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Kuo YT, Ishii T, Fuchs J, Hsieh WH, Houben A, Lin YR. The Evolutionary Dynamics of Repetitive DNA and Its Impact on the Genome Diversification in the Genus Sorghum. FRONTIERS IN PLANT SCIENCE 2021; 12:729734. [PMID: 34475879 PMCID: PMC8407070 DOI: 10.3389/fpls.2021.729734] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 07/23/2021] [Indexed: 05/11/2023]
Abstract
Polyploidization is an evolutionary event leading to structural changes of the genome(s), particularly allopolyploidization, which combines different genomes of distinct species. The tetraploid species, Sorghum halepense, is assumed an allopolyploid species formed by hybridization between diploid S. bicolor and S. propinquum. The repeat profiles of S. bicolor, S. halepense, and their relatives were compared to elucidate the repeats' role in shaping their genomes. The repeat frequencies and profiles of the three diploid accessions (S. bicolor, S. bicolor ssp. verticilliflorum, and S. bicolor var. technicum) and two tetraploid accessions (S. halepense) are similar. However, the polymorphic distribution of the subtelomeric satellites preferentially enriched in the tetraploid S. halepense indicates drastic genome rearrangements after the allopolyploidization event. Verified by CENH3 chromatin immunoprecipitation (ChIP)-sequencing and fluorescence in situ hybridization (FISH) analysis the centromeres of S. bicolor are mainly composed of the abundant satellite SorSat137 (CEN38) and diverse CRMs, Athila of Ty3_gypsy and Ty1_copia-SIRE long terminal repeat (LTR) retroelements. A similar centromere composition was found in S. halepense. The potential contribution of S. bicolor in the formation of tetraploid S. halepense is discussed.
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Affiliation(s)
- Yi-Tzu Kuo
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
- Department of Agronomy, National Taiwan University, Taipei, Taiwan
| | - Takayoshi Ishii
- Arid Land Research Center, Tottori University, Tottori, Japan
| | - Jörg Fuchs
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Wei-Hsun Hsieh
- Department of Agronomy, National Taiwan University, Taipei, Taiwan
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
- *Correspondence: Andreas Houben,
| | - Yann-Rong Lin
- Department of Agronomy, National Taiwan University, Taipei, Taiwan
- World Vegetable Center, Tainan, Taiwan
- Yann-Rong Lin,
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Giraud D, Lima O, Huteau V, Coriton O, Boutte J, Kovarik A, Leitch AR, Leitch IJ, Aïnouche M, Salmon A. Evolutionary dynamics of transposable elements and satellite DNAs in polyploid Spartina species. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 302:110671. [PMID: 33288000 DOI: 10.1016/j.plantsci.2020.110671] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 07/31/2020] [Accepted: 09/06/2020] [Indexed: 06/12/2023]
Abstract
Repeated sequences and polyploidy play a central role in plant genome dynamics. Here, we analyze the evolutionary dynamics of repeats in tetraploid and hexaploid Spartina species that diverged during the last 10 million years within the Chloridoideae, one of the poorest investigated grass lineages. From high-throughput genome sequencing, we annotated Spartina repeats and determined what sequence types account for the genome size variation among species. We examined whether differential genome size evolution correlated with ploidy levels and phylogenetic relationships. We also examined the tempo of repeat sequence dynamics associated with allopatric speciation over the last 3-6 million years between hexaploid species that diverged on the American and European Atlantic coasts and tetraploid species from North and South America. The tetraploid S. spartinae, whose phylogenetic placement has been debated, exhibits a similar repeat content as hexaploid species, suggesting common ancestry. Genome expansion or contraction resulting from repeat dynamics seems to be explained mostly by the contrasting divergence times between species, rather than by genome changes triggered by ploidy level change per se. One 370 bp satellite may be exhibiting 'meiotic drive' and driving chromosome evolution in S. alterniflora. Our results provide crucial insights for investigating the genetic and epigenetic consequences of such differential repeat dynamics on the ecology and distribution of the meso- and neopolyploid Spartina species.
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Affiliation(s)
- Delphine Giraud
- UMR CNRS 6553 ECOBIO, Université de Rennes 1, F-35042, Rennes Cedex, France.
| | - Oscar Lima
- UMR CNRS 6553 ECOBIO, Université de Rennes 1, F-35042, Rennes Cedex, France.
| | - Virginie Huteau
- Plateforme de cytogénétique moléculaire végétale, INRAE, Université de Rennes 1, Agrocampus Ouest, IGEPP, F-35650, Le Rheu, France; INRAE, Université de Rennes 1, Agrocampus Ouest, IGEPP, F-35650, Le Rheu, France.
| | - Olivier Coriton
- Plateforme de cytogénétique moléculaire végétale, INRAE, Université de Rennes 1, Agrocampus Ouest, IGEPP, F-35650, Le Rheu, France; INRAE, Université de Rennes 1, Agrocampus Ouest, IGEPP, F-35650, Le Rheu, France.
| | - Julien Boutte
- UMR CNRS 6553 ECOBIO, Université de Rennes 1, F-35042, Rennes Cedex, France; INRAE, Université de Rennes 1, Agrocampus Ouest, IGEPP, F-35650, Le Rheu, France.
| | - Ales Kovarik
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, CZ-61265, Czech Republic.
| | - Andrew R Leitch
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK.
| | - Ilia J Leitch
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, TW9 3DS, UK.
| | - Malika Aïnouche
- UMR CNRS 6553 ECOBIO, Université de Rennes 1, F-35042, Rennes Cedex, France.
| | - Armel Salmon
- UMR CNRS 6553 ECOBIO, Université de Rennes 1, F-35042, Rennes Cedex, France.
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53
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Waminal NE, Pellerin RJ, Kang SH, Kim HH. Chromosomal Mapping of Tandem Repeats Revealed Massive Chromosomal Rearrangements and Insights Into Senna tora Dysploidy. FRONTIERS IN PLANT SCIENCE 2021; 12:629898. [PMID: 33643358 PMCID: PMC7902697 DOI: 10.3389/fpls.2021.629898] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 01/21/2021] [Indexed: 05/16/2023]
Abstract
Tandem repeats can occupy a large portion of plant genomes and can either cause or result from chromosomal rearrangements, which are important drivers of dysploidy-mediated karyotype evolution and speciation. To understand the contribution of tandem repeats in shaping the extant Senna tora dysploid karyotype, we analyzed the composition and abundance of tandem repeats in the S. tora genome and compared the chromosomal distribution of these repeats between S. tora and a closely related euploid, Senna occidentalis. Using a read clustering algorithm, we identified the major S. tora tandem repeats and visualized their chromosomal distribution by fluorescence in situ hybridization. We identified eight independent repeats covering ~85 Mb or ~12% of the S. tora genome. The unit lengths and copy numbers had ranges of 7-5,833 bp and 325-2.89 × 106, respectively. Three short duplicated sequences were found in the 45S rDNA intergenic spacer, one of which was also detected at an extra-NOR locus. The canonical plant telomeric repeat (TTTAGGG)n was also detected as very intense signals in numerous pericentromeric and interstitial loci. StoTR05_180, which showed subtelomeric distribution in Senna occidentalis, was predominantly pericentromeric in S. tora. The unusual chromosomal distribution of tandem repeats in S. tora not only enabled easy identification of individual chromosomes but also revealed the massive chromosomal rearrangements that have likely played important roles in shaping its dysploid karyotype.
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Affiliation(s)
- Nomar Espinosa Waminal
- Department of Chemistry and Life Science, BioScience Institute, Sahmyook University, Seoul, South Korea
| | - Remnyl Joyce Pellerin
- Department of Chemistry and Life Science, BioScience Institute, Sahmyook University, Seoul, South Korea
| | - Sang-Ho Kang
- Genomics Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, South Korea
| | - Hyun Hee Kim
- Department of Chemistry and Life Science, BioScience Institute, Sahmyook University, Seoul, South Korea
- *Correspondence: Hyun Hee Kim
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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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55
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Machado CRD, Domit C, Pucci MB, Gazolla CB, Glugoski L, Nogaroto V, Vicari MR. Heterochromatin and microsatellites detection in karyotypes of four sea turtle species: Interspecific chromosomal differences. Genet Mol Biol 2020; 43:e20200213. [PMID: 33270075 PMCID: PMC7734918 DOI: 10.1590/1678-4685-gmb-2020-0213] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 10/08/2020] [Indexed: 12/27/2022] Open
Abstract
The wide variation in size and content of eukaryotic genomes is mainly attributed to the accumulation of repetitive DNA sequences, like microsatellites, which are tandemly repeated DNA sequences. Sea turtles share a diploid number (2n) of 56, however recent molecular cytogenetic data have shown that karyotype conservatism is not a rule in the group. In this study, the heterochromatin distribution and the chromosomal location of microsatellites (CA)n, (GA)n, (CAG)n, (GATA)n, (GAA)n, (CGC)n and (GACA)n in Chelonia mydas, Caretta caretta, Eretmochelys imbricata and Lepidochelys olivacea were comparatively investigated. The obtained data showed that just the (CA)n, (GA)n, (CAG)n and (GATA)n microsatellites were located on sea turtle chromosomes, preferentially in heterochromatic regions of the microchromosomes (mc). Variations in the location of heterochromatin and microsatellites sites, especially in some pericentromeric regions of macrochromosomes, corroborate to proposal of centromere repositioning occurrence in Cheloniidae species. Furthermore, the results obtained with the location of microsatellites corroborate with the temperature sex determination mechanism proposal and the absence of heteromorphic sex chromosomes in sea turtles. The findings are useful for understanding part of the karyotypic diversification observed in sea turtles, especially those that explain the diversification of Carettini from Chelonini species.
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Affiliation(s)
- Caroline Regina Dias Machado
- Universidade Federal do Paraná, Centro Politécnico, Departamento de
Genética, Programa de Pós-Graduação em Genética, Curitiba, Ponta Grossa, PR,
Brazil
| | - Camila Domit
- Universidade Federal do Paraná, Laboratório de Ecologia e
Conservação, Pontal do Paraná, PR, Brazil
| | | | - Camilla Borges Gazolla
- Universidade Federal do Paraná, Centro Politécnico, Departamento de
Genética, Programa de Pós-Graduação em Genética, Curitiba, Ponta Grossa, PR,
Brazil
| | - Larissa Glugoski
- Universidade Federal de São Carlos, Programa de Pós-Graduação em
Genética Evolutiva e Biologia Molecular, São Carlos, SP, Brazil
| | - Viviane Nogaroto
- Universidade Estadual de Ponta Grossa, Departamento de Biologia
Estrutural, Molecular e Genética, Ponta Grossa, PR, Brazil
| | - Marcelo Ricardo Vicari
- Universidade Federal do Paraná, Centro Politécnico, Departamento de
Genética, Programa de Pós-Graduação em Genética, Curitiba, Ponta Grossa, PR,
Brazil
- Universidade Estadual de Ponta Grossa, Departamento de Biologia
Estrutural, Molecular e Genética, Ponta Grossa, PR, Brazil
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56
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Wei L, Liu B, Zhang C, Yu Y, Yang X, Dou Q, Dong Q. Identification and characterization of satellite DNAs in Poa L. Mol Cytogenet 2020; 13:47. [PMID: 33292401 PMCID: PMC7670724 DOI: 10.1186/s13039-020-00518-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Accepted: 11/05/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Poa L. is a large genus of grass in Gramineae, among which P. pratensis is widely cultivated as turf and forage. Satellite DNA is the main components of the plant genome. Information of satellites will helpful for dissection the genome composition and definition of the phylogeny relationship of these species. However, the knowledge about the satellites in genus Poa is still limited. RESULTS Four satellite DNAs were identified using the Repeat Explorer pipeline in HiSeq Illumina reads from diploid plants in P. malaca (2n = 26). Two satellites showed high similarity with the previously identified PpTr-1 and PpTr-3, whereas two others are newly identified with the monomer of 326 bp (Poa-326) and 353 bp (Poa-353) respectively. The clone DNAs of PpTr-1 and PpTr-3, and oligonucleotides designed representing satellites Poa-326 and Poa-353 were probed to test on chromosomes across 13 Poa speceis with different polyploidy level by fluorescent in situ hybridization (FISH). PpTr-1, PpTr-3, and Poa-362 were stably positioned in the subtelomeric regions in nearly all species with the variation of hybridization sites number. However, Poa-353 showed different FISH patterns of multiple regions with the variation of hybridization intensity and distribution sites across species. In addition, 5S rDNA and 45S rDNA were used to characterize the genome of the Poa species. Four rDNA FISH patterns were revealed in the tested species. CONCLUSION Four identified satellite were high conservable across Poa species. Genome distribution of these satellites can be characterized by FISH. The variation of satellite DNAs and rDNA chromosomal distributions between species provide useful information for phylogenetic analysis in genus Poa.
