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Hubinský M, Hobza R, Starczak M, Gackowski D, Kubát Z, Janíček T, Horáková L, Rodriguez Lorenzo JL. Non-canonical bases differentially represented in the sex chromosomes of the dioecious plant Silene latifolia. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:3849-3861. [PMID: 38652039 PMCID: PMC11233409 DOI: 10.1093/jxb/erae178] [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: 09/28/2023] [Accepted: 04/22/2024] [Indexed: 04/25/2024]
Abstract
The oxidation of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC), known as oxi-mCs, garners significant interest in plants as potential epigenetic marks. While research in mammals has established a role in cell reprogramming, carcinogenesis, and gene regulation, their functions in plants remain unclear. In rice, 5hmC has been associated with transposable elements (TEs) and heterochromatin. This study utilizes Silene latifolia, a dioecious plant with heteromorphic sex chromosomes and a genome with a large proportion of TEs, which provides a favourable environment for the study of oxi-mCs in individual sexes. Notably, we detected surprisingly high levels of oxi-mCs in S. latifolia comparable with mammals. Nuclei showed enrichment in heterochromatic regions, except for 5hmC whose signal was homogeneously distributed. Intriguingly, the same X chromosome in females displayed overall enrichment of 5hmC and 5fC compared with its counterpart. This fact is shared with 5mC, resembling dosage compensation. Co-localization showed higher correlation between 5mC and 5fC than with 5hmC, indicating no potential relationship between 5hmC and 5fC. Additionally, the promoter of several sex-linked genes and sex-biased TEs clustered in a clear sex-dependent way. Together, these findings unveil a hypothetical role for oxi-mCs in S. latifolia sex chromosome development, warranting further exploration.
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Affiliation(s)
- Marcel Hubinský
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Roman Hobza
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Marta Starczak
- Department of Clinical Biochemistry, Faculty of Pharmacy, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, ul. Karlowicza 24, PO-85-092, Bydgoszcz, Poland
| | - Daniel Gackowski
- Department of Clinical Biochemistry, Faculty of Pharmacy, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, ul. Karlowicza 24, PO-85-092, Bydgoszcz, Poland
| | - Zdeněk Kubát
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Tomáš Janíček
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Lucie Horáková
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Jose Luis Rodriguez Lorenzo
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
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2
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Muyle A, Marais GAB, Bačovský V, Hobza R, Lenormand T. Dosage compensation evolution in plants: theories, controversies and mechanisms. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210222. [PMID: 35306896 PMCID: PMC8935305 DOI: 10.1098/rstb.2021.0222] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
In a minority of flowering plants, separate sexes are genetically determined by sex chromosomes. The Y chromosome has a non-recombining region that degenerates, causing a reduced expression of Y genes. In some species, the lower Y expression is accompanied by dosage compensation (DC), a mechanism that re-equalizes male and female expression and/or brings XY male expression back to its ancestral level. Here, we review work on DC in plants, which started as early as the late 1960s with cytological approaches. The use of transcriptomics fired a controversy as to whether DC existed in plants. Further work revealed that various plants exhibit partial DC, including a few species with young and homomorphic sex chromosomes. We are starting to understand the mechanisms responsible for DC in some plants, but in most species, we lack the data to differentiate between global and gene-by-gene DC. Also, it is unknown why some species evolve many dosage compensated genes while others do not. Finally, the forces that drive DC evolution remain mysterious, both in plants and animals. We review the multiple evolutionary theories that have been proposed to explain DC patterns in eukaryotes with XY or ZW sex chromosomes. This article is part of the theme issue 'Sex determination and sex chromosome evolution in land plants'.
