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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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2
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Abstract
The supernumerary B chromosome of maize is dispensable, containing no vital genes, and thus is variable in number and presence in lines of maize. In order to be maintained in populations, it has a drive mechanism consisting of nondisjunction at the pollen mitosis that produces the two sperm cells, and then the sperm with the two B chromosomes has a preference for fertilizing the egg as opposed to the central cell in the process of double fertilization. The sequence of the B chromosome coupled with B chromosomal aberrations has localized features involved with nondisjunction and preferential fertilization, which are present at the centromeric region. The predicted genes from the sequence have paralogues dispersed across all A chromosomes and have widely different divergence times suggesting that they have transposed to the B chromosome over evolutionary time followed by degradation or have been co-opted for the selfish functions of the supernumerary chromosome.
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Affiliation(s)
- James A. Birchler
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Hua Yang
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
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3
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The r-X1 deletion induces terminal deficiencies in the maize B chromosome. Chromosome Res 2021; 29:351-360. [PMID: 34480269 DOI: 10.1007/s10577-021-09671-4] [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: 05/16/2021] [Revised: 08/16/2021] [Accepted: 08/20/2021] [Indexed: 10/20/2022]
Abstract
In addition to causing the nondisjunction of maize B and normal A chromosomes at the second megaspore division during embryo sac development, the r-X1 deletion results in terminal deficiencies (TDs) in various A chromosomal arms, but whether the r-X1 deletion also induces TDs of the maize B chromosome remains unknown. To answer this question, the chromosomal composition in the r-X1-containing progeny of r-X1/R-r female parents carrying two standard B chromosomes was determined. Nine of 104 (8.7%) examined kernels contained a smaller telocentric B chromosome, and one of these (designated Bdef-1) was further identified as a TD with a breakpoint in the third distal heterochromatic region of the B chromosome. Thus, the results indicated that the r-X1 deletion could also induce TDs of the maize B chromosome during megaspore divisions. The Bdef-1 chromosome lacked nondisjunctional behavior, and this behavior was restored by the presence of the B chromosome in the cell. A transmission analysis of the Bdef-1 chromosome revealed that loss of the distal portion of the B chromosome reduced female but not male transmission of the B chromosome. Furthermore, the Bdef-1 chromosome was used to more finely map B-derived miRNA genes on the B chromosome. Our results indicate that the r-X1 deletion results in TDs of the B chromosome in maize, and the r-X1 deletion system can thus be used to generate a series of terminally truncated B chromosomes that may be used to map features of the B chromosome, including genes and properties related to B chromosome functions.
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Bednářová M, Karafiátová M, Hřibová E, Bartoš J. B Chromosomes in Genus Sorghum (Poaceae). PLANTS (BASEL, SWITZERLAND) 2021; 10:505. [PMID: 33803087 PMCID: PMC8001295 DOI: 10.3390/plants10030505] [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: 02/12/2021] [Revised: 03/04/2021] [Accepted: 03/04/2021] [Indexed: 12/30/2022]
Abstract
B chromosomes (Bs) are supernumerary dispensable genomic elements that have been reported in several thousand eukaryotic species. Since their discovery, Bs have been subjected to countless studies aiming at the clarification of their origin, composition, and influence on the carriers. Despite these efforts, we still have very limited knowledge of the processes that led to the emergence of Bs, the mechanisms of their transmission, and the effects of Bs on the hosts. In the last decade, sophisticated molecular methods, including next-generation sequencing, have provided powerful tool to help answer some of these questions, but not many species have received much attention yet. In this review, we summarize the currently available information about Bs in the genus Sorghum, which has so far been on the periphery of scientific interest. We present an overview of the occurrence and characteristics of Bs in various Sorghum species, discuss the possible mechanisms involved in their maintenance and elimination, and outline hypotheses of the origin of Bs in this genus.
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Affiliation(s)
| | | | | | - Jan Bartoš
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 31, 779 00 Olomouc, Czech Republic; (M.B.); (M.K.); (E.H.)
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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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Silva JC, Soares FAF, Sattler MC, Clarindo WR. Repetitive sequences and structural chromosome alterations promote intraspecific variations in Zea mays L. karyotype. Sci Rep 2020; 10:8866. [PMID: 32483238 PMCID: PMC7264354 DOI: 10.1038/s41598-020-65779-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 05/07/2020] [Indexed: 12/02/2022] Open
Abstract
LTR-retrotransposons, knobs and structural chromosome alterations contribute to shape the structure and organization of the Zea mays karyotype. Our initial nuclear DNA content data of Z. mays accessions revealed an intraspecific variation (2 C = 2.00 pg to 2 C = 6.10 pg), suggesting differences in their karyotypes. We aimed to compare the karyotypes of three Z. mays accessions in search of the differences and similarities among them. Karyotype divergences were demonstrated among the accessions, despite their common chromosome number (2n = 20) and ancestral origin. Cytogenomic analyses showed that repetitive sequences and structural chromosome alterations play a significant role in promoting intraspecific nuclear DNA content variation. In addition, heterozygous terminal deletion in chromosome 3 was pointed out as a cause of lower nuclear 2 C value. Besides this, translocation was also observed in the short arm of chromosome 1. Differently, higher 2 C value was associated with the more abundant distribution of LTR-retrotransposons from the family Grande in the karyotype. Moreover, heteromorphism involving the number and position of the 180-bp knob sequence was found among the accessions. Taken together, we provide insights on the pivotal role played by repetitive sequences and structural chromosome alterations in shaping the karyotype of Z. mays.
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Affiliation(s)
- Jéssica Coutinho Silva
- Laboratório de Citogenética e Citometria, Departamento de Biologia Geral, Centro de Ciências Biológicas e da Saúde, Universidade Federal de Viçosa, ZIP 36570-900, Viçosa, MG, Brazil.
| | - Fernanda Aparecida Ferrari Soares
- Laboratório de Citogenética e Citometria, Departamento de Biologia Geral, Centro de Ciências Biológicas e da Saúde, Universidade Federal de Viçosa, ZIP 36570-900, Viçosa, MG, Brazil
| | - Mariana Cansian Sattler
- Laboratório de Citogenética e Citometria, Departamento de Biologia Geral, Centro de Ciências Biológicas e da Saúde, Universidade Federal de Viçosa, ZIP 36570-900, Viçosa, MG, Brazil
| | - Wellington Ronildo Clarindo
- Laboratório de Citogenética e Citometria, Departamento de Biologia Geral, Centro de Ciências Biológicas e da Saúde, Universidade Federal de Viçosa, ZIP 36570-900, Viçosa, MG, Brazil
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8
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A universal chromosome identification system for maize and wild Zea species. Chromosome Res 2020; 28:183-194. [PMID: 32219602 DOI: 10.1007/s10577-020-09630-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 03/16/2020] [Accepted: 03/17/2020] [Indexed: 12/16/2022]
Abstract
Maize was one of the first eukaryotic species in which individual chromosomes can be identified cytologically, which made maize one of the oldest models for genetics and cytogenetics research. Nevertheless, consistent identification of all 10 chromosomes from different maize lines as well as from wild Zea species remains a challenge. We developed a new technique for maize chromosome identification based on fluorescence in situ hybridization (FISH). We developed two oligonucleotide-based probes that hybridize to 24 chromosomal regions. Individual maize chromosomes show distinct FISH signal patterns, which allow universal identification of all chromosomes from different Zea species. We developed karyotypes from three Zea mays subspecies and two additional wild Zea species based on individually identified chromosomes. A paracentric inversion was discovered on the long arm of chromosome 4 in Z. nicaraguensis and Z. luxurians based on modifications of the FISH signal patterns. Chromosomes from these two species also showed distinct distribution patterns of terminal knobs compared with other Zea species. These results support that Z. nicaraguensis and Z. luxurians are closely related species.
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Báez M, Vaio M, Dreissig S, Schubert V, Houben A, Pedrosa-Harand A. Together But Different: The Subgenomes of the Bimodal Eleutherine Karyotypes Are Differentially Organized. FRONTIERS IN PLANT SCIENCE 2019; 10:1170. [PMID: 31649686 PMCID: PMC6791338 DOI: 10.3389/fpls.2019.01170] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 08/27/2019] [Indexed: 06/10/2023]
Abstract
Bimodal karyotypes are characterized by the presence of two sets of chromosomes of contrasting size. Eleutherine bulbosa (2n = 12) presents a bimodal karyotype with a large chromosome pair, which has a pericentric inversion in permanent heterozygosity with suppressed recombination, and five pairs of three to four times smaller chromosomes. Aiming to understand whether high copy number sequence composition differs between both chromosome sets, we investigated the repetitive DNA fraction of E. bulbosa and compared it to the chromosomal organization of the related Eleutherine latifolia species, not containing the pericentric inversion. We also compared the repetitive sequence proportions between the heteromorphic large chromosomes of E. bulbosa and between E. bulbosa and E. latifolia to understand the influence of the chromosome inversion on the dynamics of repetitive sequences. The most abundant repetitive families of the genome showed a similar chromosomal distribution in both homologs of the large pair and in both species, apparently not influenced by the species-specific inversions. The repeat families Ebusat1 and Ebusat4 are localized interstitially only on the large chromosome pair, while Ebusat2 is located in the centromeric region of all chromosomes. The four most abundant retrotransposon lineages are accumulated in the large chromosome pair. Replication timing and distribution of epigenetic and transcriptional marks differ between large and small chromosomes. The differential distribution of retroelements appears to be related to the bimodal condition and is not influenced by the nonrecombining chromosome inversions in these species. Thus, the large and small chromosome subgenomes of the bimodal Eleutherine karyotype are differentially organized and probably evolved by repetitive sequences accumulation on the large chromosome set.
