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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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Nagao K, Tanaka Y, Kajitani R, Toyoda A, Itoh T, Kubota S, Goto Y. Bioinformatic and fine-scale chromosomal mapping reveal the nature and evolution of eliminated chromosomes in the Japanese hagfish, Eptatretus burgeri, through analysis of repetitive DNA families. PLoS One 2023; 18:e0286941. [PMID: 37639389 PMCID: PMC10461843 DOI: 10.1371/journal.pone.0286941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 08/14/2023] [Indexed: 08/31/2023] Open
Abstract
In the Japanese hagfish, Eptatretus burgeri, approximately 21% of the genomic DNA in germ cells (2n = 52) consists of 16 chromosomes (eliminated [E]-chromosomes) that are eliminated from presumptive somatic cells (2n = 36). To uncover the eliminated genome (E-genome), we have identified 16 eliminated repetitive DNA families from eight hagfish species, with 11 of these repeats being selectively amplified in the germline genome of E. burgeri. Furthermore, we have demonstrated that six of these sequences, namely EEEb1-6, are exclusively localized on all 16 E-chromosomes. This has led to the hypothesis that the eight pairs of E-chromosomes are derived from one pair of ancestral chromosomes via multiple duplication events over a prolonged evolutionary period. NGS analysis has recently facilitated the re-assembly of two distinct draft genomes of E. burgeri, derived from the testis and liver. This advancement allows for the prediction of not only nonrepetitive eliminated sequences but also over 100 repetitive and eliminated sequences, accomplished through K-mer-based analysis. In this study, we report four novel eliminated repetitive DNA sequences (designated as EEEb7-10) and confirm the relative chromosomal localization of all eliminated repeats (EEEb1-10) by fluorescence in situ hybridization (FISH). With the exception of EEEb10, all sequences were exclusively detected on EEEb1-positive chromosomes. Surprisingly, EEEb10 was detected as an intense signal on EEEb1-positive chromosomes and as a scattered signal on other chromosomes in germ cells. The study further divided the eight pairs of E-chromosomes into six groups based on the signal distribution of each DNA family, and fiber-FISH experiments showed that the EEEb2-10 family was dispersed in the EEEb1-positive extended chromatin fiber. These findings provide new insights into the mechanisms underlying chromosome elimination and the evolution of E-chromosomes, supporting our previous hypothesis.
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Affiliation(s)
- Kohei Nagao
- Department of Biology, Faculty of Science, Toho University, Funabashi, Chiba, Japan
| | - Yoshiki Tanaka
- Department of Life Science and Technology, School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo, Japan
| | - Rei Kajitani
- Department of Life Science and Technology, School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo, Japan
| | - Atsushi Toyoda
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka, Japan
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Takehiko Itoh
- Department of Life Science and Technology, School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo, Japan
| | - Souichirou Kubota
- Department of Biology, Faculty of Science, Toho University, Funabashi, Chiba, Japan
| | - Yuji Goto
- Department of Biology, Faculty of Science, Toho University, Funabashi, Chiba, Japan
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Vershinin AV, Elisafenko EA, Evtushenko EV. Genetic Redundancy in Rye Shows in a Variety of Ways. PLANTS (BASEL, SWITZERLAND) 2023; 12:282. [PMID: 36678994 PMCID: PMC9862056 DOI: 10.3390/plants12020282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/28/2022] [Accepted: 01/04/2023] [Indexed: 06/17/2023]
Abstract
Fifty years ago Susumu Ohno formulated the famous C-value paradox, which states that there is no correlation between the physical sizes of the genome, i.e., the amount of DNA, and the complexity of the organism, and highlighted the problem of genome redundancy. DNA that does not have a positive effect on the fitness of organisms has been characterized as "junk or selfish DNA". The controversial concept of junk DNA remains viable. Rye is a convenient subject for yet another test of the correctness and scientific significance of this concept. The genome of cultivated rye, Secale cereale L., is considered one of the largest among species of the tribe Triticeae and thus it tops the average angiosperm genome and the genomes of its closest evolutionary neighbors, such as species of barley, Hordeum (by approximately 30-35%), and diploid wheat species, Triticum (approximately 25%). The review provides an analysis of the structural organization of various regions of rye chromosomes with a description of the molecular mechanisms contributing to their size increase during evolution and the classes of DNA sequences involved in these processes. The history of the development of the concept of eukaryotic genome redundancy is traced and the current state of this problem is discussed.
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Affiliation(s)
- Alexander V. Vershinin
- Institute of Molecular and Cellular Biology, SB RAS, Acad. Lavrentiev Ave. 8/2, 630090 Novosibirsk, Russia
| | - Evgeny A. Elisafenko
- Institute of Molecular and Cellular Biology, SB RAS, Acad. Lavrentiev Ave. 8/2, 630090 Novosibirsk, Russia
- Institute of Cytology and Genetics, SB RAS, Acad. Lavrentiev Ave. 10, 630090 Novosibirsk, Russia
| | - Elena V. Evtushenko
- Institute of Molecular and Cellular Biology, SB RAS, Acad. Lavrentiev Ave. 8/2, 630090 Novosibirsk, Russia
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Aguilar M, Prieto P. Telomeres and Subtelomeres Dynamics in the Context of Early Chromosome Interactions During Meiosis and Their Implications in Plant Breeding. FRONTIERS IN PLANT SCIENCE 2021; 12:672489. [PMID: 34149773 PMCID: PMC8212018 DOI: 10.3389/fpls.2021.672489] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 05/06/2021] [Indexed: 05/08/2023]
Abstract
Genomic architecture facilitates chromosome recognition, pairing, and recombination. Telomeres and subtelomeres play an important role at the beginning of meiosis in specific chromosome recognition and pairing, which are critical processes that allow chromosome recombination between homologs (equivalent chromosomes in the same genome) in later stages. In plant polyploids, these terminal regions are even more important in terms of homologous chromosome recognition, due to the presence of homoeologs (equivalent chromosomes from related genomes). Although telomeres interaction seems to assist homologous pairing and consequently, the progression of meiosis, other chromosome regions, such as subtelomeres, need to be considered, because the DNA sequence of telomeres is not chromosome-specific. In addition, recombination operates at subtelomeres and, as it happens in rye and wheat, homologous recognition and pairing is more often correlated with recombining regions than with crossover-poor regions. In a plant breeding context, the knowledge of how homologous chromosomes initiate pairing at the beginning of meiosis can contribute to chromosome manipulation in hybrids or interspecific genetic crosses. Thus, recombination in interspecific chromosome associations could be promoted with the aim of transferring desirable agronomic traits from related genetic donor species into crops. In this review, we summarize the importance of telomeres and subtelomeres on chromatin dynamics during early meiosis stages and their implications in recombination in a plant breeding framework.
