system maintains fertility in males of this species remain undetermined. In this study we investigated the meiotic behavior of this multivalent to understand how synapse, recombination and epigenetic modifications contribute to maintaining fertility and chromosomal sexual determination in this species. Our sample had 2n = 22, with a ring formed by ten chromosomes in meiosis, indicating a new system of sex determination for this species (X1Y1X2Y2X3Y3X4Y4X5Y5). Synapsis occurs in the homologous terminal portion of the chromosomes, while part of the heterologous interstitial regions performed synaptic adjustment. The multivalent center remains asynaptic until the end of pachytene, with interlocks, gaps and rich-chromatin in histone H2A phosphorylation at serine 139 (γH2AX), suggesting transcriptional silence. In late pachytene, paired regions show repair of double strand-breaks (DSBs) with RAD51 homolog 1 (Rad51). These findings suggest that Rad51 persistence creates positive feedback at the pachytene checkpoint, allowing meiosis I to progress normally. Additionally, histone H3 trimethylation at lysine 27 in the pericentromeric heterochromatin of this anuran can suppress recombination in this region, preventing failed chromosomal segregation. Taken together, these results indicate that these meiotic adaptations are required for maintenance of fertility in L. pentadactylus.
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19
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Lukhtanov VA, Dantchenko AV, Khakimov FR, Sharafutdinov D, Pazhenkova EA. Karyotype evolution and flexible (conventional versus inverted) meiosis in insects with holocentric chromosomes: a case study based on Polyommatus butterflies. Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa077] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
The Polyommatus butterflies have holocentric chromosomes, which are characterized by kinetic activity distributed along the entire chromosome length, and the highest range of haploid chromosome numbers (n) known within a single eukaryotic genus (from n = 10 to n = 226). Previous analyses have shown that these numbers most likely evolved gradually from an ancestral karyotype, in accordance with the Brownian motion model of chromosome change accumulation. Here we studied chromosome sets within a monophyletic group of previously non-karyotyped Polyommatus species. We demonstrate that these species have a limited interspecific chromosome number variation from n = 16 to n = 25, which is consistent with the Brownian motion model prediction. We also found intra- and interpopulation variation in the chromosome numbers. These findings support the model of karyotype evolution through the gradual accumulation of neutral or weakly underdominant rearrangements that can persist in the heterozygous state within a population. For Polyommatus poseidonides we report the phenomenon of flexible meiosis in which the chromosome multivalents are able to undergo either conventional or inverted meiosis within the same individual. We hypothesise that the ability to invert the order of the meiotic events may be adaptive and can facilitate proper chromosome segregation in chromosomal heterozygotes, thus promoting rapid karyotype evolution.
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Affiliation(s)
- Vladimir A Lukhtanov
- Department of Karyosystematics, Zoological Institute of the Russian Academy of Sciences, St. Petersburg, Russia
| | - Alexander V Dantchenko
- Department of Karyosystematics, Zoological Institute of the Russian Academy of Sciences, St. Petersburg, Russia
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Fayzali R Khakimov
- Pavlovsky Institute of Zoology and Parasitology, Academy of Sciences of the Republic of Tajikistan, Dushanbe, Tajikistan
| | - Damir Sharafutdinov
- Pavlovsky Institute of Zoology and Parasitology, Academy of Sciences of the Republic of Tajikistan, Dushanbe, Tajikistan
| | - Elena A Pazhenkova
- Department of Entomology, St. Petersburg State University, St. Petersburg, Russia
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20
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de Vos JM, Augustijnen H, Bätscher L, Lucek K. Speciation through chromosomal fusion and fission in Lepidoptera. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190539. [PMID: 32654638 DOI: 10.1098/rstb.2019.0539] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Changes in chromosome numbers may strongly affect reproductive barriers, because individuals heterozygous for distinct karyotypes are typically expected to be at least partially sterile or to show reduced recombination. Therefore, several classic speciation models are based on chromosomal changes. One import mechanism generating variation in chromosome numbers is fusion and fission of existing chromosomes, which is particularly likely in species with holocentric chromosomes, i.e. chromosomes that lack a single centromere. Holocentric chromosomes evolved repeatedly across the tree of life, including in Lepidoptera. Although changes in chromosome numbers are hypothesized to be an important driver of the spectacular diversification of Lepidoptera, comparative studies across the order are lacking. We performed the first comprehensive literature survey of karyotypes for Lepidoptera species since the 1970s and tested if, and how, chromosomal variation might affect speciation. Even though a meta-analysis of karyological differences between closely related taxa did not reveal an effect on the degree of reproductive isolation, phylogenetic diversification rate analyses across the 16 best-covered genera indicated a strong, positive association of rates of chromosome number evolution and speciation. These findings suggest a macroevolutionary impact of varying chromosome numbers in Lepidoptera and likely apply to other taxonomic groups, especially to those with holocentric chromosomes. This article is part of the theme issue 'Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers'.