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Affiliation(s)
- Aline Muyle
- Laboratoire 'Biométrie et Biologie Evolutive', CNRS/Université Lyon 1, Lyon, France
| | - Gabriel A B Marais
- Laboratoire 'Biométrie et Biologie Evolutive', CNRS/Université Lyon 1, Lyon, France.,CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002 Porto, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
| | - Václav Bačovský
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, Brno, Czech Republic
| | - Roman Hobza
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, Brno, Czech Republic
| | - Thomas Lenormand
- CEFE, University of Montpellier, CNRS, EPHE, IRD, Montpellier, France
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Do Ty3/Gypsy Transposable Elements Play Preferential Roles in Sex Chromosome Differentiation? Life (Basel) 2022; 12:life12040522. [PMID: 35455013 PMCID: PMC9025612 DOI: 10.3390/life12040522] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/13/2022] [Accepted: 03/30/2022] [Indexed: 12/16/2022] Open
Abstract
Transposable elements (TEs) comprise a substantial portion of eukaryotic genomes. They have the unique ability to integrate into new locations and serve as the main source of genomic novelties by mediating chromosomal rearrangements and regulating portions of functional genes. Recent studies have revealed that TEs are abundant in sex chromosomes. In this review, we propose evolutionary relationships between specific TEs, such as Ty3/Gypsy, and sex chromosomes in different lineages based on the hypothesis that these elements contributed to sex chromosome differentiation processes. We highlight how TEs can drive the dynamics of sex-determining regions via suppression recombination under a selective force to affect the organization and structural evolution of sex chromosomes. The abundance of TEs in the sex-determining regions originates from TE-poor genomic regions, suggesting a link between TE accumulation and the emergence of the sex-determining regions. TEs are generally considered to be a hallmark of chromosome degeneration. Finally, we outline recent approaches to identify TEs and study their sex-related roles and effects in the differentiation and evolution of sex chromosomes.
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Jesionek W, Bodláková M, Kubát Z, Čegan R, Vyskot B, Vrána J, Šafář J, Puterova J, Hobza R. Fundamentally different repetitive element composition of sex chromosomes in Rumex acetosa. ANNALS OF BOTANY 2021; 127:33-47. [PMID: 32902599 PMCID: PMC7750719 DOI: 10.1093/aob/mcaa160] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 08/31/2020] [Indexed: 05/10/2023]
Abstract
BACKGROUND AND AIMS Dioecious species with well-established sex chromosomes are rare in the plant kingdom. Most sex chromosomes increase in size but no comprehensive analysis of the kind of sequences that drive this expansion has been presented. Here we analyse sex chromosome structure in common sorrel (Rumex acetosa), a dioecious plant with XY1Y2 sex determination, and we provide the first chromosome-specific repeatome analysis for a plant species possessing sex chromosomes. METHODS We flow-sorted and separately sequenced sex chromosomes and autosomes in R. acetosa using the two-dimensional fluorescence in situ hybridization in suspension (FISHIS) method and Illumina sequencing. We identified and quantified individual repeats using RepeatExplorer, Tandem Repeat Finder and the Tandem Repeats Analysis Program. We employed fluorescence in situ hybridization (FISH) to analyse the chromosomal localization of satellites and transposons. KEY RESULTS We identified a number of novel satellites, which have, in a fashion similar to previously known satellites, significantly expanded on the Y chromosome but not as much on the X or on autosomes. Additionally, the size increase of Y chromosomes is caused by non-long terminal repeat (LTR) and LTR retrotransposons, while only the latter contribute to the enlargement of the X chromosome. However, the X chromosome is populated by different LTR retrotransposon lineages than those on Y chromosomes. CONCLUSIONS The X and Y chromosomes have significantly diverged in terms of repeat composition. The lack of recombination probably contributed to the expansion of diverse satellites and microsatellites and faster fixation of newly inserted transposable elements (TEs) on the Y chromosomes. In addition, the X and Y chromosomes, despite similar total counts of TEs, differ significantly in the representation of individual TE lineages, which indicates that transposons proliferate preferentially in either the paternal or the maternal lineage.