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Affiliation(s)
- Miguel Aguilar
- Área de Fisiología Vegetal, Universidad de Córdoba, Córdoba, Spain
| | - Pilar Prieto
- Plant Breeding Department, Institute for Sustainable Agriculture, Agencia Estatal Consejo Superior de Investigaciones Científicas (CSIC), Córdoba, Spain
- *Correspondence: Pilar Prieto, ; orcid.org/0000-0002-8160-808X
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Aguilar M, Prieto P. Sequence analysis of wheat subtelomeres reveals a high polymorphism among homoeologous chromosomes. THE PLANT GENOME 2020; 13:e20065. [PMID: 33029942 DOI: 10.1002/tpg2.20065] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 07/20/2020] [Accepted: 09/08/2020] [Indexed: 05/23/2023]
Abstract
Bread wheat, Triticum aestivum L., is one of the most important crops in the world. Understanding its genome organization (allohexaploid; AABBDD; 2n = 6x = 42) is essential for geneticists and plant breeders. Particularly, the knowledge of how homologous chromosomes (equivalent chromosomes from the same genome) specifically recognize each other to pair at the beginning of meiosis, the cellular process to generate gametes in sexually reproducing organisms, is fundamental for plant breeding and has a big influence on the fertility of wheat plants. Initial homologous chromosome interactions contribute to specific recognition and pairing between homologues at the onset of meiosis. Understanding the molecular basis of these critical processes can help to develop genetic tools in a breeding context to promote interspecific chromosome associations in hybrids or interspecific genetic crosses to facilitate the transfer of desirable agronomic traits from related species into a crop like wheat. The terminal regions of chromosomes, which include telomeres and subtelomeres, participate in chromosome recognition and pairing. We present a detailed molecular analysis of subtelomeres of wheat chromosome arms 1AS, 4AS, 7AS, 7BS and 7DS. Results showed a high polymorphism in the subtelomeric region among homoeologues (equivalent chromosomes from related genomes) for all the features analyzed, including genes, transposable elements, repeats, GC content, predicted CpG islands, recombination hotspots and targeted sequence motifs for relevant DNA-binding proteins. These polymorphisms might be the molecular basis for the specificity of homologous recognition and pairing in initial chromosome interactions at the beginning of meiosis in wheat.
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Affiliation(s)
- Miguel Aguilar
- Área de Fisiología Vegetal. Universidad de Córdoba. Campus de Rabanales, edif. C4, 3a planta, Córdoba, Spain
| | - Pilar Prieto
- Plant Breeding Department, Institute for Sustainable Agriculture, Agencia Estatal Consejo Superior de Investigaciones Científicas (CSIC), Alameda del Obispo s/n, Apartado 4084, Córdoba, 14080, Spain
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Kalinka A, Achrem M. The distribution pattern of 5-methylcytosine in rye (Secale L.) chromosomes. PLoS One 2020; 15:e0240869. [PMID: 33057421 PMCID: PMC7561101 DOI: 10.1371/journal.pone.0240869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 10/04/2020] [Indexed: 12/02/2022] Open
Abstract
The rye (Secale L.) genome is large, and it contains many classes of repetitive sequences. Secale species differ in terms of genome size, heterochromatin content, and global methylation level; however, the organization of individual types of sequences in chromosomes is relatively similar. The content of the abundant subtelomeric heterochromatin fraction in rye do not correlate with the global level of cytosine methylation, hence immunofluorescence detection of 5-methylcytosine (5-mC) distribution in metaphase chromosomes was performed. The distribution patterns of 5-methylcytosine in the chromosomes of Secale species/subspecies were generally similar. 5-methylcytosine signals were dispersed along the entire length of the chromosome arms of all chromosomes, indicating high levels of methylation, especially at retrotransposon sequences. 5-mC signals were absent in the centromeric and telomeric regions, as well as in subtelomeric blocks of constitutive heterochromatin, in each of the taxa studied. Pericentromeric domains were methylated, however, there was a certain level of polymorphism in these areas, as was the case with the nucleolus organizer region. Sequence methylation within the region of the heterochromatin intercalary bands were also demonstrated to be heterogenous. Unexpectedly, there was a lack of methylation in rye subtelomeres, indicating that heterochromatin is a very diverse fraction of chromatin, and its epigenetic regulation or potential influence on adjacent regions can be more complex than has conventionally been thought. Like telomeres and centromeres, subtelomeric heterochromatin can has a specific role, and the absence of 5-mC is required to maintain the heterochromatin state.
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Affiliation(s)
- Anna Kalinka
- Institute of Biology, University of Szczecin, Szczecin, Poland
- Molecular Biology and Biotechnology Center, University of Szczecin, Szczecin, Poland
- * E-mail:
| | - Magdalena Achrem
- Institute of Biology, University of Szczecin, Szczecin, Poland
- Molecular Biology and Biotechnology Center, University of Szczecin, Szczecin, Poland
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Milani D, Ramos É, Loreto V, Martí DA, Cardoso AL, de Moraes KCM, Martins C, Cabral-de-Mello DC. The satellite DNA AflaSAT-1 in the A and B chromosomes of the grasshopper Abracris flavolineata. BMC Genet 2017; 18:81. [PMID: 28851268 PMCID: PMC5575873 DOI: 10.1186/s12863-017-0548-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 08/22/2017] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Satellite DNAs (satDNAs) are organized in repetitions directly contiguous to one another, forming long arrays and composing a large portion of eukaryote genomes. These sequences evolve according to the concerted evolution model, and homogenization of repeats is observed at the intragenomic level. Satellite DNAs are the primary component of heterochromatin, located primarily in centromeres and telomeres. Moreover, satDNA enrichment in specific chromosomes has been observed, such as in B chromosomes, that can provide clues about composition, origin and evolution of this chromosome. In this study, we isolated and characterized a satDNA in A and B chromosomes of Abracris flavolineata by integrating cytogenetic, molecular and genomics approaches at intra- and inter-population levels, with the aim to understand the evolution of satDNA and composition of B chromosomes. RESULTS AflaSAT-1 satDNA was shared with other species and in A. flavolineata, was associated with another satDNA, AflaSAT-2. Chromosomal mapping revealed centromeric blocks variable in size in almost all chromosomes (except pair 11) of A complement for both satDNAs, whereas for B chromosome, only a small centromeric signal occurred. In distinct populations, variable number of AflaSAT-1 chromosomal sites correlated with variability in copy number. Instead of such variability, low sequence diversity was observed in A complement, but monomers from B chromosome were more variable, presenting also exclusive mutations. AflaSAT-1 was transcribed in five tissues of adults in distinct life cycle phases. CONCLUSIONS The sharing of AflaSAT-1 with other species is consistent with the library hypothesis and indicates common origin in a common ancestor; however, AflaSAT-1 was highly amplified in the genome of A. flavolineata. At the population level, homogenization of repeats in distinct populations was documented, but dynamic expansion or elimination of repeats was also observed. Concerning the B chromosome, our data provided new information on the composition in A. flavolineata. Together with previous results, the sequences of heterochromatic nature were not likely highly amplified in the entire B chromosome. Finally, the constitutive transcriptional activity suggests a possible unknown functional role, which should be further investigated.
