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Schöneberg Y, Audisio TL, Ben Hamadou A, Forman M, Král J, Kořínková T, Líznarová E, Mayer C, Prokopcová L, Krehenwinkel H, Prost S, Kennedy S. Three Novel Spider Genomes Unveil Spidroin Diversification and Hox Cluster Architecture: Ryuthela nishihirai (Liphistiidae), Uloborus plumipes (Uloboridae) and Cheiracanthium punctorium (Cheiracanthiidae). Mol Ecol Resour 2024:e14038. [PMID: 39435585 DOI: 10.1111/1755-0998.14038] [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: 04/15/2024] [Revised: 09/26/2024] [Accepted: 10/04/2024] [Indexed: 10/23/2024]
Abstract
Spiders are a hyperdiverse taxon and among the most abundant predators in nearly all terrestrial habitats. Their success is often attributed to key developments in their evolution such as silk and venom production and major apomorphies such as a whole-genome duplication. Resolving deep relationships within the spider tree of life has been historically challenging, making it difficult to measure the relative importance of these novelties for spider evolution. Whole-genome data offer an essential resource in these efforts, but also for functional genomic studies. Here, we present de novo assemblies for three spider species: Ryuthela nishihirai (Liphistiidae), a representative of the ancient Mesothelae, the suborder that is sister to all other extant spiders; Uloborus plumipes (Uloboridae), a cribellate orbweaver whose phylogenetic placement is especially challenging; and Cheiracanthium punctorium (Cheiracanthiidae), which represents only the second family to be sequenced in the hyperdiverse Dionycha clade. These genomes fill critical gaps in the spider tree of life. Using these novel genomes along with 25 previously published ones, we examine the evolutionary history of spidroin gene and structural hox cluster diversity. Our assemblies provide critical genomic resources to facilitate deeper investigations into spider evolution. The near chromosome-level genome of the 'living fossil' R. nishihirai represents an especially important step forward, offering new insights into the origins of spider traits.
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Affiliation(s)
| | - Tracy Lynn Audisio
- Evolutionary Genomics Unit, Okinawa Institute of Science and Technology, Okinawa, Japan
| | - Alexander Ben Hamadou
- LOEWE-Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
- Senckenberg Forschungsinstitut und Naturmuseum, Frankfurt am Main, Germany
| | - Martin Forman
- Laboratory of Arachnid Cytogenetics, Department of Genetics and Microbiology, Faculty of Sciences, Charles University, Prague 2, Czech Republic
| | - Jiří Král
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Tereza Kořínková
- Laboratory of Arachnid Cytogenetics, Department of Genetics and Microbiology, Faculty of Sciences, Charles University, Prague 2, Czech Republic
| | - Eva Líznarová
- Laboratory of Arachnid Cytogenetics, Department of Genetics and Microbiology, Faculty of Sciences, Charles University, Prague 2, Czech Republic
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Christoph Mayer
- Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change, Bonn, Germany
| | - Lenka Prokopcová
- Laboratory of Arachnid Cytogenetics, Department of Genetics and Microbiology, Faculty of Sciences, Charles University, Prague 2, Czech Republic
| | | | - Stefan Prost
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
- South African National Biodiversity Institute, National Zoological Garden, Pretoria, South Africa
- Natural History Museum Vienna, Central Research Laboratories, Vienna, Austria
| | - Susan Kennedy
- Department of Biogeography, Trier University, Trier, Germany
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Lv Z, Addo Nyarko C, Ramtekey V, Behn H, Mason AS. Defining autopolyploidy: Cytology, genetics, and taxonomy. AMERICAN JOURNAL OF BOTANY 2024; 111:e16292. [PMID: 38439575 DOI: 10.1002/ajb2.16292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 12/15/2023] [Accepted: 12/18/2023] [Indexed: 03/06/2024]
Abstract
Autopolyploidy is taxonomically defined as the presence of more than two copies of each genome within an organism or species, where the genomes present must all originate within the same species. Alternatively, "genetic" or "cytological" autopolyploidy is defined by polysomic inheritance: random pairing and segregation of the four (or more) homologous chromosomes present, with no preferential pairing partners. In this review, we provide an overview of methods used to categorize species as taxonomic and cytological autopolyploids, including both modern and obsolete cytological methods, marker-segregation-based and genomics methods. Subsequently, we also investigated how frequently polysomic inheritance has been reliably documented in autopolyploids. Pure or predominantly polysomic inheritance was documented in 39 of 43 putative autopolyploid species where inheritance data was available (91%) and in seven of eight synthetic autopolyploids, with several cases of more mixed inheritance within species. We found no clear cases of autopolyploids with disomic inheritance, which was likely a function of our search methodology. Interestingly, we found seven species with purely polysomic inheritance and another five species with partial or predominant polysomic inheritance that appear to be taxonomic allopolyploids. Our results suggest that observations of polysomic inheritance can lead to relabeling of taxonomically allopolyploid species as autopolyploid and highlight the need for further cytogenetic and genomic investigation into polyploid origins and inheritance types.
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Affiliation(s)
- Zhenling Lv
- Plant Breeding Department, University of Bonn, Kirschallee 1, 53115, Bonn, Germany
| | - Charles Addo Nyarko
- Plant Breeding Department, University of Bonn, Kirschallee 1, 53115, Bonn, Germany
| | - Vinita Ramtekey
- Plant Breeding Department, University of Bonn, Kirschallee 1, 53115, Bonn, Germany
- ICAR-Indian Institute of Seed Science, 275103, Mau, India
| | - Helen Behn
- Plant Breeding Department, University of Bonn, Kirschallee 1, 53115, Bonn, Germany
| | - Annaliese S Mason
- Plant Breeding Department, University of Bonn, Kirschallee 1, 53115, Bonn, Germany
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Huber BA, Meng G, Dederichs TM, Michalik P, Forman M, Král J. Castaways: the Leeward Antilles endemic spider genus Papiamenta (Araneae: Pholcidae). INVERTEBR SYST 2024; 38:IS23052. [PMID: 38744495 DOI: 10.1071/is23052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 01/15/2024] [Indexed: 05/16/2024]
Abstract
Ninetinae is a group of small to tiny short-legged spiders largely restricted to arid habitats. Among daddy-long-legs spiders (Pholcidae) this is by far the least diverse subfamily but this may partly be a result of inadequate collecting, poor representation in collections or scientific neglect. We build on a large recent collection of the ninetine genus Papiamenta Huber, 2000 from the Leeward Antilles and use cytochrome oxidase 1 (COI ) sequences, extensive scanning electron microscopy data, transmission electron microscopy data and karyotyping to analyse this geographically isolated and poorly known island genus. COI sequences support the split between the two morphologically distinct species on Curaçao but genetic distances between these are surprisingly low (7.4-9.8%; mean 8.6%). The type species P. levii (Gertsch, 1982) may include more than one species but COI and morphology suggest conflicting clade limits. A third species, P. bonay Huber sp. nov. is newly described from Bonaire. Our data on sperm ultrastructure and karyology are puzzling as these suggest different phylogenetic affinities of Papiamenta to other genera. Males transfer sperm as individual sperm (cleistosperm), agreeing with the putative closest relatives as suggested by molecular data, the North American genera Pholcophora and Tolteca . The sex chromosome system (X 1 X 2 X 3 Y ) of P. levii , however, is as in the South American Ninetinae genera Gertschiola and Nerudia but different from the putative closest relatives. ZooBank: urn:lsid:zoobank.org:pub:7A6A2E84-3A61-4637-AF6F-0E31A9FA79A8.