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Affiliation(s)
- Wojciech Jesionek
- Department of Plant Developmental Genetics, The Czech Academy of Sciences, Institute of Biophysics, Královopolská, Brno, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice, Brno, Czech Republic
- For correspondence. E-mail: or
| | - Markéta Bodláková
- Department of Plant Developmental Genetics, The Czech Academy of Sciences, Institute of Biophysics, Královopolská, Brno, Czech Republic
| | - Zdeněk Kubát
- Department of Plant Developmental Genetics, The Czech Academy of Sciences, Institute of Biophysics, Královopolská, Brno, Czech Republic
| | - Radim Čegan
- Department of Plant Developmental Genetics, The Czech Academy of Sciences, Institute of Biophysics, Královopolská, Brno, Czech Republic
| | - Boris Vyskot
- Department of Plant Developmental Genetics, The Czech Academy of Sciences, Institute of Biophysics, Královopolská, Brno, Czech Republic
| | - Jan Vrána
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů, Olomouc-Holice, Czech Republic
| | - Jan Šafář
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů, Olomouc-Holice, Czech Republic
| | - Janka Puterova
- Department of Plant Developmental Genetics, The Czech Academy of Sciences, Institute of Biophysics, Královopolská, Brno, Czech Republic
- Brno University of Technology, Faculty of Information Technology, Centre of Excellence IT4Innovations, Bozetechova, Brno, Czech Republic
| | - Roman Hobza
- Department of Plant Developmental Genetics, The Czech Academy of Sciences, Institute of Biophysics, Královopolská, Brno, Czech Republic
- For correspondence. E-mail: or
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Rodríguez Lorenzo JL, Hubinský M, Vyskot B, Hobza R. Histone post-translational modifications in Silene latifolia X and Y chromosomes suggest a mammal-like dosage compensation system. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 299:110528. [PMID: 32900432 DOI: 10.1016/j.plantsci.2020.110528] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 05/07/2020] [Accepted: 05/09/2020] [Indexed: 06/11/2023]
Abstract
Silene latifolia is a model organism to study evolutionary young heteromorphic sex chromosome evolution in plants. Previous research indicates a Y-allele gene degeneration and a dosage compensation system already operating. Here, we propose an epigenetic approach based on analysis of several histone post-translational modifications (PTMs) to find the first epigenetic hints of the X:Y sex chromosome system regulation in S. latifolia. Through chromatin immunoprecipitation we interrogated six genes from X and Y alleles. Several histone PTMS linked to DNA methylation and transcriptional repression (H3K27me3, H3K23me, H3K9me2 and H3K9me3) and to transcriptional activation (H3K4me3 and H4K5, 8, 12, 16ac) were used. DNA enrichment (Immunoprecipitated DNA/input DNA) was analyzed and showed three main results: (i) promoters of the Y allele are associated with heterochromatin marks, (ii) promoters of the X allele in males are associated with activation of transcription marks and finally, (iii) promoters of X alleles in females are associated with active and repressive marks. Our finding indicates a transcription activation of X allele and transcription repression of Y allele in males. In females we found a possible differential regulation (up X1, down X2) of each female X allele. These results agree with the mammal-like epigenetic dosage compensation regulation.
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Affiliation(s)
- José Luis Rodríguez Lorenzo
- The Czech Academy of Sciences, Institute of Biophysics v.v.i., Department of Plant Developmental Genetics, Královopolská 135, 612 65, Brno, Czech Republic.
| | - Marcel Hubinský
- The Czech Academy of Sciences, Institute of Biophysics v.v.i., Department of Plant Developmental Genetics, Královopolská 135, 612 65, Brno, Czech Republic
| | - Boris Vyskot
- The Czech Academy of Sciences, Institute of Biophysics v.v.i., Department of Plant Developmental Genetics, Královopolská 135, 612 65, Brno, Czech Republic
| | - Roman Hobza
- The Czech Academy of Sciences, Institute of Biophysics v.v.i., Department of Plant Developmental Genetics, Královopolská 135, 612 65, Brno, Czech Republic
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Orozco-Arias S, Isaza G, Guyot R. Retrotransposons in Plant Genomes: Structure, Identification, and Classification through Bioinformatics and Machine Learning. Int J Mol Sci 2019; 20:E3837. [PMID: 31390781 PMCID: PMC6696364 DOI: 10.3390/ijms20153837] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 07/31/2019] [Accepted: 08/02/2019] [Indexed: 01/26/2023] Open
Abstract
Transposable elements (TEs) are genomic units able to move within the genome of virtually all organisms. Due to their natural repetitive numbers and their high structural diversity, the identification and classification of TEs remain a challenge in sequenced genomes. Although TEs were initially regarded as "junk DNA", it has been demonstrated that they play key roles in chromosome structures, gene expression, and regulation, as well as adaptation and evolution. A highly reliable annotation of these elements is, therefore, crucial to better understand genome functions and their evolution. To date, much bioinformatics software has been developed to address TE detection and classification processes, but many problematic aspects remain, such as the reliability, precision, and speed of the analyses. Machine learning and deep learning are algorithms that can make automatic predictions and decisions in a wide variety of scientific applications. They have been tested in bioinformatics and, more specifically for TEs, classification with encouraging results. In this review, we will discuss important aspects of TEs, such as their structure, importance in the evolution and architecture of the host, and their current classifications and nomenclatures. We will also address current methods and their limitations in identifying and classifying TEs.