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Affiliation(s)
- Diogo Milani
- Departamento de Biologia, UNESP - Univ Estadual Paulista, Instituto de Biociências/IB, Rio Claro, São Paulo CEP 13506-900 Brazil
| | - Érica Ramos
- Departamento de Morfologia, UNESP - Univ Estadual Paulista, Instituto de Biociências/IB, Botucatu, São Paulo Brazil
| | - Vilma Loreto
- Departamento de Genética, UFPE - Univ Federal de Pernambuco, Centro de Biociências/CB, Recife, Pernambuco Brazil
| | | | - Adauto Lima Cardoso
- Departamento de Morfologia, UNESP - Univ Estadual Paulista, Instituto de Biociências/IB, Botucatu, São Paulo Brazil
| | | | - Cesar Martins
- Departamento de Morfologia, UNESP - Univ Estadual Paulista, Instituto de Biociências/IB, Botucatu, São Paulo Brazil
| | - Diogo Cavalcanti Cabral-de-Mello
- Departamento de Biologia, UNESP - Univ Estadual Paulista, Instituto de Biociências/IB, Rio Claro, São Paulo CEP 13506-900 Brazil
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de Lima LG, Svartman M, Kuhn GCS. Dissecting the Satellite DNA Landscape in Three Cactophilic Drosophila Sequenced Genomes. G3 (BETHESDA, MD.) 2017; 7:2831-2843. [PMID: 28659292 PMCID: PMC5555486 DOI: 10.1534/g3.117.042093] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 06/26/2017] [Indexed: 01/12/2023]
Abstract
Eukaryote genomes are replete with repetitive DNAs. This class includes tandemly repeated satellite DNAs (satDNA) which are among the most abundant, fast evolving (yet poorly studied) genomic components. Here, we used high-throughput sequencing data from three cactophilic Drosophila species, D. buzzatii, D. seriema, and D. mojavensis, to access and study their whole satDNA landscape. In total, the RepeatExplorer software identified five satDNAs, three previously described (pBuM, DBC-150 and CDSTR198) and two novel ones (CDSTR138 and CDSTR130). Only pBuM is shared among all three species. The satDNA repeat length falls within only two classes, between 130 and 200 bp or between 340 and 390 bp. FISH on metaphase and polytene chromosomes revealed the presence of satDNA arrays in at least one of the following genomic compartments: centromeric, telomeric, subtelomeric, or dispersed along euchromatin. The chromosomal distribution ranges from a single chromosome to almost all chromosomes of the complement. Fiber-FISH and sequence analysis of contigs revealed interspersion between pBuM and CDSTR130 in the microchromosomes of D. mojavensis Phylogenetic analyses showed that the pBuM satDNA underwent concerted evolution at both interspecific and intraspecific levels. Based on RNA-seq data, we found transcription activity for pBuM (in D. mojavensis) and CDSTR198 (in D. buzzatii) in all five analyzed developmental stages, most notably in pupae and adult males. Our data revealed that cactophilic Drosophila present the lowest amount of satDNAs (1.9-2.9%) within the Drosophila genus reported so far. We discuss how our findings on the satDNA location, abundance, organization, and transcription activity may be related to functional aspects.
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Affiliation(s)
- Leonardo G de Lima
- Laboratório de Citogenômica Evolutiva, Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil
| | - Marta Svartman
- Laboratório de Citogenômica Evolutiva, Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil
| | - Gustavo C S Kuhn
- Laboratório de Citogenômica Evolutiva, Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil
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Palacios-Gimenez OM, Dias GB, de Lima LG, Kuhn GCES, Ramos É, Martins C, Cabral-de-Mello DC. High-throughput analysis of the satellitome revealed enormous diversity of satellite DNAs in the neo-Y chromosome of the cricket Eneoptera surinamensis. Sci Rep 2017; 7:6422. [PMID: 28743997 PMCID: PMC5527012 DOI: 10.1038/s41598-017-06822-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 06/19/2017] [Indexed: 12/31/2022] Open
Abstract
Satellite DNAs (satDNAs) constitute large portion of eukaryote genomes, comprising non-protein-coding sequences tandemly repeated. They are mostly found in heterochromatic regions of chromosomes such as around centromere or near telomeres, in intercalary heterochromatin, and often in non-recombining segments of sex chromosomes. We examined the satellitome in the cricket Eneoptera surinamensis (2n = 9, neo-X1X2Y, males) to characterize the molecular evolution of its neo-sex chromosomes. To achieve this, we analyzed illumina reads using graph-based clustering and complementary analyses. We found an unusually high number of 45 families of satDNAs, ranging from 4 bp to 517 bp, accounting for about 14% of the genome and showing different modular structures and high diversity of arrays. FISH mapping revealed that satDNAs are located mostly in C-positive pericentromeric regions of the chromosomes. SatDNAs enrichment was also observed in the neo-sex chromosomes in comparison to autosomes. Especially astonishing accumulation of satDNAs loci was found in the highly differentiated neo-Y, including 39 satDNAs over-represented in this chromosome, which is the greatest satDNAs diversity yet reported for sex chromosomes. Our results suggest possible involvement of satDNAs in genome increasing and in molecular differentiation of the neo-sex chromosomes in this species, contributing to the understanding of sex chromosome composition and evolution in Orthoptera.
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Affiliation(s)
| | - Guilherme Borges Dias
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Leonardo Gomes de Lima
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | | | - Érica Ramos
- UNESP - Univ Estadual Paulista, Instituto de Biociências/IB, Departamento de Morfologia, Botucatu, São Paulo, Brazil
| | - Cesar Martins
- UNESP - Univ Estadual Paulista, Instituto de Biociências/IB, Departamento de Morfologia, Botucatu, São Paulo, Brazil
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10
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Petrovičová L, Balážová Ž, Vivodík M, Gálová Z. Detection genetic variability of secale cereale L. by scot markers. POTRAVINARSTVO 2017. [DOI: 10.5219/726] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Rye (Secale cereale L.) is our traditional cereal used for baking. The genetic variability of grown rye has been reduced by modern agronomic practices, which subsequently prompted the importance of search for species that could be useful as a gene pool for the improving of flour quality for human consumption or for other industrial uses. Therefore, the aim of this study was to detect genetic variability among the set of 45 rye genotypes using 8 SCoT markers. Amplification of genomic DNA of 45 genotypes, using SCoT analysis, yielded 114 fragments, with an average of 14.25 polymorphic fragments per primer. The most polymorphic primer was SCoT 36, where 21 polymorphic amplification products were detected. In contract the lowest polymorphic primer was SCoT 45 with 5 polymorphic products. Genetic polymorphism was characterized based on diversity index (DI), probability of identity (PI) and polymorphic information content (PIC). The hierarchical cluster analysis showed that the rye genotypes were divided into 2 main clusters. One rye genotype Motto, origin from Poland formed a separate subcluster (1b). Subscluster 2a included only genotype Valtické (CSK). In this experiment, SCoT proved to be a rapid, reliable and practicable method for revealing of polymorphism in the rye cultivars.
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11
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Kirov IV, Kiseleva AV, Van Laere K, Van Roy N, Khrustaleva LI. Tandem repeats of Allium fistulosum associated with major chromosomal landmarks. Mol Genet Genomics 2017; 292:453-464. [PMID: 28150039 DOI: 10.1007/s00438-016-1286-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2016] [Accepted: 12/30/2016] [Indexed: 01/22/2023]
Abstract
Tandem repeats are often associated with important chromosomal landmarks, such as centromeres, telomeres, subtelomeric, and other heterochromatic regions, and can be good candidates for molecular cytogenetic markers. Tandem repeats present in many plant species demonstrate dramatic differences in unit length, proportion in the genome, and chromosomal organization. Members of genus Allium with their large genomes represent a challenging task for current genetics. Using the next generation sequencing data, molecular, and cytogenetic methods, we discovered two tandemly organized repeats in the Allium fistulosum genome (2n = 2C = 16), HAT58 and CAT36. Together, these repeats comprise 0.25% of the bunching onion genome with 160,000 copies/1 C of HAT58 and 93,000 copies/1 C of CAT36. Fluorescent in situ hybridization (FISH) and C-banding showed that HAT58 and CAT36 associated with the interstitial and pericentromeric heterochromatin of the A. fistulosum chromosomes 5, 6, 7, and 8. FISH with HAT58 and CAT36 performed on A. cepa (2n = 2C = 16) and A. wakegi (2n = 2C = 16), a natural allodiploid hybrid between A. fistulosum and A. cepa, revealed that these repeats are species specific and produced specific hybridization patterns only on A. fistulosum chromosomes. Thus, the markers can be used in interspecific breeding programs for monitoring of alien genetic material. We applied Non-denaturing FISH that allowed detection of the repeat bearing chromosomes within 3 h. A polymorphism of the HAT58 chromosome location was observed. This finding suggests that the rapid evolution of the HAT58 repeat is still ongoing.