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Affiliation(s)
- Linna Wei
- State Key Laboratory of Plateau Ecology and Agriculture in the Three River Head Waters Region, Qinghai Academy of Animal and Veterinary Science, Xining, 810001, Qinghai Province, China
- Qinghai Provincial Key Laboratory of Adaptive Management on Alpine Grassland, Qinghai University, No. 1 of Weier Road in Shengwuyuan District of Xining City, Xining, 810016, Qinghai Province, China
| | - Bo Liu
- Key Laboratory of Crop Molecular Breeding Qinghai Province, Northwest Institute of Plateau Biology, The Chinese Academy of Sciences, Xining, 810008, Qinghai Province, China
| | - Chunping Zhang
- State Key Laboratory of Plateau Ecology and Agriculture in the Three River Head Waters Region, Qinghai Academy of Animal and Veterinary Science, Xining, 810001, Qinghai Province, China
- Qinghai Provincial Key Laboratory of Adaptive Management on Alpine Grassland, Qinghai University, No. 1 of Weier Road in Shengwuyuan District of Xining City, Xining, 810016, Qinghai Province, China
| | - Yang Yu
- State Key Laboratory of Plateau Ecology and Agriculture in the Three River Head Waters Region, Qinghai Academy of Animal and Veterinary Science, Xining, 810001, Qinghai Province, China
- Qinghai Provincial Key Laboratory of Adaptive Management on Alpine Grassland, Qinghai University, No. 1 of Weier Road in Shengwuyuan District of Xining City, Xining, 810016, Qinghai Province, China
| | - Xiaoxia Yang
- State Key Laboratory of Plateau Ecology and Agriculture in the Three River Head Waters Region, Qinghai Academy of Animal and Veterinary Science, Xining, 810001, Qinghai Province, China
- Qinghai Provincial Key Laboratory of Adaptive Management on Alpine Grassland, Qinghai University, No. 1 of Weier Road in Shengwuyuan District of Xining City, Xining, 810016, Qinghai Province, China
| | - Quanwen Dou
- Key Laboratory of Crop Molecular Breeding Qinghai Province, Northwest Institute of Plateau Biology, The Chinese Academy of Sciences, Xining, 810008, Qinghai Province, China.
| | - Quanmin Dong
- State Key Laboratory of Plateau Ecology and Agriculture in the Three River Head Waters Region, Qinghai Academy of Animal and Veterinary Science, Xining, 810001, Qinghai Province, China.
- Qinghai Provincial Key Laboratory of Adaptive Management on Alpine Grassland, Qinghai University, No. 1 of Weier Road in Shengwuyuan District of Xining City, Xining, 810016, Qinghai Province, China.
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57
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Baez M, Kuo YT, Dias Y, Souza T, Boudichevskaia A, Fuchs J, Schubert V, Vanzela ALL, Pedrosa-Harand A, Houben A. Analysis of the small chromosomal Prionium serratum (Cyperid) demonstrates the importance of reliable methods to differentiate between mono- and holocentricity. Chromosoma 2020; 129:285-297. [PMID: 33165742 PMCID: PMC7665975 DOI: 10.1007/s00412-020-00745-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 10/27/2020] [Accepted: 10/28/2020] [Indexed: 12/21/2022]
Abstract
For a long time, the Cyperid clade (Thurniceae-Juncaceae-Cyperaceae) was considered a group of species possessing holocentromeres exclusively. The basal phylogenetic position of Prionium serratum (Thunb.) Drège (Thurniceae) within Cyperids makes this species an important specimen to understand the centromere evolution within this clade. In contrast to the expectation, the chromosomal distribution of the centromere-specific histone H3 (CENH3), alpha-tubulin and different centromere-associated post-translational histone modifications (H3S10ph, H3S28ph and H2AT120ph) demonstrate a monocentromeric organisation of P. serratum chromosomes. Analysis of the high-copy repeat composition resulted in the identification of two centromere-localised satellite repeats. Hence, monocentricity was the ancestral condition for the Juncaceae-Cyperaceae-Thurniaceae Cyperid clade, and holocentricity in this clade has independently arisen at least twice after differentiation of the three families, once in Juncaceae and the other one in Cyperaceae. In this context, methods suitable for the identification of holocentromeres are discussed.
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Affiliation(s)
- M Baez
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466, Stadt Seeland, Germany.,Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, Pernambuco, Brazil
| | - Y T Kuo
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466, Stadt Seeland, Germany
| | - Y Dias
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466, Stadt Seeland, Germany.,Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, Pernambuco, Brazil
| | - T Souza
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466, Stadt Seeland, Germany.,Laboratory of Cytogenetics and Plant Diversity, Department of General Biology, Center for Biological Sciences, State University of Londrina, Londrina, Paraná, 86057-970, Brazil
| | - A Boudichevskaia
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466, Stadt Seeland, Germany.,KWS SAAT SE & Co. KGaA, 37574, Einbeck, Germany
| | - J Fuchs
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466, Stadt Seeland, Germany
| | - V Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466, Stadt Seeland, Germany
| | - A L L Vanzela
- Laboratory of Cytogenetics and Plant Diversity, Department of General Biology, Center for Biological Sciences, State University of Londrina, Londrina, Paraná, 86057-970, Brazil
| | - A Pedrosa-Harand
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, Pernambuco, Brazil
| | - A Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466, Stadt Seeland, Germany.
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58
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Belyayev A, Jandová M, Josefiová J, Kalendar R, Mahelka V, Mandák B, Krak K. The major satellite DNA families of the diploid Chenopodium album aggregate species: Arguments for and against the "library hypothesis". PLoS One 2020; 15:e0241206. [PMID: 33108401 PMCID: PMC7591062 DOI: 10.1371/journal.pone.0241206] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 10/10/2020] [Indexed: 01/20/2023] Open
Abstract
Satellite DNA (satDNA) is one of the major fractions of the eukaryotic nuclear genome. Highly variable satDNA is involved in various genome functions, and a clear link between satellites and phenotypes exists in a wide range of organisms. However, little is known about the origin and temporal dynamics of satDNA. The “library hypothesis” indicates that the rapid evolutionary changes experienced by satDNAs are mostly quantitative. Although this hypothesis has received some confirmation, a number of its aspects are still controversial. A recently developed next-generation sequencing (NGS) method allows the determination of the satDNA landscape and could shed light on unresolved issues. Here, we explore low-coverage NGS data to infer satDNA evolution in the phylogenetic context of the diploid species of the Chenopodium album aggregate. The application of the Illumina read assembly algorithm in combination with Oxford Nanopore sequencing and fluorescent in situ hybridization allowed the estimation of eight satDNA families within the studied group, six of which were newly described. The obtained set of satDNA families of different origins can be divided into several categories, namely group-specific, lineage-specific and species-specific. In the process of evolution, satDNA families can be transmitted vertically and can be eliminated over time. Moreover, transposable element-derived satDNA families may appear repeatedly in the satellitome, creating an illusion of family conservation. Thus, the obtained data refute the “library hypothesis”, rather than confirming it, and in our opinion, it is more appropriate to speak about “the library of the mechanisms of origin”.
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Affiliation(s)
- Alexander Belyayev
- The Czech Academy of Sciences, Institute of Botany, Průhonice, Czech Republic
- * E-mail:
| | - Michaela Jandová
- The Czech Academy of Sciences, Institute of Botany, Průhonice, Czech Republic
| | - Jiřina Josefiová
- The Czech Academy of Sciences, Institute of Botany, Průhonice, Czech Republic
| | - Ruslan Kalendar
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
- National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Václav Mahelka
- The Czech Academy of Sciences, Institute of Botany, Průhonice, Czech Republic
| | - Bohumil Mandák
- The Czech Academy of Sciences, Institute of Botany, Průhonice, Czech Republic
- Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Praha, Suchdol, Czech Republic
| | - Karol Krak
- The Czech Academy of Sciences, Institute of Botany, Průhonice, Czech Republic
- Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Praha, Suchdol, Czech Republic
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59
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Mata-Sucre Y, Sader M, Van-Lume B, Gagnon E, Pedrosa-Harand A, Leitch IJ, Lewis GP, Souza G. How diverse is heterochromatin in the Caesalpinia group? Cytogenomic characterization of Erythrostemon hughesii Gagnon & G.P. Lewis (Leguminosae: Caesalpinioideae). PLANTA 2020; 252:49. [PMID: 32918627 DOI: 10.1007/s00425-020-03453-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 08/27/2020] [Indexed: 05/25/2023]
Abstract
Cytogenomic characterization of Erythrostemon hughesii reveals a heterogeneity of repeats in its subtelomeric heterochromatin. Comparative analyses with other Caesalpinia group species reveal a significant reduction in the abundance of Ty3-gypsy/Chromovirus Tekay retrotransposons during its evolution. In numerically stable karyotypes, repetitive DNA variability is one of the main causes of genome and chromosome variation and evolution. Species from the Caesalpinia group (Leguminosae) are karyotypically characterized by 2n = 24, with small chromosomes and highly variable CMA+ heterochromatin banding patterns that correlate with environmental variables. Erythrostemon hughesii differs from other species of the group examined to date for having subtelomeric CMA+ bands; this contrasts with most species in the group which have proximal bands. Here we analyse the repeatome of E. hughesii using genome skimming and chromosomal mapping approaches to characterize the identity of the most abundant repetitive elements and their physical location. The repetitive fraction of E. hughesii comprises 28.73% of the genome. The most abundant elements were retrotransposons (RT) with long terminal repeats (LTR-RT; 9.76%) and satellite DNAs (7.83%). Within the LTR-RTs, the most abundant lineages were: Ty1/copia-Ale (1%), Ty3/gypsy CRM (0.88%) and Ty3/gypsy Athila (0.75%). Using fluorescent in situ hybridization four satellite DNAs and several LTR-RT elements were shown to be present in most subtelomeric CMA+ bands. These results highlight how the repeatome in E. hughesii, a species from Oaxaca state in Mexico, is clearly distinct from Northeast Brazilian species of the Caesalpinia group, mainly due to its high diversity of repeats in its subtelomeric heterochromatic bands and low amount of LTR-RT Ty3/gypsy-Tekay elements. Comparative sequence analysis of Tekay elements from different species is congruent with a clade-specific origin of this LTR-RT after the divergence of the Caesalpinia group. We hypothesize that repeat-rich heterochromatin may play a role in leading to faster genomic divergence between individuals, increasing speciation and diversification.