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Affiliation(s)
- Simon Orozco-Arias
- Department of Computer Science, Universidad Autónoma de Manizales, Manizales 170001, Colombia
- Department of Systems and Informatics, Universidad de Caldas, Manizales 170001, Colombia
| | - Gustavo Isaza
- Department of Systems and Informatics, Universidad de Caldas, Manizales 170001, Colombia
| | - Romain Guyot
- Department of Electronics and Automatization, Universidad Autónoma de Manizales, Manizales 170001, Colombia.
- Institut de Recherche pour le Développement, CIRAD, University Montpellier, 34000 Montpellier, France.
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7
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Bačovský V, Houben A, Kumke K, Hobza R. The distribution of epigenetic histone marks differs between the X and Y chromosomes in Silene latifolia. PLANTA 2019; 250:487-494. [PMID: 31069521 DOI: 10.1007/s00425-019-03182-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 05/03/2019] [Indexed: 05/18/2023]
Abstract
Contrasting patterns of histone modifications between the X and Y chromosome in Silene latifolia show euchromatic histone mark depletion on the Y chromosome and indicate hyperactivation of one X chromosome in females. Silene latifolia (white campion) is a dioecious plant with heteromorphic sex chromosomes (24, XX in females and 24, XY in males), and a genetically degenerated Y chromosome that is 1.4 times larger than the X chromosome. Although the two sex chromosomes differ in their DNA content, information about epigenetic histone marks and evidence of their function are scarce. We performed immunolabeling experiments using antibodies specific for active and suppressive histone modifications as well as pericentromere-specific histone modifications. We show that the Y chromosome is partially depleted of histone modifications important for transcriptionally active chromatin, and carries these marks only in the pseudo-autosomal region, but that it is not enriched for suppressive and pericentromere histone marks. We also show that two of the active marks are specifically enriched in one of the X chromosomes in females and in the X chromosome in males. Our data support recent findings that genetic imprinting mediates dosage compensation of sex chromosomes in S. latifolia.
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Affiliation(s)
- Václav Bačovský
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 612 65, Brno, Czech Republic.
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, Gatersleben, 06466, Germany
| | - Katrin Kumke
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, Gatersleben, 06466, Germany
| | - Roman Hobza
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 612 65, Brno, Czech Republic.
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Hobza R, Hudzieczek V, Kubat Z, Cegan R, Vyskot B, Kejnovsky E, Janousek B. Sex and the flower - developmental aspects of sex chromosome evolution. ANNALS OF BOTANY 2018; 122:1085-1101. [PMID: 30032185 PMCID: PMC6324748 DOI: 10.1093/aob/mcy130] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 07/13/2018] [Indexed: 05/07/2023]
Abstract
Background The evolution of dioecious plants is occasionally accompanied by the establishment of sex chromosomes: both XY and ZW systems have been found in plants. Structural studies of sex chromosomes are now being followed up by functional studies that are gradually shedding light on the specific genetic and epigenetic processes that shape the development of separate sexes in plants. Scope This review describes sex determination diversity in plants and the genetic background of dioecy, summarizes recent progress in the investigation of both classical and emerging model dioecious plants and discusses novel findings. The advantages of interspecies hybrids in studies focused on sex determination and the role of epigenetic processes in sexual development are also overviewed. Conclusions We integrate the genic, genomic and epigenetic levels of sex determination and stress the impact of sex chromosome evolution on structural and functional aspects of plant sexual development. We also discuss the impact of dioecy and sex chromosomes on genome structure and expression.