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Affiliation(s)
- Mariana Báez
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, Brazil
| | - Magdalena Vaio
- Laboratory of Genetics, Department of Plant Biology, College of Agronomy, University of the Republic, Montevideo, Uruguay
| | - Steven Dreissig
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Veit Schubert
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Andreas Houben
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Andrea Pedrosa-Harand
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, Brazil
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Marques A, Klemme S, Houben A. Evolution of Plant B Chromosome Enriched Sequences. Genes (Basel) 2018; 9:genes9100515. [PMID: 30360448 PMCID: PMC6210368 DOI: 10.3390/genes9100515] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 10/13/2018] [Accepted: 10/18/2018] [Indexed: 01/10/2023] Open
Abstract
B chromosomes are supernumerary chromosomes found in addition to the normal standard chromosomes (A chromosomes). B chromosomes are well known to accumulate several distinct types of repeated DNA elements. Although the evolution of B chromosomes has been the subject of numerous studies, the mechanisms of accumulation and evolution of repetitive sequences are not fully understood. Recently, new genomic approaches have shed light on the origin and accumulation of different classes of repetitive sequences in the process of B chromosome formation and evolution. Here we discuss the impact of repetitive sequences accumulation on the evolution of plant B chromosomes.
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Affiliation(s)
- André Marques
- Laboratory of Genetic Resources, Federal University of Alagoas, Av. Manoel Severino Barbosa, 57309-005 Arapiraca-AL, Brazil.
| | - Sonja Klemme
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 31, CZ-37005 České Budějovice, Czech Republic.
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Gatersleben, Germany.
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11
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Vujošević M, Rajičić M, Blagojević J. B Chromosomes in Populations of Mammals Revisited. Genes (Basel) 2018; 9:E487. [PMID: 30304868 PMCID: PMC6210394 DOI: 10.3390/genes9100487] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 10/01/2018] [Accepted: 10/03/2018] [Indexed: 01/23/2023] Open
Abstract
The study of B chromosomes (Bs) started more than a century ago, while their presence in mammals dates since 1965. As the past two decades have seen huge progress in application of molecular techniques, we decided to throw a glance on new data on Bs in mammals and to review them. We listed 85 mammals with Bs that make 1.94% of karyotypically studied species. Contrary to general view, a typical B chromosome in mammals appears both as sub- or metacentric that is the same size as small chromosomes of standard complement. Both karyotypically stable and unstable species possess Bs. The presence of Bs in certain species influences the cell division, the degree of recombination, the development, a number of quantitative characteristics, the host-parasite interactions and their behaviour. There is at least some data on molecular structure of Bs recorded in nearly a quarter of species. Nevertheless, a more detailed molecular composition of Bs presently known for six mammalian species, confirms the presence of protein coding genes, and the transcriptional activity for some of them. Therefore, the idea that Bs are inert is outdated, but the role of Bs is yet to be determined. The maintenance of Bs is obviously not the same for all species, so the current models must be adapted while bearing in mind that Bs are not inactive as it was once thought.
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Affiliation(s)
- Mladen Vujošević
- Institute for Biological Research "Siniša Stanković", Department of Genetic Research, University of Belgrade, Bulevar despota Stefana 142, Belgrade 11060, Serbia.
| | - Marija Rajičić
- Institute for Biological Research "Siniša Stanković", Department of Genetic Research, University of Belgrade, Bulevar despota Stefana 142, Belgrade 11060, Serbia.
| | - Jelena Blagojević
- Institute for Biological Research "Siniša Stanković", Department of Genetic Research, University of Belgrade, Bulevar despota Stefana 142, Belgrade 11060, Serbia.
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Fourastié MF, Gottlieb AM, Poggio L, González GE. Are cytological parameters of maize landraces (Zea mays ssp. mays) adapted along an altitudinal cline? JOURNAL OF PLANT RESEARCH 2018; 131:285-296. [PMID: 29177755 DOI: 10.1007/s10265-017-0996-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 10/02/2017] [Indexed: 06/07/2023]
Abstract
The Northwestern Argentina (NWA) highland region is one of the southernmost areas of native maize cultivation. We studied variations of different cytological parameters, such as DNA contents, presence/absence of B chromosomes (Bs), and number and sequence composition of heterochromatic knobs in ten accessions of four maize landraces growing along a broad altitudinal cline in NWA. The aim of this work was to assess variations in cytological parameters and their relationship with the crop altitude of cultivation, in an adaptive context. The A-DNA content of the A chromosome complements showed 40% of difference between the lowest (4.5 pg) and the highest (6.3 pg) 2C value. This variation could be attributed to differences in number and size of heterochromatic knobs. Fluorescent in situ hybridization studies revealed the sequence composition of each knob, with a higher proportion of knobs composed of 180-bp repeats rather than TR-1 repeats, in all accessions. We also found numerical polymorphisms and the highest frequency of Bs reported in maize to this date. These results lead us to propose that the frequencies and doses of Bs are influenced by the landrace genotypical make-up. The Bs might be maintained in higher frequencies in those accessions having lower heterochromatin content, so as to preserve an optimal nucleotype. Furthermore, selective forces acting along the altitudinal gradient might be modulating the cytological parameters studied, as suggested by the significant correlations found among them.
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Affiliation(s)
- María Florencia Fourastié
- Laboratorio de Citogenética y Evolución (LaCyE), Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Alexandra Marina Gottlieb
- Laboratorio de Citogenética y Evolución (LaCyE), Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Lidia Poggio
- Laboratorio de Citogenética y Evolución (LaCyE), Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Graciela Esther González
- Laboratorio de Citogenética y Evolución (LaCyE), Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.
- Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina.
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Liu S, Zheng J, Migeon P, Ren J, Hu Y, He C, Liu H, Fu J, White FF, Toomajian C, Wang G. Unbiased K-mer Analysis Reveals Changes in Copy Number of Highly Repetitive Sequences During Maize Domestication and Improvement. Sci Rep 2017; 7:42444. [PMID: 28186206 PMCID: PMC5301235 DOI: 10.1038/srep42444] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 01/10/2017] [Indexed: 12/15/2022] Open
Abstract
The major component of complex genomes is repetitive elements, which remain recalcitrant to characterization. Using maize as a model system, we analyzed whole genome shotgun (WGS) sequences for the two maize inbred lines B73 and Mo17 using k-mer analysis to quantify the differences between the two genomes. Significant differences were identified in highly repetitive sequences, including centromere, 45S ribosomal DNA (rDNA), knob, and telomere repeats. Genotype specific 45S rDNA sequences were discovered. The B73 and Mo17 polymorphic k-mers were used to examine allele-specific expression of 45S rDNA in the hybrids. Although Mo17 contains higher copy number than B73, equivalent levels of overall 45S rDNA expression indicates that transcriptional or post-transcriptional regulation mechanisms operate for the 45S rDNA in the hybrids. Using WGS sequences of B73xMo17 doubled haploids, genomic locations showing differential repetitive contents were genetically mapped, which displayed different organization of highly repetitive sequences in the two genomes. In an analysis of WGS sequences of HapMap2 lines, including maize wild progenitor, landraces, and improved lines, decreases and increases in abundance of additional sets of k-mers associated with centromere, 45S rDNA, knob, and retrotransposons were found among groups, revealing global evolutionary trends of genomic repeats during maize domestication and improvement.
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Affiliation(s)
- Sanzhen Liu
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Jun Zheng
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R.China
| | - Pierre Migeon
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Jie Ren
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Ying Hu
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Cheng He
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R.China
| | - Hongjun Liu
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, Taian 271018, P.R. China.,College of Life Sciences, Shandong Agricultural University, Taian 271018, P.R. China
| | - Junjie Fu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R.China
| | - Frank F White
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, USA
| | | | - Guoying Wang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R.China
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Comparative Analysis of Satellite DNA in the Drosophila melanogaster Species Complex. G3-GENES GENOMES GENETICS 2017; 7:693-704. [PMID: 28007840 PMCID: PMC5295612 DOI: 10.1534/g3.116.035352] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Satellite DNAs are highly repetitive sequences that account for the majority of constitutive heterochromatin in many eukaryotic genomes. It is widely recognized that sequences and locations of satellite DNAs are highly divergent even in closely related species, contributing to the hypothesis that satellite DNA differences may underlie speciation. However, due to its repetitive nature, the mapping of satellite DNAs has been mostly left out of recent genomics analyses, hampering the use of molecular genetics techniques to better understand their role in speciation and evolution. Satellite DNAs are most extensively and comprehensively mapped in Drosophila melanogaster, a species that is also an excellent model system with which to study speciation. Yet the lack of comprehensive knowledge regarding satellite DNA identity and location in its sibling species (D. simulans, D. mauritiana, and D. sechellia) has prevented the full utilization of D. melanogaster in studying speciation. To overcome this problem, we initiated the mapping of satellite DNAs on the genomes of the D. melanogaster species complex (D. melanogaster, D. simulans, D. mauritiana, and D. sechellia) using multi-color fluorescent in situ hybridization (FISH) probes. Our study confirms a striking divergence of satellite DNAs in the D. melanogaster species complex, even among the closely related species of the D. simulans clade (D. simulans, D. mauritiana, and D. sechellia), and suggests the presence of unidentified satellite sequences in these species.
