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Félix AP, Amorim ICD, Milani D, Cabral-de-Mello DC, Moura RC. Differential amplification and contraction of satellite DNAs in the distinct lineages of the beetle Euchroma gigantea. Gene 2024; 927:148723. [PMID: 38914242 DOI: 10.1016/j.gene.2024.148723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 06/12/2024] [Accepted: 06/20/2024] [Indexed: 06/26/2024]
Abstract
Satellite DNA (satDNA) consists of tandem repeat sequences that typically evolve rapidly through evolutionary mechanisms, including unequal crossover, transposition events, and others. The evolutionary history of Euchroma gigantea is marked by complex chromosomal evolution between lineages, making this species an interesting model for understanding satDNA evolution at intraspecies level. Therefore, our aim was to comprehend the potential contribution of satDNAs to the greater chromosomal differentiation of evolutionary lineages in E. gigantea by investigating the differential patterns of amplification and contraction of the repeats. To achieve this, we employed de novo identification of satDNA using RepeatExplorer and TAREAN, allowing the satellitome characterization between lineages. A total of 26 satDNA families were identified, ranging from 18 to 1101 nucleotides in length, with most families being shared between individuals/lineages, as predicted by the library hypothesis, except for the satDNA EgiSat21-168 that was absent for Northeast Lineage. The total satDNA content of the individuals was less than 11.2%, and it appeared to increase in two directions following the chromosomal evolution model. Thirteen satDNAs exhibited different patterns of amplification, and nine ones were contracted among individuals. Additionally, most repeats showed a divergence of about 10% for these satDNAs, indicating satellitome differentiation for each lineage/individual. This scenario suggests that the expansion of the satellitome occurred differentially among individuals/lineages of E. gigantea, with the contribution of various DNA turnover mechanisms after geographical isolation, and that they could be involved with karyotype evolution.
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Affiliation(s)
- Aline Priscila Félix
- Laboratório de Biodiversidade e Genética de Insetos, Instituto de Ciências Biológicas, Universidade de Pernambuco, Recife, Pernambuco, Brazil; Pós-Graduação em Genética e Biologia Molecular, Centro de Ciências Biológicas, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
| | - Igor Costa de Amorim
- Laboratório de Biodiversidade e Genética de Insetos, Instituto de Ciências Biológicas, Universidade de Pernambuco, Recife, Pernambuco, Brazil; Departamento de Tecnologia e Ciências Sociais, Universidade do Estado da Bahia, Juazeiro, Bahia, Brazil
| | - Diogo Milani
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, São Paulo, Brazil
| | - Diogo Cavalcanti Cabral-de-Mello
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, São Paulo, Brazil
| | - Rita Cássia Moura
- Laboratório de Biodiversidade e Genética de Insetos, Instituto de Ciências Biológicas, Universidade de Pernambuco, Recife, Pernambuco, Brazil.
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Yurkevich OY, Samatadze TE, Zoshchuk SA, Amosova AV, Muravenko OV. Species of the Sections Hedysarum and Multicaulia of the Genus Hedysarum (Fabaceae): Taxonomy, Distribution, Chromosomes, Genomes, and Phylogeny. Int J Mol Sci 2024; 25:8489. [PMID: 39126057 PMCID: PMC11312482 DOI: 10.3390/ijms25158489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2024] [Revised: 07/28/2024] [Accepted: 08/01/2024] [Indexed: 08/12/2024] Open
Abstract
The genus Hedysarum L. (Fabaceae) includes about 200 species of annual and perennial herbs distributed in Asia, Europe, North Africa, and North America. Many species of this genus are valuable medicinal, melliferous, and forage resources. In this review, we consider the taxonomic history of the genus Hedysarum, the chromosomal organization of the species from the sections Hedysarum and Multicaulia, as well as phylogenetic relationships between these sections. According to morphological, genetic, and phylogenetic data, the genus Hedysarum is divided into three main sections: Hedysarum (= syn. Gamotion), Multicaulia, and Stracheya. In species of this genus, two basic chromosome numbers, x = 7 (section Hedysarum) and x = 8 (sections Multicaulia and Stracheya), were determined. The systematic positions of some species within the sections are still uncertain due to their morphological similarities. The patterns of distribution of molecular chromosomal markers (45S rDNA, 5S rDNA, and different satellite DNAs) in karyotypes of various Hedysarum species made it possible to determine their ploidy status and also specify genomic relationships within the sections Hedysarum and Multicaulia. Recent molecular phylogenetic studies clarified significantly the taxonomy and evolutionary development of the genus Hedysarum.
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Affiliation(s)
| | | | | | | | - Olga V. Muravenko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov St, 119991 Moscow, Russia
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Liu L, Zhan J, Yan J. Engineering the future cereal crops with big biological data: toward intelligence-driven breeding by design. J Genet Genomics 2024; 51:781-789. [PMID: 38531485 DOI: 10.1016/j.jgg.2024.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 03/17/2024] [Accepted: 03/17/2024] [Indexed: 03/28/2024]
Abstract
How to feed 10 billion human populations is one of the challenges that need to be addressed in the following decades, especially under an unpredicted climate change. Crop breeding, initiating from the phenotype-based selection by local farmers and developing into current biotechnology-based breeding, has played a critical role in securing the global food supply. However, regarding the changing environment and ever-increasing human population, can we breed outstanding crop varieties fast enough to achieve high productivity, good quality, and widespread adaptability? This review outlines the recent achievements in understanding cereal crop breeding, including the current knowledge about crop agronomic traits, newly developed techniques, crop big biological data research, and the possibility of integrating them for intelligence-driven breeding by design, which ushers in a new era of crop breeding practice and shapes the novel architecture of future crops. This review focuses on the major cereal crops, including rice, maize, and wheat, to explain how intelligence-driven breeding by design is becoming a reality.
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Affiliation(s)
- Lei Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
| | - Jimin Zhan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China
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Dos Santos GE, Crepaldi C, da Silva MJ, Parise-Maltempi PP. Revealing the Satellite DNA Content in Ancistrus sp. (Siluriformes: Loricariidae) by Genomic and Bioinformatic Analysis. Cytogenet Genome Res 2024; 164:52-59. [PMID: 38631304 DOI: 10.1159/000538926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 04/12/2024] [Indexed: 04/19/2024] Open
Abstract
INTRODUCTION Eukaryotic genomes are composed of simple, repetitive sequences, including satellite DNAs (satDNA), which are noncoding sequences arranged in tandem arrays. These sequences play a crucial role in genomic functions and innovations, influencing processes such as the maintenance of nuclear material, the formation of heterochromatin and the differentiation of sex chromosomes. In this genomic era, advances in next-generation sequencing and bioinformatics tools have facilitated the exhaustive cataloging of repetitive elements in genomes, particularly in non-model species. This study focuses on the satDNA content of Ancistrus sp., a diverse species of fish from the Loricariidae family. The genus Ancistrus shows significant karyotypic evolution, with extensive variability from the ancestral diploid number. METHODS By means of bioinformatic approaches, 40 satDNA families in Ancistrus sp., constituting 5.19% of the genome were identified. Analysis of the abundance and divergence landscape revealed diverse profiles, indicating recent amplification and homogenization of these satDNA sequences. RESULTS The most abundant satellite, AnSat1-142, constitutes 2.1% of the genome, while the least abundant, AnSat40-52, represents 0.0034%. The length of the monomer repeat varies from 16 to 142 base pairs, with an average length of 61 bp. These results contribute to understanding the genomic dynamics and evolution of satDNAs in Ancistrus sp. CONCLUSION The study underscores the variability of satDNAs between fish species and provides valuable information on chromosome organization and the evolution of repetitive elements in non-model organisms.
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Affiliation(s)
- Gabriel Esbrisse Dos Santos
- General and Applied Biology Department, Bioscience Institute/São Paulo State University (UNESP), Rio Claro, Brazil
| | - Carolina Crepaldi
- General and Applied Biology Department, Bioscience Institute/São Paulo State University (UNESP), Rio Claro, Brazil
| | - Marcelo João da Silva
- General and Applied Biology Department, Bioscience Institute/São Paulo State University (UNESP), Rio Claro, Brazil
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de Oliveira AM, Souza GM, Toma GA, Dos Santos N, Dos Santos RZ, Goes CAG, Deon GA, Setti PG, Porto-Foresti F, Utsunomia R, Gunski RJ, Del Valle Garnero A, Herculano Correa de Oliveira E, Kretschmer R, Cioffi MDB. Satellite DNAs, heterochromatin, and sex chromosomes of the wattled jacana (Charadriiformes; Jacanidae): a species with highly rearranged karyotype. Genome 2024; 67:109-118. [PMID: 38316150 DOI: 10.1139/gen-2023-0082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
Charadriiformes, which comprises shorebirds and their relatives, is one of the most diverse avian orders, with over 390 species showing a wide range of karyotypes. Here, we isolated and characterized the whole collection of satellite DNAs (satDNAs) at both molecular and cytogenetic levels of one of its representative species, named the wattled jacana (Jacana jacana), a species that contains a typical ZZ/ZW sex chromosome system and a highly rearranged karyotype. In addition, we also investigate the in situ location of telomeric and microsatellite repeats. A small catalog of 11 satDNAs was identified that typically accumulated on microchromosomes and on the W chromosome. The latter also showed a significant accumulation of telomeric signals, being (GA)10 the only microsatellite with positive hybridization signals among all the 16 tested ones. These current findings contribute to our understanding of the genomic organization of repetitive DNAs in a bird species with high degree of chromosomal reorganization contrary to the majority of bird species that have stable karyotypes.
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Affiliation(s)
- Alan Moura de Oliveira
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | - Guilherme Mota Souza
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | - Gustavo Akira Toma
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | | | | | | | - Geize Aparecida Deon
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | - Princia Grejo Setti
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | | | | | | | | | | | - Rafael Kretschmer
- Departamento de Ecologia, Zoologia e Genética, Instituto de Biologia, Universidade Federal de Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
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Sales-Oliveira VC, Dos Santos RZ, Goes CAG, Calegari RM, Garrido-Ramos MA, Altmanová M, Ezaz T, Liehr T, Porto-Foresti F, Utsunomia R, Cioffi MB. Evolution of ancient satellite DNAs in extant alligators and caimans (Crocodylia, Reptilia). BMC Biol 2024; 22:47. [PMID: 38413947 PMCID: PMC10900743 DOI: 10.1186/s12915-024-01847-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 02/15/2024] [Indexed: 02/29/2024] Open
Abstract
BACKGROUND Crocodilians are one of the oldest extant vertebrate lineages, exhibiting a combination of evolutionary success and morphological resilience that has persisted throughout the history of life on Earth. This ability to endure over such a long geological time span is of great evolutionary importance. Here, we have utilized the combination of genomic and chromosomal data to identify and compare the full catalogs of satellite DNA families (satDNAs, i.e., the satellitomes) of 5 out of the 8 extant Alligatoridae species. As crocodilian genomes reveal ancestral patterns of evolution, by employing this multispecies data collection, we can investigate and assess how satDNA families evolve over time. RESULTS Alligators and caimans displayed a small number of satDNA families, ranging from 3 to 13 satDNAs in A. sinensis and C. latirostris, respectively. Together with little variation both within and between species it highlighted long-term conservation of satDNA elements throughout evolution. Furthermore, we traced the origin of the ancestral forms of all satDNAs belonging to the common ancestor of Caimaninae and Alligatorinae. Fluorescence in situ experiments showed distinct hybridization patterns for identical orthologous satDNAs, indicating their dynamic genomic placement. CONCLUSIONS Alligators and caimans possess one of the smallest satDNA libraries ever reported, comprising only four sets of satDNAs that are shared by all species. Besides, our findings indicated limited intraspecific variation in satellite DNA, suggesting that the majority of new satellite sequences likely evolved from pre-existing ones.
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Affiliation(s)
- Vanessa C Sales-Oliveira
- Departamento de Genética E Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | | | | | | | - Manuel A Garrido-Ramos
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, 18071, Granada, Spain
| | - Marie Altmanová
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, 27721, Liběchov, Czech Republic
- Department of Ecology, Faculty of Science, Charles University, 12844, Prague, Czech Republic
| | - Tariq Ezaz
- Institute for Applied Ecology, University of Canberra, Canberra, Australia
| | - Thomas Liehr
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Jena, Germany.
| | | | | | - Marcelo B Cioffi
- Departamento de Genética E Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Jena, Germany
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Kretschmer R, Toma GA, Deon GA, dos Santos N, dos Santos RZ, Utsunomia R, Porto-Foresti F, Gunski RJ, Garnero ADV, Liehr T, de Oliveira EHC, de Freitas TRO, Cioffi MDB. Satellitome Analysis in the Southern Lapwing ( Vanellus chilensis) Genome: Implications for SatDNA Evolution in Charadriiform Birds. Genes (Basel) 2024; 15:258. [PMID: 38397247 PMCID: PMC10887557 DOI: 10.3390/genes15020258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 02/14/2024] [Accepted: 02/16/2024] [Indexed: 02/25/2024] Open
Abstract
Vanellus (Charadriidae; Charadriiformes) comprises around 20 species commonly referred to as lapwings. In this study, by integrating cytogenetic and genomic approaches, we assessed the satellite DNA (satDNA) composition of one typical species, Vanellus chilensis, with a highly conserved karyotype. We additionally underlined its role in the evolution, structure, and differentiation process of the present ZW sex chromosome system. Seven distinct satellite DNA families were identified within its genome, accumulating on the centromeres, microchromosomes, and the W chromosome. However, these identified satellite DNA families were not found in two other Charadriiformes members, namely Jacana jacana and Calidris canutus. The hybridization of microsatellite sequences revealed the presence of a few repetitive sequences in V. chilensis, with only two out of sixteen displaying positive hybridization signals. Overall, our results contribute to understanding the genomic organization and satDNA evolution in Charadriiform birds.
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Affiliation(s)
- Rafael Kretschmer
- Departamento de Ecologia, Zoologia e Genética, Universidade Federal de Pelotas, Pelotas 96010-900, RS, Brazil;
| | - Gustavo A. Toma
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos 13565-905, SP, Brazil; (G.A.T.); (G.A.D.); (M.d.B.C.)
| | - Geize Aparecida Deon
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos 13565-905, SP, Brazil; (G.A.T.); (G.A.D.); (M.d.B.C.)
| | - Natalia dos Santos
- Faculdade de Ciências, Universidade Estadual Paulista, Bauru 13506-900, SP, Brazil; (N.d.S.); (R.Z.d.S.); (R.U.); (F.P.-F.)
| | - Rodrigo Zeni dos Santos
- Faculdade de Ciências, Universidade Estadual Paulista, Bauru 13506-900, SP, Brazil; (N.d.S.); (R.Z.d.S.); (R.U.); (F.P.-F.)
| | - Ricardo Utsunomia
- Faculdade de Ciências, Universidade Estadual Paulista, Bauru 13506-900, SP, Brazil; (N.d.S.); (R.Z.d.S.); (R.U.); (F.P.-F.)
| | - Fabio Porto-Foresti
- Faculdade de Ciências, Universidade Estadual Paulista, Bauru 13506-900, SP, Brazil; (N.d.S.); (R.Z.d.S.); (R.U.); (F.P.-F.)
| | - Ricardo José Gunski
- Laboratório de Diversidade Genética Animal, Universidade Federal do Pampa, São Gabriel 97300-162, RS, Brazil; (R.J.G.); (A.D.V.G.)
| | - Analía Del Valle Garnero
- Laboratório de Diversidade Genética Animal, Universidade Federal do Pampa, São Gabriel 97300-162, RS, Brazil; (R.J.G.); (A.D.V.G.)
| | - Thomas Liehr
- Institute of Human Genetics, Friedrich Schiller University, University Hospital Jena, 07747 Jena, Germany
| | - Edivaldo Herculano Corra de Oliveira
- Laboratório de Citogenô mica e Mutagênese Ambiental, Seção de Meio Ambiente, Instituto Evandro Chagas, Ananindeua 67030-000, PA, Brazil;
- Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém 66075-110, PA, Brazil
| | - Thales Renato Ochotorena de Freitas
- Laboratório de Citogenética e Evolução, Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre 91509-900, RS, Brazil;
| | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos 13565-905, SP, Brazil; (G.A.T.); (G.A.D.); (M.d.B.C.)