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Affiliation(s)
- Ilya V Kirov
- Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Moscow, Russia. .,Department of Genetics, Biotechnology and Plant Breeding, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Moscow, Russia. .,Plant Sciences Unit, Applied Genetics and Breeding, Institute for Agricultural and Fisheries Research (ILVO), Melle, Belgium.
| | - Anna V Kiseleva
- Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Moscow, Russia.,Department of Genetics, Biotechnology and Plant Breeding, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Moscow, Russia
| | - Katrijn Van Laere
- Plant Sciences Unit, Applied Genetics and Breeding, Institute for Agricultural and Fisheries Research (ILVO), Melle, Belgium
| | - Nadine Van Roy
- Faculty of Medicine and Health Sciences, Center of Medical Genetics, Ghent University, Ghent, Belgium
| | - Ludmila I Khrustaleva
- Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Moscow, Russia. .,Department of Genetics, Biotechnology and Plant Breeding, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Moscow, Russia.
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Zimina OV, Parii MF, Alkhimova OG. Loss of heterozygosity at individual loci in Arabidopsis thaliana regenerants cultured with para-fluorophenylalanine. CYTOL GENET+ 2016. [DOI: 10.3103/s0095452716050157] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Evtushenko EV, Levitsky VG, Elisafenko EA, Gunbin KV, Belousov AI, Šafář J, Doležel J, Vershinin AV. The expansion of heterochromatin blocks in rye reflects the co-amplification of tandem repeats and adjacent transposable elements. BMC Genomics 2016; 17:337. [PMID: 27146967 PMCID: PMC4857426 DOI: 10.1186/s12864-016-2667-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 04/25/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND A prominent and distinctive feature of the rye (Secale cereale) chromosomes is the presence of massive blocks of subtelomeric heterochromatin, the size of which is correlated with the copy number of tandem arrays. The rapidity with which these regions have formed over the period of speciation remains unexplained. RESULTS Using a BAC library created from the short arm telosome of rye chromosome 1R we uncovered numerous arrays of the pSc200 and pSc250 tandem repeat families which are concentrated in subtelomeric heterochromatin and identified the adjacent DNA sequences. The arrays show significant heterogeneity in monomer organization. 454 reads were used to gain a representation of the expansion of these tandem repeats across the whole rye genome. The presence of multiple, relatively short monomer arrays, coupled with the mainly star-like topology of the monomer phylogenetic trees, was taken as indicative of a rapid expansion of the pSc200 and pSc250 arrays. The evolution of subtelomeric heterochromatin appears to have included a significant contribution of illegitimate recombination. The composition of transposable elements (TEs) within the regions flanking the pSc200 and pSc250 arrays differed markedly from that in the genome a whole. Solo-LTRs were strongly enriched, suggestive of a history of active ectopic exchange. Several DNA motifs were over-represented within the LTR sequences. CONCLUSION The large blocks of subtelomeric heterochromatin have arisen from the combined activity of TEs and the expansion of the tandem repeats. The expansion was likely based on a highly complex network of recombination mechanisms.
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Affiliation(s)
- E V Evtushenko
- Institute of Molecular and Cellular Biology, Siberian Branch of the RAS, Novosibirsk, Russia
| | - V G Levitsky
- Institute of Cytology and Genetics, Siberian Branch of the RAS, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - E A Elisafenko
- Institute of Cytology and Genetics, Siberian Branch of the RAS, Novosibirsk, Russia
| | - K V Gunbin
- Institute of Cytology and Genetics, Siberian Branch of the RAS, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - A I Belousov
- Institute of Molecular and Cellular Biology, Siberian Branch of the RAS, Novosibirsk, Russia
| | - J Šafář
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - J Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - A V Vershinin
- Institute of Molecular and Cellular Biology, Siberian Branch of the RAS, Novosibirsk, Russia.
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15
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New types of wheat chromosomal structural variations in derivatives of wheat-rye hybrids. PLoS One 2014; 9:e110282. [PMID: 25302962 PMCID: PMC4193885 DOI: 10.1371/journal.pone.0110282] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 09/15/2014] [Indexed: 11/25/2022] Open
Abstract
Background Chromosomal rearrangements induced by wheat-rye hybridization is a very well investigated research topic. However, the structural alterations of wheat chromosomes in wheat-rye hybrids are seldom reported. Methodology/Principal Findings Octoploid triticale lines were derived from common wheat Triticum. aestivum L. ‘Mianyang11’×rye Secale cereale L. ‘Kustro’. Some progeny were obtained by the controlled backcrossing of triticale with ‘Mianyang11’ and common wheat T. aestivum L. ‘Chuannong27’ followed by self-fertilization. Fluorescence in situ hybridization (FISH) and genomic in situ hybridization (GISH) using Oligo-pSc119.2-1, Oligo-pTa535-1 and rye genomic DNA as probes were used to analyze the mitotic chromosomes of these progeny. Alterations of wheat chromosomes including 5A, 6A, 1B, 2B, 6B, 7B, 1D, 3D and 7D were observed. 5AL arm carrying intercalary Oligo-pSc119.2-1, Oligo-pTa535-1 or both Oligo-pSc119.2-1 and Oligo-pTa535-1 signals, 6AS, 1BS and 1DL arms containing terminal Oligo-pSc119.2-1 signal, 6BS and 3DS arms without terminal Oligo-pSc119.2-1 signal, 7BS without subtelomeric Oligo-pSc119.2-1 signal and 7DL with intercalary Oligo-pSc119.2-1 signal have been observed. However, these changed wheat chromosomes have not been detected in ‘Mianyang11’ and Chuannong 27. The altered 5A, 6A, 7B and 7D chromosomes in this study have not been reported and represent several new karyotype structures of common wheat chromosomes. Conclusions/Significance These rearranged wheat chromosomes in the present study afford some new genetic variations for wheat breeding program and are valuable materials for studying the biological function of tandem repetitive DNA sequences.
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Paesold S, Borchardt D, Schmidt T, Dechyeva D. A sugar beet (Beta vulgaris L.) reference FISH karyotype for chromosome and chromosome-arm identification, integration of genetic linkage groups and analysis of major repeat family distribution. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 72:600-11. [PMID: 22775355 DOI: 10.1111/j.1365-313x.2012.05102.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
We developed a reference karyotype for B. vulgaris which is applicable to all beet cultivars and provides a consistent numbering of chromosomes and genetic linkage groups. Linkage groups of sugar beet were assigned to physical chromosome arms by FISH (fluorescent in situ hybridization) using a set of 18 genetically anchored BAC (bacterial artificial chromosome) markers. Genetic maps of sugar beet were correlated to chromosome arms, and North-South orientation of linkage groups was established. The FISH karyotype provides a technical platform for genome studies and can be applied for numbering and identification of chromosomes in related wild beet species. The discrimination of all nine chromosomes by BAC probes enabled the study of chromosome-specific distribution of the major repetitive components of sugar beet genome comprising pericentromeric, intercalary and subtelomeric satellites and 18S-5.8S-25S and 5S rRNA gene arrays. We developed a multicolor FISH procedure allowing the identification of all nine sugar beet chromosome pairs in a single hybridization using a pool of satellite DNA probes. Fiber-FISH was applied to analyse five chromosome arms in which the furthermost genetic marker of the linkage group was mapped adjacently to terminal repetitive sequences on pachytene chromosomes. Only on two arms telomere arrays and the markers are physically linked, hence these linkage groups can be considered as terminally closed making the further identification of distal informative markers difficult. The results support genetic mapping by marker localization, the anchoring of contigs and scaffolds for the annotation of the sugar beet genome sequence and the analysis of the chromosomal distribution patterns of major families of repetitive DNA.