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Affiliation(s)
- Jurriaan M de Vos
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Hannah Augustijnen
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Livio Bätscher
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Kay Lucek
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
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21
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Yoshido A, Šíchová J, Pospíšilová K, Nguyen P, Voleníková A, Šafář J, Provazník J, Vila R, Marec F. Evolution of multiple sex-chromosomes associated with dynamic genome reshuffling in Leptidea wood-white butterflies. Heredity (Edinb) 2020; 125:138-154. [PMID: 32518391 PMCID: PMC7426936 DOI: 10.1038/s41437-020-0325-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 05/21/2020] [Accepted: 05/21/2020] [Indexed: 12/13/2022] Open
Abstract
Sex-chromosome systems tend to be highly conserved and knowledge about their evolution typically comes from macroevolutionary inference. Rapidly evolving complex sex-chromosome systems represent a rare opportunity to study the mechanisms of sex-chromosome evolution at unprecedented resolution. Three cryptic species of wood-white butterflies—Leptidea juvernica, L. sinapis and L. reali—have each a unique set of multiple sex-chromosomes with 3–4 W and 3–4 Z chromosomes. Using a transcriptome-based microarray for comparative genomic hybridisation (CGH) and a library of bacterial artificial chromosome (BAC) clones, both developed in L. juvernica, we identified Z-linked Leptidea orthologs of Bombyx mori genes and mapped them by fluorescence in situ hybridisation (FISH) with BAC probes on multiple Z chromosomes. In all three species, we determined synteny blocks of autosomal origin and reconstructed the evolution of multiple sex-chromosomes. In addition, we identified W homologues of Z-linked orthologs and characterised their molecular differentiation. Our results suggest that the multiple sex-chromosome system evolved in a common ancestor as a result of dynamic genome reshuffling through repeated rearrangements between the sex chromosomes and autosomes, including translocations, fusions and fissions. Thus, the initial formation of neo-sex chromosomes could not have played a role in reproductive isolation between these Leptidea species. However, the subsequent species-specific fissions of several neo-sex chromosomes could have contributed to their reproductive isolation. Then, significantly increased numbers of Z-linked genes and independent neo-W chromosome degeneration could accelerate the accumulation of genetic incompatibilities between populations and promote their divergence resulting in speciation.
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Affiliation(s)
- Atsuo Yoshido
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 370 05, České Budějovice, Czech Republic
| | - Jindra Šíchová
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 370 05, České Budějovice, Czech Republic
| | - Kristýna Pospíšilová
- 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
| | - Petr Nguyen
- 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
| | - Anna Voleníková
- 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
| | - Jan Šafář
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, Šlechtitelů 31, 779 00, Olomouc, Czech Republic
| | - Jan Provazník
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 370 05, České Budějovice, Czech Republic.,Genomics Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Roger Vila
- Institut de Biologia Evolutiva (CSIC-UPF), Pg. Marítim de la Barceloneta 37, 08003, Barcelona, Spain
| | - František Marec
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 370 05, České Budějovice, Czech Republic.
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22
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Magalhães BRDS, Sosa-Goméz DR, Dionísio JF, Dias FC, Baldissera JNDC, Rincão MP, Da Rosa R. Cytogenetic markers applied to cytotaxonomy in two soybean pests: Anticarsia gemmatalis (Hübner, 1818) and Chrysodeixis includens (Walker, 1858). PLoS One 2020; 15:e0230244. [PMID: 32160240 PMCID: PMC7065768 DOI: 10.1371/journal.pone.0230244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 02/26/2020] [Indexed: 11/27/2022] Open
Abstract
Anticarsia gemmatalis (Hübner, 1818) and Chrysodeixis includens (Walker, 1858) are species of Lepidoptera that cause great damages in the soybean plantations of Brazil. Despite the importance they have in this regard, there are no studies on the chromosomal organization of these species and recently, A. gemmatalis, which belonged to the Noctuidae family, was allocated to the Erebidae family. Therefore, the objective of this paper was to analyze, through conventional and molecular cytogenetic markers, both species of Lepidoptera. A 2n = 62 was observed, with ZZ/ZW sex chromosome system and holokinetic chromosomes for both species. There was homogeneity in the number of 18S rDNA sites for both species. However, variations in heterochromatin distribution were observed between both species. The cytogenetic analyses enabled separation of the species, corroborating the transference of A. gemmatalis, from the family Noctuidae to the family Erebidae, suggesting new cytotaxonomic characteristics.
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Affiliation(s)
| | | | - Jaqueline Fernanda Dionísio
- Laboratório de Citogenética Animal, Departamento de Biologia Geral, Universidade Estadual de Londrina, Brasil
| | - Felipe Cordeiro Dias
- Laboratório de Citogenética Animal, Departamento de Biologia Geral, Universidade Estadual de Londrina, Brasil
| | | | - Matheus Pires Rincão
- Laboratório de Citogenética Animal, Departamento de Biologia Geral, Universidade Estadual de Londrina, Brasil
| | - Renata Da Rosa
- Laboratório de Citogenética Animal, Departamento de Biologia Geral, Universidade Estadual de Londrina, Brasil
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Advances and Challenges of Using the Sterile Insect Technique for the Management of Pest Lepidoptera. INSECTS 2019; 10:insects10110371. [PMID: 31731445 PMCID: PMC6921062 DOI: 10.3390/insects10110371] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 10/20/2019] [Accepted: 10/23/2019] [Indexed: 11/24/2022]
Abstract
Over the past 30 years, the sterile insect technique (SIT) has become a regular component of area-wide integrated pest management (AW-IPM) programs against several major agricultural pests and vectors of severe diseases. The SIT-based programs have been especially successful against dipteran pests. However, the SIT applicability for controlling lepidopteran pests has been challenging, mainly due to their high resistance to the ionizing radiation that is used to induce sterility. Nevertheless, the results of extensive research and currently operating SIT programs show that most problems with the implementation of SIT against pest Lepidoptera have been successfully resolved. Here, we summarize the cytogenetic peculiarities of Lepidoptera that should be considered in the development and application of SIT for a particular pest species. We also discuss the high resistance of Lepidoptera to ionizing radiation, and present the principle of derived technology based on inherited sterility (IS). Furthermore, we present successful SIT/IS applications against five major lepidopteran pests, and summarize the results of research on the quality control of reared and released insects, which is of great importance for their field performance. In the light of new research findings, we also discuss options for the development of genetic sexing strains, which is a challenge to further improve the applicability of SIT/IS against selected lepidopteran pests.