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Affiliation(s)
- Roman Hobza
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska, Brno, Czech Republic
| | - Vojtech Hudzieczek
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska, Brno, Czech Republic
| | - Zdenek Kubat
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska, Brno, Czech Republic
| | - Radim Cegan
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska, Brno, Czech Republic
| | - Boris Vyskot
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska, Brno, Czech Republic
| | - Eduard Kejnovsky
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska, Brno, Czech Republic
| | - Bohuslav Janousek
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska, Brno, Czech Republic
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9
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Puterova J, Kubat Z, Kejnovsky E, Jesionek W, Cizkova J, Vyskot B, Hobza R. The slowdown of Y chromosome expansion in dioecious Silene latifolia due to DNA loss and male-specific silencing of retrotransposons. BMC Genomics 2018; 19:153. [PMID: 29458354 PMCID: PMC5819184 DOI: 10.1186/s12864-018-4547-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 02/13/2018] [Indexed: 11/10/2022] Open
Abstract
Background The rise and fall of the Y chromosome was demonstrated in animals but plants often possess the large evolutionarily young Y chromosome that is thought has expanded recently. Break-even points dividing expansion and shrinkage phase of plant Y chromosome evolution are still to be determined. To assess the size dynamics of the Y chromosome, we studied intraspecific genome size variation and genome composition of male and female individuals in a dioecious plant Silene latifolia, a well-established model for sex-chromosomes evolution. Results Our genome size data are the first to demonstrate that regardless of intraspecific genome size variation, Y chromosome has retained its size in S. latifolia. Bioinformatics study of genome composition showed that constancy of Y chromosome size was caused by Y chromosome DNA loss and the female-specific proliferation of recently active dominant retrotransposons. We show that several families of retrotransposons have contributed to genome size variation but not to Y chromosome size change. Conclusions Our results suggest that the large Y chromosome of S. latifolia has slowed down or stopped its expansion. Female-specific proliferation of retrotransposons, enlarging the genome with exception of the Y chromosome, was probably caused by silencing of highly active retrotransposons in males and represents an adaptive mechanism to suppress degenerative processes in the haploid stage. Sex specific silencing of transposons might be widespread in plants but hidden in traditional hermaphroditic model plants. Electronic supplementary material The online version of this article (10.1186/s12864-018-4547-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Janka Puterova
- Department of Plant Developmental Genetics, Institute of Biophysics, Czech Academy of Sciences, Kralovopolska 135, 612 00, Brno, Czech Republic.,Department of Information Systems, Faculty of Information Technology, Brno University of Technology, 61200, Brno, Czech Republic
| | - Zdenek Kubat
- Department of Plant Developmental Genetics, Institute of Biophysics, Czech Academy of Sciences, Kralovopolska 135, 612 00, Brno, Czech Republic.
| | - Eduard Kejnovsky
- Department of Plant Developmental Genetics, Institute of Biophysics, Czech Academy of Sciences, Kralovopolska 135, 612 00, Brno, Czech Republic
| | - Wojciech Jesionek
- Department of Plant Developmental Genetics, Institute of Biophysics, Czech Academy of Sciences, Kralovopolska 135, 612 00, Brno, Czech Republic
| | - Jana Cizkova
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany, Czech Academy of Sciences, 783 71, Olomouc - Holice, Czech Republic
| | - Boris Vyskot
- Department of Plant Developmental Genetics, Institute of Biophysics, Czech Academy of Sciences, Kralovopolska 135, 612 00, Brno, Czech Republic
| | - Roman Hobza
- Department of Plant Developmental Genetics, Institute of Biophysics, Czech Academy of Sciences, Kralovopolska 135, 612 00, Brno, Czech Republic. .,Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany, Czech Academy of Sciences, 783 71, Olomouc - Holice, Czech Republic.
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10
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Bačovský V, Hobza R, Vyskot B. Technical Review: Cytogenetic Tools for Studying Mitotic Chromosomes. Methods Mol Biol 2018; 1675:509-535. [PMID: 29052211 DOI: 10.1007/978-1-4939-7318-7_30] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Significant advances in chromosome preparation and other techniques have greatly increased the potential of plant cytogenetics in recent years. Increase in longitudinal resolution using DNA extended fibers as well as new developments in imaging and signal amplification technologies have enhanced the ability of FISH to detect small gene targets. The combination of fluorescence in situ hybridization with immunocytochemistry allows the investigation of cell events, chromosomal rearrangements and chromatin features typical for plant nuclei. Chromosome manipulation techniques using microdissection and flow sorting have accelerated the analysis of complex plant genomes. Together, the different cytogenetic approaches are invaluable for the unravelling of detailed structures of plant chromosomes, which are of utmost importance for the study of genome properties, DNA replication and gene regulation. In this technical review, different cytogenetic approaches are discussed for the analysis of plant chromosomes, with a focus on mitotic chromosomes.