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Affiliation(s)
- Yennifer Mata-Sucre
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Rua Nelson Chaves S/N, Cidade Universitaria, Recife, PE, 50670-420, Brazil
| | - Mariela Sader
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Rua Nelson Chaves S/N, Cidade Universitaria, Recife, PE, 50670-420, Brazil
| | - Brena Van-Lume
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Rua Nelson Chaves S/N, Cidade Universitaria, Recife, PE, 50670-420, Brazil
| | - Edeline Gagnon
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5NZ, UK
| | - Andrea Pedrosa-Harand
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Rua Nelson Chaves S/N, Cidade Universitaria, Recife, PE, 50670-420, Brazil
| | - Ilia J Leitch
- Comparative Plant and Fungal Biology Department, Royal Botanic Gardens, Kew, Richmond, TW9 3AB, Surrey, UK
| | - Gwilym P Lewis
- Comparative Plant and Fungal Biology Department, Royal Botanic Gardens, Kew, Richmond, TW9 3AB, Surrey, UK
| | - Gustavo Souza
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Rua Nelson Chaves S/N, Cidade Universitaria, Recife, PE, 50670-420, Brazil.
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First genome survey and repeatome analysis of Chrysopogon zizanioides based on next-generation sequencing. Biologia (Bratisl) 2020. [DOI: 10.2478/s11756-020-00517-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Blommaert J. Genome size evolution: towards new model systems for old questions. Proc Biol Sci 2020; 287:20201441. [PMID: 32842932 PMCID: PMC7482279 DOI: 10.1098/rspb.2020.1441] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 07/29/2020] [Indexed: 12/20/2022] Open
Abstract
Genome size (GS) variation is a fundamental biological characteristic; however, its evolutionary causes and consequences are the topic of ongoing debate. Whether GS is a neutral trait or one subject to selective pressures, and how strong these selective pressures are, may remain open questions. Fundamentally, the genomic sequences responsible for this variation directly impact the potential evolutionary outcomes and, equally, are the targets of different evolutionary pressures. For example, duplications and deletions of genic regions (large or small) can have immediate and drastic phenotypic effects, while an expansion or contraction of non-coding DNA is less likely to cause catastrophic phenotypic effects. However, in the long term, the accumulation or deletion of ncDNA is likely to have larger effects. Modern sequencing technologies are allowing for the dissection of these proximate causes, but a combination of these new technologies with more traditional evolutionary experiments and approaches could revolutionize this debate and potentially resolve many of these arguments. Here, I discuss an ambitious way forward for GS research, putting it in context of historical debates, theories and sometimes contradictory evidence, and highlighting the promise of combining new sequencing technologies and analytical developments with more traditional experimental evolution approaches.
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Affiliation(s)
- Julie Blommaert
- Department of Organismal Biology, Uppsala University, Uppsala, Sweden
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Ávila Robledillo L, Neumann P, Koblížková A, Novák P, Vrbová I, Macas J. Extraordinary Sequence Diversity and Promiscuity of Centromeric Satellites in the Legume Tribe Fabeae. Mol Biol Evol 2020; 37:2341-2356. [PMID: 32259249 PMCID: PMC7403623 DOI: 10.1093/molbev/msaa090] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Satellite repeats are major sequence constituents of centromeres in many plant and animal species. Within a species, a single family of satellite sequences typically occupies centromeres of all chromosomes and is absent from other parts of the genome. Due to their common origin, sequence similarities exist among the centromere-specific satellites in related species. Here, we report a remarkably different pattern of centromere evolution in the plant tribe Fabeae, which includes genera Pisum, Lathyrus, Vicia, and Lens. By immunoprecipitation of centromeric chromatin with CENH3 antibodies, we identified and characterized a large and diverse set of 64 families of centromeric satellites in 14 species. These families differed in their nucleotide sequence, monomer length (33-2,979 bp), and abundance in individual species. Most families were species-specific, and most species possessed multiple (2-12) satellites in their centromeres. Some of the repeats that were shared by several species exhibited promiscuous patterns of centromere association, being located within CENH3 chromatin in some species, but apart from the centromeres in others. Moreover, FISH experiments revealed that the same family could assume centromeric and noncentromeric positions even within a single species. Taken together, these findings suggest that Fabeae centromeres are not shaped by the coevolution of a single centromeric satellite with its interacting CENH3 proteins, as proposed by the centromere drive model. This conclusion is also supported by the absence of pervasive adaptive evolution of CENH3 sequences retrieved from Fabeae species.
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Affiliation(s)
- Laura Ávila Robledillo
- Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Pavel Neumann
- Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Andrea Koblížková
- Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Petr Novák
- Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Iva Vrbová
- Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Jiří Macas
- Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
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Satellitome Analysis in the Ladybird Beetle Hippodamia variegata (Coleoptera, Coccinellidae). Genes (Basel) 2020; 11:genes11070783. [PMID: 32668664 PMCID: PMC7397073 DOI: 10.3390/genes11070783] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 07/09/2020] [Accepted: 07/09/2020] [Indexed: 12/29/2022] Open
Abstract
Hippodamia variegata is one of the most commercialized ladybirds used for the biological control of aphid pest species in many economically important crops. This species is the first Coccinellidae whose satellitome has been studied by applying new sequencing technologies and bioinformatics tools. We found that 47% of the H. variegata genome is composed of repeated sequences. We identified 30 satellite DNA (satDNA) families with a median intragenomic divergence of 5.75% and A+T content between 45.6% and 74.7%. This species shows satDNA families with highly variable sizes although the most common size is 100–200 bp. However, we highlight the existence of a satDNA family with a repeat unit of 2 kb, the largest repeat unit described in Coleoptera. PCR amplifications for fluorescence in situ hybridization (FISH) probe generation were performed for the four most abundant satDNA families. FISH with the most abundant satDNA family as a probe shows its pericentromeric location on all chromosomes. This location is coincident with the heterochromatin revealed by C-banding and DAPI staining, also analyzed in this work. Hybridization signals for other satDNA families were located only on certain bivalents and the X chromosome. These satDNAs could be very useful as chromosomal markers due to their reduced location.
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64
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Heitkam T, Weber B, Walter I, Liedtke S, Ost C, Schmidt T. Satellite DNA landscapes after allotetraploidization of quinoa (Chenopodium quinoa) reveal unique A and B subgenomes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:32-52. [PMID: 31981259 DOI: 10.1111/tpj.14705] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 12/10/2019] [Accepted: 01/17/2020] [Indexed: 06/10/2023]
Abstract
If two related plant species hybridize, their genomes may be combined and duplicated within a single nucleus, thereby forming an allotetraploid. How the emerging plant balances two co-evolved genomes is still a matter of ongoing research. Here, we focus on satellite DNA (satDNA), the fastest turn-over sequence class in eukaryotes, aiming to trace its emergence, amplification, and loss during plant speciation and allopolyploidization. As a model, we used Chenopodium quinoa Willd. (quinoa), an allopolyploid crop with 2n = 4x = 36 chromosomes. Quinoa originated by hybridization of an unknown female American Chenopodium diploid (AA genome) with an unknown male Old World diploid species (BB genome), dating back 3.3-6.3 million years. Applying short read clustering to quinoa (AABB), C. pallidicaule (AA), and C. suecicum (BB) whole genome shotgun sequences, we classified their repetitive fractions, and identified and characterized seven satDNA families, together with the 5S rDNA model repeat. We show unequal satDNA amplification (two families) and exclusive occurrence (four families) in the AA and BB diploids by read mapping as well as Southern, genomic, and fluorescent in situ hybridization. Whereas the satDNA distributions support C. suecicum as possible parental species, we were able to exclude C. pallidicaule as progenitor due to unique repeat profiles. Using quinoa long reads and scaffolds, we detected only limited evidence of intergenomic homogenization of satDNA after allopolyploidization, but were able to exclude dispersal of 5S rRNA genes between subgenomes. Our results exemplify the complex route of tandem repeat evolution through Chenopodium speciation and allopolyploidization, and may provide sequence targets for the identification of quinoa's progenitors.
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Affiliation(s)
- Tony Heitkam
- Institute of Botany, Technische Universität Dresden, 01069, Dresden, Germany
| | - Beatrice Weber
- Institute of Botany, Technische Universität Dresden, 01069, Dresden, Germany
| | - Ines Walter
- Institute of Botany, Technische Universität Dresden, 01069, Dresden, Germany
| | - Susan Liedtke
- Institute of Botany, Technische Universität Dresden, 01069, Dresden, Germany
| | - Charlotte Ost
- Institute of Botany, Technische Universität Dresden, 01069, Dresden, Germany
- Institute of Biology, Martin-Luther-Universität Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Thomas Schmidt
- Institute of Botany, Technische Universität Dresden, 01069, Dresden, Germany
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65
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Belyayev A, Josefiová J, Jandová M, Mahelka V, Krak K, Mandák B. Transposons and satellite DNA: on the origin of the major satellite DNA family in the Chenopodium genome. Mob DNA 2020; 11:20. [PMID: 32607133 PMCID: PMC7320549 DOI: 10.1186/s13100-020-00219-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 06/19/2020] [Indexed: 11/10/2022] Open
Abstract
Extensive and complex links exist between transposable elements (TEs) and satellite DNA (satDNA), which are the two largest fractions of eukaryotic genome. These relationships have a crucial effect on genome structure, function and evolution. Here, we report a novel case of mutual relationships between TEs and satDNA. In the genomes of Chenopodium s. str. species, the deletion derivatives of tnp2 conserved domain of the newly discovered CACTA-like TE Jozin are involved in generating monomers of the most abundant satDNA family of the Chenopodium satellitome. The analysis of the relative positions of satDNA and different TEs utilizing assembled Illumina reads revealed several associations between satDNA arrays and the transposases of putative CACTA-like elements when an ~ 40 bp fragment of tnp2 served as the start monomer of the satDNA array. The high degree of identity of the consensus satDNA monomers of the investigated species and the tnp2 fragment (from 82.1 to 94.9%) provides evidence of the genesis of CficCl-61-40 satDNA family monomers from analogous regions of their respective parental elements. The results were confirmed via molecular genetic methods and Oxford Nanopore sequencing. The discovered phenomenon leads to the continuous replenishment of species genomes with new identical satDNA monomers, which in turn may increase species satellitomes similarity.
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Affiliation(s)
- Alexander Belyayev
- Czech Academy of Sciences, Institute of Botany, Zámek 1, CZ-252 43 Průhonice, Czech Republic
| | - Jiřina Josefiová
- Czech Academy of Sciences, Institute of Botany, Zámek 1, CZ-252 43 Průhonice, Czech Republic
| | - Michaela Jandová
- Czech Academy of Sciences, Institute of Botany, Zámek 1, CZ-252 43 Průhonice, Czech Republic
| | - Václav Mahelka
- Czech Academy of Sciences, Institute of Botany, Zámek 1, CZ-252 43 Průhonice, Czech Republic
| | - Karol Krak
- Czech Academy of Sciences, Institute of Botany, Zámek 1, CZ-252 43 Průhonice, Czech Republic.,Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Kamýcká 129, 165 00 Praha, Suchdol Czech Republic
| | - Bohumil Mandák
- Czech Academy of Sciences, Institute of Botany, Zámek 1, CZ-252 43 Průhonice, Czech Republic.,Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Kamýcká 129, 165 00 Praha, Suchdol Czech Republic
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66
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Marta A, Dedukh D, Bartoš O, Majtánová Z, Janko K. Cytogenetic Characterization of Seven Novel satDNA Markers in Two Species of Spined Loaches ( Cobitis) and Their Clonal Hybrids. Genes (Basel) 2020; 11:genes11060617. [PMID: 32512717 PMCID: PMC7348982 DOI: 10.3390/genes11060617] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 05/31/2020] [Accepted: 06/02/2020] [Indexed: 01/11/2023] Open
Abstract
Interspecific hybridization is a powerful evolutionary force. However, the investigation of hybrids requires the application of methodologies that provide efficient and indubitable identification of both parental subgenomes in hybrid individuals. Repetitive DNA, and especially the satellite DNA sequences (satDNA), can rapidly diverge even between closely related species, hence providing a useful tool for cytogenetic investigations of hybrids. Recent progress in whole-genome sequencing (WGS) offers unprecedented possibilities for the development of new tools for species determination, including identification of species-specific satDNA markers. In this study, we focused on spined loaches (Cobitis, Teleostei), a group of fishes with frequent interspecific hybridization. Using the WGS of one species, C. elongatoides, we identified seven satDNA markers, which were mapped by fluorescence in situ hybridization on mitotic and lampbrush chromosomes of C. elongatoides, C. taenia and their triploid hybrids (C. elongatoides × 2C. taenia). Two of these markers were chromosome-specific in both species, one had centromeric localization in multiple chromosomes and four had variable patterns between tested species. Our study provided a novel set of cytogenetic markers for Cobitis species and demonstrated that NGS-based development of satDNA cytogenetic markers may provide a very efficient and easy tool for the investigation of hybrid genomes, cell ploidy, and karyotype evolution.