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24
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Talla V, Johansson A, Dincă V, Vila R, Friberg M, Wiklund C, Backström N. Lack of gene flow: Narrow and dispersed differentiation islands in a triplet ofLeptideabutterfly species. Mol Ecol 2019; 28:3756-3770. [DOI: 10.1111/mec.15188] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 07/08/2019] [Accepted: 07/12/2019] [Indexed: 01/02/2023]
Affiliation(s)
- Venkat Talla
- Department of Evolutionary Biology Evolutionary Biology Centre (EBC) Uppsala University Uppsala Sweden
| | - Anna Johansson
- Department of Medical Biochemistry and Microbiology Uppsala Biomedical Centre (BMC) Uppsala Sweden
| | - Vlad Dincă
- Department of Ecology and Genetics University of Oulu Oulu Finland
| | - Roger Vila
- Institut de Biologia Evolutiva (CSIC‐UPF) Barcelona Spain
| | - Magne Friberg
- Department of Biology, Biodiversity Unit Lund University Lund Sweden
| | - Christer Wiklund
- Division of Ecology Department of Zoology Stockholm University Stockholm Sweden
| | - Niclas Backström
- Department of Evolutionary Biology Evolutionary Biology Centre (EBC) Uppsala University Uppsala Sweden
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25
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Mackintosh A, Laetsch DR, Hayward A, Charlesworth B, Waterfall M, Vila R, Lohse K. The determinants of genetic diversity in butterflies. Nat Commun 2019; 10:3466. [PMID: 31371715 PMCID: PMC6672018 DOI: 10.1038/s41467-019-11308-4] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 07/01/2019] [Indexed: 11/09/2022] Open
Abstract
Under the neutral theory, genetic diversity is expected to increase with population size. While comparative analyses have consistently failed to find strong relationships between census population size and genetic diversity, a recent study across animals identified a strong correlation between propagule size and genetic diversity, suggesting that r-strategists that produce many small offspring, have greater long-term population sizes. Here we compare genome-wide genetic diversity across 38 species of European butterflies (Papilionoidea), a group that shows little variation in reproductive strategy. We show that genetic diversity across butterflies varies over an order of magnitude and that this variation cannot be explained by differences in current abundance, propagule size, host or geographic range. Instead, neutral genetic diversity is negatively correlated with body size and positively with the length of the genetic map. This suggests that genetic diversity is determined both by differences in long-term population size and the effect of selection on linked sites.
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Affiliation(s)
- Alexander Mackintosh
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH9 3FL, UK.
| | - Dominik R Laetsch
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH9 3FL, UK
| | - Alexander Hayward
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Cornwall, TR10 9FE, UK
| | - Brian Charlesworth
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH9 3FL, UK
| | - Martin Waterfall
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH9 3FL, UK
| | - Roger Vila
- Institut de Biologia Evolutiva (CSIC Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37, ESP-08003, Barcelona, Spain
| | - Konrad Lohse
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH9 3FL, UK.
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26
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Xu D, Sember A, Zhu Q, Oliveira EAD, Liehr T, Al-Rikabi ABH, Xiao Z, Song H, Cioffi MDB. Deciphering the Origin and Evolution of the X 1X 2Y System in Two Closely-Related Oplegnathus Species (Oplegnathidae and Centrarchiformes). Int J Mol Sci 2019; 20:E3571. [PMID: 31336568 PMCID: PMC6678977 DOI: 10.3390/ijms20143571] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 07/05/2019] [Accepted: 07/13/2019] [Indexed: 01/18/2023] Open
Abstract
Oplegnathus fasciatus and O. punctatus (Teleostei: Centrarchiformes: Oplegnathidae), are commercially important rocky reef fishes, endemic to East Asia. Both species present an X1X2Y sex chromosome system. Here, we investigated the evolutionary forces behind the origin and differentiation of these sex chromosomes, with the aim to elucidate whether they had a single or convergent origin. To achieve this, conventional and molecular cytogenetic protocols, involving the mapping of repetitive DNA markers, comparative genomic hybridization (CGH), and whole chromosome painting (WCP) were applied. Both species presented similar 2n, karyotype structure and hybridization patterns of repetitive DNA classes. 5S rDNA loci, besides being placed on the autosomal pair 22, resided in the terminal region of the long arms of both X1 chromosomes in females, and on the X1 and Y chromosomes in males. Furthermore, WCP experiments with a probe derived from the Y chromosome of O. fasciatus (OFAS-Y) entirely painted the X1 and X2 chromosomes in females and the X1, X2, and Y chromosomes in males of both species. CGH failed to reveal any sign of sequence differentiation on the Y chromosome in both species, thereby suggesting the shared early stage of neo-Y chromosome differentiation. Altogether, the present findings confirmed the origin of the X1X2Y sex chromosomes via Y-autosome centric fusion and strongly suggested their common origin.
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Affiliation(s)
- Dongdong Xu
- Key Lab of Mariculture and Enhancement of Zhejiang Province, Marine Fishery Institute of Zhejiang Province, Zhoushan 316100, China
- College of Fisheries, Zhejiang Ocean University, Zhoushan 316100, China
| | - Alexandr Sember
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 277 21 Liběchov, Czech Republic
| | - Qihui Zhu
- Key Lab of Mariculture and Enhancement of Zhejiang Province, Marine Fishery Institute of Zhejiang Province, Zhoushan 316100, China
| | - Ezequiel Aguiar de Oliveira
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos SP 13565-905, Brazil
- Secretaria de Estado de Educação de Mato Grosso-SEDUC-MT, Cuiabá MT 78049-909, Brazil
| | - Thomas Liehr
- University Clinic Jena, Institute of Human Genetics, 07747 Jena, Germany
| | | | - Zhizhong Xiao
- Laboratory for Marine Biology and Biotechnology, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China
| | - Hongbin Song
- Key Lab of Mariculture and Enhancement of Zhejiang Province, Marine Fishery Institute of Zhejiang Province, Zhoushan 316100, China
- College of Fisheries, Zhejiang Ocean University, Zhoushan 316100, China
| | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos SP 13565-905, Brazil.