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Affiliation(s)
- Václaclav Bačovský
- Department of Plant Developmental Genetics, Institute of Biophysics, Czech Academy of Sciences, Brno, Czech Republic
| | - Roman Hobza
- Department of Plant Developmental Genetics, Institute of Biophysics, Czech Academy of Sciences, Brno, Czech Republic
| | - Boris Vyskot
- Department of Plant Developmental Genetics, Institute of Biophysics, Czech Academy of Sciences, Brno, Czech Republic.
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Impact of Repetitive Elements on the Y Chromosome Formation in Plants. Genes (Basel) 2017; 8:genes8110302. [PMID: 29104214 PMCID: PMC5704215 DOI: 10.3390/genes8110302] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 10/19/2017] [Accepted: 10/26/2017] [Indexed: 12/21/2022] Open
Abstract
In contrast to animals, separate sexes and sex chromosomes in plants are very rare. Although the evolution of sex chromosomes has been the subject of numerous studies, the impact of repetitive sequences on sex chromosome architecture is not fully understood. New genomic approaches shed light on the role of satellites and transposable elements in the process of Y chromosome evolution. We discuss the impact of repetitive sequences on the structure and dynamics of sex chromosomes with specific focus on Rumex acetosa and Silene latifolia. Recent papers showed that both the expansion and shrinkage of the Y chromosome is influenced by sex-specific regulation of repetitive DNA spread. We present a view that the dynamics of Y chromosome formation is an interplay of genetic and epigenetic processes.
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Sousa A, Bellot S, Fuchs J, Houben A, Renner SS. Analysis of transposable elements and organellar DNA in male and female genomes of a species with a huge Y chromosome reveals distinct Y centromeres. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 88:387-396. [PMID: 27354172 DOI: 10.1111/tpj.13254] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 06/10/2016] [Accepted: 06/23/2016] [Indexed: 05/03/2023]
Abstract
Few angiosperms have distinct Y chromosomes. Among those that do are Silene latifolia (Caryophyllaceae), Rumex acetosa (Polygonaceae) and Coccinia grandis (Cucurbitaceae), the latter having a male/female difference of 10% of the total genome (female individuals have a 0.85 pg genome, male individuals 0.94 pg), due to a Y chromosome that arose about 3 million years ago. We compared the sequence composition of male and female C. grandis plants and determined the chromosomal distribution of repetitive and organellar DNA with probes developed from 21 types of repetitive DNA, including 16 mobile elements. The size of the Y chromosome is largely due to the accumulation of certain repeats, such as members of the Ty1/copia and Ty3/gypsy superfamilies, an unclassified element and a satellite, but also plastome- and chondriome-derived sequences. An abundant tandem repeat with a unit size of 144 bp stains the centromeres of the X chromosome and the autosomes, but is absent from the Y centromere. Immunostaining with pericentromere-specific markers for anti-histone H3Ser10ph and H2AThr120ph revealed a Y-specific extension of these histone marks. That the Y centromere has a different make-up from all the remaining centromeres raises questions about its spindle attachment, and suggests that centromeric or pericentromeric chromatin might be involved in the suppression of recombination.