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Affiliation(s)
- Bernhard A Huber
- Zoological Research Museum Alexander Koenig, LIB, Adenauerallee 127, D-53113 Bonn, Germany
| | - Guanliang Meng
- Zoological Research Museum Alexander Koenig, LIB, Adenauerallee 127, D-53113 Bonn, Germany
| | | | | | - Martin Forman
- Department of Genetics and Microbiology, Faculty of Science, Charles University, Prague, Czechia
| | - Jirí Král
- Department of Genetics and Microbiology, Faculty of Science, Charles University, Prague, Czechia
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Dutra DD, Brescovit AD, Araujo D. Chromosomal Study on Selected Small Araneomorph Spiders from Brazil, Including the First Records in Palpimanidae and Theridiosomatidae (Araneae, Araneomorphae). Zool Stud 2023; 62:e42. [PMID: 37941799 PMCID: PMC10628548 DOI: 10.6620/zs.2023.62-42] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 06/19/2023] [Indexed: 11/10/2023]
Abstract
Among the 50,474 spider species, only 849 have chromosomal data available in the literature. Fifty spider families remain unknown from a cytogenetic perspective. The aim of this study was to analyze chromosomally selected araneomorph spiders from Brazil, to contribute to the cytotaxonomy and chromosome evolution of this group. The karyotypes of 12 species belonging to families Corinnidae, Linyphiidae, Oonopidae, Palpimanidae, Theridiidae, Theridiosomatidae, Trachelidae, and Zodariidae were analyzed, including the first chromosomal record for the first two families. Specimens (with the abdomen content partially exposed by perforation) were subjected to colchicine, hypotonization, and fixation. In most cases, the total content of the abdomen was used to prepare slides by spreading of cell suspension and subsequent Giemsa staining. The results were as follows: Cinetomorpha simplex Simon, 1892 (Oonopidae) 2n♂ = 9, X0; Neotrops sp. and Neoxyphinus termitophilus (Oonopidae), 2n♂ = 7, X0; Otiothops birabeni (Palpimanidae); Agyneta sp. (Linyphiidae), 2n♂ = 24, X1X20; Coleosoma floridanum, Thymoites sp.1 and Thymoites sp.2 (Theridiidae), 2n♂ = 22, X1X20; Naatlo sp. (Theridiosomatidae), 2n♂ = 30, X1X20; Orthobula sp. (Trachelidae) 2n♂ = 21, X0; Falconina sp. (Corinnidae), 2n♂ = 28, X1X20; Epicratinus sp. (Zodariidae) 2n♂ = 42, X1X20. The chromosomal morphology was determined for all the samples except for Oonopidae. Most species exhibited telocentric chromosomes, with the exception of Palpimanidae and Theridiosomatidae. The main findings: 1) support an hypothesis on ancestral karyotype of Zodariidae and Oonopidae; 2) reveal a relatively high chromosome number in Palpimanidae that supports an idea on relatively high ancestral chromosome number (2n♂ = 42) of entelegyne spiders (Palpimanoidea is sister group of entelegyne spiders); 3) show that the karyotype found in Theridiosomatidae is exceptional within the Araneoidea.
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Affiliation(s)
- Débora Duarte Dutra
- Laboratório de Citotaxonomia e Evolução Cromossômica Animal, Programa de Pós-Graduação em Biologia Animal, Instituto de Biociências, Universidade Federal de Mato Grosso do Sul, Avenida Costa e Silva, s/n, Campo Grande, Mato Grosso do Sul, Brazil, Caixa Postal 549, CEP 79070-900. E-mail: (Araujo); (Dutra)
| | - Antônio Domingos Brescovit
- Laboratório de Coleções Zoológicas, Instituto Butantan, Av. Vital Brasil, 1500, São Paulo, São Paulo, Brazil, CEP 05503-900. E-mail: (Brescovit)
| | - Douglas Araujo
- Laboratório de Citotaxonomia e Evolução Cromossômica Animal, Programa de Pós-Graduação em Biologia Animal, Instituto de Biociências, Universidade Federal de Mato Grosso do Sul, Avenida Costa e Silva, s/n, Campo Grande, Mato Grosso do Sul, Brazil, Caixa Postal 549, CEP 79070-900. E-mail: (Araujo); (Dutra)
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Miller J, Zimin AV, Gordus A. Chromosome-level genome and the identification of sex chromosomes in Uloborus diversus. Gigascience 2022; 12:giad002. [PMID: 36762707 PMCID: PMC9912274 DOI: 10.1093/gigascience/giad002] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 11/18/2022] [Accepted: 01/03/2023] [Indexed: 02/11/2023] Open
Abstract
The orb web is a remarkable example of animal architecture that is observed in families of spiders that diverged over 200 million years ago. While several genomes exist for araneid orb-weavers, none exist for other orb-weaving families, hampering efforts to investigate the genetic basis of this complex behavior. Here we present a chromosome-level genome assembly for the cribellate orb-weaving spider Uloborus diversus. The assembly reinforces evidence of an ancient arachnid genome duplication and identifies complete open reading frames for every class of spidroin gene, which encode the proteins that are the key structural components of spider silks. We identified the 2 X chromosomes for U. diversus and identify candidate sex-determining loci. This chromosome-level assembly will be a valuable resource for evolutionary research into the origins of orb-weaving, spidroin evolution, chromosomal rearrangement, and chromosomal sex determination in spiders.