- University Clinic Jena, Institute of Human Genetics, 07747 Jena, Germany.
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Hill J, Rastas P, Hornett EA, Neethiraj R, Clark N, Morehouse N, de la Paz Celorio-Mancera M, Cols JC, Dircksen H, Meslin C, Keehnen N, Pruisscher P, Sikkink K, Vives M, Vogel H, Wiklund C, Woronik A, Boggs CL, Nylin S, Wheat CW. Unprecedented reorganization of holocentric chromosomes provides insights into the enigma of lepidopteran chromosome evolution. SCIENCE ADVANCES 2019; 5:eaau3648. [PMID: 31206013 PMCID: PMC6561736 DOI: 10.1126/sciadv.aau3648] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 05/03/2019] [Indexed: 05/04/2023]
Abstract
Chromosome evolution presents an enigma in the mega-diverse Lepidoptera. Most species exhibit constrained chromosome evolution with nearly identical haploid chromosome counts and chromosome-level gene collinearity among species more than 140 million years divergent. However, a few species possess radically inflated chromosomal counts due to extensive fission and fusion events. To address this enigma of constraint in the face of an exceptional ability to change, we investigated an unprecedented reorganization of the standard lepidopteran chromosome structure in the green-veined white butterfly (Pieris napi). We find that gene content in P. napi has been extensively rearranged in large collinear blocks, which until now have been masked by a haploid chromosome number close to the lepidopteran average. We observe that ancient chromosome ends have been maintained and collinear blocks are enriched for functionally related genes suggesting both a mechanism and a possible role for selection in determining the boundaries of these genome-wide rearrangements.
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Affiliation(s)
- Jason Hill
- Population Genetics, Department of Zoology, Stockholm University, Stockholm, Sweden
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Corresponding author. (J.H.); (C.W.W.)
| | - Pasi Rastas
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Emily A. Hornett
- Department of Zoology, University of Cambridge, Cambridge, UK
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Ramprasad Neethiraj
- Population Genetics, Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Nathan Clark
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Nathan Morehouse
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA
| | | | - Jofre Carnicer Cols
- Department of Evolutionary Biology, Ecology and Environmental Sciences, University of Barcelona, 08028 Barcelona, Spain
- CREAF, Global Ecology Unit, Autonomous University of Barcelona, 08193 Cerdanyola del Vallès, Spain
| | - Heinrich Dircksen
- Functional Morphology, Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Camille Meslin
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15260, USA
- INRA, Department of Sensory Ecology, Institute of Ecology and Environmental Sciences of Paris, Route de Saint-Cyr, 78026 Versailles Cedex, France
| | - Naomi Keehnen
- Population Genetics, Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Peter Pruisscher
- Population Genetics, Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Kristin Sikkink
- Department of Ecology, Evolution and Behavior, University of Minnesota, St Paul, MN 55108, USA
- Department of Biology, University of Mississippi, University, MS 38677, USA
| | - Maria Vives
- Department of Evolutionary Biology, Ecology and Environmental Sciences, University of Barcelona, 08028 Barcelona, Spain
- CREAF, Global Ecology Unit, Autonomous University of Barcelona, 08193 Cerdanyola del Vallès, Spain
| | - Heiko Vogel
- Department of Entomology, Max Planck Institute for Chemical Ecology, D-07745 Jena, Germany
| | - Christer Wiklund
- Population Genetics, Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Alyssa Woronik
- Population Genetics, Department of Zoology, Stockholm University, Stockholm, Sweden
- Center for Developmental Genetics, Department of Biology, New York University, 100 Washington Square East, New York, NY 10003, USA
| | - Carol L. Boggs
- Department of Biological Sciences University of South Carolina, Columbia, SC 29208, USA
| | - Sören Nylin
- Population Genetics, Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Christopher W. Wheat
- Population Genetics, Department of Zoology, Stockholm University, Stockholm, Sweden
- Corresponding author. (J.H.); (C.W.W.)
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28
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Genome-wide RAD sequencing to identify a sex-specific marker in Chinese giant salamander Andrias davidianus. BMC Genomics 2019; 20:415. [PMID: 31122206 PMCID: PMC6533744 DOI: 10.1186/s12864-019-5771-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 05/03/2019] [Indexed: 11/15/2022] Open
Abstract
Background Chinese giant salamander Andrias davidianus is an endangered species. The success of artificial breeding provides a useful way to protect this species. However, the method to identify the sex and mechanism of sex determination were unclear which hinder the improvement of the artificial breeding. Detection of a sex specific marker provides an effective approach to identify genetic sex and investigate the sex determination mechanism. Results We used restriction-site-associated DNA (RAD) sequencing to isolate a sex-specific genetic marker in A. davidianus to expand knowledge of the sex determination mechanism. Four male and four female specimens were subjected to RAD sequencing, which generated 934,072,989 reads containing approximately 134.4 Gb of sequences. The first round of comparison of the assembled sequence against the opposite sex raw reads revealed 19,097 female and 17,994 male unmatched sequences. Subsequently, 19,097 female sequences were subjected to a BLAST search against male genomic data, which revealed 308 sequences unmapped to the male genome. One hundred of these were randomly selected and validated by PCR in five male and five female specimens, and four putative sex-specific sequences were produced. Further validation was performed by PCR in another 24 females and 24 males, and all female individuals exhibited the expected specific bands, while the males did not. To apply the sex-specific marker, three specimens reversed from genetic female to physiological male were found in a group exposed to elevated temperature, and 13 individuals reversed from genetic male to physiological female were obtained in a 17β-estradiol exposed group. Conclusion This is the first report of a sex-specific marker in A. davidianus and may have potential for elucidation of its sex determination mechanism and, hence, its conservation. Electronic supplementary material The online version of this article (10.1186/s12864-019-5771-5) contains supplementary material, which is available to authorized users.