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MESH Headings
- Beta vulgaris/genetics
- Chromosomes, Artificial, Bacterial/genetics
- Chromosomes, Plant/genetics
- DNA Probes/genetics
- DNA, Plant/analysis
- DNA, Plant/genetics
- DNA, Satellite/analysis
- DNA, Satellite/genetics
- Genetic Linkage
- Genetic Markers
- Genome, Plant
- In Situ Hybridization, Fluorescence/methods
- Karyotype
- Pachytene Stage
- Physical Chromosome Mapping/methods
- RNA, Ribosomal/analysis
- RNA, Ribosomal/genetics
- RNA, Ribosomal, 18S/analysis
- RNA, Ribosomal, 18S/genetics
- RNA, Ribosomal, 5.8S/analysis
- RNA, Ribosomal, 5.8S/genetics
- Reference Standards
- Tandem Repeat Sequences
- Telomere/genetics
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Affiliation(s)
- Susanne Paesold
- Institute of Botany, Dresden University of Technology, Zellescher Weg 20b, 01217 Dresden, Germany
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Tang ZX, Fu SL, Ren ZL, Zhang T, Zou YT, Yang ZJ, Li GR, Zhou JP, Zhang HQ, Yan BJ, Zhang HY, Tan FQ. Diversity and evolution of four dispersed repetitive DNA sequences in the genus Secale. Genome 2011; 54:285-300. [PMID: 21491972 DOI: 10.1139/g10-118] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We present the first characterization of 360 sequences in six species of the genus Secale of both cultivated and wild accessions. These include four distinct kinds of dispersed repetitive DNA sequences named pSc20H, pSc119.1, pSaO5(411), and pSaD15(940) belonging to the Revolver family. During the evolution of the genus Secale from wild to cultivated accessions, the pSaO5(411)-like sequences became shorter mainly because of the deletion of a trinucleotide tandem repeating unit, the pSc20H-like sequences displayed apparent homogenization in cultivated rye, and the second intron of Revolver became longer. In addition, the pSc20H-, pSc119.1-, and pSaO5(411)-like sequences cloned from wild rye and cultivated rye could be divided into two large clades. No single case of the four kinds of repetitive elements has been inherited by each Secale accession from a lone ancestor. It is reasonable to consider the vertical transmission of the four repetitive elements during the evolution of the genus Secale. The pSc20H- and pSaO5(411)-like sequences showed evolutionary elimination at specific chromosomal locations from wild species to cultivated species. These cases imply that different repetitive DNA sequences have played different roles in the chromosome development and genomic evolution of rye. The present study adds important information to the investigations dealing with characterization of dispersed repetitive elements in wild and cultivated rye.
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Affiliation(s)
- Zong-Xiang Tang
- State Key Laboratory of Plant Breeding and Genetics, Sichuan Agriculture University, Ya'an, Sichuan 625014, China
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Heslop-Harrison JSP, Schwarzacher T. Organisation of the plant genome in chromosomes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2011; 66:18-33. [PMID: 21443620 DOI: 10.1111/j.1365-313x.2011.04544.x] [Citation(s) in RCA: 153] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The plant genome is organized into chromosomes that provide the structure for the genetic linkage groups and allow faithful replication, transcription and transmission of the hereditary information. Genome sizes in plants are remarkably diverse, with a 2350-fold range from 63 to 149,000 Mb, divided into n=2 to n= approximately 600 chromosomes. Despite this huge range, structural features of chromosomes like centromeres, telomeres and chromatin packaging are well-conserved. The smallest genomes consist of mostly coding and regulatory DNA sequences present in low copy, along with highly repeated rDNA (rRNA genes and intergenic spacers), centromeric and telomeric repetitive DNA and some transposable elements. The larger genomes have similar numbers of genes, with abundant tandemly repeated sequence motifs, and transposable elements alone represent more than half the DNA present. Chromosomes evolve by fission, fusion, duplication and insertion events, allowing evolution of chromosome size and chromosome number. A combination of sequence analysis, genetic mapping and molecular cytogenetic methods with comparative analysis, all only becoming widely available in the 21st century, is elucidating the exact nature of the chromosome evolution events at all timescales, from the base of the plant kingdom, to intraspecific or hybridization events associated with recent plant breeding. As well as being of fundamental interest, understanding and exploiting evolutionary mechanisms in plant genomes is likely to be a key to crop development for food production.
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Wang CT, Ho CH, Hseu MJ, Chen CM. The subtelomeric region of the Arabidopsis thaliana chromosome IIIR contains potential genes and duplicated fragments from other chromosomes. PLANT MOLECULAR BIOLOGY 2010; 74:155-166. [PMID: 20652368 DOI: 10.1007/s11103-010-9664-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2010] [Accepted: 07/05/2010] [Indexed: 05/29/2023]
Abstract
The subtelomere and a portion of the associated telomeric region (together named 3RTAS) of chromosome IIIR from the Arabidopsis thaliana ecotypes Columbia (Col) and Wassilewskija (Ws) were specifically amplified by polymerase chain reaction and subsequently cloned and sequenced. The centromere-proximal portion of 3RTAS from both ecotypes contained two newly identified potential genes, one encoding the chloroplast luminal 19-kDa protein precursor and the other encoding three potential alternatively spliced CCCH-type zinc finger proteins. The telomere-proximal portion of 3RTAS from the Col ecotype contained short duplicated fragments derived from chromosomes I, II, and III, and that from the Ws ecotype contained a duplicated fragment derived from chromosome V. Each duplicated fragment has diverged somewhat in sequence from that of the ectopic template. Small patches of homologous nucleotides were found within the flanking sequences of both the duplicated fragments and the corresponding ectopic template sequences. The structural characteristics of these duplicated fragments suggest that they are filler DNAs captured by non-homologous end joining during double-strand break repair. Our characterization of 3RTAS not only filled up a gap in the chromosome IIIR sequence of A. thaliana but also identified new genes with unknown functions.
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Affiliation(s)
- Chi-Ting Wang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan, Republic of China
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20
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Kuhn GCS, Schwarzacher T, Heslop-Harrison JS. The non-regular orbit: three satellite DNAs in Drosophila martensis (buzzatii complex, repleta group) followed three different evolutionary pathways. Mol Genet Genomics 2010; 284:251-62. [PMID: 20683615 DOI: 10.1007/s00438-010-0564-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2010] [Accepted: 07/20/2010] [Indexed: 11/29/2022]
Abstract
The genome of species from the buzzatii cluster (buzzatii complex, repleta group) is hosted by a number of satellite DNAs (satDNAs) showing contrasting structural characteristics, genomic organization and evolution, such as pBuM-alpha (~190 bp repeats), pBuM-alpha/beta (~370 bp repeats) and the DBC-150 (~150 bp repeats). In the present study, we aimed to investigate the evolution of these three satDNAs by looking for homologous sequences in the genome of the closest outgroup species: Drosophila martensis (buzzatii complex). After PCR, we isolated and sequenced 9 alpha, 8 alpha/beta and 11 DBC-150 sequences from this species. The results were compared to all pBuM and DBC-150 sequences available in literature. After D. martensis split from the buzzatii cluster some 6 Mya, the three satDNAs evolved differently in the genome of D. martensis by: (1) maintenance of a collection of major types of ancestral repeats in the genome (alpha); (2) fixation for a single major type of ancestral repeats (alpha/beta) or (3) fixation for new divergent species-specific repeat types (DBC-150). Curiously, D. seriema and D. martensis, although belonging to different and allopatric clusters, became independently fixed for the same major type of alpha/beta ancestral repeats, illustrating a rare case of parallelism in satDNA evolution. The contrasting pictures illustrate the diversity of evolutionary pathways a satDNA can follow, defining a "non-regular orbit" with outcomes difficult to predict.
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Affiliation(s)
- Gustavo C S Kuhn
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, Via Washington Luís, Km 235, São Carlos, SP 13565-905, Brazil.