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Affiliation(s)
- Jeremiah Miller
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Aleksey V Zimin
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Andrew Gordus
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University, Baltimore, MD 21218, USA
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Král J, Ávila Herrera IM, Šťáhlavský F, Sadílek D, Pavelka J, Chatzaki M, Huber BA. Karyotype differentiation and male meiosis in European clades of the spider genus Pholcus (Araneae, Pholcidae). COMPARATIVE CYTOGENETICS 2022; 16:185-209. [PMID: 36760487 PMCID: PMC9836407 DOI: 10.3897/compcytogen.v16i4.85059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 09/28/2022] [Indexed: 06/18/2023]
Abstract
Haplogyne araneomorphs are a diverse spider clade. Their karyotypes are usually predominated by biarmed (i.e., metacentric and submetacentric) chromosomes and have a specific sex chromosome system, X1X2Y. These features are probably ancestral for haplogynes. Nucleolus organizer regions (NORs) spread frequently from autosomes to sex chromosomes in these spiders. This study focuses on pholcids (Pholcidae), a highly diverse haplogyne family. Despite considerable recent progress in pholcid cytogenetics, knowledge on many clades remains insufficient including the most species-rich pholcid genus, Pholcus Walckenaer, 1805. To characterize the karyotype differentiation of Pholcus in Europe, we compared karyotypes, sex chromosomes, NORs, and male meiosis of seven species [P.alticeps Spassky, 1932; P.creticus Senglet, 1971; P.dentatus Wunderlich, 1995; P.fuerteventurensis Wunderlich, 1992; P.phalangioides (Fuesslin, 1775); P.opilionoides (Schrank, 1781); P.silvai Wunderlich, 1995] representing the dominant species groups in this region. The species studied show several features ancestral for Pholcus, namely the 2n♂ = 25, the X1X2Y system, and a karyotype predominated by biarmed chromosomes. Most taxa have a large acrocentric NOR-bearing pair, which evolved from a biarmed pair by a pericentric inversion. In some lineages, the acrocentric pair reverted to biarmed. Closely related species often differ in the morphology of some chromosome pairs, probably resulting from pericentric inversions and/or translocations. Such rearrangements have been implicated in the formation of reproductive barriers. While the X1 and Y chromosomes retain their ancestral metacentric morphology, the X2 chromosome shows a derived (acrocentric or subtelocentric) morphology. Pairing of this element is usually modified during male meiosis. NOR patterns are very diverse. The ancestral karyotype of Pholcus contained five or six terminal NORs including three X chromosome-linked loci. The number of NORs has been frequently reduced during evolution. In the Macaronesian clade, there is only a single NOR-bearing pair. Sex chromosome-linked NORs are lost in Madeiran species and in P.creticus. Our study revealed two cytotypes in the synanthropic species P.phalangioides (Madeiran and Czech), which differ by their NOR pattern and chromosome morphology. In the Czech cytotype, the large acrocentric pair was transformed into a biarmed pair by pericentric inversion.
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Affiliation(s)
- Jiří Král
- Laboratory of Arachnid Cytogenetics, Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, 128 44 Prague 2, Czech RepublicCharles UniversityPragueCzech Republic
| | - Ivalú M. Ávila Herrera
- Laboratory of Arachnid Cytogenetics, Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, 128 44 Prague 2, Czech RepublicCharles UniversityPragueCzech Republic
| | - František Šťáhlavský
- Laboratory of Arachnid Cytogenetics, Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, 128 44 Prague 2, Czech RepublicCharles UniversityPragueCzech Republic
| | - David Sadílek
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44 Prague 2, Czech RepublicCharles UniversityPrague 2Czech Republic
| | - Jaroslav Pavelka
- Centre of Biology, Geosciences and Environmental Education, University of West Bohemia, Univerzitní 8, 306 14 Plzeň, Czech RepublicUniversity of West BohemiaPlzeňCzech Republic
| | - Maria Chatzaki
- Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100 Alexandroupolis, GreeceDemocritus University of ThraceAlexandroupolisGreece
| | - Bernhard A. Huber
- Alexander Koenig Zoological Research Museum, Adenauerallee 127, 53113 Bonn, GermanyAlexander Koenig Zoological Research MuseumBonnGermany
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OUP accepted manuscript. Biol J Linn Soc Lond 2022. [DOI: 10.1093/biolinnean/blac039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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Zedek F, Veselý P, Tichý L, Elliott TL, Garbolino E, de Ruffray P, Bureš P. Holocentric plants are more competitive under higher UV-B doses. THE NEW PHYTOLOGIST 2022; 233:15-21. [PMID: 34547106 DOI: 10.1111/nph.17750] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 09/08/2021] [Indexed: 05/28/2023]
Affiliation(s)
- František Zedek
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic
| | - Pavel Veselý
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic
| | - Lubomír Tichý
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic
| | - Tammy L Elliott
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic
| | - Emmanuel Garbolino
- Climpact Data Science (CDS), Nova Sophia - Regus Nova, 291 rue Albert Caquot, CS 40095, 06902, Sophia Antipolis Cedex, France
| | - Patrice de Ruffray
- Institut de biologie moléculaire des plantes-CNRS, Université de Strasbourg, 12, rue du Général-Zimmer, F-67084, Strasbourg, France
| | - Petr Bureš
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic
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Harper A, Baudouin Gonzalez L, Schönauer A, Janssen R, Seiter M, Holzem M, Arif S, McGregor AP, Sumner-Rooney L. Widespread retention of ohnologs in key developmental gene families following whole-genome duplication in arachnopulmonates. G3 (BETHESDA, MD.) 2021; 11:jkab299. [PMID: 34849767 PMCID: PMC8664421 DOI: 10.1093/g3journal/jkab299] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Revised: 07/19/2021] [Accepted: 08/03/2021] [Indexed: 01/12/2023]
Abstract
Whole-genome duplications (WGDs) have occurred multiple times during animal evolution, including in lineages leading to vertebrates, teleosts, horseshoe crabs, and arachnopulmonates. These dramatic events initially produce a wealth of new genetic material, generally followed by extensive gene loss. It appears, however, that developmental genes such as homeobox genes, signaling pathway components and microRNAs are frequently retained as duplicates (so-called ohnologs) following WGD. These not only provide the best evidence for WGD, but an opportunity to study its evolutionary consequences. Although these genes are well studied in the context of vertebrate WGD, similar comparisons across the extant arachnopulmonate orders are patchy. We sequenced embryonic transcriptomes from two spider species and two amblypygid species and surveyed three important gene families, Hox, Wnt, and frizzled, across these and 12 existing transcriptomic and genomic resources for chelicerates. We report extensive retention of putative ohnologs, further supporting the ancestral arachnopulmonate WGD. We also found evidence of consistent evolutionary trajectories in Hox and Wnt gene repertoires across three of the six arachnopulmonate orders, with interorder variation in the retention of specific paralogs. We identified variation between major clades in spiders and are better able to reconstruct the chronology of gene duplications and losses in spiders, amblypygids, and scorpions. These insights shed light on the evolution of the developmental toolkit in arachnopulmonates, highlight the importance of the comparative approach within lineages, and provide substantial new transcriptomic data for future study.