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15
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Gaiero P, van de Belt J, Vilaró F, Schranz ME, Speranza P, de Jong H. Collinearity between potato (Solanum tuberosum L.) and wild relatives assessed by comparative cytogenetic mapping. Genome 2016; 60:228-240. [PMID: 28169563 DOI: 10.1139/gen-2016-0150] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A major bottleneck to introgressive hybridization is the lack of genome collinearity between the donor (alien) genome and the recipient crop genome. Structural differences between the homeologs may create unbalanced segregation of chromosomes or cause linkage drag. To assess large-scale collinearity between potato and two of its wild relatives (Solanum commersonii and Solanum chacoense), we used BAC-FISH mapping of sequences with known positions on the RH potato map. BAC probes could successfully be hybridized to the S. commersonii and S. chachoense pachytene chromosomes, confirming their correspondence with linkage groups in RH potato. Our study shows that the order of BAC signals is conserved. Distances between BAC signals were quantified and compared; some differences found suggest either small-scale rearrangements or reduction/amplification of repeats. We conclude that S. commersonii and S. chacoense are collinear with cultivated Solanum tuberosum on the whole chromosome scale, making these amenable species for efficient introgressive hybridization breeding.
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Affiliation(s)
- Paola Gaiero
- a Department of Plant Biology, Facultad de Agronomía, Universidad de la República, Garzón 780, PC 12900, Montevideo, Uruguay.,b Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, P.O. Box 16, 6708 PB, Wageningen, the Netherlands
| | - José van de Belt
- b Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, P.O. Box 16, 6708 PB, Wageningen, the Netherlands
| | - Francisco Vilaró
- c Horticulture Unit, National Institute for Agricultural Research, Ruta 48 km 10, Las Brujas, Uruguay
| | - M Eric Schranz
- d Biosystematics Group, Wageningen University, Wageningen, the Netherlands
| | - Pablo Speranza
- a Department of Plant Biology, Facultad de Agronomía, Universidad de la República, Garzón 780, PC 12900, Montevideo, Uruguay
| | - Hans de Jong
- b Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, P.O. Box 16, 6708 PB, Wageningen, the Netherlands
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16
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Fransz P, Linc G, Lee C, Aflitos SA, Lasky JR, Toomajian C, Ali H, Peters J, van Dam P, Ji X, Kuzak M, Gerats T, Schubert I, Schneeberger K, Colot V, Martienssen R, Koornneef M, Nordborg M, Juenger TE, de Jong H, Schranz ME. Molecular, genetic and evolutionary analysis of a paracentric inversion in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 88:159-178. [PMID: 27436134 PMCID: PMC5113708 DOI: 10.1111/tpj.13262] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 06/29/2016] [Accepted: 07/01/2016] [Indexed: 05/02/2023]
Abstract
Chromosomal inversions can provide windows onto the cytogenetic, molecular, evolutionary and demographic histories of a species. Here we investigate a paracentric 1.17-Mb inversion on chromosome 4 of Arabidopsis thaliana with nucleotide precision of its borders. The inversion is created by Vandal transposon activity, splitting an F-box and relocating a pericentric heterochromatin segment in juxtaposition with euchromatin without affecting the epigenetic landscape. Examination of the RegMap panel and the 1001 Arabidopsis genomes revealed more than 170 inversion accessions in Europe and North America. The SNP patterns revealed historical recombinations from which we infer diverse haplotype patterns, ancient introgression events and phylogenetic relationships. We find a robust association between the inversion and fecundity under drought. We also find linkage disequilibrium between the inverted region and the early flowering Col-FRIGIDA allele. Finally, SNP analysis elucidates the origin of the inversion to South-Eastern Europe approximately 5000 years ago and the FRI-Col allele to North-West Europe, and reveals the spreading of a single haplotype to North America during the 17th to 19th century. The 'American haplotype' was identified from several European localities, potentially due to return migration.
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Affiliation(s)
- Paul Fransz
- Department of Plant Development and (Epi)GeneticsSwammerdam Institute for Life SciencesUniversity of AmsterdamAmsterdamthe Netherlands
| | - Gabriella Linc
- Department of Plant Development and (Epi)GeneticsSwammerdam Institute for Life SciencesUniversity of AmsterdamAmsterdamthe Netherlands
- Present address: Centre for Agricultural ResearchHungarian Academy of SciencesAgricultural InstituteMartonvásárHungary
| | - Cheng‐Ruei Lee
- Gregor Mendel Institute (GMI)Austrian Academy of SciencesVienna Biocenter (VBC)Dr Bohr‐Gasse 3Vienna1030Austria
| | | | - Jesse R. Lasky
- Department of BiologyPennsylvania State UniversityUniversity ParkPAUSA
| | | | - Hoda Ali
- Department of Cytogenetics and Genome AnalysisThe Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)GaterslebenGermany
- Present address: Department of Genetics and CytologyNational Research CenterCairoEgypt
| | - Janny Peters
- Section Plant GeneticsInstitute for Wetland and Water Research Faculty of ScienceRadboud UniversityNijmegenthe Netherlands
| | - Peter van Dam
- Section Plant GeneticsInstitute for Wetland and Water Research Faculty of ScienceRadboud UniversityNijmegenthe Netherlands
- Present address: Department of Molecular Plant PathologyUniversity of AmsterdamAmsterdamThe Netherlands
| | - Xianwen Ji
- Laboratory of GeneticsWageningen UniversityWageningenthe Netherlands
| | - Mateusz Kuzak
- MAD, Dutch Genomics Service & Support ProviderSwammerdam Institute for Life SciencesUniversity of AmsterdamAmsterdamthe Netherlands
- Present address: Netherlands eScience CenterUniversity of AmsterdamAmsterdamThe Netherlands
| | - Tom Gerats
- Section Plant GeneticsInstitute for Wetland and Water Research Faculty of ScienceRadboud UniversityNijmegenthe Netherlands
| | - Ingo Schubert
- Department of Cytogenetics and Genome AnalysisThe Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)GaterslebenGermany
| | | | - Vincent Colot
- Unité de Recherche en Génomique Végétale (URGV)INRA/CNRS/UEVE 2 Rue Gaston CrémieuxEvry Cedex91057France
- Present address: Institut de Biologie de l'Ecole Normale Supérieure (IBENS)ParisFrance
| | - Rob Martienssen
- Cold Spring Harbor LaboratoryCold Spring HarborNew YorkNY11724USA
| | - Maarten Koornneef
- Laboratory of GeneticsWageningen UniversityWageningenthe Netherlands
- Max Planck Institute for Plant Breeding ResearchKöln50829Germany
| | - Magnus Nordborg
- Gregor Mendel Institute (GMI)Austrian Academy of SciencesVienna Biocenter (VBC)Dr Bohr‐Gasse 3Vienna1030Austria
| | | | - Hans de Jong
- Laboratory of GeneticsWageningen UniversityWageningenthe Netherlands
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17
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McCaw M, Graham N, Cody J, Swyers N, Zhao C, Birchler J. Fluorescence In Situ Hybridization to Maize (Zea mays) Chromosomes. CURRENT PROTOCOLS IN PLANT BIOLOGY 2016; 1:530-545. [PMID: 31725962 DOI: 10.1002/cppb.20033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Fluorescence In Situ Hybridization (FISH) is the annealing of fluorescent DNA probes to their complementary sequences on prepared chromosomes and subsequent visualization with a fluorescent microscope. In maize, FISH is useful for distinguishing each of the ten chromosomes in different accessions (karyotyping), roughly mapping single genes, transposable elements, transgene insertions, and identifying various chromosomal alterations. FISH can also be used to distinguish chromosomes between different Zea species in interspecific hybrids by use of retroelement painting. © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
- Morgan McCaw
- University of Missouri, Division of Biological Sciences, Columbia, Missouri
| | - Nathaniel Graham
- University of Missouri, Division of Biological Sciences, Columbia, Missouri
| | - Jon Cody
- University of Missouri, Division of Biological Sciences, Columbia, Missouri
| | - Nathan Swyers
- University of Missouri, Division of Biological Sciences, Columbia, Missouri
| | - Changzeng Zhao
- University of Missouri, Division of Biological Sciences, Columbia, Missouri
| | - James Birchler
- University of Missouri, Division of Biological Sciences, Columbia, Missouri
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18
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Iwata-Otsubo A, Lin JY, Gill N, Jackson SA. Highly distinct chromosomal structures in cowpea (Vigna unguiculata), as revealed by molecular cytogenetic analysis. Chromosome Res 2016; 24:197-216. [PMID: 26758200 PMCID: PMC4856725 DOI: 10.1007/s10577-015-9515-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Revised: 12/21/2015] [Accepted: 12/23/2015] [Indexed: 11/19/2022]
Abstract
Cowpea (Vigna unguiculata (L.) Walp) is an important legume, particularly in developing countries. However, little is known about its genome or chromosome structure. We used molecular cytogenetics to characterize the structure of pachytene chromosomes to advance our knowledge of chromosome and genome organization of cowpea. Our data showed that cowpea has highly distinct chromosomal structures that are cytologically visible as brightly DAPI-stained heterochromatic regions. Analysis of the repetitive fraction of the cowpea genome present at centromeric and pericentromeric regions confirmed that two retrotransposons are major components of pericentromeric regions and that a 455-bp tandem repeat is found at seven out of 11 centromere pairs in cowpea. These repeats likely evolved after the divergence of cowpea from common bean and form chromosomal structure unique to cowpea. The integration of cowpea genetic and physical chromosome maps reveals potential regions of suppressed recombination due to condensed heterochromatin and a lack of pairing in a few chromosomal termini. This study provides fundamental knowledge on cowpea chromosome structure and molecular cytogenetics tools for further chromosome studies.