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Affiliation(s)
- Aretuza Sousa
- Department of Biology, University of Munich (LMU), Munich, 80638, Germany
| | - Sidonie Bellot
- Plant Biodiversity Research, Technical University of Munich (TUM), Freising, 85354, Germany
| | - Jörg Fuchs
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Stadt Seeland, 06466, Germany
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Stadt Seeland, 06466, Germany
| | - Susanne S Renner
- Department of Biology, University of Munich (LMU), Munich, 80638, Germany
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Vrána J, Cápal P, Šimková H, Karafiátová M, Čížková J, Doležel J. Flow Analysis and Sorting of Plant Chromosomes. CURRENT PROTOCOLS IN CYTOMETRY 2016; 78:5.3.1-5.3.43. [PMID: 27723090 DOI: 10.1002/cpcy.9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Analysis and sorting of plant chromosomes (plant flow cytogenetics) is a special application of flow cytometry in plant genomics and its success depends critically on sample quality. This unit describes the methodology in a stepwise manner, starting with the induction of cell cycle synchrony and accumulation of dividing cells in mitotic metaphase, and continues with the preparation of suspensions of intact mitotic chromosomes, flow analysis and sorting of chromosomes, and finally processing of the sorted chromosomes. Each step of the protocol is described in detail as some procedures have not been used widely. Supporting histograms are presented as well as hints on dealing with plant material; the utility of sorted chromosomes for plant genomics is also discussed. © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
- Jan Vrána
- Institute of Experimental Botany, Center of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Petr Cápal
- Institute of Experimental Botany, Center of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Hana Šimková
- Institute of Experimental Botany, Center of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Miroslava Karafiátová
- Institute of Experimental Botany, Center of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Jana Čížková
- Institute of Experimental Botany, Center of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Jaroslav Doležel
- Institute of Experimental Botany, Center of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
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14
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Abstract
Structurally and functionally diverged sex chromosomes have evolved in many animals as well as in some plants. Sex chromosomes represent a specific genomic region(s) with locally suppressed recombination. As a consequence, repetitive sequences involving transposable elements, tandem repeats (satellites and microsatellites), and organellar DNA accumulate on the Y (W) chromosomes. In this paper, we review the main types of repetitive elements, their gathering on the Y chromosome, and discuss new findings showing that not only accumulation of various repeats in non-recombining regions but also opposite processes form Y chromosome. The aim of this review is also to discuss the mechanisms of repetitive DNA spread involving (retro) transposition, DNA polymerase slippage or unequal crossing-over, as well as modes of repeat removal by ectopic recombination. The intensity of these processes differs in non-recombining region(s) of sex chromosomes when compared to the recombining parts of genome. We also speculate about the relationship between heterochromatinization and the formation of heteromorphic sex chromosomes.
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Li SF, Zhang GJ, Zhang XJ, Yuan JH, Deng CL, Gu LF, Gao WJ. DPTEdb, an integrative database of transposable elements in dioecious plants. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2016; 2016:baw078. [PMID: 27173524 PMCID: PMC4865326 DOI: 10.1093/database/baw078] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Accepted: 04/22/2016] [Indexed: 02/02/2023]
Abstract
Dioecious plants usually harbor ‘young’ sex chromosomes, providing an opportunity to study the early stages of sex chromosome evolution. Transposable elements (TEs) are mobile DNA elements frequently found in plants and are suggested to play important roles in plant sex chromosome evolution. The genomes of several dioecious plants have been sequenced, offering an opportunity to annotate and mine the TE data. However, comprehensive and unified annotation of TEs in these dioecious plants is still lacking. In this study, we constructed a dioecious plant transposable element database (DPTEdb). DPTEdb is a specific, comprehensive and unified relational database and web interface. We used a combination of de novo, structure-based and homology-based approaches to identify TEs from the genome assemblies of previously published data, as well as our own. The database currently integrates eight dioecious plant species and a total of 31 340 TEs along with classification information. DPTEdb provides user-friendly web interfaces to browse, search and download the TE sequences in the database. Users can also use tools, including BLAST, GetORF, HMMER, Cut sequence and JBrowse, to analyze TE data. Given the role of TEs in plant sex chromosome evolution, the database will contribute to the investigation of TEs in structural, functional and evolutionary dynamics of the genome of dioecious plants. In addition, the database will supplement the research of sex diversification and sex chromosome evolution of dioecious plants. Database URL: http://genedenovoweb.ticp.net:81/DPTEdb/index.php
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Affiliation(s)
- Shu-Fen Li
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Guo-Jun Zhang
- School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang 453003, China
| | - Xue-Jin Zhang
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Jin-Hong Yuan
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Chuan-Liang Deng
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Lian-Feng Gu