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Affiliation(s)
- Amber Harper
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
| | - Luis Baudouin Gonzalez
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
| | - Anna Schönauer
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
| | - Ralf Janssen
- Department of Earth Sciences, Uppsala University, Geocentrum, 752 36 Uppsala, Sweden
| | - Michael Seiter
- Department of Evolutionary Biology, Unit Integrative Zoology, University of Vienna, 1090 Vienna, Austria
| | - Michaela Holzem
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
- Division of Signalling and Functional Genomics, German Cancer Research Centre (DKFZ), Heidelberg, Germany and Department of Cell and Molecular Biology, Medical Faculty Mannheim, Heidelberg University, 69120 Heidelberg, Germany
| | - Saad Arif
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
- Centre for Functional Genomics, Oxford Brookes University, Oxford OX3 0BP, UK
| | - Alistair P McGregor
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
- Centre for Functional Genomics, Oxford Brookes University, Oxford OX3 0BP, UK
| | - Lauren Sumner-Rooney
- Oxford University Museum of Natural History, University of Oxford, Oxford OX1 3PW, UK
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10
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Cerca J, Armstrong EE, Vizueta J, Fernández R, Dimitrov D, Petersen B, Prost S, Rozas J, Petrov D, Gillespie RG. The Tetragnatha kauaiensis Genome Sheds Light on the Origins of Genomic Novelty in Spiders. Genome Biol Evol 2021; 13:evab262. [PMID: 34849853 PMCID: PMC8693713 DOI: 10.1093/gbe/evab262] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/22/2021] [Indexed: 01/07/2023] Open
Abstract
Spiders (Araneae) have a diverse spectrum of morphologies, behaviors, and physiologies. Attempts to understand the genomic-basis of this diversity are often hindered by their large, heterozygous, and AT-rich genomes with high repeat content resulting in highly fragmented, poor-quality assemblies. As a result, the key attributes of spider genomes, including gene family evolution, repeat content, and gene function, remain poorly understood. Here, we used Illumina and Dovetail Chicago technologies to sequence the genome of the long-jawed spider Tetragnatha kauaiensis, producing an assembly distributed along 3,925 scaffolds with an N50 of ∼2 Mb. Using comparative genomics tools, we explore genome evolution across available spider assemblies. Our findings suggest that the previously reported and vast genome size variation in spiders is linked to the different representation and number of transposable elements. Using statistical tools to uncover gene-family level evolution, we find expansions associated with the sensory perception of taste, immunity, and metabolism. In addition, we report strikingly different histories of chemosensory, venom, and silk gene families, with the first two evolving much earlier, affected by the ancestral whole genome duplication in Arachnopulmonata (∼450 Ma) and exhibiting higher numbers. Together, our findings reveal that spider genomes are highly variable and that genomic novelty may have been driven by the burst of an ancient whole genome duplication, followed by gene family and transposable element expansion.
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Affiliation(s)
- José Cerca
- Berkeley Evolab, Department of Environmental Science, Policy, and Management, UC Berkeley, California, USA
- Frontiers in Evolutionary Zoology, Natural History Museum, University of Oslo, Norway
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Ellie E Armstrong
- Berkeley Evolab, Department of Environmental Science, Policy, and Management, UC Berkeley, California, USA
- Department of Biology, Stanford University, California, USA
| | - Joel Vizueta
- Departament de Genètica, Microbiologia i Estadística & Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Spain
- Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Denmark
| | - Rosa Fernández
- Institute of Evolutionary Biology (CSIC—Universitat Pompeu Fabra), Barcelona, Spain
| | - Dimitar Dimitrov
- Department of Natural History, University Museum of Bergen, University of Bergen, Norway
| | - Bent Petersen
- Section for Evolutionary Genomics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
- Centre of Excellence for Omics-Driven Computational Biodiscovery, Faculty of Applied Sciences, AIMST University, Kedah, Malaysia
| | - Stefan Prost
- Central Research Laboratories, Natural History Museum Vienna, Vienna, Austria
- University of Veterinary Medicine, Konrad Lorenz Institute of Ethology, Vienna, Austria
- South African National Biodiversity Institute, National Zoological Garden, Pretoria, South Africa
| | - Julio Rozas
- Departament de Genètica, Microbiologia i Estadística & Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Spain
| | - Dmitri Petrov
- Department of Biology, Stanford University, California, USA
| | - Rosemary G Gillespie
- Berkeley Evolab, Department of Environmental Science, Policy, and Management, UC Berkeley, California, USA
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Reyes Lerma AC, Šťáhlavský F, Seiter M, Carabajal Paladino LZ, Divišová K, Forman M, Sember A, Král J. Insights into the Karyotype Evolution of Charinidae, the Early-Diverging Clade of Whip Spiders (Arachnida: Amblypygi). Animals (Basel) 2021; 11:3233. [PMID: 34827965 PMCID: PMC8614469 DOI: 10.3390/ani11113233] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/05/2021] [Accepted: 11/09/2021] [Indexed: 11/16/2022] Open
Abstract
Whip spiders (Amblypygi) represent an ancient order of tetrapulmonate arachnids with a low diversity. Their cytogenetic data are confined to only a few reports. Here, we analyzed the family Charinidae, a lineage almost at the base of the amblypygids, providing an insight into the ancestral traits and basic trajectories of amblypygid karyotype evolution. We performed Giemsa staining, selected banding techniques, and detected 18S ribosomal DNA and telomeric repeats by fluorescence in situ hybridization in four Charinus and five Sarax species. Both genera exhibit a wide range of diploid chromosome numbers (2n = 42-76 and 22-74 for Charinus and Sarax, respectively). The 2n reduction was accompanied by an increase of proportion of biarmed elements. We further revealed a single NOR site (probably an ancestral condition for charinids), the presence of a (TTAGG)n telomeric motif localized mostly at the chromosome ends, and an absence of heteromorphic sex chromosomes. Our data collectively suggest a high pace of karyotype repatterning in amblypygids, with probably a high ancestral 2n and its subsequent gradual reduction by fusions, and the action of pericentric inversions, similarly to what has been proposed for neoamblypygids. The possible contribution of fissions to charinid karyotype repatterning, however, cannot be fully ruled out.
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Affiliation(s)
- Azucena Claudia Reyes Lerma
- Laboratory of Arachnid Cytogenetics, Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, 128 44 Prague, Czech Republic; (A.C.R.L.); (K.D.); (M.F.); (J.K.)
| | - František Šťáhlavský
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44 Prague, Czech Republic;
| | - Michael Seiter
- Unit Integrative Zoology, Department of Evolutionary Biology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria;
- Natural History Museum Vienna, 3. Zoology (Invertebrates), Burgring 7, 1010 Vienna, Austria
| | - Leonela Zusel Carabajal Paladino
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 370 05 České Budějovice, Czech Republic;
- Arthropod Genetics Group, The Pirbright Institute, Ash Road, Pirbright, Woking GU24 0NF, UK
| | - Klára Divišová
- Laboratory of Arachnid Cytogenetics, Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, 128 44 Prague, Czech Republic; (A.C.R.L.); (K.D.); (M.F.); (J.K.)
| | - Martin Forman
- Laboratory of Arachnid Cytogenetics, Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, 128 44 Prague, Czech Republic; (A.C.R.L.); (K.D.); (M.F.); (J.K.)
| | - Alexandr Sember
- Laboratory of Arachnid Cytogenetics, Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, 128 44 Prague, Czech Republic; (A.C.R.L.); (K.D.); (M.F.); (J.K.)
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 277 21 Liběchov, Czech Republic
| | - Jiří Král
- Laboratory of Arachnid Cytogenetics, Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, 128 44 Prague, Czech Republic; (A.C.R.L.); (K.D.); (M.F.); (J.K.)