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Affiliation(s)
- Anatolie Marta
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, 27721 Liběchov, Czech Republic; (D.D.); (O.B.); (Z.M.); (K.J.)
- Department of Zoology, Faculty of Science, Charles University in Prague, 128 00 Prague, Czech Republic
- Institute of Zoology, Academy of Science of Moldova, MD-2028, Academiei 1, 2001 Chisinau, Moldova
- Correspondence:
| | - Dmitry Dedukh
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, 27721 Liběchov, Czech Republic; (D.D.); (O.B.); (Z.M.); (K.J.)
| | - Oldřich Bartoš
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, 27721 Liběchov, Czech Republic; (D.D.); (O.B.); (Z.M.); (K.J.)
- Department of Zoology, Faculty of Science, Charles University in Prague, 128 00 Prague, Czech Republic
| | - Zuzana Majtánová
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, 27721 Liběchov, Czech Republic; (D.D.); (O.B.); (Z.M.); (K.J.)
| | - Karel Janko
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, 27721 Liběchov, Czech Republic; (D.D.); (O.B.); (Z.M.); (K.J.)
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Chittussiho 10, 710 00 Ostrava, Czech Republic
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Dwivedi SL, Stoddard FL, Ortiz R. Genomic-based root plasticity to enhance abiotic stress adaptation and edible yield in grain crops. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 295:110365. [PMID: 32534611 DOI: 10.1016/j.plantsci.2019.110365] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 11/15/2019] [Accepted: 12/01/2019] [Indexed: 06/11/2023]
Abstract
Phenotypic plasticity refers to changes expressed by a genotype across different environments and is one of the major means by which plants cope with environmental variability. Multi-fold differences in phenotypic plasticity have been noted across crops, with wild ancestors and landraces being more plastic than crops when under stress. Plasticity in response to abiotic stress adaptation, plant architecture, physio-reproductive and quality traits are multi-genic (QTL). Plasticity QTL (pQTL) were either collocated with main effect QTL and QEI (QTL × environment interaction) or located independently from the main effect QTL. For example, variations in root plasticity have been successfully introgressed to enhance abiotic stress adaptation in rice. The independence of genetic control of a trait and of its plasticity suggests that breeders may select for high or low plasticity in combination with high or low performance of economically important traits. Trait plasticity in stressful environments may be harnessed through breeding stress-tolerant crops. There exists a genetic cost associated with plasticity, so a better understanding of the trade-offs between plasticity and productivity is warranted prior to undertaking breeding for plasticity traits together with productivity in stress environments.
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Affiliation(s)
| | | | - Rodomiro Ortiz
- Swedish University of Agricultural Sciences, Department of Plant Breeding, Sundsvagen, 14 Box 101, SE 23053, Alnarp, Sweden.
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68
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Sultana N, Menzel G, Heitkam T, Kojima KK, Bao W, Serçe S. Bioinformatic and Molecular Analysis of Satellite Repeat Diversity in Vaccinium Genomes. Genes (Basel) 2020; 11:E527. [PMID: 32397417 PMCID: PMC7290377 DOI: 10.3390/genes11050527] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 05/06/2020] [Accepted: 05/06/2020] [Indexed: 12/11/2022] Open
Abstract
Bioinformatic and molecular characterization of satellite repeats was performed to understand the impact of their diversification on Vaccinium genome evolution. Satellite repeat diversity was evaluated in four cultivated and wild species, including the diploid species Vaccinium myrtillus and Vaccinium uliginosum, as well as the tetraploid species Vaccinium corymbosum and Vaccinium arctostaphylos. We comparatively characterized six satellite repeat families using in total 76 clones with 180 monomers. We observed that the monomer units of VaccSat1, VaccSat2, VaccSat5, and VaccSat6 showed a higher order repeat (HOR) structure, likely originating from the organization of two adjacent subunits with differing similarity, length and size. Moreover, VaccSat1, VaccSat3, VaccSat6, and VaccSat7 were found to have sequence similarity to parts of transposable elements. We detected satellite-typical tandem organization for VaccSat1 and VaccSat2 in long arrays, while VaccSat5 and VaccSat6 distributed in multiple sites over all chromosomes of tetraploid V. corymbosum, presumably in long arrays. In contrast, very short arrays of VaccSat3 and VaccSat7 are dispersedly distributed over all chromosomes in the same species, likely as internal parts of transposable elements. We provide a comprehensive overview on satellite species specificity in Vaccinium, which are potentially useful as molecular markers to address the taxonomic complexity of the genus, and provide information for genome studies of this genus.
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Affiliation(s)
- Nusrat Sultana
- Faculty of Life and Earth Sciences, Jagannath University, Dhaka 1100, Bangladesh
- Faculty of Biology, Technische Universität Dresden, D-01062 Dresden, Germany; (G.M.); (T.H.)
| | - Gerhard Menzel
- Faculty of Biology, Technische Universität Dresden, D-01062 Dresden, Germany; (G.M.); (T.H.)
| | - Tony Heitkam
- Faculty of Biology, Technische Universität Dresden, D-01062 Dresden, Germany; (G.M.); (T.H.)
| | - Kenji K. Kojima
- Genetic Information Research Institute, Cupertino, CA 95014, USA; (K.K.K.); (W.B.)
| | - Weidong Bao
- Genetic Information Research Institute, Cupertino, CA 95014, USA; (K.K.K.); (W.B.)
| | - Sedat Serçe
- Department of Agricultural Genetic Engineering, Ayhan Şahenk Faculty of Agricultural Sciences and Technologies, Niğde Ömer Halisdemir University, 51240 Niğde, Turkey;
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69
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McCann J, Macas J, Novák P, Stuessy TF, Villaseñor JL, Weiss-Schneeweiss H. Differential Genome Size and Repetitive DNA Evolution in Diploid Species of Melampodium sect. Melampodium (Asteraceae). FRONTIERS IN PLANT SCIENCE 2020; 11:362. [PMID: 32296454 PMCID: PMC7136903 DOI: 10.3389/fpls.2020.00362] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 03/12/2020] [Indexed: 05/18/2023]
Abstract
Plant genomes vary greatly in composition and size mainly due to the diversity of repetitive DNAs and the inherent propensity for their amplification and removal from the host genome. Most studies addressing repeatome dynamics focus on model organisms, whereas few provide comprehensive investigations across the genomes of related taxa. Herein, we analyze the evolution of repeats of the 13 species in Melampodium sect. Melampodium, representing all but two of its diploid taxa, in a phylogenetic context. The investigated genomes range in size from 0.49 to 2.27 pg/1C (ca. 4.5-fold variation), despite having the same base chromosome number (x = 10) and very strong phylogenetic affinities. Phylogenetic analysis performed in BEAST and ancestral genome size reconstruction revealed mixed patterns of genome size increases and decreases across the group. High-throughput genome skimming and the RepeatExplorer pipeline were utilized to determine the repeat families responsible for the differences in observed genome sizes. Patterns of repeat evolution were found to be highly correlated with phylogenetic position, namely taxonomic series circumscription. Major differences found were in the abundances of the SIRE (Ty1-copia), Athila (Ty3-gypsy), and CACTA (DNA transposon) lineages. Additionally, several satellite DNA families were found to be highly group-specific, although their overall contribution to genome size variation was relatively small. Evolutionary changes in repetitive DNA composition and genome size were complex, with independent patterns of genome up- and downsizing throughout the evolution of the analyzed diploids. A model-based analysis of genome size and repetitive DNA composition revealed evidence for strong phylogenetic signal and differential evolutionary rates of major lineages of repeats in the diploid genomes.
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Affiliation(s)
- Jamie McCann
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Jiří Macas
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, České Budějovice, Czechia
| | - Petr Novák
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, České Budějovice, Czechia
| | - Tod F. Stuessy
- Herbarium and Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, United States
| | - Jose L. Villaseñor
- Department of Botany, National Autonomous University of Mexico, Mexico City, Mexico
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da Silva MJ, Fogarin Destro R, Gazoni T, Narimatsu H, Pereira Dos Santos PS, Haddad CFB, Parise-Maltempi PP. Great Abundance of Satellite DNA in Proceratophrys (Anura, Odontophrynidae) Revealed by Genome Sequencing. Cytogenet Genome Res 2020; 160:141-147. [PMID: 32146462 DOI: 10.1159/000506531] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/10/2020] [Indexed: 01/04/2023] Open
Abstract
Most eukaryotic genomes contain substantial portions of repetitive DNA sequences. These are located primarily in highly compacted heterochromatin and, in many cases, are one of the most abundant components of the sex chromosomes. In this sense, the anuran Proceratophrys boiei represents an interesting model for analyses on repetitive sequences by means of cytogenetic techniques, since it has a karyotype with large blocks of heterochromatin and a ZZ/ZW sex chromosome system. The present study describes, for the first time, families of satellite DNA (satDNA) in the frog P. boiei. Its genome size was estimated at 1.6 Gb, of which 41% correspond to repetitive sequences, including satDNAs, rDNAs, transposable elements, and other elements characterized as non-repetitive. The satDNAs were mapped by FISH in the centromeric and pericentromeric regions of all chromosomes, suggesting a possible involvement of these sequences in centromere function. SatDNAs are also present in the W sex chromosome, occupying the entire heterochromatic area, indicating a probable contribution of this class of repetitive DNA to the differentiation of the sex chromosomes in this species. This study is a valuable contribution to the existing knowledge on repetitive sequences in amphibians. We show the presence of repetitive DNAs, especially satDNAs, in the genome of P. boiei that might be of relevance in genome organization and regulation, setting the stage for a deeper functional genome analysis of Proceratophrys.
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Guillaumie S, Decroocq S, Ollat N, Delrot S, Gomès E, Cookson SJ. Dissecting the control of shoot development in grapevine: genetics and genomics identify potential regulators. BMC PLANT BIOLOGY 2020; 20:43. [PMID: 31996141 PMCID: PMC6988314 DOI: 10.1186/s12870-020-2258-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Accepted: 01/20/2020] [Indexed: 05/17/2023]
Abstract
BACKGROUND Grapevine is a crop of major economic importance, yet little is known about the regulation of shoot development in grapevine or other perennial fruits crops. Here we combine genetic and genomic tools to identify candidate genes regulating shoot development in Vitis spp. RESULTS An F2 population from an interspecific cross between V. vinifera and V. riparia was phenotyped for shoot development traits, and three Quantitative Trait Loci (QTLs) were identified on linkage groups (LGs) 7, 14 and 18. Around 17% of the individuals exhibited a dwarfed phenotype. A transcriptomic study identified four candidate genes that were not expressed in dwarfed individuals and located within the confidence interval of the QTL on LG7. A deletion of 84,482 bp was identified in the genome of dwarfed plants, which included these four not expressed genes. One of these genes was VviCURLY LEAF (VviCLF), an orthologue of CLF, a regulator of shoot development in Arabidopsis thaliana. CONCLUSIONS The phenotype of the dwarfed grapevine plants was similar to that of clf mutants of A. thaliana and orthologues of the known targets of CLF in A. thaliana were differentially expressed in the dwarfed plants. This suggests that CLF, a major developmental regulator in A. thaliana, also controls shoot development in grapevine.