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Ribeiro T, Vasconcelos E, de Mendonça Filho JR, Sato S, de Argollo Marques D, Brasileiro-Vidal AC. Differential amplification of the subtelomeric satellite DNA JcSAT1 in the genus Jatropha L. (Euphorbiaceae). Genetica 2024; 152:43-49. [PMID: 38349466 DOI: 10.1007/s10709-024-00204-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 02/07/2024] [Indexed: 03/09/2024]
Abstract
Satellite DNAs (satDNAs) are highly repetitive sequences that occur in virtually all eukaryotic genomes and can undergo rapid copy number and nucleotide sequence variation among relatives. After chromosomal mapping of the satDNA JcSAT1, it was found a large accumulation at subtelomeres of Jatropha curcas (subgenus Curcas), but an absence of these monomers in J. integerrima (subgenus Jatropha). This fact suggests a dynamic scenario for this satellite repeat in Jatropha genomes. Here, we used a multitasking approach (sequence analysis, DNA blotting and chromosomal mapping) to investigate the molecular organization and chromosomal abundance and distribution of JcSAT1 in a broader group of species from the subgenus Jatropha (J. gossypiifolia, J. mollissima, J. podagrica, and J. multifida) in addition to J. curcas, with the aiming of understanding the evolution of this satDNA. Based on the analysis of BAC clone sequences of J. curcas, a large array (~ 30 kb) of 80 homogeneous monomers of JcSAT1 was identified in BAC 23J11. The monomer size was conserved (~ 358 bp) and contained a telomeric motif at the 5' end. PCR amplification coupled with a Southern blot revealed the presence of JcSAT1-like sequences in all species examined. However, a large set of genome copies was identified only in J. curcas, where a ladder-like pattern with multimers of different sizes was observed. In situ hybridization of BAC 23J11 confirmed the subtelomeric pattern for J. curcas, but showed no signals on chromosomes of species from the subgenus Jatropha. Our data indicate that JcSAT1 is a highly homogeneous satDNA that originated from a region near the telomeres and spread throughout the chromosomal subtermini, possibly due to frequent ectopic recombination between these regions. The abundance of JcSAT1 in the genome of J. curcas suggests that an amplification event occurred either at the base of the subgenus Curcas or at least in this species, although the repeat is shared by all species of the genus studied so far.
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Affiliation(s)
- Tiago Ribeiro
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco (UFPE), Recife, PE, 50670-423, Brazil.
- Current address: Integrative Plant Research Laboratory, Department of Botany and Ecology, Federal University of Mato Grosso (UFMT), Cuiabá, MT, 78060-900, Brazil.
| | - Emanuelle Vasconcelos
- Laboratory of Plant Genetics and Biotechnology, Department of Genetics, Federal University of Pernambuco (UFPE), Recife, PE, 50670-423, Brazil
| | - José Roseno de Mendonça Filho
- Laboratory of Plant Genetics and Biotechnology, Department of Genetics, Federal University of Pernambuco (UFPE), Recife, PE, 50670-423, Brazil
| | - Shusei Sato
- Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai, 980-8577, Japan
| | | | - Ana Christina Brasileiro-Vidal
- Laboratory of Plant Genetics and Biotechnology, Department of Genetics, Federal University of Pernambuco (UFPE), Recife, PE, 50670-423, Brazil.
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Gálvez-Galván A, Garrido-Ramos MA, Prieto P. Bread wheat satellitome: a complex scenario in a huge genome. PLANT MOLECULAR BIOLOGY 2024; 114:8. [PMID: 38291213 PMCID: PMC10827815 DOI: 10.1007/s11103-023-01404-x] [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: 07/26/2023] [Accepted: 11/01/2023] [Indexed: 02/01/2024]
Abstract
In bread wheat (Triticum aestivum L.), chromosome associations during meiosis are extremely regulated and initiate at the telomeres and subtelomeres, which are enriched in satellite DNA (satDNA). We present the study and characterization of the bread wheat satellitome to shed light on the molecular organization of wheat subtelomeres. Our results revealed that the 2.53% of bread wheat genome is composed by satDNA and subtelomeres are particularly enriched in such DNA sequences. Thirty-four satellite DNA (21 for the first time in this work) have been identified, analyzed and cytogenetically validated. Many of the satDNAs were specifically found at particular subtelomeric chromosome regions revealing the asymmetry in subtelomere organisation among the wheat subgenomes, which might play a role in proper homologous recognition and pairing during meiosis. An integrated physical map of the wheat satellitome was also constructed. To the best of our knowledge, our results show that the combination of both cytogenetics and genome research allowed the first comprehensive analysis of the wheat satellitome, shedding light on the complex wheat genome organization, especially on the polymorphic nature of subtelomeres and their putative implication in chromosome recognition and pairing during meiosis.
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Affiliation(s)
- Ana Gálvez-Galván
- Plant Breeding Department, Institute for Sustainable Agriculture, Agencia Estatal Consejo Superior de Investigaciones Científicas (CSIC), Avda. Menéndez Pidal, Campus Alameda del Obispo S/N, 14004, Córdoba, Spain
| | - Manuel A Garrido-Ramos
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Avda. Fuentenueva S/N, 18071, Granada, Spain.
| | - Pilar Prieto
- Plant Breeding Department, Institute for Sustainable Agriculture, Agencia Estatal Consejo Superior de Investigaciones Científicas (CSIC), Avda. Menéndez Pidal, Campus Alameda del Obispo S/N, 14004, Córdoba, Spain.
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Liu J, Lin X, Wang X, Feng L, Zhu S, Tian R, Fang J, Tao A, Fang P, Qi J, Zhang L, Huang Y, Xu J. Genomic and cytogenetic analyses reveal satellite repeat signature in allotetraploid okra (Abelmoschus esculentus). BMC PLANT BIOLOGY 2024; 24:71. [PMID: 38267860 PMCID: PMC10809672 DOI: 10.1186/s12870-024-04739-9] [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: 09/20/2023] [Accepted: 01/10/2024] [Indexed: 01/26/2024]
Abstract
BACKGROUND Satellite repeats are one of the most rapidly evolving components in eukaryotic genomes and play vital roles in genome regulation, genome evolution, and speciation. As a consequence, the composition, abundance and chromosome distribution of satellite repeats often exhibit variability across various species, genome, and even individual chromosomes. However, we know little about the satellite repeat evolution in allopolyploid genomes. RESULTS In this study, we investigated the satellite repeat signature in five okra (Abelmoschus esculentus) accessions using genomic and cytogenetic methods. In each of the five accessions, we identified eight satellite repeats, which exhibited a significant level of intraspecific conservation. Through fluorescence in situ hybridization (FISH) experiments, we observed that the satellite repeats generated multiple signals and exhibited variations in copy number across chromosomes. Intriguingly, we found that five satellite repeats were interspersed with centromeric retrotransposons, signifying their involvement in centromeric satellite repeat identity. We confirmed subgenome-biased amplification patterns of these satellite repeats through existing genome assemblies or dual-color FISH, indicating their distinct dynamic evolution in the allotetraploid okra subgenome. Moreover, we observed the presence of multiple chromosomes harboring the 35 S rDNA loci, alongside another chromosomal pair carrying the 5 S rDNA loci in okra using FISH assay. Remarkably, the intensity of 35 S rDNA hybridization signals varied among chromosomes, with the signals predominantly localized within regions of relatively weak DAPI staining, associated with GC-rich heterochromatin regions. Finally, we observed a similar localization pattern between 35 S rDNA and three satellite repeats with high GC content and confirmed their origin in the intergenic spacer region of the 35 S rDNA. CONCLUSIONS Our findings uncover a unique satellite repeat signature in the allotetraploid okra, contributing to our understanding of the composition, abundance, and chromosomal distribution of satellite repeats in allopolyploid genomes, further enriching our understanding of their evolutionary dynamics in complex allopolyploid genomes.
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Affiliation(s)
- Jiarui Liu
- Scientific Observing and Experimental Station of Southeastern kenaf & jute, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Provincial Key Laboratory of Crop Breeding by Design, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xinyi Lin
- Scientific Observing and Experimental Station of Southeastern kenaf & jute, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Provincial Key Laboratory of Crop Breeding by Design, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xiaojie Wang
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Liqing Feng
- College of Life Science, Fujian Normal University, Fuzhou, 350117, China
| | - Shixin Zhu
- Scientific Observing and Experimental Station of Southeastern kenaf & jute, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Provincial Key Laboratory of Crop Breeding by Design, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Runmeng Tian
- Scientific Observing and Experimental Station of Southeastern kenaf & jute, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Provincial Key Laboratory of Crop Breeding by Design, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jingping Fang
- College of Life Science, Fujian Normal University, Fuzhou, 350117, China
| | - Aifen Tao
- Scientific Observing and Experimental Station of Southeastern kenaf & jute, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Provincial Key Laboratory of Crop Breeding by Design, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Pingping Fang
- Scientific Observing and Experimental Station of Southeastern kenaf & jute, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Provincial Key Laboratory of Crop Breeding by Design, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jianmin Qi
- Scientific Observing and Experimental Station of Southeastern kenaf & jute, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Provincial Key Laboratory of Crop Breeding by Design, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Liwu Zhang
- Scientific Observing and Experimental Station of Southeastern kenaf & jute, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Provincial Key Laboratory of Crop Breeding by Design, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yongji Huang
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, College of Geography and Oceanography, Minjiang University, Fuzhou, 350108, China.
| | - Jiantang Xu
- Scientific Observing and Experimental Station of Southeastern kenaf & jute, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Provincial Key Laboratory of Crop Breeding by Design, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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11
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Mann L, Balasch K, Schmidt N, Heitkam T. High-fidelity (repeat) consensus sequences from short reads using combined read clustering and assembly. BMC Genomics 2024; 25:109. [PMID: 38267856 PMCID: PMC10809544 DOI: 10.1186/s12864-023-09948-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 12/28/2023] [Indexed: 01/26/2024] Open
Abstract
BACKGROUND Despite the many cheap and fast ways to generate genomic data, good and exact genome assembly is still a problem, with especially the repeats being vastly underrepresented and often misassembled. As short reads in low coverage are already sufficient to represent the repeat landscape of any given genome, many read cluster algorithms were brought forward that provide repeat identification and classification. But how can trustworthy, reliable and representative repeat consensuses be derived from unassembled genomes? RESULTS Here, we combine methods from repeat identification and genome assembly to derive these robust consensuses. We test several use cases, such as (1) consensus building from clustered short reads of non-model genomes, (2) from genome-wide amplification setups, and (3) specific repeat-centred questions, such as the linked vs. unlinked arrangement of ribosomal genes. In all our use cases, the derived consensuses are robust and representative. To evaluate overall performance, we compare our high-fidelity repeat consensuses to RepeatExplorer2-derived contigs and check, if they represent real transposable elements as found in long reads. Our results demonstrate that it is possible to generate useful, reliable and trustworthy consensuses from short reads by a combination from read cluster and genome assembly methods in an automatable way. CONCLUSION We anticipate that our workflow opens the way towards more efficient and less manual repeat characterization and annotation, benefitting all genome studies, but especially those of non-model organisms.
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Affiliation(s)
- Ludwig Mann
- Faculty of Biology, Technische Universität Dresden, D-01069, Dresden, Germany
| | - Kristin Balasch
- Faculty of Biology, Technische Universität Dresden, D-01069, Dresden, Germany
| | - Nicola Schmidt
- Faculty of Biology, Technische Universität Dresden, D-01069, Dresden, Germany
| | - Tony Heitkam
- Faculty of Biology, Technische Universität Dresden, D-01069, Dresden, Germany.
- Institute of Biology, NAWI Graz, Karl-Franzens-Universität, Graz, A-8010, Austria.
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12
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Gultyaev AP, Koster C, van Batenburg DC, Sistermans T, van Belle N, Vijfvinkel D, Roussis A. Conserved structured domains in plant non-coding RNA enod40, their evolution and recruitment of sequences from transposable elements. NAR Genom Bioinform 2023; 5:lqad091. [PMID: 37850034 PMCID: PMC10578108 DOI: 10.1093/nargab/lqad091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 07/22/2023] [Accepted: 09/22/2023] [Indexed: 10/19/2023] Open
Abstract
Plant long noncoding RNA enod40 is involved in the regulation of symbiotic associations with bacteria, in particular, in nitrogen-fixing root nodules of legumes, and with fungi in phosphate-acquiring arbuscular mycorrhizae formed by various plants. The presence of enod40 genes in plants that do not form such symbioses indicates its other roles in cell physiology. The molecular mechanisms of enod40 RNA function are poorly understood. Enod40 RNAs form several structured domains, conserved to different extents. Due to relatively low sequence similarity, identification of enod40 sequences in plant genomes is not straightforward, and many enod40 genes remain unannotated even in complete genomes. Here, we used comparative structure analysis and sequence similarity searches in order to locate enod40 genes and determine enod40 RNA structures in nitrogen-fixing clade plants and in grasses. The structures combine conserved features with considerable diversity of structural elements, including insertions of structured domain modules originating from transposable elements. Remarkably, these insertions contain sequences similar to tandem repeats and several stem-loops are homologous to microRNA precursors.