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Tomita M, Asao M, Kuraki A. Effective isolation of retrotransposons and repetitive DNA families from the wheat genome. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2010; 52:679-691. [PMID: 20590997 DOI: 10.1111/j.1744-7909.2010.00954.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
New classes of repetitive DNA elements were effectively identified by isolating small fragments of the elements from the wheat genome. A wheat A genome library was constructed from Triticum monococcum by degenerate cleavage with EcoO109I, the recognition sites of which consisted of 5'-PuGGNCCPy-3' multi-sequences. Three novel repetitive sequences pTm6, pTm69 and pTm58 derived from the A genome were screened and tested for high copy number using a blotting approach. pTm6 showed identity with integrase domains of the barley Ty1-Copia-retrotransposon BARE-1 and pTm58 showed similarity to the barley Ty3-gypsy-like retrotransposon Romani. pTm69, however, constituted a tandem array with useful genomic specificities, but did not share any identity with known repetitive elements. This study also sought to isolate wheat D-genome-specific repetitive elements regardless of the level of methylation, by genomic subtraction. Total genomic DNA of Aegilops tauschii was cleaved into short fragments with a methylation-insensitive 4 bp cutter, MboI, and then common DNA sequences between Ae. tauschii and Triticum turgidum were subtracted by annealing with excess T. turgidum genomic DNA. The D genome repetitive sequence pAt1 was isolated and used to identify an additional novel repetitive sequence family from wheat bacterial artificial chromosomes with a size range of 1 395-1 850 bp. The methods successfully led pathfinding of two unique repetitive families.
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Affiliation(s)
- Motonori Tomita
- Molecular Genetics Laboratory, Faculty of Agriculture, Tottori University, Tottori 680-8553, Japan.
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22
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Evtushenko EV, Elisafenko EA, Vershinin AV. The relationship between two tandem repeat families in rye heterochromatin. Mol Biol 2010. [DOI: 10.1134/s0026893310010012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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23
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Salina EA, Sergeeva EM, Adonina IG, Shcherban AB, Afonnikov DA, Belcram H, Huneau C, Chalhoub B. Isolation and sequence analysis of the wheat B genome subtelomeric DNA. BMC Genomics 2009; 10:414. [PMID: 19732459 PMCID: PMC2756281 DOI: 10.1186/1471-2164-10-414] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2009] [Accepted: 09/05/2009] [Indexed: 12/17/2022] Open
Abstract
Background Telomeric and subtelomeric regions are essential for genome stability and regular chromosome replication. In this work, we have characterized the wheat BAC (bacterial artificial chromosome) clones containing Spelt1 and Spelt52 sequences, which belong to the subtelomeric repeats of the B/G genomes of wheats and Aegilops species from the section Sitopsis. Results The BAC library from Triticum aestivum cv. Renan was screened using Spelt1 and Spelt52 as probes. Nine positive clones were isolated; of them, clone 2050O8 was localized mainly to the distal parts of wheat chromosomes by in situ hybridization. The distribution of the other clones indicated the presence of different types of repetitive sequences in BACs. Use of different approaches allowed us to prove that seven of the nine isolated clones belonged to the subtelomeric chromosomal regions. Clone 2050O8 was sequenced and its sequence of 119 737 bp was annotated. It is composed of 33% transposable elements (TEs), 8.2% Spelt52 (namely, the subfamily Spelt52.2) and five non-TE-related genes. DNA transposons are predominant, making up 24.6% of the entire BAC clone, whereas retroelements account for 8.4% of the clone length. The full-length CACTA transposon Caspar covers 11 666 bp, encoding a transposase and CTG-2 proteins, and this transposon accounts for 40% of the DNA transposons. The in situ hybridization data for 2050O8 derived subclones in combination with the BLAST search against wheat mapped ESTs (expressed sequence tags) suggest that clone 2050O8 is located in the terminal bin 4BL-10 (0.95-1.0). Additionally, four of the predicted 2050O8 genes showed significant homology to four putative orthologous rice genes in the distal part of rice chromosome 3S and confirm the synteny to wheat 4BL. Conclusion Satellite DNA sequences from the subtelomeric regions of diploid wheat progenitor can be used for selecting the BAC clones from the corresponding regions of hexaploid wheat chromosomes. It has been demonstrated for the first time that Spelt52 sequences were involved in the evolution of terminal regions of common wheat chromosomes. Our research provides new insights into the microcollinearity in the terminal regions of wheat chromosomes 4BL and rice chromosome 3S.
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Affiliation(s)
- Elena A Salina
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Science, pr, Lavrentieva 10, Novosibirsk, 630090, Russia.
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Anamthawat-Jónsson K, Wenke T, Thórsson AT, Sveinsson S, Zakrzewski F, Schmidt T. Evolutionary diversification of satellite DNA sequences from Leymus (Poaceae: Triticeae). Genome 2009; 52:381-90. [PMID: 19370093 DOI: 10.1139/g09-013] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The genus Leymus (lymegrass) comprises about 30 polyploid, perennial, temperate grass species in the tribe Triticeae (family Poaceae). Previous studies indicated a large diversity in the Leymus genome, and therefore, the aim of this study was to isolate new repetitive DNA sequences that can be used for differentiating Leymus species and elucidating their genomic relationships. A C0t-1 DNA plasmid library was generated from genomic DNA of American tetraploid species Leymus triticoides. A family of highly repetitive satellite DNA sequences, designated Lt1, was obtained from this library. The Lt1 family consisted of 380 bp SacI repeating units arranging in tandem arrays. A 120 bp MspI subfamily was discovered within this family, indicating that cytosine methylation may have played an important role in the evolution of satellite sequences. The Lt1 satellite was localized in the subtelomeric heterochromatic blocks of L. triticoides chromosomes, which are present on all chromosomes and often on both arms. The Lt1 sequences are abundant in L. triticoides but absent in its closely related species Leymus racemosus. Significant homology was found between the Lt1 family and numerous repetitive sequences from Poaceae species, indicating that the Lt1 is an ancient family of tandemly repeated sequences in grasses.
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Tomita M, Akai K, Morimoto T. Genomic Subtraction Recovers Rye-Specific DNA Elements Enriched in the Rye Genome. Mol Biotechnol 2009; 42:160-7. [DOI: 10.1007/s12033-009-9151-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2008] [Accepted: 01/22/2009] [Indexed: 11/24/2022]
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Evolutionary dynamics and sites of illegitimate recombination revealed in the interspersion and sequence junctions of two nonhomologous satellite DNAs in cactophilic Drosophila species. Heredity (Edinb) 2009; 102:453-64. [PMID: 19259119 DOI: 10.1038/hdy.2009.9] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Satellite DNA (satDNA) is a major component of genomes but relatively little is known about the fine-scale organization of unrelated satDNAs residing at the same chromosome location, and the sequence structure and dynamics of satDNA junctions. We studied the organization and sequence junctions of two nonhomologous satDNAs, pBuM and DBC-150, in three species from the neotropical Drosophila buzzatii cluster (repleta group). In situ hybridization to microchromosomes, interphase nuclei and extended DNA fibers showed frequent interspersion of the two satellites in D. gouveai, D. antonietae and, to a lesser extent, D. seriema. We isolated by PCR six pBuM x DBC-150 junctions: four are exclusive to D. gouveai and two are exclusive to D. antonietae. The six junction breakpoints occur at different positions within monomers, suggesting independent origin. Four junctions showed abrupt transitions between the two satellites, whereas two junctions showed a distinct 10 bp tandem duplication before the junction. Unlike pBuM, DBC-150 junction repeats are more variable than randomly cloned monomers and showed diagnostic features in common to a 3-monomer higher-order repeat seen in the sister species D. serido. The high levels of interspersion between pBuM and DBC-150 repeats suggest extensive rearrangements between the two satellites, maybe favored by specific features of the microchromosomes. Our interpretation is that the junctions evolved by multiples events of illegitimate recombination between nonhomologous satDNA repeats, with subsequent rounds of unequal crossing-over expanding the copy number of some of the junctions.