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Affiliation(s)
- Sabine Guillaumie
- UMR1287 EGFV, Bordeaux Sciences Agro, INRAE, University of Bordeaux, Villenave d'Ornon, France.
| | - Stéphane Decroocq
- UMR1332 BFP, INRAE, University of Bordeaux, Villenave d'Ornon, France
| | - Nathalie Ollat
- UMR1287 EGFV, Bordeaux Sciences Agro, INRAE, University of Bordeaux, Villenave d'Ornon, France
| | - Serge Delrot
- UMR1287 EGFV, Bordeaux Sciences Agro, INRAE, University of Bordeaux, Villenave d'Ornon, France
| | - Eric Gomès
- UMR1287 EGFV, Bordeaux Sciences Agro, INRAE, University of Bordeaux, Villenave d'Ornon, France
| | - Sarah J Cookson
- UMR1287 EGFV, Bordeaux Sciences Agro, INRAE, University of Bordeaux, Villenave d'Ornon, France
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Setiawan AB, Teo CH, Kikuchi S, Sassa H, Kato K, Koba T. Centromeres of Cucumis melo L. comprise Cmcent and two novel repeats, CmSat162 and CmSat189. PLoS One 2020; 15:e0227578. [PMID: 31945109 PMCID: PMC6964814 DOI: 10.1371/journal.pone.0227578] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 12/20/2019] [Indexed: 12/29/2022] Open
Abstract
Centromeres are prerequisite for accurate segregation and are landmarks of primary constrictions of metaphase chromosomes in eukaryotes. In melon, high-copy-number satellite DNAs (SatDNAs) were found at various chromosomal locations such as centromeric, pericentromeric, and subtelomeric regions. In the present study, utilizing the published draft genome sequence of melon, two new SatDNAs (CmSat162 and CmSat189) of melon were identified and their chromosomal distributions were confirmed using fluorescence in situ hybridization. DNA probes prepared from these SatDNAs were successfully hybridized to melon somatic and meiotic chromosomes. CmSat162 was located on 12 pairs of melon chromosomes and co-localized with the centromeric repeat, Cmcent, at the centromeric regions. In contrast, CmSat189 was found to be located not only on centromeric regions but also on specific regions of the chromosomes, allowing the characterization of individual chromosomes of melon. It was also shown that these SatDNAs were transcribed in melon. These results suggest that CmSat162 and CmSat189 might have some functions at the centromeric regions.
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Affiliation(s)
- Agus Budi Setiawan
- Laboratory of Genetics and Plant Breeding, Graduate School of Horticulture, Chiba University, Matsudo, Chiba, Japan
| | - Chee How Teo
- Center for Research in Biotechnology for Agriculture, University of Malaya, Kuala Lumpur, Malaysia
| | - Shinji Kikuchi
- Laboratory of Genetics and Plant Breeding, Graduate School of Horticulture, Chiba University, Matsudo, Chiba, Japan
| | - Hidenori Sassa
- Laboratory of Genetics and Plant Breeding, Graduate School of Horticulture, Chiba University, Matsudo, Chiba, Japan
| | - Kenji Kato
- Graduate School of Environmental and Life Science, Okayama University, Kita-ku, Okayama, Japan
| | - Takato Koba
- Laboratory of Genetics and Plant Breeding, Graduate School of Horticulture, Chiba University, Matsudo, Chiba, Japan
- * E-mail:
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Vondrak T, Ávila Robledillo L, Novák P, Koblížková A, Neumann P, Macas J. Characterization of repeat arrays in ultra-long nanopore reads reveals frequent origin of satellite DNA from retrotransposon-derived tandem repeats. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:484-500. [PMID: 31559657 PMCID: PMC7004042 DOI: 10.1111/tpj.14546] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 09/09/2019] [Accepted: 09/12/2019] [Indexed: 05/21/2023]
Abstract
Amplification of monomer sequences into long contiguous arrays is the main feature distinguishing satellite DNA from other tandem repeats, yet it is also the main obstacle in its investigation because these arrays are in principle difficult to assemble. Here we explore an alternative, assembly-free approach that utilizes ultra-long Oxford Nanopore reads to infer the length distribution of satellite repeat arrays, their association with other repeats and the prevailing sequence periodicities. Using the satellite DNA-rich legume plant Lathyrus sativus as a model, we demonstrated this approach by analyzing 11 major satellite repeats using a set of nanopore reads ranging from 30 to over 200 kb in length and representing 0.73× genome coverage. We found surprising differences between the analyzed repeats because only two of them were predominantly organized in long arrays typical for satellite DNA. The remaining nine satellites were found to be derived from short tandem arrays located within LTR-retrotransposons that occasionally expanded in length. While the corresponding LTR-retrotransposons were dispersed across the genome, this array expansion occurred mainly in the primary constrictions of the L. sativus chromosomes, which suggests that these genome regions are favourable for satellite DNA accumulation.
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Affiliation(s)
- Tihana Vondrak
- Biology CentreCzech Academy of SciencesBranišovská 31České BudějoviceCZ‐37005Czech Republic
- Faculty of ScienceUniversity of South BohemiaČeské BudějoviceCzech Republic
| | - Laura Ávila Robledillo
- Biology CentreCzech Academy of SciencesBranišovská 31České BudějoviceCZ‐37005Czech Republic
- Faculty of ScienceUniversity of South BohemiaČeské BudějoviceCzech Republic
| | - Petr Novák
- Biology CentreCzech Academy of SciencesBranišovská 31České BudějoviceCZ‐37005Czech Republic
| | - Andrea Koblížková
- Biology CentreCzech Academy of SciencesBranišovská 31České BudějoviceCZ‐37005Czech Republic
| | - Pavel Neumann
- Biology CentreCzech Academy of SciencesBranišovská 31České BudějoviceCZ‐37005Czech Republic
| | - Jiří Macas
- Biology CentreCzech Academy of SciencesBranišovská 31České BudějoviceCZ‐37005Czech Republic
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Dogan M, Pouch M, Mandáková T, Hloušková P, Guo X, Winter P, Chumová Z, Van Niekerk A, Mummenhoff K, Al-Shehbaz IA, Mucina L, Lysak MA. Evolution of Tandem Repeats Is Mirroring Post-polyploid Cladogenesis in Heliophila (Brassicaceae). FRONTIERS IN PLANT SCIENCE 2020; 11:607893. [PMID: 33510751 PMCID: PMC7835680 DOI: 10.3389/fpls.2020.607893] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 11/16/2020] [Indexed: 05/02/2023]
Abstract
The unigeneric tribe Heliophileae encompassing more than 100 Heliophila species is morphologically the most diverse Brassicaceae lineage. The tribe is endemic to southern Africa, confined chiefly to the southwestern South Africa, home of two biodiversity hotspots (Cape Floristic Region and Succulent Karoo). The monospecific Chamira (C. circaeoides), the only crucifer species with persistent cotyledons, is traditionally retrieved as the closest relative of Heliophileae. Our transcriptome analysis revealed a whole-genome duplication (WGD) ∼26.15-29.20 million years ago, presumably preceding the Chamira/Heliophila split. The WGD was then followed by genome-wide diploidization, species radiations, and cladogenesis in Heliophila. The expanded phylogeny based on nuclear ribosomal DNA internal transcribed spacer (ITS) uncovered four major infrageneric clades (A-D) in Heliophila and corroborated the sister relationship between Chamira and Heliophila. Herein, we analyzed how the diploidization process impacted the evolution of repetitive sequences through low-coverage whole-genome sequencing of 15 Heliophila species, representing the four clades, and Chamira. Despite the firmly established infrageneric cladogenesis and different ecological life histories (four perennials vs. 11 annual species), repeatome analysis showed overall comparable evolution of genome sizes (288-484 Mb) and repeat content (25.04-38.90%) across Heliophila species and clades. Among Heliophila species, long terminal repeat (LTR) retrotransposons were the predominant components of the analyzed genomes (11.51-22.42%), whereas tandem repeats had lower abundances (1.03-12.10%). In Chamira, the tandem repeat content (17.92%, 16 diverse tandem repeats) equals the abundance of LTR retrotransposons (16.69%). Among the 108 tandem repeats identified in Heliophila, only 16 repeats were found to be shared among two or more species; no tandem repeats were shared by Chamira and Heliophila genomes. Six "relic" tandem repeats were shared between any two different Heliophila clades by a common descent. Four and six clade-specific repeats shared among clade A and C species, respectively, support the monophyly of these two clades. Three repeats shared by all clade A species corroborate the recent diversification of this clade revealed by plastome-based molecular dating. Phylogenetic analysis based on repeat sequence similarities separated the Heliophila species to three clades [A, C, and (B+D)], mirroring the post-polyploid cladogenesis in Heliophila inferred from rDNA ITS and plastome sequences.
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Affiliation(s)
- Mert Dogan
- CEITEC, Masaryk University, Brno, Czechia
- NCBR, Faculty of Science, Masaryk University, Brno, Czechia
| | - Milan Pouch
- CEITEC, Masaryk University, Brno, Czechia
- NCBR, Faculty of Science, Masaryk University, Brno, Czechia
| | - Terezie Mandáková
- CEITEC, Masaryk University, Brno, Czechia
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | | | - Xinyi Guo
- CEITEC, Masaryk University, Brno, Czechia
| | - Pieter Winter
- South African National Biodiversity Institute (SANBI), Kirstenbosch, Cape Town, South Africa
| | - Zuzana Chumová
- Institute of Botany, Czech Academy of Sciences, Prùhonice, Czechia
| | - Adriaan Van Niekerk
- Department of Geography & Environmental Studies, Stellenbosch University, Stellenbosch, South Africa
| | - Klaus Mummenhoff
- Department of Biology, Botany, Osnabrück University, Osnabrück, Germany
| | | | - Ladislav Mucina
- Department of Geography & Environmental Studies, Stellenbosch University, Stellenbosch, South Africa
- Harry Butler Institute, Murdoch University, Perth, WA, Australia
| | - Martin A. Lysak
- CEITEC, Masaryk University, Brno, Czechia
- NCBR, Faculty of Science, Masaryk University, Brno, Czechia
- *Correspondence: Martin A. Lysak, ;
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Genetic and Genomic Diversity in a Tarwi (Lupinus mutabilis Sweet) Germplasm Collection and Adaptability to Mediterranean Climate Conditions. AGRONOMY-BASEL 2019. [DOI: 10.3390/agronomy10010021] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Lupinus mutabilis (tarwi) is a species of Andean origin with high protein and oil content and regarded as a potential crop in Europe. The success in the introduction of this crop depends in part on in depth knowledge of the intra-specific genetic variability of the collections, enabling the establishment of breeding and conservation programs. In this study, we used morphological traits, Inter-Simple Sequence Repeat markers and genome size to assess genetic and genomic diversity of 23 tarwi accessions under Mediterranean conditions. Phenotypic analyses and yield component studies point out accession LM268 as that achieving the highest seed production, producing large seeds and efficiently using primary branches as an important component of total yield, similar to the L. albus cultivars used as controls. By contrast, accession JKI-L295 presents high yield concentrated on the main stem, suggesting a semi-determinate development pattern. Genetic and genomic analyses revealed important levels of diversity, however not relatable to phenotypic diversity, reflecting the recent domestication of this crop. This is the first study of genome size diversity within L. mutabilis, revealing an average size of 2.05 pg/2C (2001 Mbp) with 9.2% variation (1897–2003 Mbp), prompting further studies for the exploitation of this diversity.