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Affiliation(s)
- Alexander P Gultyaev
- Leiden Institute of Advanced Computer Science, Leiden University, PO Box 9512, 2300 RA Leiden, The Netherlands
- Department of Viroscience, Erasmus Medical Center, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Celine Koster
- Life Science & Technology Honours College, Leiden University, PO Box 9502, 2300 RA Leiden, The Netherlands
- Amsterdam University Medical Center, Department of Human Genetics, section Ophthalmogenetics, Location AMC, Meibergdreef 9, Amsterdam, The Netherlands
| | - Diederik Cames van Batenburg
- Leiden Institute of Advanced Computer Science, Leiden University, PO Box 9512, 2300 RA Leiden, The Netherlands
- CareRate, Unit E1.165, Stationsplein 45, 3013 AK Rotterdam, The Netherlands
| | - Tom Sistermans
- Leiden Institute of Advanced Computer Science, Leiden University, PO Box 9512, 2300 RA Leiden, The Netherlands
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
| | - Niels van Belle
- Leiden Institute of Advanced Computer Science, Leiden University, PO Box 9512, 2300 RA Leiden, The Netherlands
| | - Daan Vijfvinkel
- Leiden Institute of Advanced Computer Science, Leiden University, PO Box 9512, 2300 RA Leiden, The Netherlands
| | - Andreas Roussis
- National & Kapodistrian University of Athens, Faculty of Biology, Section of Botany, Group Molecular Plant Physiology, Panepistimiopolis - Zografou - Athens, 15784, Greece
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13
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Serrano-León IM, Prieto P, Aguilar M. Telomere and subtelomere high polymorphism might contribute to the specificity of homologous recognition and pairing during meiosis in barley in the context of breeding. BMC Genomics 2023; 24:642. [PMID: 37884878 PMCID: PMC10601145 DOI: 10.1186/s12864-023-09738-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 10/12/2023] [Indexed: 10/28/2023] Open
Abstract
Barley (Hordeum vulgare) is one of the most popular cereal crops globally. Although it is a diploid species, (2n = 2x = 14) the study of its genome organization is necessary in the framework of plant breeding since barley is often used in crosses with other cereals like wheat to provide them with advantageous characters. We already have an extensive knowledge on different stages of the meiosis, the cell division to generate the gametes in species with sexual reproduction, such as the formation of the synaptonemal complex, recombination, and chromosome segregation. But meiosis really starts with the identification of homologous chromosomes and pairing initiation, and it is still unclear how chromosomes exactly choose a partner to appropriately pair for additional recombination and segregation. In this work we present an exhaustive molecular analysis of both telomeres and subtelomeres of barley chromosome arms 2H-L, 3H-L and 5H-L. As expected, the analysis of multiple features, including transposable elements, repeats, GC content, predicted CpG islands, recombination hotspots, G4 quadruplexes, genes and targeted sequence motifs for key DNA-binding proteins, revealed a high degree of variability both in telomeres and subtelomeres. The molecular basis for the specificity of homologous recognition and pairing occurring in the early chromosomal interactions at the start of meiosis in barley may be provided by these polymorphisms. A more relevant role of telomeres and most distal part of subtelomeres is suggested.
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Affiliation(s)
- I M Serrano-León
- Plant Breeding Department, Institute for Sustainable Agriculture, Agencia Estatal Consejo Superior de Investigaciones Científicas (CSIC), Avenida Menéndez Pidal S/N., Campus Alameda del Obispo, 14004, Córdoba, Spain
| | - P Prieto
- Plant Breeding Department, Institute for Sustainable Agriculture, Agencia Estatal Consejo Superior de Investigaciones Científicas (CSIC), Avenida Menéndez Pidal S/N., Campus Alameda del Obispo, 14004, Córdoba, Spain.
| | - M Aguilar
- Área de Fisiología Vegetal, Universidad de Córdoba, Campus de Rabanales, Edif. C4, 3ª Planta, Córdoba, Spain
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14
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Ferraz ME, Ribeiro T, Sader M, Nascimento T, Pedrosa-Harand A. Comparative analysis of repetitive DNA in dysploid and non-dysploid Phaseolus beans. Chromosome Res 2023; 31:30. [PMID: 37812264 DOI: 10.1007/s10577-023-09739-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/31/2023] [Accepted: 09/15/2023] [Indexed: 10/10/2023]
Abstract
Structural karyotype changes result from ectopic recombination events frequently associated with repetitive DNA. Although most Phaseolus species present relatively stable karyotypes with 2n = 22 chromosomes, the karyotypes of species of the Leptostachyus group show high rates of structural rearrangements, including a nested chromosome fusion that led to the dysploid chromosome number of the group (2n = 20). We examined the roles of repetitive landscapes in the rearrangements of species of the Leptostachyus group using genome-skimming data to characterize the repeatome in a range of Phaseolus species and compared them to species of that group (P. leptostachyus and P. macvaughii). LTR retrotransposons, especially the Ty3/gypsy lineage Chromovirus, were the most abundant elements in the genomes. Differences in the abundance of Tekay, Retand, and SIRE elements between P. macvaughii and P. leptostachyus were reflected in their total amounts of Ty3/gypsy and Ty1/copia. The satellite DNA fraction was the most divergent among the species, varying both in abundance and distribution, even between P. leptostachyus and P. macvaughii. The rapid turnover of repeats in the Leptostachyus group may be associated with the several rearrangements observed.
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Affiliation(s)
- Maria Eduarda Ferraz
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Biosciences Centre, Federal University of Pernambuco, Recife, PE, Brazil
| | - Tiago Ribeiro
- Integrative Plant Research Lab, Department of Botany and Ecology, Institute of Biosciences, Federal University of Mato Grosso, Cuiabá, MT, Brazil
| | - Mariela Sader
- Multidisciplinary Institute of Plant Biology, National Council for Scientific and Technical Research, National University of Córdoba, Córdoba, Argentina
| | - Thiago Nascimento
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Biosciences Centre, Federal University of Pernambuco, Recife, PE, Brazil
| | - Andrea Pedrosa-Harand
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Biosciences Centre, Federal University of Pernambuco, Recife, PE, Brazil.
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15
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de Assis R, Gonçalves LSA, Guyot R, Vanzela ALL. Abundance of distal repetitive DNA sequences in Capsicum L. (Solanaceae) chromosomes. Genome 2023; 66:269-280. [PMID: 37364373 DOI: 10.1139/gen-2022-0083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
Chili peppers (Solanaceae family) have great commercial value. They are commercialized in natura and used as spices and for ornamental and medicinal purposes. Although three whole genomes have been published, limited information about satellite DNA sequences, their composition, and genomic distribution has been provided. Here, we exploited the noncoding repetitive fraction, represented by satellite sequences, that tends to accumulate in blocks along chromosomes, especially near the chromosome ends of peppers. Two satellite DNA sequences were identified (CDR-1 and CDR-2), characterized and mapped in silico in three Capsicum genomes (C. annuum, C. chinense, and C. baccatum) using data from the published high-coverage sequencing and repeats finding bioinformatic tools. Localization using FISH in the chromosomes of these species and in two others (C. frutescens and C. chacoense), totaling five species, showed signals adjacent to the rDNA sites. A sequence comparison with existing Solanaceae repeats showed that CDR-1 and CDR-2 have different origins but without homology to rDNA sequences. Satellites occupied subterminal chromosomal regions, sometimes collocated with or adjacent to 35S rDNA sequences. Our results expand knowledge about the diversity of subterminal regions of Capsicum chromosomes, showing different amounts and distributions within and between karyotypes. In addition, these sequences may be useful for future phylogenetic studies.
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Affiliation(s)
- Rafael de Assis
- Laboratório de Citogenética e Diversidade Vegetal, Departamento de Biologia Geral, Centro de Ciências Biológicas, Universidade Estadual de Londrina, Londrina 86097-570, Paraná, Brazil
| | | | - Romain Guyot
- Institute de Recherche pour le Développement, CIRAD, Université de Montpellier, UMR DIADE, Montpellier, France
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16
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Guo D, Wang R, Fang J, Zhong Y, Qi X. Development of sex-linked markers for gender identification of Actinidia arguta. Sci Rep 2023; 13:12780. [PMID: 37550389 PMCID: PMC10406875 DOI: 10.1038/s41598-023-39561-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 07/27/2023] [Indexed: 08/09/2023] Open
Abstract
The fruit of the dioecious plant Actinidia arguta has become a great attraction recently. It has long been difficult to distinguish the genders of hybrid seedlings before flowering, therefore increasing the expenditures of breeding. To produce reliable molecular marker for gender identification, this research utilized whole-genome re-sequencing of 15 males and 15 females from an 8-year-old cross population to develop gender specific markers. P51 and P11 were identified as sex-linked markers after verification. Both of these markers, according to the PCR results, only amplified a single band in male samples. These two markers were tested in 97 hybrids (52 females and 45 males) and 31 wild individuals (13 females and 18 males), with an accuracy of 96.88% and 96.09%, correspondingly. This research also verified the universalities of the two markers in Actinidia chinensis samples, and it could be inferred from the PCR results that neither marker was applicable to A. chinensis samples. The BLAST results of the two markers demonstrated that the two markers were closely aligned with different parts of the Y male-specific region of A. chinensis genome, thus they were likely to be useful for the research on the mechanism of sex determination of A. arguta. The two male-linked makers, P51 and P11, have already been used in sex-identification of A. arguta seedlings.
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Affiliation(s)
- Dandan Guo
- Key Laboratory for Fruit Tree Growth, Development and Quality Control, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
| | - Ran Wang
- Key Laboratory for Fruit Tree Growth, Development and Quality Control, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
| | - Jinbao Fang
- Key Laboratory for Fruit Tree Growth, Development and Quality Control, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
| | - Yunpeng Zhong
- Key Laboratory for Fruit Tree Growth, Development and Quality Control, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China.
| | - Xiujuan Qi
- Key Laboratory for Fruit Tree Growth, Development and Quality Control, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China.
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17
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Liu ZW, Liu J, Liu F, Zhong X. Depositing centromere repeats induces heritable intragenic heterochromatin establishment and spreading in Arabidopsis. Nucleic Acids Res 2023; 51:6039-6054. [PMID: 37094065 PMCID: PMC10325890 DOI: 10.1093/nar/gkad306] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 04/10/2023] [Accepted: 04/19/2023] [Indexed: 04/26/2023] Open
Abstract
Stable transmission of non-DNA-sequence-based epigenetic information contributes to heritable phenotypic variants and thus to biological diversity. While studies on spontaneous natural epigenome variants have revealed an association of epialleles with a wide range of biological traits in both plants and animals, the function, transmission mechanism, and stability of an epiallele over generations in a locus-specific manner remain poorly investigated. Here, we invented a DNA sequence deposition strategy to generate a locus-specific epiallele by depositing CEN180 satellite repeats into a euchromatic target locus in Arabidopsis. Using CRISPR/Cas9-mediated knock-in system, we demonstrated that depositing CEN180 repeats can induce heterochromatin nucleation accompanied by DNA methylation, H3K9me2, and changes in the nucleosome occupancy at the insertion sites. Interestingly, both DNA methylation and H3K9me2 are restricted within the depositing sites and depletion of an H3K9me2 demethylase IBM1 enables the outward heterochromatin propagation into the neighboring regions, leading to inheritable target gene silencing to persist for at least five generations. Together, these results demonstrate the promise of employing a cis-engineering system for the creation of stable and site-specific epialleles and provide important insights into functional epigenome studies and locus-specific transgenerational epigenetic inheritance.
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Affiliation(s)
- Zhang-Wei Liu
- Department of Biology, Washington University in St Louis, St Louis, MO 63130, USA
- Wisconsin Institute for Discovery & Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jie Liu
- Department of Biology, Washington University in St Louis, St Louis, MO 63130, USA
- Wisconsin Institute for Discovery & Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Fengquan Liu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu 210014, China
| | - Xuehua Zhong
- Department of Biology, Washington University in St Louis, St Louis, MO 63130, USA
- Wisconsin Institute for Discovery & Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
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18
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Chen J, Wang Z, Tan K, Huang W, Shi J, Li T, Hu J, Wang K, Wang C, Xin B, Zhao H, Song W, Hufford MB, Schnable JC, Jin W, Lai J. A complete telomere-to-telomere assembly of the maize genome. Nat Genet 2023:10.1038/s41588-023-01419-6. [PMID: 37322109 DOI: 10.1038/s41588-023-01419-6] [Citation(s) in RCA: 56] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 05/05/2023] [Indexed: 06/17/2023]
Abstract
A complete telomere-to-telomere (T2T) finished genome has been the long pursuit of genomic research. Through generating deep coverage ultralong Oxford Nanopore Technology (ONT) and PacBio HiFi reads, we report here a complete genome assembly of maize with each chromosome entirely traversed in a single contig. The 2,178.6 Mb T2T Mo17 genome with a base accuracy of over 99.99% unveiled the structural features of all repetitive regions of the genome. There were several super-long simple-sequence-repeat arrays having consecutive thymine-adenine-guanine (TAG) tri-nucleotide repeats up to 235 kb. The assembly of the entire nucleolar organizer region of the 26.8 Mb array with 2,974 45S rDNA copies revealed the enormously complex patterns of rDNA duplications and transposon insertions. Additionally, complete assemblies of all ten centromeres enabled us to precisely dissect the repeat compositions of both CentC-rich and CentC-poor centromeres. The complete Mo17 genome represents a major step forward in understanding the complexity of the highly recalcitrant repetitive regions of higher plant genomes.
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Affiliation(s)
- Jian Chen
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, P. R. China
| | - Zijian Wang
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, P. R. China
| | - Kaiwen Tan
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, P. R. China
| | - Wei Huang
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, P. R. China
| | - Junpeng Shi
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, P. R. China
| | - Tong Li
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, P. R. China
| | - Jiang Hu
- Grandomics Biosciences, Wuhan, P. R. China
| | - Kai Wang
- Grandomics Biosciences, Wuhan, P. R. China
| | - Chao Wang
- Grandomics Biosciences, Wuhan, P. R. China
| | - Beibei Xin
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, P. R. China
| | - Haiming Zhao
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, P. R. China
| | - Weibin Song
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, P. R. China
| | - Matthew B Hufford
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - James C Schnable
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Weiwei Jin
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, P. R. China
| | - Jinsheng Lai
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, P. R. China.
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, P. R. China.
- Sanya Institute of China Agricultural University, Sanya, P. R. China.
- Hainan Yazhou Bay Seed Laboratory, Sanya, P. R. China.
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19
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Costa L, Marques A, Buddenhagen CE, Pedrosa-Harand A, Souza G. Investigating the diversification of holocentromeric satellite DNA Tyba in Rhynchospora (Cyperaceae). ANNALS OF BOTANY 2023; 131:813-825. [PMID: 36815646 PMCID: PMC10184444 DOI: 10.1093/aob/mcad036] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 02/21/2023] [Indexed: 05/16/2023]
Abstract
BACKGROUND AND AIMS Satellite DNAs (satDNAs) are repetitive sequences composed by tandemly arranged, often highly homogenized units called monomers. Although satDNAs are usually fast evolving, some satDNA families can be conserved across species separated by several millions of years, probably because of their functional roles in the genomes. Tyba was the first centromere-specific satDNA described for a holocentric organism, until now being characterized for only eight species of the genus Rhynchospora Vahl. (Cyperaceae). Here, we characterized Tyba across a broad sampling of the genus, analysing and comparing its evolutionary patterns with other satDNAs. METHODS We characterized the structure and sequence evolution of satDNAs across a robust dadated phylogeny based on Hybrid Target-Capture Sequencing (hyb-seq) of 70 species. We mined the repetitive fraction for Tyba-like satellites to compare its features with other satDNAs and to construct a Tyba-based phylogeny for the genus. KEY RESULTS Our results show that Tyba is present in the majority of examined species of the genus, spanning four of the five major clades and maintaining intrafamily pairwise identity of 70.9% over 31 Myr. In comparison, other satellite families presented higher intrafamily pairwise identity but are phylogenetically restricted. Furthermore, Tyba sequences could be divided into 12 variants grouped into three different clade-specific subfamilies, showing evidence of traditional models of satDNA evolution, such as the concerted evolution and library models. Besides, a Tyba-based phylogeny showed high congruence with the hyb-seq topology. Our results show structural indications of a possible relationship of Tyba with nucleosomes, given its high curvature peaks over conserved regions and overall high bendability values compared with other non-centromeric satellites. CONCLUSIONS Overall, Tyba shows a remarkable sequence conservation and phylogenetic significance across the genus Rhynchospora, which suggests that functional roles might lead to long-term stability and conservation for satDNAs in the genome.