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Affiliation(s)
- Aiko Iwata-Otsubo
- Center for Applied Genetic Technologies, University of Georgia, 111 Riverbend Road, Athens, GA, 30602, USA.,Department of Biology, University of Pennsylvania, Philadelphia, 19104, PA, USA
| | - Jer-Young Lin
- Department of Agronomy, Purdue University, 170 S. University Street, West Lafayette, IN, USA.,Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA, 90095, USA
| | - Navdeep Gill
- Department of Agronomy, Purdue University, 170 S. University Street, West Lafayette, IN, USA.,Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Scott A Jackson
- Center for Applied Genetic Technologies, University of Georgia, 111 Riverbend Road, Athens, GA, 30602, USA.
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Mondin M, Santos-Serejo JA, Bertäo MR, Laborda P, Pizzaia D, Aguiar-Perecin MLR. Karyotype variability in tropical maize sister inbred lines and hybrids compared with KYS standard line. FRONTIERS IN PLANT SCIENCE 2014; 5:544. [PMID: 25352856 PMCID: PMC4195276 DOI: 10.3389/fpls.2014.00544] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 09/24/2014] [Indexed: 05/27/2023]
Abstract
Maize karyotype variability has been extensively investigated. The identification of maize somatic and pachytene chromosomes has improved with the development of fluorescence in situ hybridization (FISH) using tandemly repeated DNA sequences as probes. We identified the somatic chromosomes of sister inbred lines that were derived from a tropical flint maize population (Jac Duro [JD]), and hybrids between them, using FISH probes for the 180-bp knob repeat, centromeric satellite (CentC), centromeric satellite 4 (Cent4), subtelomeric clone 4-12-1, 5S ribosomal DNA and nucleolus organizing region DNA sequences. The observations were integrated with data based on C-banded mitotic metaphases and conventional analysis of pachytene chromosomes. Heterochromatic knobs visible at pachynema were coincident with C-bands and 180-bp FISH signals on somatic chromosomes, and most of them were large. Variation in the presence of some knobs was observed among lines. Small 180-bp knob signals were invariant on the short arms of chromosomes 1, 6, and 9. The subtelomeric 4-12-1 signal was also invariant and useful for identifying some chromosomes. The centromere location of chromosomes 2 and 4 differed from previous reports on standard maize lines. Somatic chromosomes of a JD line and the commonly used KYS line were compared by FISH in a hybrid of these lines. The pairing behavior of chromosomes 2 and 4 at pachytene stage in this hybrid was investigated using FISH with chromosome-specific probes. The homologues were fully synapsed, including the 5S rDNA and CentC sites on chromosome 2, and Cent4 and subtelomeric 4-12-1 sites on chromosome 4. This suggests that homologous chromosomes could pair through differential degrees of chromatin packaging in homologous arms differing in size. The results contribute to current knowledge of maize global diversity and also raise questions concerning the meiotic pairing of homologous chromosomes possibly differing in their amounts of repetitive DNA.
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Affiliation(s)
- Mateus Mondin
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of SãoPaulo, Piracicaba, Brazil
| | - Janay A. Santos-Serejo
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of SãoPaulo, Piracicaba, Brazil
- Embrapa Cassava and Fruits, Brazilian Agricultural Research CorporationCruz das Almas, Brazil
| | - Mônica R. Bertäo
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of SãoPaulo, Piracicaba, Brazil
- Department of Biological Sciences, Faculty of Sciences and Letters, São Paulo State UniversityAssis, Brazil
| | - Prianda Laborda
- Center for Molecular Biology and Genetic Engineering, State University of CampinasCampinas, Brazil
| | - Daniel Pizzaia
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of SãoPaulo, Piracicaba, Brazil
- Herminio Ometto University Center, Herminio Ometto FoundationAraras, Brazil
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20
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Characterization of four B-chromosome-specific RAPDs and the development of SCAR markers on the maize B-chromosome. Mol Genet Genomics 2014; 290:431-41. [PMID: 25258187 DOI: 10.1007/s00438-014-0926-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 09/17/2014] [Indexed: 10/24/2022]
Abstract
Understanding the molecular organization of the maize B-chromosome is hindered by its high homology with A-chromosomes. Recently, various approaches have been employed to overcome this hindrance, and several B-chromosome-specific sequences have been identified. Here, we cloned and characterized four previously published B-chromosome-specific RAPD fragments in detail. The results of sequence analysis, Southern hybridization and fluorescence in situ hybridization revealed that the four RAPD fragments are repetitive and present on both the B- and A-chromosomes, which supports an A-chromosome origin of the B-chromosome. We further developed four sequence-characterized amplified region (SCAR) markers derived from the four B-chromosome-specific RAPDs. These markers amplified PCR products exclusively in plants with B-chromosomes and were further mapped to definite distal heterochromatic regions of the B-chromosome by 15 B-A translocations. Furthermore, reverse transcriptase-PCR revealed that two of the four B-chromosome-specific RAPD fragments are transcriptionally active. These results demonstrate the feasibility of using B-chromosome-specific RAPD sequences to generate SCAR markers specific to the B-chromosome and might apply to other sequences of the maize B-chromosome.
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21
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Chromosomal organizations of major repeat families on potato (Solanum tuberosum) and further exploring in its sequenced genome. Mol Genet Genomics 2014; 289:1307-19. [PMID: 25106953 DOI: 10.1007/s00438-014-0891-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2014] [Accepted: 07/18/2014] [Indexed: 10/24/2022]
Abstract
One of the most powerful technologies in unraveling the organization of a eukaryotic plant genome is high-resolution Fluorescent in situ hybridization of repeats and single copy DNA sequences on pachytene chromosomes. This technology allows the integration of physical mapping information with chromosomal positions, including centromeres, telomeres, nucleolar-organizing region, and euchromatin and heterochromatin. In this report, we established chromosomal positions of different repeat fractions of the potato genomic DNA (Cot100, Cot500 and Cot1000) on the chromosomes. We also analysed various repeat elements that are unique to potato including the moderately repetitive P5 and REP2 elements, where the REP2 is part of a larger Gypsy-type LTR retrotransposon and cover most chromosome regions, with some brighter fluorescing spots in the heterochromatin. The most abundant tandem repeat is the potato genomic repeat 1 that covers subtelomeric regions of most chromosome arms. Extensive multiple alignments of these repetitive sequences in the assembled RH89-039-16 potato BACs and the draft assembly of the DM1-3 516 R44 genome shed light on the conservation of these repeats within the potato genome. The consensus sequences thus obtained revealed the native complete transposable elements from which they were derived.
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22
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Gao Z, Han F, Danilova TV, Lamb JC, Albert PS, Birchler JA. Labeling meiotic chromosomes in maize with fluorescence in situ hybridization. Methods Mol Biol 2013; 990:35-43. [PMID: 23559200 DOI: 10.1007/978-1-62703-333-6_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
Fluorescence in situ hybridization (FISH) can be used to visualize chromosomal features using repetitive or single gene probes above a minimum target size. When applied to meiosis, each chromosome of the karyotypic complement can be identified, which can facilitate an understanding of the interrelationship of different chromosomes during this process. On the other hand, the pachytene stage of early meiosis is characterized by slightly but not strongly condensed chromosomes that permit more detailed analyses of adjacent features than can be achieved with somatic metaphase chromosomes.