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12
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Câmara AS, Schubert V, Mascher M, Houben A. A simple model explains the cell cycle-dependent assembly of centromeric nucleosomes in holocentric species. Nucleic Acids Res 2021; 49:9053-9065. [PMID: 34352103 PMCID: PMC8450114 DOI: 10.1093/nar/gkab648] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 06/24/2021] [Accepted: 07/21/2021] [Indexed: 11/25/2022] Open
Abstract
Centromeres are essential for chromosome movement. In independent taxa, species with holocentric chromosomes exist. In contrast to monocentric species, where no obvious dispersion of centromeres occurs during interphase, the organization of holocentromeres differs between condensed and decondensed chromosomes. During interphase, centromeres are dispersed into a large number of CENH3-positive nucleosome clusters in a number of holocentric species. With the onset of chromosome condensation, the centromeric nucleosomes join and form line-like holocentromeres. Using polymer simulations, we propose a mechanism relying on the interaction between centromeric nucleosomes and structural maintenance of chromosomes (SMC) proteins. Different sets of molecular dynamic simulations were evaluated by testing four parameters: (i) the concentration of Loop Extruders (LEs) corresponding to SMCs, (ii) the distribution and number of centromeric nucleosomes, (iii) the effect of centromeric nucleosomes on interacting LEs and (iv) the assembly of kinetochores bound to centromeric nucleosomes. We observed the formation of a line-like holocentromere, due to the aggregation of the centromeric nucleosomes when the chromosome was compacted into loops. A groove-like holocentromere structure formed after a kinetochore complex was simulated along the centromeric line. Similar mechanisms may also organize a monocentric chromosome constriction, and its regulation may cause different centromere types during evolution.
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Affiliation(s)
- Amanda Souza Câmara
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany
| | - Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany
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13
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Ávila Herrera IM, Král J, Pastuchová M, Forman M, Musilová J, Kořínková T, Šťáhlavský F, Zrzavá M, Nguyen P, Just P, Haddad CR, Hiřman M, Koubová M, Sadílek D, Huber BA. Evolutionary pattern of karyotypes and meiosis in pholcid spiders (Araneae: Pholcidae): implications for reconstructing chromosome evolution of araneomorph spiders. BMC Ecol Evol 2021; 21:75. [PMID: 33941079 PMCID: PMC8091558 DOI: 10.1186/s12862-021-01750-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 01/25/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Despite progress in genomic analysis of spiders, their chromosome evolution is not satisfactorily understood. Most information on spider chromosomes concerns the most diversified clade, entelegyne araneomorphs. Other clades are far less studied. Our study focused on haplogyne araneomorphs, which are remarkable for their unusual sex chromosome systems and for the co-evolution of sex chromosomes and nucleolus organizer regions (NORs); some haplogynes exhibit holokinetic chromosomes. To trace the karyotype evolution of haplogynes on the family level, we analysed the number and morphology of chromosomes, sex chromosomes, NORs, and meiosis in pholcids, which are among the most diverse haplogyne families. The evolution of spider NORs is largely unknown. RESULTS Our study is based on an extensive set of species representing all major pholcid clades. Pholcids exhibit a low 2n and predominance of biarmed chromosomes, which are typical haplogyne features. Sex chromosomes and NOR patterns of pholcids are diversified. We revealed six sex chromosome systems in pholcids (X0, XY, X1X20, X1X2X30, X1X2Y, and X1X2X3X4Y). The number of NOR loci ranges from one to nine. In some clades, NORs are also found on sex chromosomes. CONCLUSIONS The evolution of cytogenetic characters was largely derived from character mapping on a recently published molecular phylogeny of the family. Based on an extensive set of species and mapping of their characters, numerous conclusions regarding the karyotype evolution of pholcids and spiders can be drawn. Our results suggest frequent autosome-autosome and autosome-sex chromosome rearrangements during pholcid evolution. Such events have previously been attributed to the reproductive isolation of species. The peculiar X1X2Y system is probably ancestral for haplogynes. Chromosomes of the X1X2Y system differ considerably in their pattern of evolution. In some pholcid clades, the X1X2Y system has transformed into the X1X20 or XY systems, and subsequently into the X0 system. The X1X2X30 system of Smeringopus pallidus probably arose from the X1X20 system by an X chromosome fission. The X1X2X3X4Y system of Kambiwa probably evolved from the X1X2Y system by integration of a chromosome pair. Nucleolus organizer regions have frequently expanded on sex chromosomes, most probably by ectopic recombination. Our data suggest the involvement of sex chromosome-linked NORs in achiasmatic pairing.
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Affiliation(s)
- Ivalú M. Ávila Herrera
- Laboratory of Arachnid Cytogenetics, Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, 128 44 Prague 2, Czech Republic
| | - Jiří Král
- Laboratory of Arachnid Cytogenetics, Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, 128 44 Prague 2, Czech Republic
| | - Markéta Pastuchová
- Laboratory of Arachnid Cytogenetics, Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, 128 44 Prague 2, Czech Republic
| | - Martin Forman
- Laboratory of Arachnid Cytogenetics, Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, 128 44 Prague 2, Czech Republic
| | - Jana Musilová
- Laboratory of Arachnid Cytogenetics, Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, 128 44 Prague 2, Czech Republic
- Research Team of Plant Stress Biology and Biotechnology, Division of Crop Genetics and Breeding, Crop Research Institute, Drnovská 507/73, 161 00 Prague 6, Czech Republic
| | - Tereza Kořínková
- Laboratory of Arachnid Cytogenetics, Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, 128 44 Prague 2, Czech Republic
- Prague 1, Czech Republic
| | - František Šťáhlavský
- Invertebrate Zoology Unit, Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44 Prague 2, Czech Republic
| | - Magda Zrzavá
- Laboratory of Molecular Cytogenetics, Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, Branišovská 31, 370 05 České Budějovice, Czech Republic
- Laboratory of Molecular Cytogenetics, Department of Molecular Biology and Genetics, Institute of Entomology, Biology Centre CAS, Branišovská 31, 370 05 České Budějovice, Czech Republic
| | - Petr Nguyen
- Laboratory of Molecular Cytogenetics, Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, Branišovská 31, 370 05 České Budějovice, Czech Republic
- Laboratory of Molecular Cytogenetics, Department of Molecular Biology and Genetics, Institute of Entomology, Biology Centre CAS, Branišovská 31, 370 05 České Budějovice, Czech Republic
| | - Pavel Just
- Laboratory of Arachnid Cytogenetics, Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, 128 44 Prague 2, Czech Republic
- Invertebrate Zoology Unit, Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44 Prague 2, Czech Republic
| | - Charles R. Haddad
- Research Group of Arachnid Systematics and Ecology, Department of Zoology and Entomology, Faculty of Natural and Agricultural Sciences, University of the Free State, P.O. Box 339, Bloemfontein, 9300 Republic of South Africa