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Affiliation(s)
- Lucas Costa
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife-PE, Brazil
| | - André Marques
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | | | - Andrea Pedrosa-Harand
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife-PE, Brazil
| | - Gustavo Souza
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife-PE, Brazil
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20
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Peona V, Kutschera VE, Blom MPK, Irestedt M, Suh A. Satellite DNA evolution in Corvoidea inferred from short and long reads. Mol Ecol 2023; 32:1288-1305. [PMID: 35488497 DOI: 10.1111/mec.16484] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 04/11/2022] [Accepted: 04/17/2022] [Indexed: 11/29/2022]
Abstract
Satellite DNA (satDNA) is a fast-evolving portion of eukaryotic genomes. The homogeneous and repetitive nature of such satDNA causes problems during the assembly of genomes, and therefore it is still difficult to study it in detail in nonmodel organisms as well as across broad evolutionary timescales. Here, we combined the use of short- and long-read data to explore the diversity and evolution of satDNA between individuals of the same species and between genera of birds spanning ~40 millions of years of bird evolution using birds-of-paradise (Paradisaeidae) and crow (Corvus) species. These avian species highlighted the presence of a GC-rich Corvoidea satellitome composed of 61 satellite families and provided a set of candidate satDNA monomers for being centromeric on the basis of length, abundance, homogeneity and transcription. Surprisingly, we found that the satDNA of crow species rapidly diverged between closely related species while the satDNA appeared more similar between birds-of-paradise species belonging to different genera.
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Affiliation(s)
- Valentina Peona
- Department of Organismal Biology - Systematic Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Verena E Kutschera
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - Mozes P K Blom
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Museum für Naturkunde, Leibniz Institut für Evolutions- und Biodiversitätsforschung, Berlin, Germany
| | - Martin Irestedt
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Alexander Suh
- Department of Organismal Biology - Systematic Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.,School of Biological Sciences-Organisms and the Environment, University of East Anglia, Norwich, UK
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21
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Venancio S, Noleto RB, Azambuja M, Gazolla CB, Santos BR, Nogaroto V, Vicari MR. Comparative cytogenetics among Boana species (Anura, Hylidae): focus on evolutionary variability of repetitive DNA. Genet Mol Biol 2023; 45:e20220203. [PMID: 36622243 PMCID: PMC9827724 DOI: 10.1590/1678-4685-gmb-2022-0203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 11/08/2022] [Indexed: 01/10/2023] Open
Abstract
Boana comprises a diverse genus of Neotropical treefrogs, currently rearranged into seven taxonomic species groups. Although cytogenetic studies have demonstrated diversity in its representatives, the chromosomal mapping of repetitive DNA sequences is still scarce. In this study, Boana albopunctata, Boana faber, and Boana prasina were subjected to in situ localization of different repetitive DNA units to evaluate trends of chromosomal evolution in this genus. Boana faber and B. prasina had 2n=24 chromosomes, while B. albopunctata has 2n=22 and an intra-individual variation related to the presence/absence of one B chromosome. The location of 45S rDNA sites was different in the analyzed karyotypes, corroborating with what was found in the distinct phylogenetic groups of Boana. We presented the first description of 5S rDNA in a Boana species, which showed markings resulting from transposition/translocation mechanisms. In situ localization of microsatellite loci proved to be a helpful marker for karyotype comparison in Boana, commonly with cis accumulation in the heterochromatin. On the other hand, genomic dispersion of microsatellites may be associated with hitchhiking effects during the spreading of transposable elements. The obtained results corroborated the independent diversification of these lineages of species from three distinct phylogenetic groups of Boana.
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Affiliation(s)
- Sebastião Venancio
- Universidade Federal do Paraná, Centro Politécnico, Departamento de
Genética, Programa de Pós-Graduação em Genética, Curitiba, PR, Brazil
| | - Rafael Bueno Noleto
- Universidade Estadual do Paraná, Departamento de Biologia, União da
Vitória, PR, Brazil
| | - Matheus Azambuja
- Universidade Federal do Paraná, Centro Politécnico, Departamento de
Genética, Programa de Pós-Graduação em Genética, Curitiba, PR, Brazil
| | - Camilla Borges Gazolla
- Universidade Federal do Paraná, Centro Politécnico, Departamento de
Genética, Programa de Pós-Graduação em Genética, Curitiba, PR, Brazil
| | - Bianca Rocha Santos
- Universidade Estadual do Paraná, Departamento de Biologia, União da
Vitória, PR, Brazil
| | - Viviane Nogaroto
- Universidade Estadual de Ponta Grossa, Departamento de Biologia
Estrutural, Molecular e Genética, Ponta Grossa, PR, Brazil
| | - Marcelo Ricardo Vicari
- Universidade Federal do Paraná, Centro Politécnico, Departamento de
Genética, Programa de Pós-Graduação em Genética, Curitiba, PR, Brazil.,Universidade Estadual de Ponta Grossa, Departamento de Biologia
Estrutural, Molecular e Genética, Ponta Grossa, PR, Brazil
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22
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Kroupin PY, Badaeva ED, Sokolova VM, Chikida NN, Belousova MK, Surzhikov SA, Nikitina EA, Kocheshkova AA, Ulyanov DS, Ermolaev AS, Khuat TML, Razumova OV, Yurkina AI, Karlov GI, Divashuk MG. Aegilops crassa Boiss. repeatome characterized using low-coverage NGS as a source of new FISH markers: Application in phylogenetic studies of the Triticeae. FRONTIERS IN PLANT SCIENCE 2022; 13:980764. [PMID: 36325551 PMCID: PMC9621091 DOI: 10.3389/fpls.2022.980764] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 08/29/2022] [Indexed: 06/13/2023]
Abstract
Aegilops crassa Boiss. is polyploid grass species that grows in the eastern part of the Fertile Crescent, Afghanistan, and Middle Asia. It consists of tetraploid (4x) and hexaploid (6x) cytotypes (2n = 4x = 28, D1D (Abdolmalaki et al., 2019) XcrXcr and 2n = 6x = 42, D1D (Abdolmalaki et al., 2019) XcrXcrD2D (Adams and Wendel, 2005), respectively) that are similar morphologically. Although many Aegilops species were used in wheat breeding, the genetic potential of Ae. crassa has not yet been exploited due to its uncertain origin and significant genome modifications. Tetraploid Ae. crassa is thought to be the oldest polyploid Aegilops species, the subgenomes of which still retain some features of its ancient diploid progenitors. The D1 and D2 subgenomes of Ae. crassa were contributed by Aegilops tauschii (2n = 2x = 14, DD), while the Xcr subgenome donor is still unknown. Owing to its ancient origin, Ae. crassa can serve as model for studying genome evolution. Despite this, Ae. crassa is poorly studied genetically and no genome sequences were available for this species. We performed low-coverage genome sequencing of 4x and 6x cytotypes of Ae. crassa, and four Ae. tauschii accessions belonging to different subspecies; diploid wheatgrass Thinopyrum bessarabicum (Jb genome), which is phylogenetically close to D (sub)genome species, was taken as an outgroup. Subsequent data analysis using the pipeline RepeatExplorer2 allowed us to characterize the repeatomes of these species and identify several satellite sequences. Some of these sequences are novel, while others are found to be homologous to already known satellite sequences of Triticeae species. The copy number of satellite repeats in genomes of different species and their subgenome (D1 or Xcr) affinity in Ae. crassa were assessed by means of comparative bioinformatic analysis combined with quantitative PCR (qPCR). Fluorescence in situ hybridization (FISH) was performed to map newly identified satellite repeats on chromosomes of common wheat, Triticum aestivum, 4x and 6x Ae. crassa, Ae. tauschii, and Th. bessarabicum. The new FISH markers can be used in phylogenetic analyses of the Triticeae for chromosome identification and the assessment of their subgenome affinities and for evaluation of genome/chromosome constitution of wide hybrids or polyploid species.
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Affiliation(s)
- Pavel Yu. Kroupin
- All-Russia Research Institute of Agricultural Biotechnology, Kurchatov Genomics Centre – ARRIAB, Moscow, Russia
| | - Ekaterina D. Badaeva
- N.I.Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Victoria M. Sokolova
- All-Russia Research Institute of Agricultural Biotechnology, Kurchatov Genomics Centre – ARRIAB, Moscow, Russia
| | - Nadezhda N. Chikida
- All-Russian Institute of Plant Genetic Resources (VIR), Department of Wheat Genetic Resources, St. Petersburg, Russia
| | - Maria Kh. Belousova
- All-Russian Institute of Plant Genetic Resources (VIR), Department of Wheat Genetic Resources, St. Petersburg, Russia
| | - Sergei A. Surzhikov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Ekaterina A. Nikitina
- All-Russia Research Institute of Agricultural Biotechnology, Kurchatov Genomics Centre – ARRIAB, Moscow, Russia
| | - Alina A. Kocheshkova
- All-Russia Research Institute of Agricultural Biotechnology, Kurchatov Genomics Centre – ARRIAB, Moscow, Russia
| | - Daniil S. Ulyanov
- All-Russia Research Institute of Agricultural Biotechnology, Kurchatov Genomics Centre – ARRIAB, Moscow, Russia
| | - Aleksey S. Ermolaev
- All-Russia Research Institute of Agricultural Biotechnology, Kurchatov Genomics Centre – ARRIAB, Moscow, Russia
| | - Thi Mai Luong Khuat
- Agricultural Genetics Institute, Department of Molecular Biology, Hanoi, Vietnam
| | - Olga V. Razumova
- All-Russia Research Institute of Agricultural Biotechnology, Kurchatov Genomics Centre – ARRIAB, Moscow, Russia
| | - Anna I. Yurkina
- All-Russia Research Institute of Agricultural Biotechnology, Kurchatov Genomics Centre – ARRIAB, Moscow, Russia
| | - Gennady I. Karlov
- All-Russia Research Institute of Agricultural Biotechnology, Kurchatov Genomics Centre – ARRIAB, Moscow, Russia
| | - Mikhail G. Divashuk
- All-Russia Research Institute of Agricultural Biotechnology, Kurchatov Genomics Centre – ARRIAB, Moscow, Russia
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23
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Chumová Z, Belyayev A, Mandáková T, Zeisek V, Hodková E, Šemberová K, Euston-Brown D, Trávníček P. The relationship between transposable elements and ecological niches in the Greater Cape Floristic Region: A study on the genus Pteronia (Asteraceae). FRONTIERS IN PLANT SCIENCE 2022; 13:982852. [PMID: 36247607 PMCID: PMC9559566 DOI: 10.3389/fpls.2022.982852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 09/02/2022] [Indexed: 06/16/2023]
Abstract
Non-coding repetitive DNA (repeatome) is an active part of the nuclear genome, involved in its structure, evolution and function. It is dominated by transposable elements (TEs) and satellite DNA and is prone to the most rapid changes over time. The TEs activity presumably causes the global genome reorganization and may play an adaptive or regulatory role in response to environmental challenges. This assumption is applied here for the first time to plants from the Cape Floristic hotspot to determine whether changes in repetitive DNA are related to responses to a harsh, but extremely species-rich environment. The genus Pteronia (Asteraceae) serves as a suitable model group because it shows considerable variation in genome size at the diploid level and has high and nearly equal levels of endemism in the two main Cape biomes, Fynbos and Succulent Karoo. First, we constructed a phylogeny based on multiple low-copy genes that served as a phylogenetic framework for detecting quantitative and qualitative changes in the repeatome. Second, we performed a comparative analysis of the environments of two groups of Pteronia differing in their TEs bursts. Our results suggest that the environmental transition from the Succulent Karoo to the Fynbos is accompanied by TEs burst, which is likely also driving phylogenetic divergence. We thus hypothesize that analysis of rapidly evolving repeatome could serve as an important proxy for determining the molecular basis of lineage divergence in rapidly radiating groups.
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Affiliation(s)
- Zuzana Chumová
- Institute of Botany of the Czech Academy of Sciences, Průhonice, Czechia
- Department of Botany, Faculty of Science, Charles University, Prague, Czechia
| | - Alexander Belyayev
- Institute of Botany of the Czech Academy of Sciences, Průhonice, Czechia
| | - Terezie Mandáková
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czechia
- Faculty of Science, Masaryk University, Brno, Czechia
| | - Vojtěch Zeisek
- Institute of Botany of the Czech Academy of Sciences, Průhonice, Czechia
| | - Eva Hodková
- Institute of Botany of the Czech Academy of Sciences, Průhonice, Czechia
| | - Kristýna Šemberová
- Institute of Botany of the Czech Academy of Sciences, Průhonice, Czechia
| | | | - Pavel Trávníček
- Institute of Botany of the Czech Academy of Sciences, Průhonice, Czechia
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24
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Telomeres and Their Neighbors. Genes (Basel) 2022; 13:genes13091663. [PMID: 36140830 PMCID: PMC9498494 DOI: 10.3390/genes13091663] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/08/2022] [Accepted: 09/09/2022] [Indexed: 11/21/2022] Open
Abstract
Telomeres are essential structures formed from satellite DNA repeats at the ends of chromosomes in most eukaryotes. Satellite DNA repeat sequences are useful markers for karyotyping, but have a more enigmatic role in the eukaryotic cell. Much work has been done to investigate the structure and arrangement of repetitive DNA elements in classical models with implications for species evolution. Still more is needed until there is a complete picture of the biological function of DNA satellite sequences, particularly when considering non-model organisms. Celebrating Gregor Mendel’s anniversary by going to the roots, this review is designed to inspire and aid new research into telomeres and satellites with a particular focus on non-model organisms and accessible experimental and in silico methods that do not require specialized equipment or expensive materials. We describe how to identify telomere (and satellite) repeats giving many examples of published (and some unpublished) data from these techniques to illustrate the principles behind the experiments. We also present advice on how to perform and analyse such experiments, including details of common pitfalls. Our examples are a selection of recent developments and underexplored areas of research from the past. As a nod to Mendel’s early work, we use many examples from plants and insects, especially as much recent work has expanded beyond the human and yeast models traditional in telomere research. We give a general introduction to the accepted knowledge of telomere and satellite systems and include references to specialized reviews for the interested reader.