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29
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Carabajal Paladino LZ, Provazníková I, Berger M, Bass C, Aratchige NS, López SN, Marec F, Nguyen P. Sex Chromosome Turnover in Moths of the Diverse Superfamily Gelechioidea. Genome Biol Evol 2019; 11:1307-1319. [PMID: 31028711 PMCID: PMC6486803 DOI: 10.1093/gbe/evz075] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/05/2019] [Indexed: 01/22/2023] Open
Abstract
Sex chromosomes play a central role in genetics of speciation and their turnover was suggested to promote divergence. In vertebrates, sex chromosome-autosome fusions resulting in neo-sex chromosomes occur frequently in male heterogametic taxa (XX/XY), but are rare in groups with female heterogamety (WZ/ZZ). We examined sex chromosomes of seven pests of the diverse lepidopteran superfamily Gelechioidea and confirmed the presence of neo-sex chromosomes in their karyotypes. Two synteny blocks, which correspond to autosomes 7 (LG7) and 27 (LG27) in the ancestral lepidopteran karyotype exemplified by the linkage map of Biston betularia (Geometridae), were identified as sex-linked in the tomato leafminer, Tuta absoluta (Gelechiidae). Testing for sex-linkage performed in other species revealed that while LG7 fused to sex chromosomes in a common ancestor of all Gelechioidea, the second fusion between the resulting neo-sex chromosome and the other autosome is confined to the tribe Gnoreschemini (Gelechiinae). Our data accentuate an emerging pattern of high incidence of neo-sex chromosomes in Lepidoptera, the largest clade with WZ/ZZ sex chromosome system, which suggest that the paucity of neo-sex chromosomes is not an intrinsic feature of female heterogamety. Furthermore, LG7 contains one of the major clusters of UDP-glucosyltransferases, which are involved in the detoxification of plant secondary metabolites. Sex chromosome evolution in Gelechioidea thus supports an earlier hypothesis postulating that lepidopteran sex chromosome-autosome fusions can be driven by selection for association of Z-linked preference or host-independent isolation genes with larval performance and thus can contribute to ecological specialization and speciation of moths.
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Affiliation(s)
- Leonela Z Carabajal Paladino
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czech Republic
- The Pirbright Institute, Surrey, United Kingdom
| | - Irena Provazníková
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czech Republic
- University of South Bohemia, Faculty of Science, České Budějovice, Czech Republic
| | - Madeleine Berger
- Rothamsted Research, Department of Biointeractions and Crop Protection, Herts, United Kingdom
| | - Chris Bass
- University of Exeter, College of Life and Environmental Sciences, Biosciences, Penryn, Cornwall, United Kingdom
| | - Nayanie S Aratchige
- Coconut Research Institute of Sri Lanka, Crop Protection Division, Bandirippuwa Estate, Lunuwila, Sri Lanka
| | - Silvia N López
- Instituto Nacional de Tecnología Agropecuaria, Instituto de Microbiología y Zoología Agrícola, Hurlingham, Buenos Aires, Argentina
| | - František Marec
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czech Republic
| | - Petr Nguyen
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czech Republic
- University of South Bohemia, Faculty of Science, České Budějovice, Czech Republic
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30
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Versatility of multivalent orientation, inverted meiosis, and rescued fitness in holocentric chromosomal hybrids. Proc Natl Acad Sci U S A 2018; 115:E9610-E9619. [PMID: 30266792 DOI: 10.1073/pnas.1802610115] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Chromosomal rearrangements (e.g., fusions/fissions) have the potential to drive speciation. However, their accumulation in a population is generally viewed as unlikely, because chromosomal heterozygosity should lead to meiotic problems and aneuploid gametes. Canonical meiosis involves segregation of homologous chromosomes in meiosis I and sister chromatid segregation during meiosis II. In organisms with holocentric chromosomes, which are characterized by kinetic activity distributed along almost the entire chromosome length, this order may be inverted depending on their metaphase I orientation. Here we analyzed the evolutionary role of this intrinsic versatility of holocentric chromosomes, which is not available to monocentric ones, by studying F1 to F4 hybrids between two chromosomal races of the Wood White butterfly (Leptidea sinapis), separated by at least 24 chromosomal fusions/fissions. We found that these chromosomal rearrangements resulted in multiple meiotic multivalents, and, contrary to the theoretical prediction, the hybrids displayed relatively high reproductive fitness (42% of that of the control lines) and regular behavior of meiotic chromosomes. In the hybrids, we also discovered inverted meiosis, in which the first and critical stage of chromosome number reduction was replaced by the less risky stage of sister chromatid separation. We hypothesize that the ability to invert the order of the main meiotic events facilitates proper chromosome segregation and hence rescues fertility and viability in chromosomal hybrids, potentially promoting dynamic karyotype evolution and chromosomal speciation.