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Affiliation(s)
- Zhi Gao
- Division of Biological Sciences, University of Missouri-Columbia, Columbia, MO, USA
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23
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In vivo modification of a maize engineered minichromosome. Chromosoma 2013; 122:221-32. [DOI: 10.1007/s00412-013-0403-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2012] [Revised: 02/25/2013] [Accepted: 02/27/2013] [Indexed: 10/27/2022]
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Waminal NE, Park HM, Ryu KB, Kim JH, Yang TJ, Kim HH. Karyotype analysis of Panax ginseng C.A.Meyer, 1843 (Araliaceae) based on rDNA loci and DAPI band distribution. COMPARATIVE CYTOGENETICS 2012; 6:425-41. [PMID: 24260682 PMCID: PMC3834566 DOI: 10.3897/compcytogen.v6i4.3740] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Accepted: 10/26/2012] [Indexed: 05/26/2023]
Abstract
Ginseng has long been considered a valuable plant owing to its medicinal properties; however, genomic information based on chromosome characterization and physical mapping of cytogenetic markers has been very limited. Dual-color FISH karyotype and DAPI banding analyses of Panax ginseng C. A. Meyer, 1843 were conducted using 5S and 45S rDNA probes. The somatic chromosome complement was 2n=48 with lengths from 3.3 μm to 6.3 μm. The karyotype was composed of 12 metacentric, 9 submetacentric, and 3 subtelocentric pairs. The 5S rDNA probe localized to the intercalary region of the short arm of pair 11, while the 45S rDNA was located at the secondary constriction of the subtelocentric satellited chromosome 14. DAPI bands were clearly observed for most chromosomes, with various signal intensities and chromosomal distributions that consequently improved chromosome identification. As a result, all 24 chromosomes could be distinguished and numbers were assigned to each chromosome for the first time. The results presented here will be useful for the on-going ginseng genome sequencing and further molecular-cytogenetic studies and breeding programs of ginseng.
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Affiliation(s)
- Nomar Espinosa Waminal
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151–921, Korea
- Plant Biotechnology Institute, Department of Life Science, Sahmyook University, Seoul, 139–742, Korea
| | - Hye Mi Park
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151–921, Korea
- Plant Biotechnology Institute, Department of Life Science, Sahmyook University, Seoul, 139–742, Korea
| | - Kwang Bok Ryu
- Plant Biotechnology Institute, Department of Life Science, Sahmyook University, Seoul, 139–742, Korea
- Department of Horticultural Science, Kyungpook National University, Daegu, 702–701, Korea
| | - Joo Hyung Kim
- Plant Biotechnology Institute, Department of Life Science, Sahmyook University, Seoul, 139–742, Korea
| | - Tae-Jin Yang
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151–921, Korea
| | - Hyun Hee Kim
- Plant Biotechnology Institute, Department of Life Science, Sahmyook University, Seoul, 139–742, Korea
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25
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Hu Y, Zhang L, He S, Huang M, Tan J, Zhao L, Yan S, Li H, Zhou K, Liang Y, Li L. Cold stress selectively unsilences tandem repeats in heterochromatin associated with accumulation of H3K9ac. PLANT, CELL & ENVIRONMENT 2012; 35:2130-42. [PMID: 22616903 DOI: 10.1111/j.1365-3040.2012.02541.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Knobs are cytologically observable major interstitial heterochromatin present on maize nuclei, which consist of highly tandem-repetitive elements that are always silenced. Here we investigated the genome-wide change of H3K9ac, an active chromatin mark, during cold stress using chromatin immunoprecipitation sequencing (ChIP-Seq) and identified differential cold-induced H3K9ac enrichment at repetitive sequences in maize. More detailed analysis of two knob-associated tandem-repetitive sequences, 180-bp and TR-1, demonstrated that cold activated their transcription and this cold-induced transcriptional activation of repetitive sequences is selective, transient, and associated with an increase in H3K9ac and a reduction in DNA methylation and H3K9me2. Furthermore, knob sequence expression is accompanied by localized chromatin remodelling and silencing is recovered upon prolonged treatment. In addition, no evidence of copy number change and rearrangement of these repetitive elements are found in plants subjected to cold stress. These results suggest that cold-mediated unsilencing of heterochromatic tandem-repeated sequences, accompanied with epigenetic regulation, might play an important role in the adaptation of plants to cold stimuli.
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Affiliation(s)
- Yong Hu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
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26
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A model of DNA repeat-assembled mitotic chromosomal skeleton. Genes (Basel) 2011; 2:661-70. [PMID: 24710285 PMCID: PMC3927603 DOI: 10.3390/genes2040661] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Revised: 09/15/2011] [Accepted: 09/21/2011] [Indexed: 01/01/2023] Open
Abstract
Despite intensive investigation for decades, the principle of higher-order organization of mitotic chromosomes is unclear. Here, I describe a novel model that emphasizes a critical role of interactions of homologous DNA repeats (repetitive elements; repetitive sequences) in mitotic chromosome architecture. According to the model, DNA repeats are assembled, via repeat interactions (pairing), into compact core structures that govern the arrangement of chromatins in mitotic chromosomes. Tandem repeat assemblies form a chromosomal axis to coordinate chromatins in the longitudinal dimension, while dispersed repeat assemblies form chromosomal nodes around the axis to organize chromatins in the halo. The chromosomal axis and nodes constitute a firm skeleton on which non-skeletal chromatins can be anchored, folded, and supercoiled.
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27
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Zhao X, Lu J, Zhang Z, Hu J, Huang S, Jin W. Comparison of the distribution of the repetitive DNA sequences in three variants of Cucumis sativus reveals their phylogenetic relationships. J Genet Genomics 2011; 38:39-45. [PMID: 21338951 DOI: 10.1016/j.jcg.2010.12.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2010] [Revised: 12/20/2010] [Accepted: 12/24/2010] [Indexed: 01/08/2023]
Abstract
Repetitive DNA sequences with variability in copy number or/and sequence polymorphism can be employed as useful molecular markers to study phylogenetics and identify species/chromosomes when combined with fluorescence in situ hybridization (FISH). Cucumis sativus has three variants, Cucumis sativus L. var. sativus, Cucumis sativus L. var. hardwickii and Cucumis sativus L. var. xishuangbannesis. The phylogenetics among these three variants has not been well explored using cytological landmarks. Here, we concentrate on the organization and distribution of highly repetitive DNA sequences in cucumbers, with emphasis on the differences between cultivar and wild cucumber. The diversity of chromosomal karyotypes in cucumber and its relatives was detected in our study. Thereby, sequential FISH with three sets of multi-probe cocktails (combined repetitive DNA with chromosome-specific fosmid clones as probes) were conducted on the same metaphase cell, which helped us to simultaneously identify each of the 7 metaphase chromosomes of wild cucumber C. sativus var. hardwickii. A standardized karyotype of somatic metaphase chromosomes was constructed. Our data also indicated that the relationship between cultivar cucumber and C. s. var. xishuangbannesis was closer than that of C. s. var. xishuangbannesis and C. s. var. hardwickii.
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Affiliation(s)
- Xin Zhao
- National Maize Improvement Center of China, Key Laboratory of Crop Genetic Improvement and Genome of Ministry of Agriculture, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
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28
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Tenaillon MI, Hufford MB, Gaut BS, Ross-Ibarra J. Genome size and transposable element content as determined by high-throughput sequencing in maize and Zea luxurians. Genome Biol Evol 2011; 3:219-29. [PMID: 21296765 PMCID: PMC3068001 DOI: 10.1093/gbe/evr008] [Citation(s) in RCA: 124] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The genome of maize (Zea mays ssp. mays) consists mostly of transposable elements (TEs) and varies in size among lines. This variation extends to other species in the genus Zea: although maize and Zea luxurians diverged only ∼140,000 years ago, their genomes differ in size by ∼50%. We used paired-end Illumina sequencing to evaluate the potential contribution of TEs to the genome size difference between these two species. We aligned the reads both to a filtered gene set and to an exemplar database of unique repeats representing 1,514 TE families; ∼85% of reads mapped against TE repeats in both species. The relative contribution of TE families to the B73 genome was highly correlated with previous estimates, suggesting that reliable estimates of TE content can be obtained from short high-throughput sequencing reads, even at low coverage. Because we used paired-end reads, we could assess whether a TE was near a gene by determining if one paired read mapped to a TE and the second read mapped to a gene. Using this method, Class 2 DNA elements were found significantly more often in genic regions than Class 1 RNA elements, but Class 1 elements were found more often near other TEs. Overall, we found that both Class 1 and 2 TE families account for ∼70% of the genome size difference between B73 and luxurians. Interestingly, the relative abundance of TE families was conserved between species (r = 0.97), suggesting genome-wide control of TE content rather than family-specific effects.