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Tang ZX, Fu SL, Ren ZL, Zhou JP, Yan BJ, Zhang HQ. Variations of tandem repeat, regulatory element, and promoter regions revealed by wheat–rye amphiploids. Genome 2008; 51:399-408. [DOI: 10.1139/g08-027] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
To better understand the evolution of allopolyploids, 4 different combinations between wheat ( Triticum aestivum L.) and rye ( Secale cereale L.) including 12 F1hybrids and 12 derived amphiploids were analyzed and compared with their direct parental plants by PCR analysis using 150 wheat SSR (single sequence repeat) markers and by FISH analysis using a rye-specific repetitive sequence (pSc200) as a probe. Nine SSR markers amplified rye-specific fragments whose sizes ranged from 471 bp to 1089 bp. These fragments contain regulatory elements and (or) promoters. Some of these fragments were amplified from all 24 progenies, while others were amplified from a subset of the progenies. The disappearance of rye-specific fragments from some progenies was caused by sequence elimination or DNA modification. Marker Xgwm320 amplified a new fragment (403 bp), a rye-specific tandem repeat, from some of the progenies. Twenty-eight SSR markers displayed microsatellite variation in progenies derived from ‘Chinese Spring’ × ‘Jinzhou-heimai’, but none of the 150 SSR markers displayed microsatellite variation in the progenies derived from the other three combinations. FISH signals of pSc200 were eliminated from one telomere/subtelomere of 4 chromosomes of ‘Kustro’ during allopolyploidization and expanded in amphiploids derived from ‘Chinese Spring’ × ‘AR106BONE’. Thus, allopolyploidization in wheat–rye can be accompanied by rapid variation of tandem repeats, regulatory elements, and promoter regions. The alterations of repetitive sequence pSc200 indicate coordination between the constituent genomes of the newly formed amphiploids. Different genetic backgrounds of parents appear to affect genome changes during allopolyploidization.
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Affiliation(s)
- Zong-Xiang Tang
- State Key Laboratory of Plant Breeding and Genetics, Sichuan Agricultural University, Ya’an, Sichuan 625014, China
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Shu-Lan Fu
- State Key Laboratory of Plant Breeding and Genetics, Sichuan Agricultural University, Ya’an, Sichuan 625014, China
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Zheng-Long Ren
- State Key Laboratory of Plant Breeding and Genetics, Sichuan Agricultural University, Ya’an, Sichuan 625014, China
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Jian-Ping Zhou
- State Key Laboratory of Plant Breeding and Genetics, Sichuan Agricultural University, Ya’an, Sichuan 625014, China
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Ben-Ju Yan
- State Key Laboratory of Plant Breeding and Genetics, Sichuan Agricultural University, Ya’an, Sichuan 625014, China
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Huai-Qiong Zhang
- State Key Laboratory of Plant Breeding and Genetics, Sichuan Agricultural University, Ya’an, Sichuan 625014, China
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
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Gill N, Hans CS, Jackson S. An overview of plant chromosome structure. Cytogenet Genome Res 2008; 120:194-201. [PMID: 18504347 DOI: 10.1159/000121067] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/04/2008] [Indexed: 11/19/2022] Open
Affiliation(s)
- N Gill
- Department of Agronomy, Purdue University, West Lafayette, IN 47906, USA
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Sequence analysis, chromosomal distribution and long-range organization show that rapid turnover of new and old pBuM satellite DNA repeats leads to different patterns of variation in seven species of the Drosophila buzzatii cluster. Chromosome Res 2008; 16:307-24. [PMID: 18266060 DOI: 10.1007/s10577-007-1195-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2007] [Revised: 12/07/2007] [Accepted: 12/07/2007] [Indexed: 10/22/2022]
Abstract
We aimed to study patterns of variation and factors influencing the evolutionary dynamics of a satellite DNA, pBuM, in all seven Drosophila species from the buzzatii cluster (repleta group). We analyzed 117 alpha pBuM-1 (monomer length 190 bp) and 119 composite alpha/beta (370 bp) pBuM-2 repeats and determined the chromosome location and long-range organization on DNA fibers of major sequence variants. Such combined methodologies in the study of satDNAs have been used in very few organisms. In most species, concerted evolution is linked to high copy number of pBuM repeats. Species presenting low-abundance and scattered distributed pBuM repeats did not undergo concerted evolution and maintained part of the ancestral inter-repeat variability. The alpha and alpha/beta repeats colocalized in heterochromatic regions and were distributed on multiple chromosomes, with notable differences between species. High-resolution FISH revealed array sizes of a few kilobases to over 0.7 Mb and mutual arrangements of alpha and alpha/beta repeats along the same DNA fibers, but with considerable changes in the amount of each variant across species. From sequence, chromosomal and phylogenetic data, we could infer that homogenization and amplification events involved both new and ancestral pBuM variants. Altogether, the data on the structure and organization of the pBuM satDNA give insights into genome evolution including mechanisms that contribute to concerted evolution and diversification.
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30
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Robledo G, Seijo G. Characterization of the Arachis (Leguminosae) D genome using fluorescence in situ hybridization (FISH) chromosome markers and total genome DNA hybridization. Genet Mol Biol 2008. [DOI: 10.1590/s1415-47572008000400019] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
| | - Guillermo Seijo
- Instituto de Botánica del Nordeste, Argentina; Universidad Nacional del Nordeste
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31
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Dechyeva D, Schmidt T. Molecular organization of terminal repetitive DNA in Beta species. Chromosome Res 2007; 14:881-97. [PMID: 17195925 DOI: 10.1007/s10577-006-1096-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2006] [Revised: 10/19/2007] [Accepted: 10/19/2006] [Indexed: 09/29/2022]
Abstract
We have isolated families of subtelomeric satellite DNA sequences from species of four sections of the genus Beta and from spinach, a related Chenopodiaceae. Twenty-five clones were sequenced and representative repeats of each family were characterized by Southern blotting and FISH. The families of ApaI restriction satellite repeats were designated pAv34, pAc34, the families of RsaI repeats pRp34, pRn34 and pRs34. The repeating units are 344-362 bp long and 45.7-98.8% homologous with a clear species-specific divergence. Each satellite monomer consists of two subrepeats SR1 and SR2 of 165-184 bp, respectively. The repeats of each subrepeat group are highly identical across species, but share only a homology of 40.8-54.8% with members of the other subrepeat group. Two evolutionary steps could be supposed in the phylogeny of the subtelomeric satellite family: the diversification of an ancestor satellite into groups representing SR1 and SR2 in the progenitor of Beta and Spinacea species, followed by the dimerization and diversification of the resulting 360 bp repeats into section-specific satellite DNA families during species radiation. The chromosomal localization of telomeric, subtelomeric and rDNA tandem repeats was investigated by multi-colour FISH. High-resolution analysis by fibre FISH revealed a unique physical organization of B. vulgaris chromosome ends with telomeric DNA and subtelomeric satellites extending over a maximum of 63 kb and 125 kb, respectively.