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31
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Sex Chromosomes of the Iconic Moth Abraxas grossulariata (Lepidoptera, Geometridae) and Its Congener A. sylvata. Genes (Basel) 2018; 9:genes9060279. [PMID: 29857494 PMCID: PMC6027526 DOI: 10.3390/genes9060279] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 05/25/2018] [Accepted: 05/28/2018] [Indexed: 01/28/2023] Open
Abstract
The magpie moth, Abraxas grossulariata, is an iconic species in which female heterogamety was discovered at the beginning of the 20th century. However, the sex chromosomes of this species have not yet been cytologically identified. We describe the sex chromosomes of A. grossulariata and its congener, A. sylvata. Although these species split only around 9.5 million years ago, and both species have the expected WZ/ZZ chromosomal system of sex determination and their sex chromosomes share the major ribosomal DNA (rDNA) representing the nucleolar organizer region (NOR), we found major differences between their karyotypes, including between their sex chromosomes. The species differ in chromosome number, which is 2n = 56 in A. grossularita and 2n = 58 in A. sylvata. In addition, A. grossularita autosomes exhibit massive autosomal blocks of heterochromatin, which is a very rare phenomenon in Lepidoptera, whereas the autosomes of A. sylvata are completely devoid of distinct heterochromatin. Their W chromosomes differ greatly. Although they are largely composed of female-specific DNA sequences, as shown by comparative genomic hybridization, cross-species W-chromosome painting revealed considerable sequence differences between them. The results suggest a relatively rapid molecular divergence of Abraxas W chromosomes by the independent spreading of female-specific repetitive sequences.
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32
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More sex chromosomes than autosomes in the Amazonian frog Leptodactylus pentadactylus. Chromosoma 2018; 127:269-278. [PMID: 29372309 DOI: 10.1007/s00412-018-0663-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 01/15/2018] [Accepted: 01/16/2018] [Indexed: 12/15/2022]
Abstract
Heteromorphic sex chromosomes are common in eukaryotes and largely ubiquitous in birds and mammals. The largest number of multiple sex chromosomes in vertebrates known today is found in the monotreme platypus (Ornithorhynchus anatinus, 2n = 52) which exhibits precisely 10 sex chromosomes. Interestingly, fish, amphibians, and reptiles have sex determination mechanisms that do or do not involve morphologically differentiated sex chromosomes. Relatively few amphibian species carry heteromorphic sex chromosomes, and when present, they are frequently represented by only one pair, either XX:XY or ZZ:ZW types. Here, in contrast, with several evidences, from classical and molecular cytogenetic analyses, we found 12 sex chromosomes in a Brazilian population of the smoky jungle frog, designated as Leptodactylus pentadactylus Laurenti, 1768 (Leptodactylinae), which has a karyotype with 2n = 22 chromosomes. Males exhibited an astonishing stable ring-shaped meiotic chain composed of six X and six Y chromosomes. The number of sex chromosomes is larger than the number of autosomes found, and these data represent the largest number of multiple sex chromosomes ever found among vertebrate species. Additionally, sequence and karyotype variation data suggest that this species may represent a complex of species, in which the chromosomal rearrangements may possibly have played an important role in the evolution process.
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Pereira TTP, dos Reis ACCC, Cardoso DC, Cristiano MP. Molecular phylogenetic reconstruction and localization of the (TTAGG)n telomeric repeats in the chromosomes of Acromyrmex striatus (Roger, 1863) suggests a lower ancestral karyotype for leafcutter ants (Hymenoptera). COMPARATIVE CYTOGENETICS 2018; 12:13-21. [PMID: 29362670 PMCID: PMC5770561 DOI: 10.3897/compcytogen.v12i1.21799] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Accepted: 11/27/2017] [Indexed: 05/24/2023]
Abstract
Chromosome counts and karyotype characterization have proved to be important features of a genome. Chromosome changes during the diversification of ants might play an important role, given the diversity and success of Formicidae. Comparative karyotype analyses on ants have enriched and helped ant systematics. Among leafcutter ants, two major chromosome counts have been described, one frequent in Atta Fabricius, 1804 (2n = 22 in all Atta spp. whose karyotype is known) and the other frequent in Acromyrmex Mayr, 1865 (2n = 38 in the majority of species whose karyotype is known). The main exception is Acromyrmex striatus (Roger, 1863), which harbors a diploid chromosome set of 22. Here we describe the use of fluorescence in situ hybridization (FISH) with telomeric probes with (TTAGG)6 repeats to describe the telomere composition of A. striatus and to recover potential interstitial non-telomeric signals that may reflect fusion events during the evolution of leafcutter lineage from 38 to 22 chromosomes. Further, we reconstruct the ancestral chromosome numbers of the leafcutter clade based on a recently proposed molecular phylogenetic hypothesis and phylogenomic tree. Distinct signals have been observed in both extremities on the telomere chromosomes of A. striatus. Non-telomeric signals have not been retrieved in our analysis. It could be supposed that the low-numbered karyotype indeed represents the ancestral chromosome number of leafcutters. The phylogenetic reconstruction also recovered a low chromosome number from the diverse approaches implemented, suggesting that n = 11 is the most likely ancestral karyotype of the leafcutter ants and is a plesiomorphic feature shared between A. striatus and Atta spp.