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25
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Integration of Repeatomic and Cytogenetic Data on Satellite DNA for the Genome Analysis in the Genus Salvia (Lamiaceae). PLANTS 2022; 11:plants11172244. [PMID: 36079625 PMCID: PMC9460151 DOI: 10.3390/plants11172244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/25/2022] [Accepted: 08/25/2022] [Indexed: 11/17/2022]
Abstract
Within the complicated and controversial taxonomy of cosmopolitan genus Salvia L. (Lamiaceae) are valuable species Salvia officinalis L. and Salvia sclarea L., which are important for the pharmaceutical, ornamental horticulture, food, and perfume industries. Genome organization and chromosome structure of these essential oil species remain insufficiently studied. For the first time, the comparative repeatome analysis of S. officinalis and S. sclarea was performed using the obtained NGS data, RepeatExplorer/TAREAN pipelines and FISH-based chromosome mapping of the revealed satellite DNA families (satDNAs). In repeatomes of these species, LTR retrotransposons made up the majority of their repetitive DNA. Interspecific variations in genome abundance of Class I and Class II transposable elements, ribosomal DNA, and satellite DNA were revealed. Four (S. sclarea) and twelve (S. officinalis) putative satDNAs were identified. Based on patterns of chromosomal distribution of 45S rDNA; 5S rDNA and the revealed satDNAs, karyograms of S. officinalis and S. sclarea were constructed. Promising satDNAs which can be further used as chromosome markers to assess inter- and intraspecific chromosome variability in Salvia karyotypes were determined. The specific localization of homologous satDNA and 45S rDNA on chromosomes of the studied Salvia species confirmed their common origin, which is consistent with previously reported molecular phylogenetic data.
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26
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Samoluk SS, Vaio M, Ortíz AM, Chalup LMI, Robledo G, Bertioli DJ, Seijo G. Comparative repeatome analysis reveals new evidence on genome evolution in wild diploid Arachis (Fabaceae) species. PLANTA 2022; 256:50. [PMID: 35895167 DOI: 10.1007/s00425-022-03961-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 07/12/2022] [Indexed: 06/15/2023]
Abstract
Opposing changes in the abundance of satellite DNA and long terminal repeat (LTR) retroelements are the main contributors to the variation in genome size and heterochromatin amount in Arachis diploids. The South American genus Arachis (Fabaceae) comprises 83 species organized in nine taxonomic sections. Among them, section Arachis is characterized by species with a wide genome and karyotype diversity. Such diversity is determined mainly by the amount and composition of repetitive DNA. Here we performed computational analysis on low coverage genome sequencing to infer the dynamics of changes in major repeat families that led to the differentiation of genomes in diploid species (x = 10) of genus Arachis, focusing on section Arachis. Estimated repeat content ranged from 62.50 to 71.68% of the genomes. Species with different genome composition tended to have different landscapes of repeated sequences. Athila family retrotransposons were the most abundant and variable lineage among Arachis repeatomes, with peaks of transpositional activity inferred at different times in the evolution of the species. Satellite DNAs (satDNAs) were less abundant, but differentially represented among species. High rates of evolution of an AT-rich superfamily of satDNAs led to the differential accumulation of heterochromatin in Arachis genomes. The relationship between genome size variation and the repetitive content is complex. However, largest genomes presented a higher accumulation of LTR elements and lower contents of satDNAs. In contrast, species with lowest genome sizes tended to accumulate satDNAs in detriment of LTR elements. Phylogenetic analysis based on repetitive DNA supported the genome arrangement of section Arachis. Altogether, our results provide the most comprehensive picture on the repeatome dynamics that led to the genome differentiation of Arachis species.
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Affiliation(s)
- Sergio S Samoluk
- Instituto de Botánica del Nordeste (UNNE-CONICET), Facultad de Ciencias Agrarias, Corrientes, Argentina.
| | - Magdalena Vaio
- Laboratory of Plant Genome Evolution and Domestication, Department of Plant Biology, Faculty of Agronomy, University of the Republic, Montevideo, Uruguay
| | - Alejandra M Ortíz
- Instituto de Botánica del Nordeste (UNNE-CONICET), Facultad de Ciencias Agrarias, Corrientes, Argentina
| | - Laura M I Chalup
- Instituto de Botánica del Nordeste (UNNE-CONICET), Facultad de Ciencias Agrarias, Corrientes, Argentina
| | - Germán Robledo
- Instituto de Botánica del Nordeste (UNNE-CONICET), Facultad de Ciencias Agrarias, Corrientes, Argentina
- Facultad de Ciencias Exactas y Naturales y Agrimensura, Universidad Nacional del Nordeste, Corrientes, Argentina
| | - David J Bertioli
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
| | - Guillermo Seijo
- Instituto de Botánica del Nordeste (UNNE-CONICET), Facultad de Ciencias Agrarias, Corrientes, Argentina
- Facultad de Ciencias Exactas y Naturales y Agrimensura, Universidad Nacional del Nordeste, Corrientes, Argentina
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27
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de Souza TB, Parteka LM, de Assis R, Vanzela ALL. Diversity of the repetitive DNA fraction in Cestrum, the genus with the largest genomes within Solanaceae. Mol Biol Rep 2022; 49:8785-8799. [PMID: 35809181 DOI: 10.1007/s11033-022-07728-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 06/17/2022] [Indexed: 10/17/2022]
Abstract
BACKGROUND Cestrum species present large genomes (2 C = ~ 24 pg), a high occurrence of B chromosomes and great diversity in heterochromatin bands. Despite this diversity, karyotypes maintain the chromosome number 2n = 16 (except when they present B chromosomes), and a relative similarity in chromosome morphology and symmetry. To deepen our knowledge of the Cestrum genome composition, low-coverage sequencing data of C. strigilatum and C. elegans were compared, including cytogenomic analyses of seven species. METHODS AND RESULTS Bioinformatics analyses showed retrotransposons comprising more than 70% of the repetitive fraction, followed by DNA transposons (~ 17%), but FISH assays using retrotransposon probes revealed inconspicuous and scattered signals. The four satellite DNA families here analyzed represented approximately 2.48% of the C. strigilatum dataset, and these sequences were used as probes in FISH assays. Hybridization signals were colocalized with all AT- and GC-rich sequences associated with heterochromatin, including AT-rich Cold-Sensitive Regions (CSRs). Although satellite probes hybridized in almost all tested species, a satDNA family named CsSat49 was highlighted because it predominates in centromeric regions. CONCLUSIONS Data suggest that the satDNA fraction is conserved in the genus, although there is variation in the number of FISH signals between karyotypes. Except to the absence of FISH signals with probes CsSat1 and CsSat72 in two species, the other satellites occurred in species of different phylogenetic clades. Some satDNA sequences have been detected in the B chromosomes, indicating that they are rich in preexisting sequences in the chromosomes of the A complement. This comparative study provides an important advance in the knowledge on genome organization and heterochromatin composition in Cestrum, especially on the distribution of satellite fractions between species and their importance for the B chromosome composition.
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Affiliation(s)
- Thaíssa Boldieri de Souza
- Laboratório de Citogenética e Diversidade Vegetal, Departamento de Biologia Geral, Centro de Ciências Biológicas, Universidade Estadual de Londrina, Londrina, Paraná, 86097-570, Brazil.,Programa de Pós-graduação em Genética e Biologia Molecular, Centro de Ciências Biológicas, Universidade Estadual de Londrina, Londrina, Paraná, 86097-570, Brazil
| | - Letícia Maria Parteka
- Laboratório de Citogenética e Diversidade Vegetal, Departamento de Biologia Geral, Centro de Ciências Biológicas, Universidade Estadual de Londrina, Londrina, Paraná, 86097-570, Brazil.,Programa de Pós-graduação em Genética e Biologia Molecular, Centro de Ciências Biológicas, Universidade Estadual de Londrina, Londrina, Paraná, 86097-570, Brazil
| | - Rafael de Assis
- Laboratório de Citogenética e Diversidade Vegetal, Departamento de Biologia Geral, Centro de Ciências Biológicas, Universidade Estadual de Londrina, Londrina, Paraná, 86097-570, Brazil.,Programa de Pós-graduação em Genética e Biologia Molecular, Centro de Ciências Biológicas, Universidade Estadual de Londrina, Londrina, Paraná, 86097-570, Brazil
| | - André Luís Laforga Vanzela
- Laboratório de Citogenética e Diversidade Vegetal, Departamento de Biologia Geral, Centro de Ciências Biológicas, Universidade Estadual de Londrina, Londrina, Paraná, 86097-570, Brazil.
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28
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Alexandrov OS, Romanov DV, Divashuk MG, Razumova OV, Ulyanov DS, Karlov GI. Study and Physical Mapping of the Species-Specific Tandem Repeat CS-237 Linked with 45S Ribosomal DNA Intergenic Spacer in Cannabis sativa L. PLANTS (BASEL, SWITZERLAND) 2022; 11:1396. [PMID: 35684169 PMCID: PMC9183113 DOI: 10.3390/plants11111396] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 05/11/2022] [Accepted: 05/20/2022] [Indexed: 06/15/2023]
Abstract
Hemp (Cannabis sativa L.) is a valuable crop and model plant for studying sex chromosomes. The scientific interest in the plant has led to its whole genome sequencing and the determination of its cytogenetic characteristics. A range of cytogenetic markers (subtelomeric repeat CS-1, 5S rDNA, and 45S rDNA) has been mapped onto hemp's chromosomes by fluorescent in situ hybridization (FISH). In this study, another cytogenetic marker (the tandem repeat CS-237, with a 237 bp monomer) was found, studied, and localized on chromosomes by FISH. The signal distribution and karyotyping revealed that the CS-237 probe was localized in chromosome 6 with one hybridization site and in chromosome 8 with two hybridization sites, one of which colocalizes with the 45S rDNA probe (with which a nucleolus organizer region, NOR, was detected). A BLAST analysis of the genomic data and PCR experiments showed that the modified CS-237 monomers (delCS-237, 208 bp in size) were present in the intergenic spacers (IGSs) of hemp 45S rDNA monomers. Such a feature was firstly observed in Cannabaceae species. However, IGS-linked DNA repeats were found in several plant species of other families (Fabaceae, Solanaceae, and Asteraceae). This phenomenon is discussed in this article. The example of CS-237 may be useful for further studying the phenomenon as well as for the physical mapping of hemp chromosomes.
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29
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Yurkevich OY, Samatadze TE, Selyutina IY, Suprun NA, Suslina SN, Zoshchuk SA, Amosova AV, Muravenko OV. Integration of Genomic and Cytogenetic Data on Tandem DNAs for Analyzing the Genome Diversity Within the Genus Hedysarum L. (Fabaceae). FRONTIERS IN PLANT SCIENCE 2022; 13:865958. [PMID: 35574118 PMCID: PMC9101955 DOI: 10.3389/fpls.2022.865958] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 03/28/2022] [Indexed: 06/15/2023]
Abstract
The section Multicaulia is the largest clade in the genus Hedysarum L. (Fabaceae). Representatives of the sect. Multicaulia are valuable plants used for medicinal and fodder purposes. The taxonomy and phylogeny of the sect. Multicaulia are still ambiguous. To clarify the species relationships within sect. Multicaulia, we, for the first time, explored repeatomes of H. grandiflorum Pall., H. zundukii Peschkova, and H. dahuricum Turcz. using next-generation sequencing technologies and a subsequent bioinformatic analysis by RepeatExplorer/TAREAN pipelines. The comparative repeatome analysis showed that mobile elements made up 20-24% (Class I) and about 2-2.5% (Class II) of their repetitive DNAs. The amount of ribosomal DNA varied from 1 to 2.6%, and the content of satellite DNA ranged from 2.7 to 5.1%. For each species, five high confident putative tandem DNA repeats and 5-10 low confident putative DNA repeats were identified. According to BLAST, these repeats demonstrated high sequence similarity within the studied species. FISH-based mapping of 35S rDNA, 5S rDNA, and satDNAs made it possible to detect new effective molecular chromosome markers for Hedysarum species and construct the species karyograms. Comparison of the patterns of satDNA localization on chromosomes of the studied species allowed us to assess genome diversity within the sect. Multicaulia. In all studied species, we revealed intra- and interspecific variabilities in patterns of the chromosomal distribution of molecular chromosome markers. In H. gmelinii Ledeb. and H. setigerum Turcz. ex Fisch. et Meyer, similar subgenomes were detected, which confirmed the polyploid status of their genomes. Our findings demonstrated a close genomic relationship among six studied species indicating their common origin and confirmed the taxonomic status of H. setigerum as a subspecies of H. gmelinii as well as the validity of combining the sect. Multicaulia and Subacaulia into one sect. Multicaulia.
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Affiliation(s)
- Olga Yu. Yurkevich
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Tatiana E. Samatadze
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- Peoples’ Friendship University of Russia, Moscow, Russia
| | - Inessa Yu. Selyutina
- Central Siberian Botanical Garden, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | | | | | | | - Alexandra V. Amosova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Olga V. Muravenko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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30
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Amosova AV, Yurkevich OY, Bolsheva NL, Samatadze TE, Zoshchuk SA, Muravenko OV. Repeatome Analyses and Satellite DNA Chromosome Patterns in Deschampsia sukatschewii, D. cespitosa, and D. antarctica (Poaceae). Genes (Basel) 2022; 13:genes13050762. [PMID: 35627148 PMCID: PMC9141916 DOI: 10.3390/genes13050762] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 04/20/2022] [Accepted: 04/22/2022] [Indexed: 02/05/2023] Open
Abstract
Subpolar and polar ecotypes of Deschampsia sukatschewii (Popl.) Roshev, D. cespitosa (L.) P. Beauv, and D. antarctica E. Desv. are well adapted to stressful environmental conditions, which make them useful model plants for genetic research and breeding. For the first time, the comparative repeatome analyses of subpolar and polar D. sukatschewii, D. cespitosa, and D. antarctica was performed using RepeatExplorer/TAREAN pipelines and FISH-based chromosomal mapping of the identified satellite DNA families (satDNAs). In the studied species, mobile genetic elements of class 1 made up the majority of their repetitive DNA; interspecific variations in the total amount of Ty3/Gypsy and Ty1/Copia retroelements, DNA transposons, ribosomal, and satellite DNA were revealed; 12–18 high confident and 7–9 low confident putative satDNAs were identified. According to BLAST, most D. sukatschewii satDNAs demonstrated sequence similarity with satDNAs of D. antarctica and D. cespitosa indicating their common origin. Chromosomal mapping of 45S rDNA, 5S rDNA, and satDNAs of D. sukatschewii allowed us to construct the species karyograms and detect new molecular chromosome markers important for Deschampsia species. Our findings confirmed that genomes of D. sukatschewii and D. cespitosa were more closely related compared to D. antarctica according to repeatome composition and patterns of satDNA chromosomal distribution.
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31
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Choi IS, Wojciechowski MF, Steele KP, Hunter SG, Ruhlman TA, Jansen RK. Born in the mitochondrion and raised in the nucleus: evolution of a novel tandem repeat family in Medicago polymorpha (Fabaceae). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:389-406. [PMID: 35061308 DOI: 10.1111/tpj.15676] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 01/13/2022] [Indexed: 06/14/2023]
Abstract
Plant nuclear genomes harbor sequence elements derived from the organelles (mitochondrion and plastid) through intracellular gene transfer (IGT). Nuclear genomes also show a dramatic range of repeat content, suggesting that any sequence can be readily amplified. These two aspects of plant nuclear genomes are well recognized but have rarely been linked. Through investigation of 31 Medicago taxa we detected exceptionally high post-IGT amplification of mitochondrial (mt) DNA sequences containing rps10 in the nuclear genome of Medicago polymorpha and closely related species. The amplified sequences were characterized as tandem arrays of five distinct repeat motifs (2157, 1064, 987, 971, and 587 bp) that have diverged from the mt genome (mitogenome) in the M. polymorpha nuclear genome. The mt rps10-like arrays were identified in seven loci (six intergenic and one telomeric) of the nuclear chromosome assemblies and were the most abundant tandem repeat family, representing 1.6-3.0% of total genomic DNA, a value approximately three-fold greater than the entire mitogenome in M. polymorpha. Compared to a typical mt gene, the mt rps10-like sequence coverage level was 691.5-7198-fold higher in M. polymorpha and closely related species. In addition to the post-IGT amplification, our analysis identified the canonical telomeric repeat and the species-specific satellite arrays that are likely attributable to an ancestral chromosomal fusion in M. polymorpha. A possible relationship between chromosomal instability and the mt rps10-like tandem repeat family in the M. polymorpha clade is discussed.