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Affiliation(s)
- Daryna Dechyeva
- Institute of Botany, Dresden University of Technology, Zellescher Weg 20b, 01062 Dresden, Germany
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32
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González-García M, González-Sánchez M, Puertas MJ. The high variability of subtelomeric heterochromatin and connections between nonhomologous chromosomes, suggest frequent ectopic recombination in rye meiocytes. Cytogenet Genome Res 2006; 115:179-85. [PMID: 17065801 DOI: 10.1159/000095240] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2006] [Accepted: 05/19/2006] [Indexed: 11/19/2022] Open
Abstract
The position of telomeres, centromeres and subtelomeric heterochromatin (SH) has been studied by FISH in rye meiocytes. We compare the morphology of the signals from zygotene to telophase II mainly to determine differences in SH and telomere positions between plants with and without neocentromeres. Plants from two varieties were used: Paldang showing neocentromeres, and Puyo without neocentromeres but with two B chromosomes. In both varieties, at zygotene and pachytene the SH is observed forming clumps often including two or more bivalent ends. At diplotene the SH is stretched suggesting that it is close to the nuclear envelope. In these cases, the telomere signals are not stretched and lay behind the SH. Frequently, two or more bivalents are joined by conspicuous SH connections at diplotene strongly suggesting ectopic recombination. Probably as a result, differential distribution of the SH between recombinant homologues or the whole meiotic products is observed. From diplotene onwards, the large heterochromatic blocks cover the telomeres, the SH being the morphological end of the bivalents, both in plants with or without neocentromeres. The Bs are tightly associated only at the telomeric end of the long arm from diplotene to metaphase I. The high variability between homologous chromosomes and the frequent nonhomologous bindings of SH, strongly suggest that rye SH is in dynamic state and frequently changes in chromosome position during meiosis.
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Affiliation(s)
- M González-García
- Departamento de Genética, Facultad de Biología, Universidad Complutense, Madrid, Spain
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33
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Mikhailova EI, Phillips D, Sosnikhina SP, Lovtsyus AV, Jones RN, Jenkins G. Molecular assembly of meiotic proteins Asy1 and Zyp1 and pairing promiscuity in rye (Secale cereale L.) and its synaptic mutant sy10. Genetics 2006; 174:1247-58. [PMID: 16980383 PMCID: PMC1667052 DOI: 10.1534/genetics.106.064105] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Assembly of two orthologous proteins associated with meiotic chromosome axes in Arabidopsis thaliana (Asy1 and Zyp1) was studied immunologically at meiotic prophase of meiosis of wild-type rye (Secale cereale) and its synaptic mutant sy10, using antibodies derived from A. thaliana. The temporal and spatial expression of the two proteins were similar in wild-type rye, but with one notable difference. Unlike A. thaliana, in which foci of the transverse filament protein Zyp1 appear to linearize commensurately with synapsis, linear tracts of Asy1 and Zyp1 protein form independently at leptotene and early zygotene of rye and coalign into triple structures resembling synaptonemal complexes (SCs) only at later stages of synapsis. The sy10 mutant used in this study also forms spatially separate linear tracts of Asy1 and Zyp1 proteins at leptotene and early zygotene, and these coalign but do not form regular triple structures at midprophase. Electron microscopy of spread axial elements reveals extensive asynapsis with some exchanges of pairing partners. Indiscriminate SCs support nonhomologous chiasma formation at metaphase I, as revealed by multi-color fluorescence in situ hybridization enabling reliable identification of all the chromosomes of the complement. Scrutiny of chiasmate associations of chromosomes at this stage revealed some specificity in the associations of homologous and nonhomologous chromosomes. Inferences about the nature of synapsis in this mutant were drawn from such observations.
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Affiliation(s)
- E I Mikhailova
- Department of Genetics, Saint Petersburg State University, Russian Academy of Sciences, Russia
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35
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Macas J, Navrátilová A, Koblízková A. Sequence homogenization and chromosomal localization of VicTR-B satellites differ between closely related Vicia species. Chromosoma 2006; 115:437-47. [PMID: 16788823 DOI: 10.1007/s00412-006-0070-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2006] [Revised: 05/04/2006] [Accepted: 05/05/2006] [Indexed: 11/28/2022]
Abstract
Satellite sequences of the VicTR-B family are specific for the genus Vicia (Leguminosae), but their abundance varies among the species, being the highest in Vicia sativa and Vicia grandiflora. In this study, we have sequenced multiple randomly cloned VicTR-B fragments from these two species and analyzed their sequence variability, periodicity, and chromosomal localization. We have found that V. sativa VicTR-B sequences are homogeneous with respect to their nucleotide sequences and periodicity (monomers of 38 bp), whereas V. grandiflora repeats are considerably more variable, occurring in at least four distinct sequence subfamilies. Although the periodicity of 38 bp was conserved in most of the V. grandiflora sequences, one of the subfamilies was composed of higher-order repeats of 186 bp, which originated from a pentamer of the basic repeated unit. Individual VicTR-B subfamilies were preferentially located in either intercalary or subtelomeric regions of chromosomes. Interestingly, two V. grandiflora subfamilies with the highest similarity to V. sativa VicTR-B sequences were located in intercalary heterochromatic bands, showing similar chromosomal distribution as the majority of VicTR-B repeats in V. sativa. The other two V. grandiflora subfamilies showing a considerable divergence from V. sativa sequences were found to be accumulated at subtelomeric regions of V. grandiflora chromosomes.
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Affiliation(s)
- Jirí Macas
- Institute of Plant Molecular Biology, Branisovská 31, Ceské Budejovice, 37005, Czech Republic.
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Kuo HF, Olsen KM, Richards EJ. Natural variation in a subtelomeric region of Arabidopsis: implications for the genomic dynamics of a chromosome end. Genetics 2006; 173:401-17. [PMID: 16547105 PMCID: PMC1461430 DOI: 10.1534/genetics.105.055202] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2005] [Accepted: 03/07/2006] [Indexed: 11/18/2022] Open
Abstract
We investigated genome dynamics at a chromosome end in the model plant Arabidopsis thaliana through a study of natural variation in 35 wild accessions. We focused on the single-copy subtelomeric region of chromosome 1 north (approximately 3.5 kb), which represents the relatively simple organization of subtelomeric regions in this species. PCR fragment-length variation across the subtelomeric region indicated that the 1.4-kb distal region showed elevated structural variation relative to the centromere-proximal region. Examination of nucleotide sequences from this 1.4-kb region revealed diverse DNA rearrangements, including an inversion, several deletions, and an insertion of a retrotransposon LTR. The structures at the deletion and inversion breakpoints are characteristic of simple deletion-associated nonhomologous end-joining (NHEJ) events. There was strong linkage disequilibrium between the distal subtelomeric region and the proximal telomere, which contains degenerate and variant telomeric repeats. Variation in the proximal telomere was characterized by the expansion and deletion of blocks of repeats. Our sample of accessions documented two independent chromosome-healing events associated with terminal deletions of the subtelomeric region as well as the capture of a scrambled mitochondrial DNA segment in the proximal telomeric array. This natural variation study highlights the variety of genomic events that drive the fluidity of chromosome termini.
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Affiliation(s)
- Hui-Fen Kuo
- Department of Biology, Washington University, St. Louis, Missouri 63130, USA
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37
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Abstract
The structures of specific chromosome regions, centromeres and telomeres, present a number of puzzles. As functions performed by these regions are ubiquitous and essential, their DNA, proteins and chromatin structure are expected to be conserved. Recent studies of centromeric DNA from human, Drosophila and plant species have demonstrated that a hidden universal centromere-specific sequence is highly unlikely. The DNA of telomeres is more conserved consisting of a tandemly repeated 6-8 bp Arabidopsis-like sequence in a majority of organisms as diverse as protozoan, fungi, mammals and plants. However, there are alternatives to short DNA repeats at the ends of chromosomes and for telomere elongation by telomerase. Here we focus on the similarities and diversity that exist among the structural elements, DNA sequences and proteins, that make up terminal domains (telomeres and subtelomeres), and how organisms use these in different ways to fulfil the functions of end-replication and end-protection.
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Affiliation(s)
- Edward J Louis
- Department of Genetics, University of Leicester, Leicester UK.
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