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Affiliation(s)
- Tássia Tatiane Pontes Pereira
- Departamento de Biodiversidade, Evolução e Meio Ambiente, Universidade Federal de Ouro Preto, Ouro Preto, MG, Brazil
- Programa de Pós-graduação em Genética, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | | | - Danon Clemes Cardoso
- Departamento de Biodiversidade, Evolução e Meio Ambiente, Universidade Federal de Ouro Preto, Ouro Preto, MG, Brazil
- Programa de Pós-graduação em Genética, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Maykon Passos Cristiano
- Departamento de Biodiversidade, Evolução e Meio Ambiente, Universidade Federal de Ouro Preto, Ouro Preto, MG, Brazil
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34
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Lukhtanov VA, Dantchenko AV. A new butterfly species from south Russia revealed through chromosomal and molecular analysis of the Polyommatus (Agrodiaetus) damonides complex (Lepidoptera, Lycaenidae). COMPARATIVE CYTOGENETICS 2017; 11:769-795. [PMID: 29302297 PMCID: PMC5740405 DOI: 10.3897/compcytogen.v11i4.20072] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Accepted: 10/22/2017] [Indexed: 05/26/2023]
Abstract
Finding a new species is a rare event in easy-to-see and well-studied organisms like butterflies, especially if they inhabit well-explored areas such as the Western Palaearctic. However, even in this region, gaps in taxonomic knowledge still exist and here we report such a discovery. Using a combined analysis of chromosomal and molecular markers we demonstrate that Polyommatus blue populations from Daghestan (South Russia), previously identified as P. aserbeidschanus, represent in fact a new species which is described here as P. australorossicussp. n. We also show that the enigmatic Polyommatus damonides described as a form of Polyommatus damone and later considered as an entity similar to P. poseidon or P. ninae is conspecific with a taxon previously known as P. elbursicus. As a result of our study, we propose several taxonomic changes within the P. damonides species complex and suggest the following new combinations: P. damonides elbursicus Forster, 1956, comb. n. and P. damonides gilanensis Eckweiler, 2002, comb. n.
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Affiliation(s)
- Vladimir A. Lukhtanov
- Department of Karyosystematics, Zoological Institute of the Russian Academy of Sciences, Universitetskaya nab. 1, St. Petersburg 199034, Russia
- Department of Entomology, St. Petersburg State University, Universitetskaya nab 7/9, St. Petersburg 199034, Russia
| | - Alexander V. Dantchenko
- Faculty of Chemistry, Lomonosov Moscow State University, GSP-1, Leninskiye Gory 1/13, Moscow119991, Russia
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Talla V, Suh A, Kalsoom F, Dincă V, Vila R, Friberg M, Wiklund C, Backström N. Rapid Increase in Genome Size as a Consequence of Transposable Element Hyperactivity in Wood-White (Leptidea) Butterflies. Genome Biol Evol 2017; 9:2491-2505. [PMID: 28981642 PMCID: PMC5737376 DOI: 10.1093/gbe/evx163] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/22/2016] [Indexed: 12/14/2022] Open
Abstract
Characterizing and quantifying genome size variation among organisms and understanding if genome size evolves as a consequence of adaptive or stochastic processes have been long-standing goals in evolutionary biology. Here, we investigate genome size variation and association with transposable elements (TEs) across lepidopteran lineages using a novel genome assembly of the common wood-white (Leptidea sinapis) and population re-sequencing data from both L. sinapis and the closely related L. reali and L. juvernica together with 12 previously available lepidopteran genome assemblies. A phylogenetic analysis confirms established relationships among species, but identifies previously unknown intraspecific structure within Leptidea lineages. The genome assembly of L. sinapis is one of the largest of any lepidopteran taxon so far (643 Mb) and genome size is correlated with abundance of TEs, both in Lepidoptera in general and within Leptidea where L. juvernica from Kazakhstan has considerably larger genome size than any other Leptidea population. Specific TE subclasses have been active in different Lepidoptera lineages with a pronounced expansion of predominantly LINEs, DNA elements, and unclassified TEs in the Leptidea lineage after the split from other Pieridae. The rate of genome expansion in Leptidea in general has been in the range of four Mb/Million year (My), with an increase in a particular L. juvernica population to 72 Mb/My. The considerable differences in accumulation rates of specific TE classes in different lineages indicate that TE activity plays a major role in genome size evolution in butterflies and moths.
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Affiliation(s)
- Venkat Talla
- Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Sweden
| | - Alexander Suh
- Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Sweden
| | - Faheema Kalsoom
- Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Sweden
| | - Vlad Dincă
- Animal Biodiversity and Evolution Program, Institut de Biologia Evolutiva (CSIC-UPF), Barcelona, Spain
| | - Roger Vila
- Animal Biodiversity and Evolution Program, Institut de Biologia Evolutiva (CSIC-UPF), Barcelona, Spain
| | - Magne Friberg
- Department of Plant Ecology and Evolution, Evolutionary Biology Centre (EBC), Uppsala University, Sweden
| | - Christer Wiklund
- Division of Ecology, Department of Zoology, Stockholm University, Sweden
| | - Niclas Backström
- Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Sweden
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Vershinina AO, Lukhtanov VA. Evolutionary mechanisms of runaway chromosome number change in Agrodiaetus butterflies. Sci Rep 2017; 7:8199. [PMID: 28811556 PMCID: PMC5557896 DOI: 10.1038/s41598-017-08525-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 07/10/2017] [Indexed: 11/17/2022] Open
Abstract
Despite predictions of the classic, hybrid-sterility model of chromosomal speciation, some organisms demonstrate high rate of karyotype evolution. This rate is especially impressive in Agrodiaetus butterflies that rapidly evolved the greatest chromosome number diversity known in animal kingdom within a single subgenus. Here we analyzed karyotype evolution in Agrodiaetus using phylogenetic comparative methods. We found that chromosome numbers possess a strong phylogenetic signal. This disproves the chromosome megaevolution model that proposes multiple chromosome rearrangements to accumulate independently in each of closely related species. We found that Brownian motion gives a more adequate description of observed trait changes than Ornstein-Uhlenbeck model. This indicates that chromosome numbers evolve via random walk along branches of the phylogeny. We discovered a correlation between karyotype changes and phylogeny branch lengths. This gradual pattern is inconsistent with the hybrid-sterility model which, due to association of major chromosome changes with cladogenetic events, predicts a high degree of punctualism in karyotype evolution. Thus, low underdominace of chromosomal rearrangements and/or prevalence of the recombination-suppression model over the hybrid-sterility model of chromosome speciation are the most common engines of the runaway chromosome number change observed.