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Affiliation(s)
- In-Su Choi
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | | | - Kelly P Steele
- Division of Science and Mathematics, Arizona State University, Mesa, AZ, 85212, USA
| | - Sarah G Hunter
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA
| | - Tracey A Ruhlman
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA
| | - Robert K Jansen
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA
- Centre of Excellence in Bionanoscience Research, Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
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32
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Mascagni F, Barghini E, Ceccarelli M, Baldoni L, Trapero C, Díez CM, Natali L, Cavallini A, Giordani T. The Singular Evolution of Olea Genome Structure. FRONTIERS IN PLANT SCIENCE 2022; 13:869048. [PMID: 35432417 PMCID: PMC9009077 DOI: 10.3389/fpls.2022.869048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 03/07/2022] [Indexed: 06/14/2023]
Abstract
The current view of plant genome evolution proposes that genome size has mainly been determined by polyploidisation and amplification/loss of transposons, with a minor role played by other repeated sequences, such as tandem repeats. In cultivated olive (Olea europaea subsp. europaea var. europaea), available data suggest a singular model of genome evolution, in which a massive expansion of tandem-repeated sequences accompanied changes in nuclear architecture. This peculiar scenario highlights the importance of focusing on Olea genus evolution, to shed light on mechanisms that led to its present genomic structure. Next-generation sequencing technologies, bioinformatics and in situ hybridisation were applied to study the genomic structure of five related Olea taxa, which originated at different times from their last common ancestor. On average, repetitive DNA in the Olea taxa ranged from ~59% to ~73% of the total genome, showing remarkable differences in terms of composition. Among repeats, we identified 11 major families of tandem repeats, with different abundances in the analysed taxa, five of which were novel discoveries. Interestingly, overall tandem repeat abundance was inversely correlated to that of retrotransposons. This trend might imply a competition in the proliferation of these repeat classes. Indeed, O. paniculata, the species closest to the Olea common ancestor, showed very few tandem-repeated sequences, while it was rich in long terminal repeat retrotransposons, suggesting that the amplification of tandem repeats occurred after its divergence from the Olea ancestor. Furthermore, some tandem repeats were physically localised in closely related O. europaea subspecies (i.e., cultivated olive and O. europaea subsp. cuspidata), which showed a significant difference in tandem repeats abundance. For 4 tandem repeats families, a similar number of hybridisation signals were observed in both subspecies, apparently indicating that, after their dissemination throughout the olive genome, these tandem repeats families differentially amplified maintaining the same positions in each genome. Overall, our research identified the temporal dynamics shaping genome structure during Olea speciation, which represented a singular model of genome evolution in higher plants.
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Affiliation(s)
- Flavia Mascagni
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Elena Barghini
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Marilena Ceccarelli
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Luciana Baldoni
- CNR, Institute of Biosciences and BioResources, Perugia, Italy
| | - Carlos Trapero
- CSIRO Agriculture & Food, Narrabri, NSW, Australia
- Agronomy Department, University of Cordoba, Cordoba, Spain
| | | | - Lucia Natali
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Andrea Cavallini
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Tommaso Giordani
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
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33
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Wang K, Xiang D, Xia K, Sun B, Khurshid H, Esh AMH, Zhang H. Characterization of Repetitive DNA in Saccharum officinarum and Saccharum spontaneum by Genome Sequencing and Cytological Assays. FRONTIERS IN PLANT SCIENCE 2022; 13:814620. [PMID: 35273624 PMCID: PMC8902033 DOI: 10.3389/fpls.2022.814620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 01/28/2022] [Indexed: 06/14/2023]
Abstract
In most plant species, DNA repeated elements such as satellites and retrotransposons are composing the majority of their genomes. Saccharum officinarum (2n = 8x = 80) and S. spontaneum (2n = 40-128) are the two fundamental donors of modern sugarcane cultivars. These two species are polyploids with large genome sizes and are enriched in repetitive elements. In this work, we adopted a de novo strategy to isolate highly repetitive and abundant sequences in S. officinarum LA Purple and S. spontaneum SES208. The findings obtained from alignment to the genome assemblies revealed that the vast majority of the repeats (97.9% in LA Purple and 96.5% in SES208) were dispersed in the respective genomes. Fluorescence in situ hybridization assays were performed on 27 representative repeats to investigate their distributions and abundances. The results showed that the copies of some highly repeated sequences, including rDNA and centromeric or telomeric repeats, were underestimated in current genome assemblies. The analysis of the raw read mapping strategy showed more copy numbers for all studied repeats, suggesting that copy number underestimation is common for highly repeated sequences in current genome assemblies of LA Purple and SES208. In addition, the data showed that the centromeric retrotransposons in all SES208 centromeres were absent in certain S. spontaneum clones with different ploidies. This rapid turnover of centromeric DNA in sugarcane provides new clues regarding the pattern of centromeric retrotransposon formation and accumulation.
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Affiliation(s)
- Kai Wang
- School of Life Sciences, Nantong University, Nantong, China
| | - Dong Xiang
- Guangxi Key Laboratory of Sugarcane Biology & Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Kai Xia
- Guangxi Key Laboratory of Sugarcane Biology & Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Bo Sun
- Guangxi Key Laboratory of Sugarcane Biology & Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Haris Khurshid
- Oilseeds Research Program, National Agricultural Research Centre, Islamabad, Pakistan
| | - Ayman M. H. Esh
- Sugar Crops Research Institute, Agriculture Research Center, Giza, Egypt
| | - Hui Zhang
- School of Life Sciences, Nantong University, Nantong, China
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34
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Camacho JPM, Cabrero J, López-León MD, Martín-Peciña M, Perfectti F, Garrido-Ramos MA, Ruiz-Ruano FJ. Satellitome comparison of two oedipodine grasshoppers highlights the contingent nature of satellite DNA evolution. BMC Biol 2022; 20:36. [PMID: 35130900 PMCID: PMC8822648 DOI: 10.1186/s12915-021-01216-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 12/16/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The full catalog of satellite DNA (satDNA) within a same genome constitutes the satellitome. The Library Hypothesis predicts that satDNA in relative species reflects that in their common ancestor, but the evolutionary mechanisms and pathways of satDNA evolution have never been analyzed for full satellitomes. We compare here the satellitomes of two Oedipodine grasshoppers (Locusta migratoria and Oedaleus decorus) which shared their most recent common ancestor about 22.8 Ma ago. RESULTS We found that about one third of their satDNA families (near 60 in every species) showed sequence homology and were grouped into 12 orthologous superfamilies. The turnover rate of consensus sequences was extremely variable among the 20 orthologous family pairs analyzed in both species. The satDNAs shared by both species showed poor association with sequence signatures and motives frequently argued as functional, except for short inverted repeats allowing short dyad symmetries and non-B DNA conformations. Orthologous satDNAs frequently showed different FISH patterns at both intra- and interspecific levels. We defined indices of homogenization and degeneration and quantified the level of incomplete library sorting between species. CONCLUSIONS Our analyses revealed that satDNA degenerates through point mutation and homogenizes through partial turnovers caused by massive tandem duplications (the so-called satDNA amplification). Remarkably, satDNA amplification increases homogenization, at intragenomic level, and diversification between species, thus constituting the basis for concerted evolution. We suggest a model of satDNA evolution by means of recursive cycles of amplification and degeneration, leading to mostly contingent evolutionary pathways where concerted evolution emerges promptly after lineages split.
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Affiliation(s)
| | - Josefa Cabrero
- Departamento de Genética, Universidad de Granada, 18071, Granada, Spain
| | | | | | - Francisco Perfectti
- Departamento de Genética, Universidad de Granada, 18071, Granada, Spain.,Research Unit Modeling Nature, Universidad de Granada, Granada, Spain
| | | | - Francisco J Ruiz-Ruano
- Department of Organismal Biology - Systematic Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36, Uppsala, Sweden. .,School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TU, UK.
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35
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Kretschmer R, Goes CAG, Bertollo LAC, Ezaz T, Porto-Foresti F, Toma GA, Utsunomia R, de Bello Cioffi M. Satellitome analysis illuminates the evolution of ZW sex chromosomes of Triportheidae fishes (Teleostei: Characiformes). Chromosoma 2022; 131:29-45. [PMID: 35099570 DOI: 10.1007/s00412-022-00768-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 01/09/2022] [Accepted: 01/12/2022] [Indexed: 12/14/2022]
Abstract
Satellites are an abundant source of repetitive DNAs that play an essential role in the chromosomal organization and are tightly linked with the evolution of sex chromosomes. Among fishes, Triportheidae stands out as the only family where almost all species have a homeologous ZZ/ZW sex chromosomes system. While the Z chromosome is typically conserved, the W is always smaller, with variations in size and morphology between species. Here, we report an analysis of the satellitome of Triportheus auritus (TauSat) by integrating genomic and chromosomal data, with a special focus on the highly abundant and female-biased satDNAs. In addition, we investigated the evolutionary trajectories of the ZW sex chromosomes in the Triportheidae family by mapping satDNAs in selected representative species of this family. The satellitome of T. auritus comprised 53 satDNA families of which 24 were also hybridized by FISH. Most satDNAs differed significantly between sexes, with 19 out of 24 being enriched on the W chromosome of T. auritus. The number of satDNAs hybridized into the W chromosomes of T. signatus and T. albus decreased to six and four, respectively, in accordance with the size of their W chromosomes. No TauSat probes produced FISH signals on the chromosomes of Agoniates halecinus. Despite its apparent conservation, our results indicate that each species differs in the satDNA accumulation on the Z chromosome. Minimum spanning trees (MSTs), generated for three satDNA families with different patterns of FISH mapping data, revealed different homogenization rates between the Z and W chromosomes. These results were linked to different levels of recombination between them. The most abundant satDNA family (TauSat01) was exclusively hybridized in the centromeres of all 52 chromosomes of T. auritus, and its putative role in the centromere evolution was also highlighted. Our results identified a high differentiation of both ZW chromosomes regarding satellites composition, highlighting their dynamic role in the sex chromosomes evolution.
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Affiliation(s)
- Rafael Kretschmer
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | | | | | - Tariq Ezaz
- Institute for Applied Ecology, University of Canberra, Canberra, Australia
| | | | - Gustavo Akira Toma
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | - Ricardo Utsunomia
- Instituto de Ciências Biológicas e da Saúde, ICBS, Universidade Federal Rural do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil.
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36
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Ibiapino A, Báez M, García MA, Costea M, Stefanović S, Pedrosa-Harand A. Karyotype asymmetry in Cuscuta L. subgenus Pachystigma reflects its repeat DNA composition. Chromosome Res 2022; 30:91-107. [PMID: 35089455 DOI: 10.1007/s10577-021-09683-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 12/24/2021] [Accepted: 12/27/2021] [Indexed: 12/25/2022]
Abstract
Cuscuta is a cytogenetically diverse genus, with karyotypes varying 18-fold in chromosome number and 127-fold in genome size. Each of its four subgenera also presents particular chromosomal features, such as bimodal karyotypes in Pachystigma. We used low coverage sequencing of the Cuscuta nitida genome (subgenus Pachystigma), as well as chromosome banding and molecular cytogenetics of three subgenus representatives, to understand the origin of bimodal karyotypes. All three species, C. nitida, C. africana (2n = 28) and C. angulata (2n = 30), showed heterochromatic bands mainly in the largest chromosome pairs. Eighteen satellite DNAs were identified in C. nitida genome, two showing similarity to mobile elements. The most abundant were present at the largest pairs, as well as the highly abundant ribosomal DNAs. The most abundant Ty1/Copia and Ty3/Gypsy elements were also highly enriched in the largest pairs, except for the Ty3/Gypsy CRM, which also labelled the pericentromeric regions of the smallest chromosomes. This accumulation of repetitive DNA in the larger pairs indicates that these sequences are largely responsible for the formation of bimodal karyotypes in the subgenus Pachystigma. The repetitive DNA fraction is directly linked to karyotype evolution in Cuscuta.
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Affiliation(s)
- Amalia Ibiapino
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, Brazil
| | - Mariana Báez
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, Brazil.,Plant Breeding Department, University of Bonn, Bonn, Germany
| | | | - Mihai Costea
- Department of Biology, Wilfrid Laurier University, Waterloo, Ontario, Canada
| | - Saša Stefanović
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - Andrea Pedrosa-Harand
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, Brazil.
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Reis AC, Chester M, de Sousa SM, Campos VR, de Queiroz Nascimento LS, Pacheco Júnior S, Franco AL, Viccini LF. Chromosomal view of Lippia alba, a tropical polyploid complex under genome stabilization process. PROTOPLASMA 2022; 259:33-46. [PMID: 33760982 DOI: 10.1007/s00709-021-01636-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 03/12/2021] [Indexed: 06/12/2023]
Abstract
Lippia alba is a phenotypically variable tropical shrub thought to comprise a young autopolyploid complex. Chromosome numbers in L. alba include 2n = 30, 38, 45, 60, and 90. High levels of chemical and phenotypic variation associated with economic and medicinal importance were reported. However, the genetic background including chromosome composition remains under-explored. Furthermore, the occurrence of at least four ploidal levels in L. alba and the lack of data for polyploid plants in tropical areas also merit further study of L. alba. Here we assessed the chromosome composition using two new satellite repeats (CL98 and CL66) applied as FISH probes to mitotic chromosomes, and we proposed to calculate the degree of homozygosis for CL66 satDNA (named as index h) and to associate it to meiotic instability. The CL98 mapping showed few variations in both number of signals and position. However, the levels of structural homozygosity for a satellite repeat CL66 were very variable. The numbers of CL66-bearing-chromosomes were under-represented in tetraploids relative to diploids implying that CL66 arrays have been lost in tetraploid lineages as a result of increased meiotic instability. High percentage of irregularities was observed in meiotic cells, especially in polyploids. L. alba complex comprised a mixture of homomorphic and heteromorphic chromosomes. Overall, the polyploid complex presents features typical of both young and older stable polyploids. It seems that L. alba genome is still in the process of stabilization.
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Affiliation(s)
- Aryane Campos Reis
- Department of Biology, Federal University of Juiz de Fora, Juiz de Fora, MG, 36036-900, Brazil
| | | | - Saulo Marçal de Sousa
- Department of Biology, Federal University of Juiz de Fora, Juiz de Fora, MG, 36036-900, Brazil
| | - Victória Rabelo Campos
- Department of Biology, Federal University of Juiz de Fora, Juiz de Fora, MG, 36036-900, Brazil
| | | | | | - Ana Luiza Franco
- Department of Biology, Federal University of Juiz de Fora, Juiz de Fora, MG, 36036-900, Brazil
| | - Lyderson Facio Viccini
- Department of Biology, Federal University of Juiz de Fora, Juiz de Fora, MG, 36036-900, Brazil.