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Affiliation(s)
- Maud I Tenaillon
- CNRS, UMR de Génétique Végétale, INRA/CNRS/Univ Paris-Sud/AgroParisTech, Ferme du Moulon, Gif-sur-Yvette, France
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The selection and use of sorghum (Sorghum propinquum) bacterial artificial chromosomes as cytogenetic FISH probes for maize (Zea mays L.). J Biomed Biotechnol 2011; 2011:386862. [PMID: 21234422 PMCID: PMC3014715 DOI: 10.1155/2011/386862] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2010] [Accepted: 11/02/2010] [Indexed: 02/03/2023] Open
Abstract
The integration of genetic and physical maps of maize is progressing rapidly, but the cytogenetic maps lag behind, with the exception of the pachytene fluorescence in situ hybridization (FISH) maps of maize chromosome 9. We sought to produce integrated FISH maps of other maize chromosomes using Core Bin Marker loci. Because these 1 Kb restriction fragment length polymorphism (RFLP) probes are below the FISH detection limit, we used BACs from sorghum, a small-genome relative of maize, as surrogate clones for FISH mapping. We sequenced 151 maize RFLP probes and compared in silico BAC selection methods to that of library filter hybridization and found the latter to be the best. BAC library screening, clone verification, and single-clone selection criteria are presented along with an example of transgenomic BAC FISH mapping. This strategy has been used to facilitate the integration of RFLP and FISH maps in other large-genome species.
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30
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Kato A, Lamb JC, Albert PS, Danilova T, Han F, Gao Z, Findley S, Birchler JA. Chromosome painting for plant biotechnology. Methods Mol Biol 2011; 701:67-96. [PMID: 21181525 DOI: 10.1007/978-1-61737-957-4_4] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Fluorescence in situ hybridization (FISH) is an invaluable tool for chromosome analysis and engineering. The ability to visually localize endogenous genes, transposable elements, transgenes, naturally occurring organellar DNA insertions - essentially any unique sequence larger than 2 kb - greatly facilitates progress. This chapter details the labeling procedures and chromosome preparation techniques used to produce high-quality FISH signals on somatic metaphase and meiotic pachytene spreads.
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Affiliation(s)
- Akio Kato
- Division of Biological Sciences, University of Missouri, Columbia, MO, USA
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31
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Abstract
B chromosomes are dispensable elements of the genome that do not recombine with the A chromosomes of the regular complement and that follow their own evolutionary pathway. Here, we survey current knowledge on the DNA/chromatin composition, origin, and drive mechanisms of B chromosomes and discuss the potential research applications of supernumerary chromosomes.
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Affiliation(s)
- Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
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32
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Maize centromere structure and evolution: sequence analysis of centromeres 2 and 5 reveals dynamic Loci shaped primarily by retrotransposons. PLoS Genet 2009; 5:e1000743. [PMID: 19956743 PMCID: PMC2776974 DOI: 10.1371/journal.pgen.1000743] [Citation(s) in RCA: 136] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2009] [Accepted: 10/13/2009] [Indexed: 01/20/2023] Open
Abstract
We describe a comprehensive and general approach for mapping centromeres and present a detailed characterization of two maize centromeres. Centromeres are difficult to map and analyze because they consist primarily of repetitive DNA sequences, which in maize are the tandem satellite repeat CentC and interspersed centromeric retrotransposons of maize (CRM). Centromeres are defined epigenetically by the centromeric histone H3 variant, CENH3. Using novel markers derived from centromere repeats, we have mapped all ten centromeres onto the physical and genetic maps of maize. We were able to completely traverse centromeres 2 and 5, confirm physical maps by fluorescence in situ hybridization (FISH), and delineate their functional regions by chromatin immunoprecipitation (ChIP) with anti-CENH3 antibody followed by pyrosequencing. These two centromeres differ substantially in size, apparent CENH3 density, and arrangement of centromeric repeats; and they are larger than the rice centromeres characterized to date. Furthermore, centromere 5 consists of two distinct CENH3 domains that are separated by several megabases. Succession of centromere repeat classes is evidenced by the fact that elements belonging to the recently active recombinant subgroups of CRM1 colonize the present day centromeres, while elements of the ancestral subgroups are also found in the flanking regions. Using abundant CRM and non-CRM retrotransposons that inserted in and near these two centromeres to create a historical record of centromere location, we show that maize centromeres are fluid genomic regions whose borders are heavily influenced by the interplay of retrotransposons and epigenetic marks. Furthermore, we propose that CRMs may be involved in removal of centromeric DNA (specifically CentC), invasion of centromeres by non-CRM retrotransposons, and local repositioning of the CENH3. Centromeres tend to be the last regions to be assembled in genome projects, as their mapping is hampered by their characteristically high repeat DNA content and lack of genetic recombination. Using unique markers derived from these repeat-rich regions, we were able to generate and annotate physical maps of two maize centromeres. Functional centromeres are defined not so much by their primary DNA sequence as by the presence of CENH3, a special histone that replaces canonical histone H3 in centromeric nucleosomes. Little is known about how deposition of CENH3 is regulated, or about the interplay between centromeric repeats and CENH3. By graphing the density of CENH3 nucleosomes onto the physical map, we delineated the functional centromeres in today's maize genome. We then used the large number of LTR retrotransposon insertions, for which the corn genome is well known, as “archeological evidence” to reconstruct the historic centromere boundaries. This was possible because i) some retrotransposon families of maize (CRM) appear to possess a unique ability to preferentially target centromeres during integration and ii) insertion times of individual retrotransposons can be calculated. Here we show that the centromere boundaries in maize have changed over time and are heavily influenced by centromeric and non-centromeric repeats.
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David P, Chen NW, Pedrosa-Harand A, Thareau V, Sévignac M, Cannon SB, Debouck D, Langin T, Geffroy V. A nomadic subtelomeric disease resistance gene cluster in common bean. PLANT PHYSIOLOGY 2009; 151:1048-65. [PMID: 19776165 PMCID: PMC2773105 DOI: 10.1104/pp.109.142109] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2009] [Accepted: 09/17/2009] [Indexed: 05/18/2023]
Abstract
The B4 resistance (R) gene cluster is one of the largest clusters known in common bean (Phaseolus vulgaris [Pv]). It is located in a peculiar genomic environment in the subtelomeric region of the short arm of chromosome 4, adjacent to two heterochromatic blocks (knobs). We sequenced 650 kb spanning this locus and annotated 97 genes, 26 of which correspond to Coiled-Coil-Nucleotide-Binding-Site-Leucine-Rich-Repeat (CNL). Conserved microsynteny was observed between the Pv B4 locus and corresponding regions of Medicago truncatula and Lotus japonicus in chromosomes Mt6 and Lj2, respectively. The notable exception was the CNL sequences, which were completely absent in these regions. The origin of the Pv B4-CNL sequences was investigated through phylogenetic analysis, which reveals that, in the Pv genome, paralogous CNL genes are shared among nonhomologous chromosomes (4 and 11). Together, our results suggest that Pv B4-CNL was derived from CNL sequences from another cluster, the Co-2 cluster, through an ectopic recombination event. Integration of the soybean (Glycine max) genome data enables us to date more precisely this event and also to infer that a single CNL moved from the Co-2 to the B4 cluster. Moreover, we identified a new 528-bp satellite repeat, referred to as khipu, specific to the Phaseolus genus, present both between B4-CNL sequences and in the two knobs identified at the B4 R gene cluster. The khipu repeat is present on most chromosomal termini, indicating the existence of frequent ectopic recombination events in Pv subtelomeric regions. Our results highlight the importance of ectopic recombination in R gene evolution.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Valérie Geffroy
- Institut de Biotechnologie des Plantes, UMR-CNRS 8618, Université Paris-Sud, 91405 Orsay cedex, France (P.D., N.W.G.C., V.T., M.S., T.L., V.G.); Unité Mixte de Recherche de Génétique Végétale, Institut National de la Recherche Agronomique, 91190 Gif-sur-Yvette, France (V.G.); Laboratório de Citogenética Vegetal, Departamento de Botânica-Centro de Ciências Biológicas, Universidade Federal de Pernambuco, Recife-Pernambuco 50670–420, Brazil (A.P.-H.); United States Department of Agriculture-Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Ames, Iowa 50011 (S.B.C.); and Genetic Resources Unit, Centro Internacional de Agricultura Tropical, AA 6713 Cali, Colombia (D.D.)
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34
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Allopolyploid origin of Mediterranean species inHelictotrichon(Poaceae) and its consequences for karyotype repatterning and homogenisation of rDNA repeat units. SYST BIODIVERS 2009. [DOI: 10.1017/s1477200009003041] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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35
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Staton SE, Ungerer MC, Moore RC. The genomic organization of Ty3/gypsy-like retrotransposons in Helianthus (Asteraceae) homoploid hybrid species. AMERICAN JOURNAL OF BOTANY 2009; 96:1646-1655. [PMID: 21622351 DOI: 10.3732/ajb.0800337] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The origin of new diploid, or homoploid, hybrid species is associated with rapid genomic restructuring in the hybrid neospecies. This mode of speciation has been best characterized in wild sunflower species in the genus Helianthus, where three homoploid hybrid species (H. anomalus, H. deserticola, and H. paradoxus) have independently arisen via ancient hybridization events between the same two parental species (H. annuus and H. petiolaris). Most previous work examining genomic restructuring in these sunflower hybrid species has focused on chromosomal rearrangements. However, the origin of all three homoploid hybrid sunflower species also is associated with massive proliferation events of Ty3/gypsy-like retrotransposons in the hybrid species' genomes. We compared the genomic organization of these elements in the parent species and two of the homoploid hybrid species using fluorescence in situ hybridization (FISH). We found a significant expansion of Ty3/gypsy-like retrotransposons confined to the pericentromeric regions of two hybrid sunflower species, H. deserticola and H. paradoxus. In contrast, we detected no significant increase in the frequency or extent of dispersed retrotransposon populations in the hybrid species within the resolution limits of our assay. We discuss the potential role that transposable element proliferation and localization plays in the evolution of homoploid hybrid species.