| | - Matyáš Hiřman
- Invertebrate Zoology Unit, Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44 Prague 2, Czech Republic
| | - Martina Koubová
- Laboratory of Arachnid Cytogenetics, Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, 128 44 Prague 2, Czech Republic
| | - David Sadílek
- Laboratory of Arachnid Cytogenetics, Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, 128 44 Prague 2, Czech Republic
- Invertebrate Zoology Unit, Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44 Prague 2, Czech Republic
| | - Bernhard A. Huber
- Arachnida Section, Alexander Koenig Zoological Research Museum, Adenauerallee 160, 53113 Bonn, Germany
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Hofstatter PG, Thangavel G, Castellani M, Marques A. Meiosis Progression and Recombination in Holocentric Plants: What Is Known? FRONTIERS IN PLANT SCIENCE 2021; 12:658296. [PMID: 33968114 PMCID: PMC8100227 DOI: 10.3389/fpls.2021.658296] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 03/22/2021] [Indexed: 05/02/2023]
Abstract
Differently from the common monocentric organization of eukaryotic chromosomes, the so-called holocentric chromosomes present many centromeric regions along their length. This chromosomal organization can be found in animal and plant lineages, whose distribution suggests that it has evolved independently several times. Holocentric chromosomes present an advantage: even broken chromosome parts can be correctly segregated upon cell division. However, the evolution of holocentricity brought about consequences to nuclear processes and several adaptations are necessary to cope with this new organization. Centromeres of monocentric chromosomes are involved in a two-step cohesion release during meiosis. To deal with that holocentric lineages developed different adaptations, like the chromosome remodeling strategy in Caenorhabditis elegans or the inverted meiosis in plants. Furthermore, the frequency of recombination at or around centromeres is normally very low and the presence of centromeric regions throughout the entire length of the chromosomes could potentially pose a problem for recombination in holocentric organisms. However, meiotic recombination happens, with exceptions, in those lineages in spite of their holocentric organization suggesting that the role of centromere as recombination suppressor might be altered in these lineages. Most of the available information about adaptations to meiosis in holocentric organisms is derived from the animal model C. elegans. As holocentricity evolved independently in different lineages, adaptations observed in C. elegans probably do not apply to other lineages and very limited research is available for holocentric plants. Currently, we still lack a holocentric model for plants, but good candidates may be found among Cyperaceae, a large angiosperm family. Besides holocentricity, chiasmatic and achiasmatic inverted meiosis are found in the family. Here, we introduce the main concepts of meiotic constraints and adaptations with special focus in meiosis progression and recombination in holocentric plants. Finally, we present the main challenges and perspectives for future research in the field of chromosome biology and meiosis in holocentric plants.
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15
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Zedek F, Plačková K, Veselý P, Šmerda J, Šmarda P, Horová L, Bureš P. Endopolyploidy is a common response to UV-B stress in natural plant populations, but its magnitude may be affected by chromosome type. ANNALS OF BOTANY 2020; 126:883-889. [PMID: 32582956 PMCID: PMC7750947 DOI: 10.1093/aob/mcaa109] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 06/18/2020] [Indexed: 05/08/2023]
Abstract
BACKGROUND AND AIMS Ultraviolet-B radiation (UV-B) radiation damages the DNA, cells and photosynthetic apparatus of plants. Plants commonly prevent this damage by synthetizing UV-B-protective compounds. Recent laboratory experiments in Arabidopsis and cucumber have indicated that plants can also respond to UV-B stress with endopolyploidy. Here we test the generality of this response in natural plant populations, considering their monocentric or holocentric chromosomal structure. METHODS We measured the endopolyploidy index (flow cytometry) and the concentration of UV-B-protective compounds in leaves of 12 herbaceous species (1007 individuals) from forest interiors and neighbouring clearings where they were exposed to increased UV-B radiation (103 forest + clearing populations). We then analysed the data using phylogenetic mixed models. KEY RESULTS The concentration of UV-B protectives increased with UV-B doses estimated from hemispheric photographs of the sky above sample collection sites, but the increase was more rapid in species with monocentric chromosomes. Endopolyploidy index increased with UV-B doses and with concentrations of UV-B-absorbing compounds only in species with monocentric chromosomes, while holocentric species responded negligibly. CONCLUSIONS Endopolyploidy seems to be a common response to increased UV-B in monocentric plants. Low sensitivity to UV-B in holocentric species might relate to their success in high-UV-stressed habitats and corroborates the hypothesized role of holocentric chromosomes in plant terrestrialization.
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Affiliation(s)
- František Zedek
- Department of Botany and Zoology, Masaryk University, Brno, Czech Republic
| | - Klára Plačková
- Department of Botany and Zoology, Masaryk University, Brno, Czech Republic
| | - Pavel Veselý
- Department of Botany and Zoology, Masaryk University, Brno, Czech Republic
| | - Jakub Šmerda
- Department of Botany and Zoology, Masaryk University, Brno, Czech Republic
| | - Petr Šmarda
- Department of Botany and Zoology, Masaryk University, Brno, Czech Republic
| | - Lucie Horová
- Department of Botany and Zoology, Masaryk University, Brno, Czech Republic
| | - Petr Bureš
- Department of Botany and Zoology, Masaryk University, Brno, Czech Republic
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Šťáhlavský F, Nguyen P, Sadílek D, Štundlová J, Just P, Haddad CR, Koç H, Ranawana KB, Stockmann M, Yağmur EA, Kovařík F. Evolutionary dynamics of rDNA clusters on chromosomes of buthid scorpions (Chelicerata: Arachnida). Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
We examined the distribution of genes for major ribosomal RNAs (rDNA) on holokinetic chromosomes of 74 species belonging to 19 genera of scorpions from the family Buthidae using fluorescence in situ hybridization (FISH). Our analysis revealed differences between the two main evolutionary lineages within the family. The genera belonging to the ‘Buthus group’, with a proposed Laurasian origin, possess one pair of rDNA mainly in an interstitial position, with the only exceptions being the terminal location found in some Hottentotta and Buthacus species, possibly as a result of chromosome fissions. All the remaining buthid ‘groups’ possess rDNA found strictly in a terminal position. However, the number of signals may increase from an ancestral state of one pair of rDNA loci to up to seven signals in Reddyanus ceylonensis Kovařík et al., 2016. Despite the differences in evolutionary dynamics of the rDNA clusters between the ‘Buthus group’ and other lineages investigated, we found a high incidence of reciprocal translocations and presence of multivalent associations during meiosis in the majority of the genera studied. These phenomena seem to be typical for the whole family Buthidae.