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38
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Bayat S, Lysak MA, Mandáková T. Genome structure and evolution in the cruciferous tribe Thlaspideae (Brassicaceae). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:1768-1785. [PMID: 34661331 DOI: 10.1111/tpj.15542] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 09/30/2021] [Accepted: 10/11/2021] [Indexed: 06/13/2023]
Abstract
Whole-genome duplications (WGDs) and chromosome rearrangements (CRs) play the key role in driving the diversification and evolution of plant lineages. Although the direct link between WGDs and plant diversification is well documented, relatively few studies focus on the evolutionary significance of CRs. The cruciferous tribe Thlaspideae represents an ideal model system to address the role of large-scale chromosome alterations in genome evolution, as most Thlaspideae species share the same diploid chromosome number (2n = 2x = 14). Here we constructed the genome structure in 12 Thlaspideae species, including field pennycress (Thlaspi arvense) and garlic mustard (Alliaria petiolata). We detected and precisely characterized genus- and species-specific CRs, mostly pericentric inversions, as the main genome-diversifying drivers in the tribe. We reconstructed the structure of seven chromosomes of an ancestral Thlaspideae genome, identified evolutionary stable chromosomes versus chromosomes prone to CRs, estimated the rate of CRs, and uncovered an allohexaploid origin of garlic mustard from diploid taxa closely related to A. petiolata and Parlatoria cakiloidea. Furthermore, we performed detailed bioinformatic analysis of the Thlaspideae repeatomes, and identified repetitive elements applicable as unique species- and genus-specific barcodes and chromosome landmarks. This study deepens our general understanding of the evolutionary role of CRs, particularly pericentric inversions, in plant genome diversification, and provides a robust base for follow-up whole-genome sequencing efforts.
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Affiliation(s)
- Soheila Bayat
- CEITEC, Masaryk University, Brno, 62500, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, 62500, Czech Republic
| | - Martin A Lysak
- CEITEC, Masaryk University, Brno, 62500, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, 62500, Czech Republic
| | - Terezie Mandáková
- CEITEC, Masaryk University, Brno, 62500, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, 62500, Czech Republic
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39
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Cintra LA, Souza TBD, Parteka LM, Barreto LM, Pereira LFP, Gaeta ML, Guyot R, Vanzela ALL. An 82 bp tandem repeat family typical of 3' non-coding end of Gypsy/TAT LTR retrotransposons is conserved in Coffea spp. pericentromeres. Genome 2021; 65:137-151. [PMID: 34727516 DOI: 10.1139/gen-2021-0045] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Coffea spp. chromosomes are very small and accumulate a variety of repetitive DNA families around the centromeres. However, the proximal regions of Coffea chromosomes remain poorly understood, especially regarding the nature and organisation of the sequences. Taking advantage of the genome sequences of C. arabica (2n = 44), C. canephora, and C. eugenioides (C. arabica progenitors with 2n = 22) and good coverage genome sequencing of dozens of other wild Coffea spp., repetitive DNA sequences were identified, and the genomes were compared to decipher particularities of pericentromeric structures. The searches revealed a short tandem repeat (82 bp length) typical of Gypsy/TAT LTR retrotransposons, named Coffea_sat11. This repeat organises clusters with fragments of other transposable elements, comprising regions of non-coding RNA production. Cytogenomic analyses showed that Coffea_sat11 extends from the pericentromeres towards the middle of the chromosomal arms. This arrangement was observed in the allotetraploid C. arabica chromosomes, as well as in its progenitors. This study improves our understanding of the role of the Gypsy/TAT LTR retrotransposon lineage in the organisation of Coffea pericentromeres, as well as the conservation of Coffea_sat11 within the genus. The relationships between fragments of other transposable elements and the functional aspects of these sequences on the pericentromere chromatin were also evaluated. Highlights: A scattered short tandem repeat, typical of Gypsy/TAT LTR retrotransposons, associated with several fragments of other transposable elements, accumulates in the pericentromeres of Coffea chromosomes. This arrangement is preserved in all clades of the genus and appears to have a strong regulatory role in the organisation of chromatin around centromeres.
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Affiliation(s)
- Leonardo Adabo Cintra
- Laboratório de Citogenética e Diversidade Vegetal, Departamento de Biologia Geral, Centro de Ciências Biológicas, Universidade Estadual de Londrina, Londrina, 86097-570, Paraná, Brazil.,Programa de Pós-graduação em Genética e Biologia Molecular, Centro de Ciências Biológicas, Universidade Estadual de Londrina, Londrina, 86097-570, Paraná, Brazil
| | - Thaíssa Boldieri de Souza
- Laboratório de Citogenética e Diversidade Vegetal, Departamento de Biologia Geral, Centro de Ciências Biológicas, Universidade Estadual de Londrina, Londrina, 86097-570, Paraná, Brazil.,Programa de Pós-graduação em Genética e Biologia Molecular, Centro de Ciências Biológicas, Universidade Estadual de Londrina, Londrina, 86097-570, Paraná, Brazil
| | - Letícia Maria Parteka
- Laboratório de Citogenética e Diversidade Vegetal, Departamento de Biologia Geral, Centro de Ciências Biológicas, Universidade Estadual de Londrina, Londrina, 86097-570, Paraná, Brazil.,Programa de Pós-graduação em Genética e Biologia Molecular, Centro de Ciências Biológicas, Universidade Estadual de Londrina, Londrina, 86097-570, Paraná, Brazil
| | - Lucas Mesquita Barreto
- Laboratório de Citogenética e Diversidade Vegetal, Departamento de Biologia Geral, Centro de Ciências Biológicas, Universidade Estadual de Londrina, Londrina, 86097-570, Paraná, Brazil.,Programa de Pós-graduação em Genética e Biologia Molecular, Centro de Ciências Biológicas, Universidade Estadual de Londrina, Londrina, 86097-570, Paraná, Brazil
| | | | - Marcos Letaif Gaeta
- Laboratório de Citogenética e Diversidade Vegetal, Departamento de Biologia Geral, Centro de Ciências Biológicas, Universidade Estadual de Londrina, Londrina, 86097-570, Paraná, Brazil
| | - Romain Guyot
- Institut de Recherche pour le Développement, CIRAD, Université Montpellier, 34394, Montpellier, France.,Department of Electronics and Automation, Universidad Autónoma de Manizales, 170002, Manizales, Caldas, Colombia
| | - André Luís Laforga Vanzela
- Laboratório de Citogenética e Diversidade Vegetal, Departamento de Biologia Geral, Centro de Ciências Biológicas, Universidade Estadual de Londrina, Londrina, 86097-570, Paraná, Brazil
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40
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Pellicer J, Fernández P, Fay MF, Michálková E, Leitch IJ. Genome Size Doubling Arises From the Differential Repetitive DNA Dynamics in the Genus Heloniopsis (Melanthiaceae). Front Genet 2021; 12:726211. [PMID: 34552621 PMCID: PMC8450539 DOI: 10.3389/fgene.2021.726211] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 08/19/2021] [Indexed: 12/23/2022] Open
Abstract
Plant genomes are highly diverse in size and repetitive DNA composition. In the absence of polyploidy, the dynamics of repetitive elements, which make up the bulk of the genome in many species, are the main drivers underpinning changes in genome size and the overall evolution of the genomic landscape. The advent of high-throughput sequencing technologies has enabled investigation of genome evolutionary dynamics beyond model plants to provide exciting new insights in species across the biodiversity of life. Here we analyze the evolution of repetitive DNA in two closely related species of Heloniopsis (Melanthiaceae), which despite having the same chromosome number differ nearly twofold in genome size [i.e., H. umbellata (1C = 4,680 Mb), and H. koreana (1C = 2,480 Mb)]. Low-coverage genome skimming and the RepeatExplorer2 pipeline were used to identify the main repeat families responsible for the significant differences in genome sizes. Patterns of repeat evolution were found to correlate with genome size with the main classes of transposable elements identified being twice as abundant in the larger genome of H. umbellata compared with H. koreana. In addition, among the satellite DNA families recovered, a single shared satellite (HeloSAT) was shown to have contributed significantly to the genome expansion of H. umbellata. Evolutionary changes in repetitive DNA composition and genome size indicate that the differences in genome size between these species have been underpinned by the activity of several distinct repeat lineages.
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Affiliation(s)
- Jaume Pellicer
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Barcelona, Spain.,Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Pol Fernández
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Barcelona, Spain
| | - Michael F Fay
- Royal Botanic Gardens, Kew, Richmond, United Kingdom.,School of Plant Biology, University of Western Australia, Crawley, WA, Australia
| | | | - Ilia J Leitch
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
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41
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González ML, Chiapella JO, Urdampilleta JD. Chromosomal Differentiation of Deschampsia (Poaceae) Based on Four Satellite DNA Families. Front Genet 2021; 12:728664. [PMID: 34621294 PMCID: PMC8490763 DOI: 10.3389/fgene.2021.728664] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 09/06/2021] [Indexed: 11/19/2022] Open
Abstract
Diverse families of satellite DNA (satDNA) were detected in heterochromatin regions of Deschampsia. This kind of repetitive DNA consists of tandem repeat sequences forming big arrays in genomes, and can contribute to lineages differentiation. The differentiation between types of satDNA is related to their sequence identity, the size and number of monomers forming the array, and their chromosomal location. In this work, four families of satDNA (D2, D3, D12, D13), previously isolated by genomic analysis, were studied on chromosomal preparations of 12 species of Deschampsia (D. airiformis, D. antarctica, D. cespitosa, D. cordillerarum, D. elongata, D. kingii, D. laxa, D. mendocina, D. parvula, D. patula, D. venustula, and Deschampsia sp) and one of Deyeuxia (D. eminens). Despite the number of satDNA loci showing interspecific variation, the general distribution pattern of each satDNA family is maintained. The four satDNA families are AT-rich and associated with DAPI + heterochromatin regions. D2, D3, and D12 have mainly subterminal distribution, while D13 is distributed in intercalary regions. Such conservation of satDNA patterns suggests a not random distribution in genomes, where the variation between species is mainly associated with the array size and the loci number. The presence of satDNA in all species studied suggests a low genetic differentiation of sequences. On the other hand, the variation of the distribution pattern of satDNA has no clear association with phylogeny. This may be related to high differential amplification and contraction of sequences between lineages, as explained by the library model.
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Affiliation(s)
- María Laura González
- Instituto Multidisciplinario de Biología Vegetal (Consejo Nacional de Investigaciones Científicas y Técnicas - Universidad Nacional de Córdoba), Córdoba, Argentina
| | - Jorge Oscar Chiapella
- Instituto de Investigaciones en Biodiversidad y Medioambiente (Consejo Nacional de Investigaciones Científicas y Técnicas - Universidad Nacional Del Comahue), Bariloche, Argentina
| | - Juan Domingo Urdampilleta
- Instituto Multidisciplinario de Biología Vegetal (Consejo Nacional de Investigaciones Científicas y Técnicas - Universidad Nacional de Córdoba), Córdoba, Argentina
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42
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Garrido-Ramos MA. The Genomics of Plant Satellite DNA. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2021; 60:103-143. [PMID: 34386874 DOI: 10.1007/978-3-030-74889-0_5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
The twenty-first century began with a certain indifference to the research of satellite DNA (satDNA). Neither genome sequencing projects were able to accurately encompass the study of satDNA nor classic methodologies were able to go further in undertaking a better comprehensive study of the whole set of satDNA sequences of a genome. Nonetheless, knowledge of satDNA has progressively advanced during this century with the advent of new analytical techniques. The enormous advantages that genome-wide approaches have brought to its analysis have now stimulated a renewed interest in the study of satDNA. At this point, we can look back and try to assess more accurately many of the key questions that were left unsolved in the past about this enigmatic and important component of the genome. I review here the understanding gathered on plant satDNAs over the last few decades with an eye on the near future.
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43
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Ebrahimzadegan R, Orooji F, Ma P, Mirzaghaderi G. Differentially Amplified Repetitive Sequences Among Aegilops tauschii Subspecies and Genotypes. FRONTIERS IN PLANT SCIENCE 2021; 12:716750. [PMID: 34490015 PMCID: PMC8417419 DOI: 10.3389/fpls.2021.716750] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Accepted: 07/27/2021] [Indexed: 06/13/2023]
Abstract
Genomic repetitive sequences commonly show species-specific sequence type, abundance, and distribution patterns, however, their intraspecific characteristics have been poorly described. We quantified the genomic repetitive sequences and performed single nucleotide polymorphism (SNP) analysis between 29 Ae. tauschii genotypes and subspecies using publicly available raw genomic Illumina sequence reads and used fluorescence in situ hybridization (FISH) to experimentally analyze some repeats. The majority of the identified repetitive sequences had similar contents and proportions between anathera, meyeri, and strangulata subspecies. However, two Ty3/gypsy retrotransposons (CL62 and CL87) showed significantly higher abundances, and CL1, CL119, CL213, CL217 tandem repeats, and CL142 retrotransposon (Ty1/copia type) showed significantly lower abundances in subspecies strangulata compared with the subspecies anathera and meyeri. One tandem repeat and 45S ribosomal DNA (45S rDNA) abundances showed a high variation between genotypes but their abundances were not subspecies specific. Phylogenetic analysis using the repeat abundances of the aforementioned clusters placed the strangulata subsp. in a distinct clade but could not discriminate anathera and meyeri. A near complete differentiation of anathera and strangulata subspecies was observed using SNP analysis; however, var. meyeri showed higher genetic diversity. FISH using major tandem repeats couldn't detect differences between subspecies, although (GAA)10 signal patterns generated two different karyotype groups. Taken together, the different classes of repetitive DNA sequences have differentially accumulated between strangulata and the other two subspecies of Ae. tauschii that is generally in agreement with spike morphology, implying that factors affecting repeatome evolution are variable even among highly closely related lineages.
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Affiliation(s)
- Rahman Ebrahimzadegan
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran
| | - Fatemeh Orooji
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran
| | - Pengtao Ma
- College of Life Sciences, Yantai University, Yantai, China
| | - Ghader Mirzaghaderi
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran
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44
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The B Chromosomes of Prochilodus lineatus (Teleostei, Characiformes) Are Highly Enriched in Satellite DNAs. Cells 2021; 10:cells10061527. [PMID: 34204462 PMCID: PMC8235050 DOI: 10.3390/cells10061527] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/07/2021] [Accepted: 06/11/2021] [Indexed: 12/18/2022] Open
Abstract
B or supernumerary chromosomes are dispensable elements that are widely present in numerous eukaryotes. Due to their non-recombining nature, there is an evident tendency for repetitive DNA accumulation in these elements. Thus, satellite DNA plays an important role in the evolution and diversification of B chromosomes and can provide clues regarding their origin. The characiform Prochilodus lineatus was one of the first discovered fish species bearing B chromosomes, with all populations analyzed so far showing one to nine micro-B chromosomes and exhibiting at least three morphological variants (Ba, Bsm, and Bm). To date, a single satellite DNA is known to be located on the B chromosomes of this species, but no information regarding the differentiation of the proposed B-types is available. Here, we characterized the satellitome of P. lineatus and mapped 35 satellite DNAs against the chromosomes of P. lineatus, of which six were equally located on all B-types and this indicates a similar genomic content. In addition, we describe, for the first time, an entire population without B chromosomes.