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77
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Van-Lume B, Mata-Sucre Y, Báez M, Ribeiro T, Huettel B, Gagnon E, Leitch IJ, Pedrosa-Harand A, Lewis GP, Souza G. Evolutionary convergence or homology? Comparative cytogenomics of Caesalpinia group species (Leguminosae) reveals diversification in the pericentromeric heterochromatic composition. PLANTA 2019; 250:2173-2186. [PMID: 31696317 DOI: 10.1007/s00425-019-03287-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 09/25/2019] [Indexed: 05/02/2023]
Abstract
We demonstrated by cytogenomic analysis that the proximal heterochromatin of the Northeast Brazilian species of Caesalpinia group is enriched with phylogenetically conserved Ty3/Gypsy-Tekay RT, but diverge in the presence of Ty3/Gypsy-Athila RT and satDNA. The Caesalpinia Group includes 225 species and 27 monophyletic genera of which four occur in Northeastern Brazil: Erythrostemon (1 sp.), Cenostigma (7 spp.), Libidibia (1 sp.), and Paubrasilia (1 sp.). The last three genera are placed in different clades in the Caesalpinia Group phylogeny, and yet they are characterized by having a numerically stable karyotype 2n = 24 (16 M+8A) and GC-rich heterochromatic bands (chromomycin A3 positive/CMA+ bands) in the proximal chromosome regions. To characterize the composition of their heterochromatin and test for the homology of these chromosomal regions, genomic DNA was extracted from Cenostigma microphyllum, Libidibia ferrea, and Paubrasilia echinata, and sequenced at low coverage using the Illumina platform. The genomic repetitive fractions were characterized using a Galaxy/RepeatExplorer-Elixir platform. The most abundant elements of each genome were chromosomally located by fluorescent in situ hybridization (FISH) and compared to the CMA+ heterochromatin distribution. The repetitive fraction of the genomes of C. microphyllum, L. ferrea, and P. echinata were estimated to be 41.70%, 38.44%, and 72.51%, respectively. Ty3/Gypsy retrotransposons (RT), specifically the Tekay lineage, were the most abundant repeats in each of the three genomes. FISH mapping revealed species-specific patterns for the Tekay elements in the proximal regions of the chromosomes, co-localized with CMA+ bands. Other species-specific patterns were observed, e.g., for the Ty3/Gypsy RT Athila elements which were found in all the proximal heterochromatin of L. ferrea or restricted to the acrocentric chromosomes of C. microphyllum. This Athila labeling co-localized with satellite DNAs (satDNAs). Although the Caesalpinia Group diverged around 55 Mya, our results suggest an ancestral colonization of Tekay RT in the proximal heterochromatin. Thus, the present-day composition of the pericentromeric heterochromatin in these Northeast Brazilian species is a combination of the maintenance of an ancestral Tekay distribution with a species-specific accumulation of other repeats.
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Affiliation(s)
- Brena Van-Lume
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Rua Nelson Chaves S/N, Cidade Universitária, Recife, PE, 50670-420, Brazil
| | - Yennifer Mata-Sucre
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Rua Nelson Chaves S/N, Cidade Universitária, Recife, PE, 50670-420, Brazil
| | - Mariana Báez
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Rua Nelson Chaves S/N, Cidade Universitária, Recife, PE, 50670-420, Brazil
| | - Tiago Ribeiro
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Rua Nelson Chaves S/N, Cidade Universitária, Recife, PE, 50670-420, Brazil
- Department of Botany and Ecology, Institute of Biosciences, Federal University of Mato Grosso, Av. Fernando Correa da Costa, 2.367, Boa Esperança, Cuiabá, MT, 78060-900, Brazil
| | | | - Edeline Gagnon
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5NZ, UK
| | - Ilia J Leitch
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK
| | - Andrea Pedrosa-Harand
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Rua Nelson Chaves S/N, Cidade Universitária, Recife, PE, 50670-420, Brazil
| | - Gwilym P Lewis
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK
| | - Gustavo Souza
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Rua Nelson Chaves S/N, Cidade Universitária, Recife, PE, 50670-420, Brazil.
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Finke A, Mandáková T, Nawaz K, Vu GTH, Novák P, Macas J, Lysak MA, Pecinka A. Genome invasion by a hypomethylated satellite repeat in Australian crucifer Ballantinia antipoda. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 99:1066-1079. [PMID: 31074166 DOI: 10.1111/tpj.14380] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 04/02/2019] [Accepted: 04/24/2019] [Indexed: 06/09/2023]
Abstract
Repetitive sequences are ubiquitous components of all eukaryotic genomes. They contribute to genome evolution and the regulation of gene transcription. However, the uncontrolled activity of repetitive sequences can negatively affect genome functions and stability. Therefore, repetitive DNAs are embedded in a highly repressive heterochromatic environment in plant cell nuclei. Here, we analyzed the sequence, composition and the epigenetic makeup of peculiar non-pericentromeric heterochromatic segments in the genome of the Australian crucifer Ballantinia antipoda. By the combination of high throughput sequencing, graph-based clustering and cytogenetics, we found that the heterochromatic segments consist of a mixture of unique sequences and an A-T-rich 174 bp satellite repeat (BaSAT1). BaSAT1 occupies about 10% of the B. antipoda nuclear genome in >250 000 copies. Unlike many other highly repetitive sequences, BaSAT1 repeats are hypomethylated; this contrasts with the normal patterns of DNA methylation in the B. antipoda genome. Detailed analysis of several copies revealed that these non-methylated BaSAT1 repeats were also devoid of heterochromatic histone H3K9me2 methylation. However, the factors decisive for the methylation status of BaSAT1 repeats remain currently unknown. In summary, we show that even highly repetitive sequences can exist as hypomethylated in the plant nuclear genome.
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Affiliation(s)
- Andreas Finke
- Max Planck Institute for Plant Breeding Research (MPIPZ), Cologne, 50829, Germany
| | - Terezie Mandáková
- Plant Cytogenomics Research Group, CEITEC - Central-European Institute of Technology, Masaryk University, Brno, 62500, Czech Republic
| | - Kashif Nawaz
- Max Planck Institute for Plant Breeding Research (MPIPZ), Cologne, 50829, Germany
- The Czech Academy of Sciences, Institute of Experimental Botany (IEB), Centre of the Region Haná for Agricultural and Biotechnological Research (CRH), Olomouc, 77900, Czech Republic
| | - Giang T H Vu
- Max Planck Institute for Plant Breeding Research (MPIPZ), Cologne, 50829, Germany
| | - Petr Novák
- Biology Centre, The Czech Academy of Sciences, České Budejovice, 37005, Czech Republic
| | - Jiri Macas
- Biology Centre, The Czech Academy of Sciences, České Budejovice, 37005, Czech Republic
| | - Martin A Lysak
- Plant Cytogenomics Research Group, CEITEC - Central-European Institute of Technology, Masaryk University, Brno, 62500, Czech Republic
| | - Ales Pecinka
- Max Planck Institute for Plant Breeding Research (MPIPZ), Cologne, 50829, Germany
- The Czech Academy of Sciences, Institute of Experimental Botany (IEB), Centre of the Region Haná for Agricultural and Biotechnological Research (CRH), Olomouc, 77900, Czech Republic
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Escudeiro A, Adega F, Robinson TJ, Heslop-Harrison JS, Chaves R. Conservation, Divergence, and Functions of Centromeric Satellite DNA Families in the Bovidae. Genome Biol Evol 2019; 11:1152-1165. [PMID: 30888421 PMCID: PMC6475130 DOI: 10.1093/gbe/evz061] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/18/2019] [Indexed: 12/18/2022] Open
Abstract
Repetitive satellite DNA (satDNA) sequences are abundant in eukaryote genomes, with a structural and functional role in centromeric function. We analyzed the nucleotide sequence and chromosomal location of the five known cattle (Bos taurus) satDNA families in seven species from the tribe Tragelaphini (Bovinae subfamily). One of the families (SAT1.723) was present at the chromosomes’ centromeres of the Tragelaphini species, as well in two more distantly related bovid species, Ovis aries and Capra hircus. Analysis of the interaction of SAT1.723 with centromeric proteins revealed that this satDNA sequence is involved in the centromeric activity in all the species analyzed and that it is preserved for at least 15–20 Myr across Bovidae species. The satDNA sequence similarity among the analyzed species reflected different stages of homogeneity/heterogeneity, revealing the evolutionary history of each satDNA family. The SAT1.723 monomer-flanking regions showed the presence of transposable elements, explaining the extensive shuffling of this satDNA between different genomic regions.
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Affiliation(s)
- Ana Escudeiro
- Department of Genetics and Biotechnology, CAG - Laboratory of Cytogenomics and Animal Genomics, University of Trás-os-Montes e Alto Douro, Vila Real, Portugal.,BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Portugal
| | - Filomena Adega
- Department of Genetics and Biotechnology, CAG - Laboratory of Cytogenomics and Animal Genomics, University of Trás-os-Montes e Alto Douro, Vila Real, Portugal.,BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Portugal
| | | | | | - Raquel Chaves
- Department of Genetics and Biotechnology, CAG - Laboratory of Cytogenomics and Animal Genomics, University of Trás-os-Montes e Alto Douro, Vila Real, Portugal.,BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Portugal
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80
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Rodrigues PHDM, Dos Santos RZ, Silva DMZDA, Goes CAG, Oliveira C, Foresti F, Porto-Foresti F, Utsunomia R. Chromosomal and Genomic Dynamics of Satellite DNAs in Characidae (Characiformes, Teleostei) Species. Zebrafish 2019; 16:408-414. [PMID: 31145041 DOI: 10.1089/zeb.2019.1738] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Satellite DNAs (satDNAs) are tandemly repeated DNA sequences with great abundance in eukaryotic genomes. A single species may carry up to hundreds of satDNA families, which is collectively called as "satellitome," each showing its own dynamics and evolution rates. In this context, all live species contain a satDNA library that may be partially or totally shared with other related species/populations. In the late few years, next-generation sequencing (NGS) and novel bioinformatic tools facilitated the massive characterization of these sequences at low costs, and consequently, comparing satDNAs between species. In this study, we characterized two novel satDNAs (MsaSat03-80 and MsaSat04-142) in three characid fish (Astyanax paranae and Astyanax fasciatus and two populations of Moenkhausia sanctaefilomenae) and mapped their chromosomal location to unveil the evolutionary dynamics of satDNA repeats in those species. Our results evidenced that MsaSat03 is present in the genomes of all analyzed species, but is clustered only in the chromosomes of M. sanctaefilomenae, exhibiting a conserved number and location of sites. Conversely, MsaSat04 sequences is restricted to M. sanctaefilomenae and shows a differential distribution between the two analyzed populations. Altogether, our analyses point to a complex history of satDNA families in characid fish and the utility of NGS data for comparative satDNA analysis.