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Affiliation(s)
- S Evan Staton
- Miami University, Department of Botany, 316 Pearson Hall, Oxford, Ohio 45056 USA
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36
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Hale CJ, Erhard KF, Lisch D, Hollick JB. Production and processing of siRNA precursor transcripts from the highly repetitive maize genome. PLoS Genet 2009; 5:e1000598. [PMID: 19680464 PMCID: PMC2725412 DOI: 10.1371/journal.pgen.1000598] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2009] [Accepted: 07/14/2009] [Indexed: 11/18/2022] Open
Abstract
Mutations affecting the maintenance of heritable epigenetic states in maize identify multiple RNA–directed DNA methylation (RdDM) factors including RMR1, a novel member of a plant-specific clade of Snf2-related proteins. Here we show that RMR1 is necessary for the accumulation of a majority of 24 nt small RNAs, including those derived from Long-Terminal Repeat (LTR) retrotransposons, the most common repetitive feature in the maize genome. A genetic analysis of DNA transposon repression indicates that RMR1 acts upstream of the RNA–dependent RNA polymerase, RDR2 (MOP1). Surprisingly, we show that non-polyadenylated transcripts from a sampling of LTR retrotransposons are lost in both rmr1 and rdr2 mutants. In contrast, plants deficient for RNA Polymerase IV (Pol IV) function show an increase in polyadenylated LTR RNA transcripts. These findings support a model in which Pol IV functions independently of the small RNA accumulation facilitated by RMR1 and RDR2 and support that a loss of Pol IV leads to RNA Polymerase II–based transcription. Additionally, the lack of changes in general genome homeostasis in rmr1 mutants, despite the global loss of 24 nt small RNAs, challenges the perceived roles of siRNAs in maintaining functional heterochromatin in the genomes of outcrossing grass species. Most eukaryotic genomes are divided into two functional classes of regulation: the euchromatic and the heterochromatic. Heterochromatic regions, often composed of potentially deleterious transposons and retrotransposons, are typically viewed as “silent” or not transcribed. Paradoxically, evidence from multiple organisms indicates that heterochromatic regions must be transcribed to maintain a heterochromatic character. In plants, specialized RNA polymerase complexes are thought to specifically process repetitive regions of the genome into small RNA molecules that facilitate maintenance of a heterochromatic environment. We investigated the role of this specialized polymerase pathway in maintaining maize genome homeostasis with particular focus on RMR1, a novel protein related to a family of DNA repair proteins, whose function in modifying repetitive regions of the genome is unknown. We find most small RNA generation is dependent on RMR1, which appears to function downstream of the specialized polymerase, RNA polymerase IV. However, we provide evidence that the function of RNA polymerase IV is not disrupted by the absence of small RNA generation. Our results suggest the division of the plant genome into euchromatin and heterochromatin is maintained by template competition between the specialized plant polymerases and canonical RNA polymerase II, and not by the subsequent generation of small RNA molecules.
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Affiliation(s)
- Christopher J. Hale
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Karl F. Erhard
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Damon Lisch
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Jay B. Hollick
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, United States of America
- * E-mail:
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37
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Topp CN, Okagaki RJ, Melo JR, Kynast RG, Phillips RL, Dawe RK. Identification of a maize neocentromere in an oat-maize addition line. Cytogenet Genome Res 2009; 124:228-38. [PMID: 19556776 DOI: 10.1159/000218128] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/11/2008] [Indexed: 12/17/2022] Open
Abstract
We report a neocentromere event on maize chromosome 3 that occurred due to chromosome breakage. The neocentromere lies on a fragment of the short arm that lacks the primary centromere DNA elements, CentC and CRM. It is transmitted in the genomic background of oat via a new centromere (and kinetochore), as shown by immunolocalization of the oat CENH3 protein. Despite normal transmission of the maize fragment in most progeny, neocentromeres appear to vary in size within the same tissue, as shown by fluorescent measurements. A secondary truncation in one line lowered mitotic transmission to 3% and precipitously reduced the size of the chromosome. The results support the view that neocentromere formation is generally associated with major genomic disturbances such as wide species crosses or deletion of an existing centromere. The data further suggest that new centromeres may undergo a period of instability that is corrected over a period of several generations.
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Affiliation(s)
- C N Topp
- Department of Plant Biology, University of Georgia, Athens, GA 30602-1755, USA
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38
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Tandem organization of StarkB element (22.8 kb) in the maize B chromosome. Mol Genet Genomics 2009; 282:131-9. [PMID: 19418069 DOI: 10.1007/s00438-009-0452-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2009] [Accepted: 04/17/2009] [Indexed: 10/20/2022]
Abstract
A very large repetitive element (StarkB, 22.8 kb) is present in the maize B chromosome, presumably not organized as tandem arrays. Results of the current study are contrary to this notion. Out of eighteen StarkB-carrying sequences, nine were the expected internal fragment of StarkB, and nine others were fragments spanning two StarkB elements. One of the two StarkB components, GrandeB, was flanked in all clones with identical target sequences, as opposed to other Grandes that are associated with different target sequences. Also observed was a prominent Southern signal associated with a fragment representing the junction of two adjacent StarkB units. A clone possessing a structure inverse to that of the second component of StarkB is proposed to be the initial element into which a GrandeB inserted to derive StarkB. Most, if not all, isolated StarkB arrays were not the original form, being disrupted by the invasion of various mobile elements intertwined with various stages of amplification.
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39
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Epigenetic Phenomena and Epigenomics in Maize. Epigenomics 2008. [DOI: 10.1007/978-1-4020-9187-2_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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40
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Histone modifications associated with both A and B chromosomes of maize. Chromosome Res 2008; 16:1203-14. [PMID: 18987983 DOI: 10.1007/s10577-008-1269-8] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2008] [Revised: 09/18/2008] [Accepted: 09/18/2008] [Indexed: 01/11/2023]
Abstract
We report the distribution of several histone modifications along the arms and in centromeric regions of somatic chromosomes of maize, including the supernumerary B chromosome. Acetylated H3 and H4 as well as H3K4me2, modifications associated with euchromatin, were enriched in the distal parts of the A chromosomes, but were progressively depleted toward the centromeres of the A chromosomes and were depleted in the heterochromatic portions of the B chromosome. Classical histone modifications associated with heterochromatin, including H3K9me2, H3K27me1 and H3K27me2, were distributed throughout both A and B chromosomes. However, H3K27me2 showed a reduced level on the B chromosome compared with the A chromosomes and was not associated with some classes of constitutive heterochromatin. We monitored the presence of each histone modification in the centromeric regions using a YFP-tagged centromere-specific histone, CENH3. We observed the presence of H3K9me2 and absence of H3K4me2 in the centromeric regions of both A and B chromosomes of maize, which is in contrast to the presence of H3K4me2 and absence of H3K9me2 in animal centromeres. These results show a diversity of epigenetic modifications associated with centromeric chromatin in different eukaryotes.
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41
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Mandáková T, Lysak MA. Chromosomal phylogeny and karyotype evolution in x=7 crucifer species (Brassicaceae). THE PLANT CELL 2008; 20:2559-70. [PMID: 18836039 PMCID: PMC2590746 DOI: 10.1105/tpc.108.062166] [Citation(s) in RCA: 120] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2008] [Revised: 09/06/2008] [Accepted: 09/17/2008] [Indexed: 05/18/2023]
Abstract
Karyotype evolution in species with identical chromosome number but belonging to distinct phylogenetic clades is a long-standing question of plant biology, intractable by conventional cytogenetic techniques. Here, we apply comparative chromosome painting (CCP) to reconstruct karyotype evolution in eight species with x=7 (2n=14, 28) chromosomes from six Brassicaceae tribes. CCP data allowed us to reconstruct an ancestral Proto-Calepineae Karyotype (PCK; n=7) shared by all x=7 species analyzed. The PCK has been preserved in the tribes Calepineae, Conringieae, and Noccaeeae, whereas karyotypes of Eutremeae, Isatideae, and Sisymbrieae are characterized by an additional translocation. The inferred chromosomal phylogeny provided compelling evidence for a monophyletic origin of the x=7 tribes. Moreover, chromosomal data along with previously published gene phylogenies strongly suggest the PCK to represent an ancestral karyotype of the tribe Brassiceae prior to its tribe-specific whole-genome triplication. As the PCK shares five chromosomes and conserved associations of genomic blocks with the putative Ancestral Crucifer Karyotype (n=8) of crucifer Lineage I, we propose that both karyotypes descended from a common ancestor. A tentative origin of the PCK via chromosome number reduction from n=8 to n=7 is outlined. Comparative chromosome maps of two important model species, Noccaea caerulescens and Thellungiella halophila, and complete karyotypes of two purported autotetraploid Calepineae species (2n=4x=28) were reconstructed by CCP.