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Affiliation(s)
- František Šťáhlavský
- Department of Zoology, Faculty of Science, Charles University, Viničná, Prague, Czech Republic
| | - Petr Nguyen
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia in České Budějovice, Branišovská, České Budějovice, Czech Republic
| | - David Sadílek
- Department of Zoology, Faculty of Science, Charles University, Viničná, Prague, Czech Republic
| | - Jana Štundlová
- Department of Zoology, Faculty of Science, Charles University, Viničná, Prague, Czech Republic
| | - Pavel Just
- Department of Zoology, Faculty of Science, Charles University, Viničná, Prague, Czech Republic
| | - Charles R Haddad
- Department of Zoology and Entomology, University of the Free State, Bloemfontein, South Africa
| | - Halil Koç
- Department of Biology, Faculty of Arts and Science, Sinop University, Sinop, Turkey
| | - Kithsiri B Ranawana
- Department of Zoology, Faculty of Science, University of Peradeniya, Sri Lanka
| | | | - Ersen Aydin Yağmur
- Alaşehir Vocational School, Celal Bayar University, Alaşehir, Manisa, Turkey
| | - František Kovařík
- Department of Zoology, Faculty of Science, Charles University, Viničná, Prague, Czech Republic
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17
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Sember A, Pappová M, Forman M, Nguyen P, Marec F, Dalíková M, Divišová K, Doležálková-Kaštánková M, Zrzavá M, Sadílek D, Hrubá B, Král J. Patterns of Sex Chromosome Differentiation in Spiders: Insights from Comparative Genomic Hybridisation. Genes (Basel) 2020; 11:E849. [PMID: 32722348 PMCID: PMC7466014 DOI: 10.3390/genes11080849] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 07/21/2020] [Accepted: 07/21/2020] [Indexed: 01/21/2023] Open
Abstract
Spiders are an intriguing model to analyse sex chromosome evolution because of their peculiar multiple X chromosome systems. Y chromosomes were considered rare in this group, arising after neo-sex chromosome formation by X chromosome-autosome rearrangements. However, recent findings suggest that Y chromosomes are more common in spiders than previously thought. Besides neo-sex chromosomes, they are also involved in the ancient X1X2Y system of haplogyne spiders, whose origin is unknown. Furthermore, spiders seem to exhibit obligatorily one or two pairs of cryptic homomorphic XY chromosomes (further cryptic sex chromosome pairs, CSCPs), which could represent the ancestral spider sex chromosomes. Here, we analyse the molecular differentiation of particular types of spider Y chromosomes in a representative set of ten species by comparative genomic hybridisation (CGH). We found a high Y chromosome differentiation in haplogyne species with X1X2Y system except for Loxosceles spp. CSCP chromosomes exhibited generally low differentiation. Possible mechanisms and factors behind the observed patterns are discussed. The presence of autosomal regions marked predominantly or exclusively with the male or female probe was also recorded. We attribute this pattern to intraspecific variability in the copy number and distribution of certain repetitive DNAs in spider genomes, pointing thus to the limits of CGH in this arachnid group. In addition, we confirmed nonrandom association of chromosomes belonging to particular CSCPs at spermatogonial mitosis and spermatocyte meiosis and their association with multiple Xs throughout meiosis. Taken together, our data suggest diverse evolutionary pathways of molecular differentiation in different types of spider Y chromosomes.
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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;
- Laboratory of Arachnid Cytogenetics, Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, 128 44 Prague, Czech Republic; (M.P.); (M.F.); (K.D.); (D.S.); (B.H.); (J.K.)
| | - Michaela Pappová
- Laboratory of Arachnid Cytogenetics, Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, 128 44 Prague, Czech Republic; (M.P.); (M.F.); (K.D.); (D.S.); (B.H.); (J.K.)
| | - Martin Forman
- Laboratory of Arachnid Cytogenetics, Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, 128 44 Prague, Czech Republic; (M.P.); (M.F.); (K.D.); (D.S.); (B.H.); (J.K.)
| | - Petr Nguyen
- Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05 České Budějovice, Czech Republic; (P.N.); (M.D.); (M.Z.)
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 370 05 České Budějovice, Czech Republic;
| | - František Marec
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 370 05 České Budějovice, Czech Republic;
| | - Martina Dalíková
- Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05 České Budějovice, Czech Republic; (P.N.); (M.D.); (M.Z.)
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 370 05 České Budějovice, Czech Republic;
| | - Klára Divišová
- Laboratory of Arachnid Cytogenetics, Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, 128 44 Prague, Czech Republic; (M.P.); (M.F.); (K.D.); (D.S.); (B.H.); (J.K.)
| | - Marie Doležálková-Kaštánková
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 277 21 Liběchov, Czech Republic;
- Laboratory of Arachnid Cytogenetics, Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, 128 44 Prague, Czech Republic; (M.P.); (M.F.); (K.D.); (D.S.); (B.H.); (J.K.)
| | - Magda Zrzavá
- Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05 České Budějovice, Czech Republic; (P.N.); (M.D.); (M.Z.)
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 370 05 České Budějovice, Czech Republic;
| | - David Sadílek
- Laboratory of Arachnid Cytogenetics, Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, 128 44 Prague, Czech Republic; (M.P.); (M.F.); (K.D.); (D.S.); (B.H.); (J.K.)
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44 Prague, Czech Republic
| | - Barbora Hrubá
- Laboratory of Arachnid Cytogenetics, Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, 128 44 Prague, Czech Republic; (M.P.); (M.F.); (K.D.); (D.S.); (B.H.); (J.K.)
| | - Jiří Král
- Laboratory of Arachnid Cytogenetics, Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, 128 44 Prague, Czech Republic; (M.P.); (M.F.); (K.D.); (D.S.); (B.H.); (J.K.)
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Schubert V, Neumann P, Marques A, Heckmann S, Macas J, Pedrosa-Harand A, Schubert I, Jang TS, Houben A. Super-Resolution Microscopy Reveals Diversity of Plant Centromere Architecture. Int J Mol Sci 2020; 21:E3488. [PMID: 32429054 PMCID: PMC7278974 DOI: 10.3390/ijms21103488] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/11/2020] [Accepted: 05/11/2020] [Indexed: 12/20/2022] Open
Abstract
Centromeres are essential for proper chromosome segregation to the daughter cells during mitosis and meiosis. Chromosomes of most eukaryotes studied so far have regional centromeres that form primary constrictions on metaphase chromosomes. These monocentric chromosomes vary from point centromeres to so-called "meta-polycentromeres", with multiple centromere domains in an extended primary constriction, as identified in Pisum and Lathyrus species. However, in various animal and plant lineages centromeres are distributed along almost the entire chromosome length. Therefore, they are called holocentromeres. In holocentric plants, centromere-specific proteins, at which spindle fibers usually attach, are arranged contiguously (line-like), in clusters along the chromosomes or in bands. Here, we summarize findings of ultrastructural investigations using immunolabeling with centromere-specific antibodies and super-resolution microscopy to demonstrate the structural diversity of plant centromeres. A classification of the different centromere types has been suggested based on the distribution of spindle attachment sites. Based on these findings we discuss the possible evolution and advantages of holocentricity, and potential strategies to segregate holocentric chromosomes correctly.
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Affiliation(s)
- Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany; (S.H.); (I.S.); (A.H.)
| | - Pavel Neumann
- Biology Centre, Czech Academy of Sciences, 37005 České Budějovice, Czech Republic; (P.N.); (J.M.); (T.-S.J.)
| | - André Marques
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany;
| | - Stefan Heckmann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany; (S.H.); (I.S.); (A.H.)
| | - Jiri Macas
- Biology Centre, Czech Academy of Sciences, 37005 České Budějovice, Czech Republic; (P.N.); (J.M.); (T.-S.J.)
| | - Andrea Pedrosa-Harand
- Department of Botany, Federal University of Pernambuco (UFPE), Recife 50670-901, Pernambuco, Brazil;
| | - Ingo Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany; (S.H.); (I.S.); (A.H.)
| | - Tae-Soo Jang
- Biology Centre, Czech Academy of Sciences, 37005 České Budějovice, Czech Republic; (P.N.); (J.M.); (T.-S.J.)