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Affiliation(s)
| | - Rodrigo Zeni Dos Santos
- 1Departamento de Ciências Biológicas, Faculdade de Ciências, Universidade Estadual Paulista-UNESP, Bauru, Brazil
| | | | - Caio Augusto Gomes Goes
- 1Departamento de Ciências Biológicas, Faculdade de Ciências, Universidade Estadual Paulista-UNESP, Bauru, Brazil
| | - Claudio Oliveira
- 2Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista-UNESP, Botucatu, Brazil
| | - Fausto Foresti
- 2Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista-UNESP, Botucatu, Brazil
| | - Fábio Porto-Foresti
- 1Departamento de Ciências Biológicas, Faculdade de Ciências, Universidade Estadual Paulista-UNESP, Bauru, Brazil
| | - Ricardo Utsunomia
- 1Departamento de Ciências Biológicas, Faculdade de Ciências, Universidade Estadual Paulista-UNESP, Bauru, Brazil.,2Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista-UNESP, Botucatu, Brazil
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81
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Zhou HC, Waminal NE, Kim HH. In silico mining and FISH mapping of a chromosome-specific satellite DNA in Capsicum annuum L. Genes Genomics 2019; 41:1001-1006. [PMID: 31134590 DOI: 10.1007/s13258-019-00832-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 05/15/2019] [Indexed: 12/13/2022]
Abstract
BACKGROUND A large proportion of eukaryote nuclear genomes is composed of repetitive DNA. Tracing the dynamics of repetitive elements in the genomes of related taxa can reveal important information about their phylogenic relationships as well as traits that have become distinct to a lineage. OBJECTIVE Study the genomic abundance and chromosomal location of repetitive DNA in Capsicum annuum L. to understand the repeat dynamics. METHOD We quantified repeated DNA content in the C. annuum genome using the RepeatExplorer pipeline. RESULTS About 42% of the C. annuum genome dataset comprised repetitive elements. Of these, 0.011, 0.98, 3.09, and 0.024% represented high and low confidence satellite repeats, putative long-terminal repeats (LTRs), and rDNA sequences, respectively. One novel high confidence 167-bp satellite repeat with a genomic proportion of 0.011%, Ca167TR, was identified. Furthermore, FISH with Ca167TR on metaphase chromosomes of C. annuum revealed signals in the subtelomeric regions of the short and long arms of chromosome 3 and 4, respectively. CONCLUSION Further understanding of the origin and associated functions of Ca167TR and other repeats in Capsicum will give us insights into the genomic relationships and functions of the genome.
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Affiliation(s)
- Hui Chao Zhou
- Department of Life Sciences, Chromosome Research Institute, Sahmyook University, Seoul, 01795, Republic of Korea
| | - Nomar Espinosa Waminal
- Department of Life Sciences, Chromosome Research Institute, Sahmyook University, Seoul, 01795, Republic of Korea
| | - Hyun Hee Kim
- Department of Life Sciences, Chromosome Research Institute, Sahmyook University, Seoul, 01795, Republic of Korea.
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82
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Luo X, Liu J. Fluorescence In Situ Hybridization (FISH) Analysis of the Locations of the Oligonucleotides 5S rDNA, (AGGGTTT) 3, and (TTG) 6 in Three Genera of Oleaceae and Their Phylogenetic Framework. Genes (Basel) 2019; 10:genes10050375. [PMID: 31108932 PMCID: PMC6562466 DOI: 10.3390/genes10050375] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 05/09/2019] [Accepted: 05/10/2019] [Indexed: 11/29/2022] Open
Abstract
We report the cytogenetic map for a collection of species in the Oleaceae, and test similarities among the karyotypes relative to their known species phylogeny. The oligonucleotides 5S ribosomal DNA (rDNA), (AGGGTTT)3, and (TTG)6 were used as fluorescence in situ hybridization (FISH) probes to locate the corresponding chromosomes in three Oleaceae genera: Fraxinus pennsylvanica, Syringa oblata, Ligustrum lucidum, and Ligustrum × vicaryi. Forty-six small chromosomes were identified in four species. (AGGGTTT)3 signals were observed on almost all chromosome ends of four species, but (AGGGTTT)3 played no role in distinguishing the chromosomes but displayed intact chromosomes and could thus be used as a guide for finding chromosome counts. (TTG)6 and 5S rDNA signals discerned several chromosomes located at subterminal or central regions. Based on the similarity of the signal pattern (mainly in number and location and less in intensity) of the four species, the variations in the 5S rDNA and (TTG)6 distribution can be ordered as L. lucidum < L. × vicaryi < F. pennsylvanica < S. oblata. Variations have observed in the three genera. The molecular cytogenetic data presented here might serve as a starting point for further larger-scale elucidation of the structure of the Oleaceae genome, and comparison with the known phylogeny of Oleaceae family.
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Affiliation(s)
- Xiaomei Luo
- College of Forestry, Sichuan Agricultural University, Wenjiang District, Chengdu 611130, China.
| | - Juncheng Liu
- College of Forestry, Sichuan Agricultural University, Wenjiang District, Chengdu 611130, China.
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Deng H, Cai Z, Xiang S, Guo Q, Huang W, Liang G. Karyotype Analysis of Diploid and Spontaneously Occurring Tetraploid Blood Orange [ Citrus sinensis (L.) Osbeck] Using Multicolor FISH With Repetitive DNA Sequences as Probes. FRONTIERS IN PLANT SCIENCE 2019; 10:331. [PMID: 30967887 PMCID: PMC6440391 DOI: 10.3389/fpls.2019.00331] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 03/04/2019] [Indexed: 05/17/2023]
Abstract
Blood orange [Citrus sinensis (L.) Osbeck] has been increasingly appreciated by consumers worldwide owing to its brilliant red color, abundant anthocyanin and other health-promoting compounds. However, there is still relatively little known about its cytogenetic characteristics, probably because of the small size and similar morphology of metaphase chromosomes and the paucity of chromosomal landmarks. In our previous study, a naturally occurring tetraploid blood orange plant was obtained via seedling screening. Before this tetraploid germplasm can be manipulated into a citrus triploid seedless breeding program, it is of great importance to determine its chromosome characterization and composition. In the present study, an integrated karyotype of blood orange was constructed using sequential multicolor fluorescence in situ hybridization (FISH) with four satellite repeats, two ribosomal DNAs (rDNAs), a centromere-like repeat and an oligonucleotide of telomere repeat (TTTAGGG)3 as probes. Satellite repeats were preferentially located at the terminal regions of the chromosomes of blood orange. Individual somatic chromosome pairs of blood orange were unambiguously identified by repetitive DNA-based multicolor FISH. These probes proved to be effective chromosomal landmarks. The karyotype was formulated as 2n = 2x = 18 = 16m+2sm (1sat) with the karyotype asymmetry degree belonging to 2B. The chromosomal distribution pattern of these repetitive DNAs in this spontaneously occurring tetraploid was identical to that of the diploid, but the tetraploid carried twice the number of hybridization sites as the diploid, indicating a possible pathway involving the spontaneous duplication of chromosome sets in nucellar cells. Our work may facilitate the molecular cytogenetic study of blood orange and provide chromosomal characterization for the future utilization of this tetraploid germplasm in the service of seedless breeding programs.
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Affiliation(s)
- Honghong Deng
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
| | - Zexi Cai
- College of Agronomy and Biotechnology, National Maize Improvement Center, China Agricultural University, Beijing, China
| | - Suqiong Xiang
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
| | - Qigao Guo
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
| | - Wei Huang
- College of Agronomy and Biotechnology, National Maize Improvement Center, China Agricultural University, Beijing, China
| | - Guolu Liang
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
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84
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Ruiz-Ruano FJ, Navarro-Domínguez B, Camacho JPM, Garrido-Ramos MA. Characterization of the satellitome in lower vascular plants: the case of the endangered fern Vandenboschia speciosa. ANNALS OF BOTANY 2019; 123:587-599. [PMID: 30357311 PMCID: PMC6417484 DOI: 10.1093/aob/mcy192] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 10/04/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND AND AIMS Vandenboschia speciosa is a highly vulnerable fern species, with a large genome (10.5 Gb). Haploid gametophytes and diploid sporophytes are perennial, can reproduce vegetatively, and certain populations are composed only of independent gametophytes. These features make this fern a good model: (1) for high-throughput analysis of satellite DNA (satDNA) to investigate possible evolutionary trends in satDNA sequence features; (2) to determine the relative contribution of satDNA and other repetitive DNAs to its large genome; and (3) to analyse whether the reproduction mode or phase alternation between long-lasting haploid and diploid stages influences satDNA abundance or divergence. METHODS We analysed the repetitive fraction of the genome of this species in three different populations (one comprised only of independent gametophytes) using Illumina sequencing and bioinformatic analysis with RepeatExplorer and satMiner. KEY RESULTS The satellitome of V. speciosa is composed of 11 satDNA families, most of them showing a short repeat length and being A + T rich. Some satDNAs had complex repeats composed of sub-repeats, showing high similarity to shorter satDNAs. Three families had particular structural features and highly conserved motifs. SatDNA only amounts to approx. 0.4 % of its genome. Likewise, microsatellites do not represent more than 2 %, but transposable elements (TEs) represent approx. 50 % of the sporophytic genomes. We found high resemblance in satDNA abundance and divergence between both gametophyte and sporophyte samples from the same population and between populations. CONCLUSIONS (1) Longer (and older) satellites in V. speciosa have a higher A + T content and evolve from shorter ones and, in some cases, microsatellites were a source of new satDNAs; (2) the satellitome does not explain the huge genome size in this species while TEs are the major repetitive component of the V. speciosa genome and mostly contribute to its large genome; and (3) reproduction mode or phase alternation between gametophytes and sporophytes does not entail accumulation or divergence of satellites.
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Affiliation(s)
- F J Ruiz-Ruano
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | - B Navarro-Domínguez
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | - J P M Camacho
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | - M A Garrido-Ramos
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Granada, Spain
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85
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Natural History of a Satellite DNA Family: From the Ancestral Genome Component to Species-Specific Sequences, Concerted and Non-Concerted Evolution. Int J Mol Sci 2019; 20:ijms20051201. [PMID: 30857296 PMCID: PMC6429384 DOI: 10.3390/ijms20051201] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 03/04/2019] [Accepted: 03/06/2019] [Indexed: 12/20/2022] Open
Abstract
Satellite DNA (satDNA) is the most variable fraction of the eukaryotic genome. Related species share a common ancestral satDNA library and changing of any library component in a particular lineage results in interspecific differences. Although the general developmental trend is clear, our knowledge of the origin and dynamics of satDNAs is still fragmentary. Here, we explore whole genome shotgun Illumina reads using the RepeatExplorer (RE) pipeline to infer satDNA family life stories in the genomes of Chenopodium species. The seven diploids studied represent separate lineages and provide an example of a species complex typical for angiosperms. Application of the RE pipeline allowed by similarity searches a determination of the satDNA family with a basic monomer of ~40 bp and to trace its transformation from the reconstructed ancestral to the species-specific sequences. As a result, three types of satDNA family evolutionary development were distinguished: (i) concerted evolution with mutation and recombination events; (ii) concerted evolution with a trend toward increased complexity and length of the satellite monomer; and (iii) non-concerted evolution, with low levels of homogenization and multidirectional trends. The third type is an example of entire repeatome transformation, thus producing a novel set of satDNA families, and genomes showing non-concerted evolution are proposed as a significant source for genomic diversity.
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86
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Deng H, Xiang S, Guo Q, Jin W, Cai Z, Liang G. Molecular cytogenetic analysis of genome-specific repetitive elements in Citrus clementina Hort. Ex Tan. and its taxonomic implications. BMC PLANT BIOLOGY 2019; 19:77. [PMID: 30770721 PMCID: PMC6377768 DOI: 10.1186/s12870-019-1676-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 02/07/2019] [Indexed: 05/26/2023]
Abstract
BACKGROUND Clementine mandarin (Citrus clementina Hort. ex Tan.) is one of the most famous and widely grown citrus cultivars worldwide. Variations in relation to the composition and distribution of repetitive DNA sequences that dominate greatly in eukaryote genomes are considered to be species-, genome-, or even chromosome-specific. Repetitive DNA-based fluorescence in situ hybridization (FISH) is a powerful tool for molecular cytogenetic study. However, to date few studies have involved in the repetitive elements and cytogenetic karyotype of Clementine. RESULTS A graph-based similarity sequence read clustering methodology was performed to analyze the repetitive DNA families in the Clementine genome. The bioinformatics analysis showed that repetitive DNAs constitute 41.95% of the Clementine genome, and the majority of repetitive elements are retrotransposons and satellite DNAs. Sequential multicolor FISH using a probe mix that contained CL17, four satellite DNAs, two rDNAs and an oligonucleotide of (TTTAGGG)3 was performed with Clementine somatic metaphase chromosomes. An integrated karyotype of Clementine was established based on unequivocal and reproducible chromosome discriminations. The distribution patterns of these probes in several Citrus, Poncirus and Fortunella species were summarized through extensive FISH analyses. Polymorphism and heterozygosity were commonly observed in the three genera. Some asymmetrical FISH loci in Clementine were in agreement with its hybrid origin. CONCLUSIONS The composition and abundance of repetitive elements in the Clementine genome were reanalyzed. Multicolor FISH-based karyotyping provided direct visual proof of the heterozygous nature of Clementine chromosomes with conspicuous asymmetrical FISH hybridization signals. We detected some similar and variable distribution patterns of repetitive DNAs in Citrus, Poncirus, and Fortunella, which revealed notable conservation among these genera, as well as obvious polymorphism and heterozygosity, indicating the potential utility of these repetitive element markers for the study of taxonomic, phylogenetic and evolutionary relationships in the future.