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Affiliation(s)
- Terezie Mandáková
- Department of Functional Genomics and Proteomics, Institute of Experimental Biology, Masaryk University, Brno CZ-625 00, Czech Republic
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42
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Koo DH, Jiang J. Extraordinary tertiary constrictions of Tripsacum dactyloides chromosomes: implications for karyotype evolution of polyploids driven by segmental chromosome losses. Genetics 2008; 179:1119-23. [PMID: 18558656 PMCID: PMC2429865 DOI: 10.1534/genetics.108.087726] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2008] [Accepted: 04/02/2008] [Indexed: 11/18/2022] Open
Abstract
Tripsacum dactyloides (2n = 2x = 36) is an ancient tetraploid species. Here we report that T. dactyloides chromosomes contain an extraordinary tertiary constriction, which causes a radical and distant separation of a terminal segment from the chromosome. The relationships between extraordinary tertiary constriction and segmental chromosome loss as well as karyotype evolution of polyploid species are discussed.
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Affiliation(s)
- Dal-Hoe Koo
- Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706, USA
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43
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Jones RN, González-Sánchez M, González-García M, Vega JM, Puertas MJ. Chromosomes with a life of their own. Cytogenet Genome Res 2008; 120:265-80. [PMID: 18504356 DOI: 10.1159/000121076] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/05/2007] [Indexed: 01/05/2023] Open
Abstract
B chromosomes (Bs) can be described as 'passengers in the genome', a term that has been used for the repetitive DNA which comprises the bulk of the genome in large genome species, except that Bs have a life of their own as independent chromosomes. As with retrotransposons they can accumulate in number, but in this case by various processes of mitotic or meiotic drive, based on their own autonomous ways of using spindles, especially in the gametophyte phase of the life cycle of flowering plants. This selfish property of drive ensures their survival and spread in natural populations, even against a gradient of harmful effects on the host plant phenotype. Bs are inhabitants of the nucleus and they are subject to control by 'genes' in the A chromosome (As) complement. This interaction with the As, together with the balance between drive and harmful effects makes a dynamic system in the life of a B chromosome, notwithstanding the fact that we are only now beginning to unravel the story in a few favoured species. In this review we concentrate mainly on recent developments in the Bs of rye and maize, two of the species currently receiving most attention. We focus on their population dynamics and on the molecular basis of their structural organisation and mechanisms of drive, as well as on their mode of origin and potential applications in plant biotechnology.
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Affiliation(s)
- R N Jones
- Aberystwyth University, Institute of Biological Sciences, Aberystwyth, UK
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44
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Villasante A, Abad JP, Méndez-Lago M. Centromeres were derived from telomeres during the evolution of the eukaryotic chromosome. Proc Natl Acad Sci U S A 2007; 104:10542-7. [PMID: 17557836 PMCID: PMC1965549 DOI: 10.1073/pnas.0703808104] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2005] [Indexed: 12/24/2022] Open
Abstract
The centromere is the DNA region of the eukaryotic chromosome that determines kinetochore formation and sister chromatid cohesion. Centromeres interact with spindle microtubules to ensure the segregation of chromatids during mitosis and of homologous chromosomes in meiosis. The origin of centromeres, therefore, is inseparable from the evolution of cytoskeletal components that distribute chromosomes to offspring cells. Although the origin of the nucleus has been debated, no explanation for the evolutionary appearance of centromeres is available. We propose an evolutionary scenario: The centromeres originated from telomeres. The breakage of the ancestral circular genophore activated the transposition of retroelements at DNA ends that allowed the formation of telomeres by a recombination-dependent replication mechanism. Afterward, the modification of the tubulin-based cytoskeleton that allowed specific subtelomeric repeats to be recognized as new cargo gave rise to the first centromere. This switch from actin-based genophore partition to a tubulin-based mechanism generated a transition period during which both types of cytoskeleton contributed to fidelity of chromosome segregation. During the transition, pseudodicentric chromosomes increased the tendency toward chromosomal breakage and instability. This instability generated multiple telocentric chromosomes that eventually evolved into metacentric or holocentric chromosomes.
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Affiliation(s)
- Alfredo Villasante
- Centro de Biología Molecular Severo Ochoa, Universidad Autonóma de Madrid, Cantoblanco, 28049 Madrid, Spain.
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45
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Lamb JC, Riddle NC, Cheng YM, Theuri J, Birchler JA. Localization and transcription of a retrotransposon-derived element on the maize B chromosome. Chromosome Res 2007; 15:383-98. [PMID: 17429746 DOI: 10.1007/s10577-007-1135-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2007] [Revised: 02/21/2007] [Accepted: 02/21/2007] [Indexed: 10/23/2022]
Abstract
Dispensable chromosomes in addition to the normal complement in diverse taxa are called B chromosomes. The maize B chromosome is discernible in mitotic chromosome spreads as a small compact chromosome composed mainly of heterochromatin. Although much of this chromosome consists of repetitive elements common to the A chromosomes, several sequences specific to the B chromosome have been identified. In the work described here we used the sequence from a B-specific RAPD (random amplification of polymorphic DNA) marker, pBGBM18.2, to isolate another DNA element, StarkB, present in many copies on the B chromosome. StarkB was mapped to the third and fourth blocks of distal heterochromatin using translocation breakpoints and fluorescent in-situ hybridization (FISH). Sequence analysis revealed that StarkB is composed of fragments from the A genome as well as B-specific sequences. The StarkB element is much larger than the other B-specific elements and is not present in large tandem arrays. Different copies of StarkB varied by small insertions, deletions, and duplications as well as single-nucleotide polymorphisms. Reverse transcriptase PCR showed that portions of the StarkB element are expressed. Using the LTR divergence of retroelements interrupting the B-specific sequences, the minimum age of the StarkB repeat array and, by inference, of the B chromosome, was estimated to be 2 million years.
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Affiliation(s)
- Jonathan C Lamb
- Division of Biological Sciences, University of Missouri-Columbia, Columbia, MO 65211, USA
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Lamb JC, Meyer JM, Birchler JA. A hemicentric inversion in the maize line knobless Tama flint created two sites of centromeric elements and moved the kinetochore-forming region. Chromosoma 2007; 116:237-47. [PMID: 17256108 DOI: 10.1007/s00412-007-0096-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2006] [Revised: 12/30/2006] [Accepted: 01/07/2007] [Indexed: 12/16/2022]
Abstract
A maize line, knobless Tama flint (KTF), was found to contain a version of chromosome 8 with two spatially distinct regions of centromeric elements, one at the original genetic position and the other at a novel location on the long arm. The new site of centromeric elements functions as the kinetochore-forming region resulting in a change of arm length ratio. Examination of fluorescence in situ hybridization markers on chromosome 8 revealed an inversion between the two centromere sites relative to standard maize lines, indicating that this chromosome 8 resulted from a hemicentric inversion with one breakpoint approximately 20 centi-McClintocks (cMc) on the long arm (20% of the total arm length from the centromere) and the other in the original cluster of centromere repeats. This inversion moved the kinetochore-forming region but left the remainder of the centromere repeats. In a hybrid between a standard line (Mo17) and KTF, both chromosome 8 homologues were completely synapsed at pachytene despite the inversion. Although the homologous centromeres were not paired, they were always correctly oriented at anaphase and migrated to opposite poles. Additionally, recombination on 8L was severely repressed in the hybrid.
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Affiliation(s)
- Jonathan C Lamb
- Division of Biological Sciences, University of Missouri-Columbia, 117 Tucker Hall, Columbia, MO 65211, USA
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Lamb JC, Danilova T, Bauer MJ, Meyer JM, Holland JJ, Jensen MD, Birchler JA. Single-gene detection and karyotyping using small-target fluorescence in situ hybridization on maize somatic chromosomes. Genetics 2007; 175:1047-58. [PMID: 17237520 PMCID: PMC1840074 DOI: 10.1534/genetics.106.065573] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Combined with a system for identifying each of the chromosomes in a genome, visualizing the location of individual genetic loci by fluorescence in situ hybridization (FISH) would aid in assembling physical and genetic maps. Previously, large genomic clones have been successfully used as FISH probes onto somatic chromosomes but this approach is complicated in species with abundant repetitive elements. In this study, repeat-free portions of sequences that were anchored to particular chromosomes including genes, gene clusters, large cDNAs, and portions of BACs obtained from public databases were used to label the corresponding physical location using FISH. A collection of probes that includes at least one marker on each chromosome in the maize complement was assembled, allowing a small-target karyotyping system to be developed. This set provides the foundation onto which additional loci could be added to strengthen further the ability to perform chromosomal identification in maize and its relatives. The probes were demonstrated to produce signals in several wild relatives of maize, including Zea luxurians, Z. diploperennis, and Tripsacum dactyloides.
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Affiliation(s)
- Jonathan C Lamb
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211, USA
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