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45
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Cytogenomics of Deschampsia P. Beauv. (Poaceae) Species Based on Sequence Analyses and FISH Mapping of CON/COM Satellite DNA Families. PLANTS 2021; 10:plants10061105. [PMID: 34070920 PMCID: PMC8229069 DOI: 10.3390/plants10061105] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/19/2021] [Accepted: 05/26/2021] [Indexed: 02/06/2023]
Abstract
The genus Deschampsia P. Beauv. (Poaceae) involves a group of widespread polymorphic species, and many of them are highly tolerant to stressful environmental conditions. Genome diversity and chromosomal phylogeny within the genus are still insufficiently studied. Satellite DNAs, including CON/COM families, are the main components of the plant repeatome, which contribute to chromosome organization. For the first time, using PCR-based (Polymerase Chain Reaction) techniques and sequential BLAST (Basic Local Alignment Search Tool) and MSA (Multiple Sequence Alignment) analyses, we identified and classified CON/COM repeats in genomes of eleven Deschampsia accessions and three accessions from related genera. High homology of CON/COM sequences were revealed in the studied species though differences in single-nucleotide alteration profiles detected in homologous CON/COM regions indicated that they tended to diverge independently. The performed chromosome mapping of 45S rDNA, 5S rDNA, and CON/COM repeats in six Deschampsia species demonstrated interspecific variability in localization of these cytogenetic markers and facilitated the identification of different chromosomal rearrangements. Based on the obtained data, the studied Deschampsia species were distinguished into karyological groups, and MSA-based schematic trees were built, which could clarify the relationships within the genus. Our findings can be useful for further genetic and phylogenetic studies.
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46
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Lopes M, Louzada S, Gama-Carvalho M, Chaves R. Genomic Tackling of Human Satellite DNA: Breaking Barriers through Time. Int J Mol Sci 2021; 22:4707. [PMID: 33946766 PMCID: PMC8125562 DOI: 10.3390/ijms22094707] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/24/2021] [Accepted: 04/27/2021] [Indexed: 12/12/2022] Open
Abstract
(Peri)centromeric repetitive sequences and, more specifically, satellite DNA (satDNA) sequences, constitute a major human genomic component. SatDNA sequences can vary on a large number of features, including nucleotide composition, complexity, and abundance. Several satDNA families have been identified and characterized in the human genome through time, albeit at different speeds. Human satDNA families present a high degree of sub-variability, leading to the definition of various subfamilies with different organization and clustered localization. Evolution of satDNA analysis has enabled the progressive characterization of satDNA features. Despite recent advances in the sequencing of centromeric arrays, comprehensive genomic studies to assess their variability are still required to provide accurate and proportional representation of satDNA (peri)centromeric/acrocentric short arm sequences. Approaches combining multiple techniques have been successfully applied and seem to be the path to follow for generating integrated knowledge in the promising field of human satDNA biology.
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Affiliation(s)
- Mariana Lopes
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (M.L.); (S.L.)
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal;
| | - Sandra Louzada
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (M.L.); (S.L.)
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal;
| | - Margarida Gama-Carvalho
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal;
| | - Raquel Chaves
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (M.L.); (S.L.)
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal;
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Vondrak T, Oliveira L, Novák P, Koblížková A, Neumann P, Macas J. Complex sequence organization of heterochromatin in the holocentric plant Cuscuta europaea elucidated by the computational analysis of nanopore reads. Comput Struct Biotechnol J 2021; 19:2179-2189. [PMID: 33995911 PMCID: PMC8091179 DOI: 10.1016/j.csbj.2021.04.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/31/2021] [Accepted: 04/03/2021] [Indexed: 12/20/2022] Open
Abstract
Repeat-rich regions of higher plant genomes are usually associated with constitutive heterochromatin, a specific type of chromatin that forms tightly packed nuclear chromocenters and chromosome bands. There is a large body of cytogenetic evidence that these chromosome regions are often composed of tandemly organized satellite DNA. However, comparatively little is known about the sequence arrangement within heterochromatic regions, which are difficult to assemble due to their repeated nature. Here, we explore long-range sequence organization of heterochromatin regions containing the major satellite repeat CUS-TR24 in the holocentric plant Cuscuta europaea. Using a combination of ultra-long read sequencing with assembly-free sequence analysis, we reveal the complex structure of these loci, which are composed of short arrays of CUS-TR24 interrupted frequently by emerging simple sequence repeats and targeted insertions of a specific lineage of LINE retrotransposons. These data suggest that the organization of satellite repeats constituting heterochromatic chromosome bands can be more complex than previously envisioned, and demonstrate that heterochromatin organization can be efficiently investigated without the need for genome assembly.
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Affiliation(s)
- Tihana Vondrak
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 31, České Budějovice CZ-37005, Czech Republic
- University of South Bohemia, Faculty of Science, České Budějovice, Czech Republic
| | - Ludmila Oliveira
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 31, České Budějovice CZ-37005, Czech Republic
| | - Petr Novák
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 31, České Budějovice CZ-37005, Czech Republic
| | - Andrea Koblížková
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 31, České Budějovice CZ-37005, Czech Republic
| | - Pavel Neumann
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 31, České Budějovice CZ-37005, Czech Republic
| | - Jiří Macas
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 31, České Budějovice CZ-37005, Czech Republic
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48
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Sader M, Vaio M, Cauz-Santos LA, Dornelas MC, Vieira MLC, Melo N, Pedrosa-Harand A. Large vs small genomes in Passiflora: the influence of the mobilome and the satellitome. PLANTA 2021; 253:86. [PMID: 33792791 DOI: 10.1007/s00425-021-03598-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 03/18/2021] [Indexed: 05/22/2023]
Abstract
While two lineages of retrotransposons were more abundant in larger Passiflora genomes, the satellitome was more diverse and abundant in the smallest genome analysed. Repetitive sequences are ubiquitous and fast-evolving elements responsible for size variation and large-scale organization of plant genomes. Within Passiflora genus, a tenfold variation in genome size, not attributed to polyploidy, is known. Here, we applied a combined in silico and cytological approach to study the organization and diversification of repetitive elements in three species of this genus representing its known range in genome size variation. Sequences were classified in terms of type and repetitiveness and the most abundant were mapped to chromosomes. We identified long terminal repeat (LTR) retrotransposons as the most abundant elements in the three genomes, showing a considerable variation among species. Satellite DNAs (satDNAs) were less representative, but highly diverse between subgenera. Our results clearly confirm that the largest genome species (Passiflora quadrangularis) presents a higher accumulation of repetitive DNA sequences, specially Angela and Tekay elements, making up most of its genome. Passiflora cincinnata, with intermediate genome and from the same subgenus, showed similarity with P. quadrangularis regarding the families of repetitive DNA sequences, but in different proportions. On the other hand, Passiflora organensis, the smallest genome, from a different subgenus, presented greater diversity and the highest proportion of satDNA. Altogether, our data indicates that while large genomes evolved by an accumulation of retrotransposons, the smallest genome known for the genus has evolved by diversification of different repeat types, particularly satDNAs.
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Affiliation(s)
- Mariela Sader
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, Pernambuco, Brazil.
| | - Magdalena Vaio
- Laboratory of Plant Genome Evolution and Domestication, Department of Plant Biology, Faculty of Agronomy, University of the Republic, Montevideo, Uruguay
| | - Luiz Augusto Cauz-Santos
- Genetics Department, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | | | - Maria Lucia Carneiro Vieira
- Genetics Department, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Natoniel Melo
- Laboratory of Biotechnology, Embrapa Semiarid, Petrolina, Pernambuco, Brazil
| | - Andrea Pedrosa-Harand
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, Pernambuco, Brazil
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49
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dos Santos RZ, Calegari RM, Silva DMZDA, Ruiz-Ruano FJ, Melo S, Oliveira C, Foresti F, Uliano-Silva M, Porto-Foresti F, Utsunomia R. A Long-Term Conserved Satellite DNA That Remains Unexpanded in Several Genomes of Characiformes Fish Is Actively Transcribed. Genome Biol Evol 2021; 13:evab002. [PMID: 33502491 PMCID: PMC8210747 DOI: 10.1093/gbe/evab002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/03/2021] [Indexed: 12/12/2022] Open
Abstract
Eukaryotic genomes contain large amounts of repetitive DNA sequences, such as tandemly repeated satellite DNAs (satDNAs). These sequences are highly dynamic and tend to be genus- or species-specific due to their particular evolutionary pathways, although there are few unusual cases of conserved satDNAs over long periods of time. Here, we used multiple approaches to reveal that an satDNA named CharSat01-52 originated in the last common ancestor of Characoidei fish, a superfamily within the Characiformes order, ∼140-78 Ma, whereas its nucleotide composition has remained considerably conserved in several taxa. We show that 14 distantly related species within Characoidei share the presence of this satDNA, which is highly amplified and clustered in subtelomeric regions in a single species (Characidium gomesi), while remained organized as small clusters in all the other species. Defying predictions of the molecular drive of satellite evolution, CharSat01-52 shows similar values of intra- and interspecific divergence. Although we did not provide evidence for a specific functional role of CharSat01-52, its transcriptional activity was demonstrated in different species. In addition, we identified short tandem arrays of CharSat01-52 embedded within single-molecule real-time long reads of Astyanax paranae (536 bp-3.1 kb) and A. mexicanus (501 bp-3.9 kb). Such arrays consisted of head-to-tail repeats and could be found interspersed with other sequences, inverted sequences, or neighbored by other satellites. Our results provide a detailed characterization of an old and conserved satDNA, challenging general predictions of satDNA evolution.
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Affiliation(s)
- Rodrigo Zeni dos Santos
- Departamento de Ciências Biológicas, Faculdade de Ciências, Universidade
Estadual Paulista, UNESP, Campus de Bauru, Bauru, Sao Paulo, Brazil
| | - Rodrigo Milan Calegari
- Departamento de Ciências Biológicas, Faculdade de Ciências, Universidade
Estadual Paulista, UNESP, Campus de Bauru, Bauru, Sao Paulo, Brazil
| | | | - Francisco J Ruiz-Ruano
- Department of Organismal Biology—Systematic Biology, Evolutionary Biology
Centre, Uppsala University, Uppsala, Sweden
| | - Silvana Melo
- Departamento de Biologia Estrutural e Funcional, Instituto de Biociências de
Botucatu, Universidade Estadual Paulista, UNESP, Botucatu, Sao Paulo,
Brazil
| | - Claudio Oliveira
- Departamento de Biologia Estrutural e Funcional, Instituto de Biociências de
Botucatu, Universidade Estadual Paulista, UNESP, Botucatu, Sao Paulo,
Brazil
| | - Fausto Foresti
- Departamento de Biologia Estrutural e Funcional, Instituto de Biociências de
Botucatu, Universidade Estadual Paulista, UNESP, Botucatu, Sao Paulo,
Brazil
| | | | - Fábio Porto-Foresti
- Departamento de Ciências Biológicas, Faculdade de Ciências, Universidade
Estadual Paulista, UNESP, Campus de Bauru, Bauru, Sao Paulo, Brazil
| | - Ricardo Utsunomia
- Departamento de Ciências Biológicas, Faculdade de Ciências, Universidade
Estadual Paulista, UNESP, Campus de Bauru, Bauru, Sao Paulo, Brazil
- Departamento de Genética, Instituto de Ciências Biológicas e da Saúde, ICBS,
Universidade Federal Rural do Rio de Janeiro, Seropédica, Rio de Janerio,
Brazil
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50
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Boštjančić LL, Bonassin L, Anušić L, Lovrenčić L, Besendorfer V, Maguire I, Grandjean F, Austin CM, Greve C, Hamadou AB, Mlinarec J. The Pontastacus leptodactylus (Astacidae) Repeatome Provides Insight Into Genome Evolution and Reveals Remarkable Diversity of Satellite DNA. Front Genet 2021; 11:611745. [PMID: 33552130 PMCID: PMC7859515 DOI: 10.3389/fgene.2020.611745] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 12/21/2020] [Indexed: 12/14/2022] Open
Abstract
Pontastacus leptodactylus is a native European crayfish species found in both freshwater and brackish environments. It has commercial importance for fisheries and aquaculture industries. Up till now, most studies concerning P. leptodactylus have focused onto gaining knowledge about its phylogeny and population genetics. However, little is known about the chromosomal evolution and genome organization of this species. Therefore, we performed clustering analysis of a low coverage genomic dataset to identify and characterize repetitive DNA in the P. leptodactylus genome. In addition, the karyogram of P. leptodactylus (2n = 180) is presented here for the first time consisting of 75 metacentric, 14 submetacentric, and a submetacentric/metacentric heteromorphic chromosome pair. We determined the genome size to be at ~18.7 gigabase pairs. Repetitive DNA represents about 54.85% of the genome. Satellite DNA repeats are the most abundant type of repetitive DNA, making up to ~28% of the total amount of repetitive elements, followed by the Ty3/Gypsy retroelements (~15%). Our study established a surprisingly high diversity of satellite repeats in P. leptodactylus. The genome of P. leptodactylus is by far the most satellite-rich genome discovered to date with 258 satellite families described. Of the five mapped satellite DNA families on chromosomes, PlSAT3-411 co-localizes with the AT-rich DAPI positive probable (peri)centromeric heterochromatin on all chromosomes, while PlSAT14-79 co-localizes with the AT-rich DAPI positive (peri)centromeric heterochromatin on one chromosome and is also located subterminally and intercalary on some chromosomes. PlSAT1-21 is located intercalary in the vicinity of the (peri)centromeric heterochromatin on some chromosomes, while PlSAT6-70 and PlSAT7-134 are located intercalary on some P. leptodactylus chromosomes. The FISH results reveal amplification of interstitial telomeric repeats (ITRs) in P. leptodactylus. The prevalence of repetitive elements, especially the satellite DNA repeats, may have provided a driving force for the evolution of the P. leptodactylus genome.
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Affiliation(s)
| | - Lena Bonassin
- Division of Molecular Biology, Department of Biology, University of Zagreb, Zagreb, Croatia
| | - Lucija Anušić
- Division of Molecular Biology, Department of Biology, University of Zagreb, Zagreb, Croatia
| | - Leona Lovrenčić
- Division of Zoology, Department of Biology, University of Zagreb, Zagreb, Croatia
| | - Višnja Besendorfer
- Division of Molecular Biology, Department of Biology, University of Zagreb, Zagreb, Croatia
| | - Ivana Maguire
- Division of Zoology, Department of Biology, University of Zagreb, Zagreb, Croatia
| | - Frederic Grandjean
- Laboratoire Ecologie Biologie des Interactions-UMR CNRS 7267, University of Poitiers, Poitiers, France
| | - Christopher M. Austin
- Centre of Integrative Ecology, School of Life and Environmental Sciences Deakin University, Geelong, VIC, Australia
| | - Carola Greve
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt, Germany
| | - Alexander Ben Hamadou
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt, Germany
| | - Jelena Mlinarec
- Division of Molecular Biology, Department of Biology, University of Zagreb, Zagreb, Croatia
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