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Korea
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany; (S.H.); (I.S.); (A.H.)
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19
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Araujo D, Schneider MC, Zacaro AA, de Oliveira EG, Martins R, Brescovit AD, Knysak I, Cella DM. Venomous Loxosceles Species (Araneae, Haplogynae, Sicariidae) from Brazil: 2n♂ = 23 and X1X2Y Sex Chromosome System as Shared Characteristics. Zoolog Sci 2020; 37:128-139. [DOI: 10.2108/zs190128] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 01/01/2020] [Indexed: 11/17/2022]
Affiliation(s)
- Douglas Araujo
- Universidade Federal de Mato Grosso do Sul - UFMS, Setor de Biologia Geral, Instituto de Biociências, Cidade Universitária, Bairro Universitário, 79070-900, Campo Grande, Mato Grosso do Sul, Brazil
| | - Marielle Cristina Schneider
- Universidade Federal de Mato Grosso, UFMT, Departamento de Biologia e Zoologia, Av. Fernando Côrrea da Costa, 2367, 78060-900, Cuiabá, Mato Grosso, Brazil
| | - Adilson Ariza Zacaro
- Universidade Federal de Viçosa - UFV, Centro de Ciências Biológicas e da Saúde, Departamento de Biologia Geral, Av. P.H. Rolfs, s/n°, Campus Universitário, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Edson Gabriel de Oliveira
- Universidade Estadual Paulista - UNESP, Instituto de Biociências, Departamento de Biologia, Av. 24-A, 1515, Bela Vista, Rio Claro, São Paulo, 13506-900, Brazil
| | - Rosana Martins
- Instituto Butantan, Laboratório Especial de Coleções Zoológicas, Av. Vital Brasil, 1500, 05503-900, São Paulo, São Paulo, Brazil
| | - Antonio Domingos Brescovit
- Instituto Butantan, Laboratório Especial de Coleções Zoológicas, Av. Vital Brasil, 1500, 05503-900, São Paulo, São Paulo, Brazil
| | - Irene Knysak
- Instituto Butantan, Laboratório Especial de Coleções Zoológicas, Av. Vital Brasil, 1500, 05503-900, São Paulo, São Paulo, Brazil
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Šťáhlavský F, Forman M, Just P, Denič F, Haddad CR, Opatova V. Cytogenetics of entelegyne spiders (Arachnida, Araneae) from southern Africa. COMPARATIVE CYTOGENETICS 2020; 14:107-138. [PMID: 32194919 PMCID: PMC7066264 DOI: 10.3897/compcytogen.v14i1.48667] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 01/17/2020] [Indexed: 06/10/2023]
Abstract
Spiders represent one of the most studied arachnid orders. They are particularly intriguing from a cytogenetic point of view, due to their complex and dynamic sex chromosome determination systems. Despite intensive research on this group, cytogenetic data from African spiders are still mostly lacking. In this study, we describe the karyotypes of 38 species of spiders belonging to 16 entelegyne families from South Africa and Namibia. In the majority of analysed families, the observed chromosome numbers and morphology (mainly acrocentric) did not deviate from the family-level cytogenetic characteristics based on material from other continents: Tetragnathidae (2n♂ = 24), Ctenidae and Oxyopidae (2n♂ = 28), Sparassidae (2n♂ = 42), Gnaphosidae, Trachelidae and Trochanteriidae (2n♂ = 22), and Salticidae (2n♂ = 28). On the other hand, we identified interspecific variability within Hersiliidae (2n♂ = 33 and 35), Oecobiidae (2n♂ = 19 and 25), Selenopidae (2n♂ = 26 and 29) and Theridiidae (2n♂ = 21 and 22). We examined the karyotypes of Ammoxenidae and Gallieniellidae for the first time. Their diploid counts (2n♂ = 22) correspond to the superfamily Gnaphosoidea and support their placement in this lineage. On the other hand, the karyotypes of Prodidominae (2n♂ = 28 and 29) contrast with all other Gnaphosoidea. Similarly, the unusually high diploid number in Borboropactus sp. (2n♂ = 28) within the otherwise cytogenetically uniform family Thomisidae (mainly 2n♂ = 21-24) supports molecular data suggesting a basal position of the genus in the family. The implementation of FISH methods for visualisation of rDNA clusters facilitated the detection of complex dynamics of numbers of these loci. We identified up to five loci of the 18S rDNA clusters in our samples. Three different sex chromosome systems (X0, X1X20 and X1X2X30) were also detected among the studied taxa.
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Affiliation(s)
- František Šťáhlavský
- Department of Zoology, Charles University, Faculty of Science, Viničná 7, CZ-12844 Praha, Czech Republic
| | - Martin Forman
- Department of Genetics and Microbiology, Charles University, Faculty of Science, Viničná 5, CZ-12844 Praha, Czech Republic
| | - Pavel Just
- Department of Zoology, Charles University, Faculty of Science, Viničná 7, CZ-12844 Praha, Czech Republic
| | - Filip Denič
- Department of Genetics and Microbiology, Charles University, Faculty of Science, Viničná 5, CZ-12844 Praha, Czech Republic
| | - Charles R. Haddad
- Department of Zoology and Entomology, University of the Free State, P.O. Box 339, Bloemfontein 9300, South Africa
| | - Vera Opatova
- Department of Zoology, Charles University, Faculty of Science, Viničná 7, CZ-12844 Praha, Czech Republic
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Zedek F, Bureš P. Pest Arthropods with Holocentric Chromosomes are More Resistant to Sterilizing Ionizing Radiation. Radiat Res 2019; 191:255-261. [PMID: 30702973 DOI: 10.1667/rr15208.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
It has been hypothesized that species with holocentric chromosomes have a selective evolutionary advantage for developmental and reproductive success because holocentric chromosomes are less susceptible to chromosome breakage than monocentric chromosomes. We analyzed data on sterilizing doses of ionizing radiation for more than 250 species of arthropods to test whether the minimal dose for reproductive sterilization is higher for species with holocentric chromosomes than for species with monocentric chromosomes. Using linear mixed models that account for phylogeny, we show that holocentric arthropods are more tolerant of sterilizing radiation than monocentrics. Moreover, higher dose rates correlate with lower sterilizing doses in monocentrics, but not in holocentrics, which is a novel finding that may be of importance for radiosanitation practice. Under the dose rate of 1 Gy/min, holocentric arthropods are sterilized on average with a 2.9 times higher minimal dose than monocentrics. Life stage and sex have significant but considerably weaker effects on sterilizing dose than chromosome type. Adults and males require 1.2 and 1.4 times higher sterilizing doses than juveniles and females, respectively. These results support the hypothesis that holocentric lineages may originate and thrive better in times of increased exposure to chromosome-breaking factors.
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Affiliation(s)
- František Zedek
- 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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