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Affiliation(s)
- Alisa O Vershinina
- Department of Karyosystematics, Zoological Institute of Russian Academy of Sciences, Universitetskaya nab. 1, 199034, St. Petersburg, Russia.
- Department of Ecology & Evolutionary Biology, University of California Santa Cruz, 95064, Santa Cruz, CA, USA.
| | - Vladimir A Lukhtanov
- Department of Karyosystematics, Zoological Institute of Russian Academy of Sciences, Universitetskaya nab. 1, 199034, St. Petersburg, Russia.
- Department of Entomology, St Petersburg State University, Universitetskaya nab. 7/9, 199034, St. Petersburg, Russia.
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Veleba A, Šmarda P, Zedek F, Horová L, Šmerda J, Bureš P. Evolution of genome size and genomic GC content in carnivorous holokinetics (Droseraceae). ANNALS OF BOTANY 2017; 119:409-416. [PMID: 28025291 PMCID: PMC5314647 DOI: 10.1093/aob/mcw229] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2016] [Revised: 09/06/2016] [Accepted: 09/26/2016] [Indexed: 05/04/2023]
Abstract
BACKGROUND AND AIMS Studies in the carnivorous family Lentibulariaceae in the last years resulted in the discovery of the smallest plant genomes and an unusual pattern of genomic GC content evolution. However, scarcity of genomic data in other carnivorous clades still prevents a generalization of the observed patterns. Here the aim was to fill this gap by mapping genome evolution in the second largest carnivorous family, Droseraceae, where this evolution may be affected by chromosomal holokinetism in Drosera METHODS: The genome size and genomic GC content of 71 Droseraceae species were measured by flow cytometry. A dated phylogeny was constructed, and the evolution of both genomic parameters and their relationship to species climatic niches were tested using phylogeny-based statistics. KEY RESULTS The 2C genome size of Droseraceae varied between 488 and 10 927 Mbp, and the GC content ranged between 37·1 and 44·7 %. The genome sizes and genomic GC content of carnivorous and holocentric species did not differ from those of their non-carnivorous and monocentric relatives. The genomic GC content positively correlated with genome size and annual temperature fluctuations. The genome size and chromosome numbers were inversely correlated in the Australian clade of Drosera CONCLUSIONS: Our results indicate that neither carnivory (nutrient scarcity) nor the holokinetism have a prominent effect on size and DNA base composition of Droseraceae genomes. However, the holokinetic drive seems to affect karyotype evolution in one of the major clades of Drosera Our survey confirmed that the evolution of GC content is tightly connected with the evolution of genome size and also with environmental conditions.
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Affiliation(s)
- Adam Veleba
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno, CZ 61137, Czech Republic
| | - Petr Šmarda
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno, CZ 61137, Czech Republic
| | - František Zedek
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno, CZ 61137, Czech Republic
| | - Lucie Horová
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno, CZ 61137, Czech Republic
| | - Jakub Šmerda
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno, CZ 61137, Czech Republic
| | - Petr Bureš
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno, CZ 61137, Czech Republic
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Zedek F, Veselý P, Horová L, Bureš P. Flow cytometry may allow microscope-independent detection of holocentric chromosomes in plants. Sci Rep 2016; 6:27161. [PMID: 27255216 PMCID: PMC4891681 DOI: 10.1038/srep27161] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 05/13/2016] [Indexed: 01/03/2023] Open
Abstract
Two chromosomal structures, known as monocentric and holocentric chromosomes, have evolved in eukaryotes. Acentric fragments of monocentric chromosomes are unequally distributed to daughter cells and/or lost, while holocentric fragments are inherited normally. In monocentric species, unequal distribution should generate chimeras of cells with different nuclear DNA content. We investigated whether such differences in monocentric species are detectable by flow cytometry (FCM) as (i) a decreased nuclear DNA content and (ii) an increased coefficient of variance (CV) of the G1 peak after gamma radiation-induced fragmentation. We compared 13 monocentric and 9 holocentric plant species. Unexpectedly, monocentrics and holocentrics did not differ with respect to parameters (i) and (ii) in their response to gamma irradiation. However, we found that the proportion of G2 nuclei was highly elevated in monocentrics after irradiation, while holocentrics were negligibly affected. Therefore, we hypothesize that DNA-damaging agents induce cell cycle arrest leading to endopolyploidy only in monocentric and not (or to much lesser extent) in holocentric plants. While current microscope-dependent methods for holocentrism detection are unreliable for small and numerous chromosomes, which are common in holocentrics, FCM can use somatic nuclei. Thus, FCM may be a rapid and reliable method of high-throughput screening for holocentric candidates across plant phylogeny.
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Affiliation(s)
- František Zedek
- Department of Botany and Zoology, Masaryk University, Kotlarska 2, 611 37 Brno, Czech Republic
| | - Pavel Veselý
- Department of Botany and Zoology, Masaryk University, Kotlarska 2, 611 37 Brno, Czech Republic
| | - Lucie Horová
- Department of Botany and Zoology, Masaryk University, Kotlarska 2, 611 37 Brno, Czech Republic
| | - Petr Bureš
- Department of Botany and Zoology, Masaryk University, Kotlarska 2, 611 37 Brno, Czech Republic
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