- Basic Forestry and Proteomics Center, Haixia Institute of Science and Technology (HIST), Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Wu-Jun Gao
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
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Li SF, Zhang GJ, Yuan JH, Deng CL, Gao WJ. Repetitive sequences and epigenetic modification: inseparable partners play important roles in the evolution of plant sex chromosomes. PLANTA 2016; 243:1083-95. [PMID: 26919983 DOI: 10.1007/s00425-016-2485-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Accepted: 02/07/2016] [Indexed: 05/03/2023]
Abstract
The present review discusses the roles of repetitive sequences played in plant sex chromosome evolution, and highlights epigenetic modification as potential mechanism of repetitive sequences involved in sex chromosome evolution. Sex determination in plants is mostly based on sex chromosomes. Classic theory proposes that sex chromosomes evolve from a specific pair of autosomes with emergence of a sex-determining gene(s). Subsequently, the newly formed sex chromosomes stop recombination in a small region around the sex-determining locus, and over time, the non-recombining region expands to almost all parts of the sex chromosomes. Accumulation of repetitive sequences, mostly transposable elements and tandem repeats, is a conspicuous feature of the non-recombining region of the Y chromosome, even in primitive one. Repetitive sequences may play multiple roles in sex chromosome evolution, such as triggering heterochromatization and causing recombination suppression, leading to structural and morphological differentiation of sex chromosomes, and promoting Y chromosome degeneration and X chromosome dosage compensation. In this article, we review the current status of this field, and based on preliminary evidence, we posit that repetitive sequences are involved in sex chromosome evolution probably via epigenetic modification, such as DNA and histone methylation, with small interfering RNAs as the mediator.
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Affiliation(s)
- Shu-Fen Li
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Guo-Jun Zhang
- School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, 453003, China
| | - Jin-Hong Yuan
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Chuan-Liang Deng
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Wu-Jun Gao
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China.
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17
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Abstract
Nuclear genomes of many important plant species are tremendously complicated to map and sequence. The ability to isolate single chromosomes, which represent small units of nuclear genome, is priceless in many areas of plant research including cytogenetics, genomics, and proteomics. Flow cytometry is the only technique which can provide large quantities of pure chromosome fractions suitable for downstream applications including physical mapping, preparation of chromosome-specific BAC libraries, sequencing, and optical mapping. Here, we describe step-by-step procedure of preparation of liquid suspensions of intact mitotic metaphase chromosomes and their flow cytometric analysis and sorting.
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Affiliation(s)
- Jan Vrána
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Šlechtitelů 31, 783 71, Olomouc, Czech Republic.
| | - Petr Cápal
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Šlechtitelů 31, 783 71, Olomouc, Czech Republic
| | - Jarmila Číhalíková
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Šlechtitelů 31, 783 71, Olomouc, Czech Republic
| | - Marie Kubaláková
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Šlechtitelů 31, 783 71, Olomouc, Czech Republic
| | - Jaroslav Doležel
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Šlechtitelů 31, 783 71, Olomouc, Czech Republic
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18
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Vyskot B, Hobza R. The genomics of plant sex chromosomes. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 236:126-35. [PMID: 26025526 DOI: 10.1016/j.plantsci.2015.03.019] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2014] [Revised: 02/27/2015] [Accepted: 03/26/2015] [Indexed: 05/18/2023]
Abstract
Around six percent of flowering species are dioecious, with separate female and male individuals. Sex determination is mostly based on genetics, but morphologically distinct sex chromosomes have only evolved in a few species. Of these, heteromorphic sex chromosomes have been most clearly described in the two model species - Silene latifolia and Rumex acetosa. In both species, the sex chromosomes are the largest chromosomes in the genome. They are hence easily distinguished, can be physically separated and analyzed. This review discusses some recent experimental data on selected model dioecious species, with a focus on S. latifolia. Phylogenetic analyses show that dioecy in plants originated independently and repeatedly even within individual genera. A cogent question is whether there is genetic degeneration of the non-recombining part of the plant Y chromosome, as in mammals, and, if so, whether reduced levels of gene expression in the heterogametic sex are equalized by dosage compensation. Current data provide no clear conclusion. We speculate that although some transcriptome analyses indicate the first signs of degeneration, especially in S. latifolia, the evolutionary processes forming plant sex chromosomes in plants may, to some extent, differ from those in animals.
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Affiliation(s)
- Boris Vyskot
- Department of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, 61265 Brno, Czech Republic.
| | - Roman Hobza
- Department of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, 61265 Brno, Czech Republic
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