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Affiliation(s)
- Honghong Deng
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715 China
| | - Suqiong Xiang
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715 China
| | - Qigao Guo
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715 China
| | - Weiwei Jin
- National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193 China
| | - Zexi Cai
- National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193 China
| | - Guolu Liang
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715 China
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87
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Kroupin P, Kuznetsova V, Romanov D, Kocheshkova A, Karlov G, Dang TX, Khuat TML, Kirov I, Alexandrov O, Polkhovskiy A, Razumova O, Divashuk M. Pipeline for the Rapid Development of Cytogenetic Markers Using Genomic Data of Related Species. Genes (Basel) 2019; 10:E113. [PMID: 30717300 PMCID: PMC6409974 DOI: 10.3390/genes10020113] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 01/23/2019] [Accepted: 01/28/2019] [Indexed: 11/19/2022] Open
Abstract
Repetitive DNA including tandem repeats (TRs) is a significant part of most eukaryotic genomes. TRs include rapidly evolving satellite DNA (satDNA) that can be shared by closely related species, their abundance may be associated with evolutionary divergence, and they have been widely used for chromosome karyotyping using fluorescence in situ hybridization (FISH). The recent progress in the development of whole-genome sequencing and bioinformatics tools enables rapid and cost-effective searches for TRs including satDNA that can be converted into molecular cytogenetic markers. In the case of closely related taxa, the genome sequence of one species (donor) can be used as a base for the development of chromosome markers for related species or genomes (target). Here, we present a pipeline for rapid and high-throughput screening for new satDNA TRs in whole-genome sequencing of the donor genome and the development of chromosome markers based on them that can be applied in the target genome. One of the main peculiarities of the developed pipeline is that preliminary estimation of TR abundance using qPCR and ranking found TRs according to their copy number in the target genome; it facilitates the selection of the most prospective (most abundant) TRs that can be converted into cytogenetic markers. Another feature of our pipeline is the probe preparation for FISH using PCR with primers designed on the aligned TR unit sequences and the genomic DNA of a target species as a template that enables amplification of a whole pool of monomers inherent in the chromosomes of the target species. We demonstrate the efficiency of the developed pipeline by the example of FISH probes developed for A, B, and R subgenome chromosomes of hexaploid triticale (BBAARR) based on a bioinformatics analysis of the D genome of Aegilops tauschii (DD) whole-genome sequence. Our pipeline can be used to develop chromosome markers in closely related species for comparative cytogenetics in evolutionary and breeding studies.
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Affiliation(s)
- Pavel Kroupin
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, Moscow 127550, Russia.
- Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Timiryazevskaya str. 49, Moscow 127550, Russia.
| | - Victoria Kuznetsova
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, Moscow 127550, Russia.
- Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Timiryazevskaya str. 49, Moscow 127550, Russia.
| | - Dmitry Romanov
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, Moscow 127550, Russia.
| | - Alina Kocheshkova
- Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Timiryazevskaya str. 49, Moscow 127550, Russia.
| | - Gennady Karlov
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, Moscow 127550, Russia.
| | - Thi Xuan Dang
- Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Timiryazevskaya str. 49, Moscow 127550, Russia.
| | - Thi Mai L Khuat
- Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Timiryazevskaya str. 49, Moscow 127550, Russia.
| | - Ilya Kirov
- Laboratory of Marker-Assisted and Genomic Selection of Plants, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, Moscow 127550, Russia.
| | - Oleg Alexandrov
- Laboratory of Plant Cell Engineering, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, Moscow 127550, Russia.
| | - Alexander Polkhovskiy
- Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Timiryazevskaya str. 49, Moscow 127550, Russia.
| | - Olga Razumova
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, Moscow 127550, Russia.
| | - Mikhail Divashuk
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, Moscow 127550, Russia.
- Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Timiryazevskaya str. 49, Moscow 127550, Russia.
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88
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Kroupin PY, Kuznetsova VM, Nikitina EA, Martirosyan YT, Karlov GI, Divashuk MG. Development of new cytogenetic markers for Thinopyrum ponticum (Podp.) Z.-W. Liu & R.-C. Wang. COMPARATIVE CYTOGENETICS 2019; 13:231-243. [PMID: 31440353 PMCID: PMC6702164 DOI: 10.3897/compcytogen.v13i3.36112] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Accepted: 07/22/2019] [Indexed: 05/19/2023]
Abstract
Thinopyrum ponticum (Podpěra, 1902) Z.-W. Liu & R.-C.Wang, 1993 is an important polyploid wild perennial Triticeae species that is widely used as a source of valuable genes for wheat but its genomic constitution has long been debated. For its chromosome identification, only a limited set of FISH probes has been used. The development of new cytogenetic markers for Th. ponticum chromosomes is of great importance both for cytogenetic characterization of wheat-wheatgrass hybrids and for fundamental comparative studies of phylogenetic relationships between species. Here, we report on the development of five cytogenetic markers for Th. ponticum based on repetitive satellite DNA of which sequences were selected from the whole genome sequence of Aegilops tauschii Cosson, 1849. Using real-time quantitative PCR we estimated the abundance of the found repeats: P720 and P427 had the highest abundance and P132, P332 and P170 had lower quantity in Th. ponticum genome. Using fluorescence in situ hybridization (FISH) we localized five repeats to different regions of the chromosomes of Th. ponticum. Using reprobing multicolor FISH we colocalized the probes between each other. The distribution of these found repeats in the Triticeae genomes and its usability as cytogenetic markers for chromosomes of Th. ponticum are discussed.
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Affiliation(s)
- Pavel Yu Kroupin
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, Moscow 127550, Russia All-Russia Research Institute of Agricultural Biotechnology Moscow Russia
- Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Timiryazevskaya str. 49, Moscow 127550, Russia Russian State Agrarian University-Moscow Timiryazev Agricultural Academ Moscow Russia
| | - Victoria M Kuznetsova
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, Moscow 127550, Russia All-Russia Research Institute of Agricultural Biotechnology Moscow Russia
- Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Timiryazevskaya str. 49, Moscow 127550, Russia Russian State Agrarian University-Moscow Timiryazev Agricultural Academ Moscow Russia
| | - Ekaterina A Nikitina
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, Moscow 127550, Russia All-Russia Research Institute of Agricultural Biotechnology Moscow Russia
| | - Yury Ts Martirosyan
- Group of Aeroponic Plant Growing Technologies, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, Moscow 127550, Russia Russian State Agrarian University-Moscow Timiryazev Agricultural Acade Moscow Russia
| | - Gennady I Karlov
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, Moscow 127550, Russia All-Russia Research Institute of Agricultural Biotechnology Moscow Russia
- Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Timiryazevskaya str. 49, Moscow 127550, Russia Russian State Agrarian University-Moscow Timiryazev Agricultural Academ Moscow Russia
| | - Mikhail G Divashuk
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, Moscow 127550, Russia All-Russia Research Institute of Agricultural Biotechnology Moscow Russia
- Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Timiryazevskaya str. 49, Moscow 127550, Russia Russian State Agrarian University-Moscow Timiryazev Agricultural Academ Moscow Russia
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89
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Mccann J, Jang TS, Macas J, Schneeweiss GM, Matzke NJ, Novák P, Stuessy TF, Villaseñor JL, Weiss-Schneeweiss H. Dating the Species Network: Allopolyploidy and Repetitive DNA Evolution in American Daisies (Melampodium sect. Melampodium, Asteraceae). Syst Biol 2018; 67:1010-1024. [PMID: 29562303 PMCID: PMC6193527 DOI: 10.1093/sysbio/syy024] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 02/17/2018] [Accepted: 03/15/2018] [Indexed: 12/04/2022] Open
Abstract
Allopolyploidy has played an important role in the evolution of the flowering plants. Genome mergers are often accompanied by significant and rapid alterations of genome size and structure via chromosomal rearrangements and altered dynamics of tandem and dispersed repetitive DNA families. Recent developments in sequencing technologies and bioinformatic methods allow for a comprehensive investigation of the repetitive component of plant genomes. Interpretation of evolutionary dynamics following allopolyploidization requires both the knowledge of parentage and the age of origin of an allopolyploid. Whereas parentage is typically inferred from cytogenetic and phylogenetic data, age inference is hampered by the reticulate nature of the phylogenetic relationships. Treating subgenomes of allopolyploids as if they belonged to different species (i.e., no recombination among subgenomes) and applying cross-bracing (i.e., putting a constraint on the age difference of nodes pertaining to the same event), we can infer the age of allopolyploids within the framework of the multispecies coalescent within BEAST2. Together with a comprehensive characterization of the repetitive DNA fraction using the RepeatExplorer pipeline, we apply the dating approach in a group of closely related allopolyploids and their progenitor species in the plant genus Melampodium (Asteraceae). We dated the origin of both the allotetraploid, Melampodium strigosum, and its two allohexaploid derivatives, Melampodium pringlei and Melampodium sericeum, which share both parentage and the direction of the cross, to the Pleistocene ($<$1.4 Ma). Thus, Pleistocene climatic fluctuations may have triggered formation of allopolyploids possibly in short intervals, contributing to difficulties in inferring the precise temporal order of allopolyploid species divergence of M. sericeum and M. pringlei. The relatively recent origin of the allopolyploids likely played a role in the near-absence of major changes in the repetitive fraction of the polyploids' genomes. The repetitive elements most affected by the postpolyploidization changes represented retrotransposons of the Ty1-copia lineage Maximus and, to a lesser extent, also Athila elements of Ty3-gypsy family.
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Affiliation(s)
- Jamie Mccann
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, Austria
| | - Tae-Soo Jang
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, Austria
- Department of Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon, South Korea
| | - Jiři Macas
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 31, České Budějovice, Czech Republic
| | - Gerald M Schneeweiss
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, Austria
| | - Nicholas J Matzke
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Petr Novák
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 31, České Budějovice, Czech Republic
| | - Tod F Stuessy
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, Austria
- Herbarium and Department of Evolution, Ecology and Organismal Biology, 1315 Kinnear Road, The Ohio State University, Columbus, Ohio, USA
| | - José L Villaseñor
- Department of Botany, UNAM, Tercer Circuito s/n, Ciudad Universitaria, Delegación Coyoacán, MX-04510 México, D.F., México
| | - Hanna Weiss-Schneeweiss
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, Austria
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90
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Lee YI, Yap JW, Izan S, Leitch IJ, Fay MF, Lee YC, Hidalgo O, Dodsworth S, Smulders MJM, Gravendeel B, Leitch AR. Satellite DNA in Paphiopedilum subgenus Parvisepalum as revealed by high-throughput sequencing and fluorescent in situ hybridization. BMC Genomics 2018; 19:578. [PMID: 30068293 PMCID: PMC6090851 DOI: 10.1186/s12864-018-4956-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 07/23/2018] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Satellite DNA is a rapidly diverging, largely repetitive DNA component of many eukaryotic genomes. Here we analyse the evolutionary dynamics of a satellite DNA repeat in the genomes of a group of Asian subtropical lady slipper orchids (Paphiopedilum subgenus Parvisepalum and representative species in the other subgenera/sections across the genus). A new satellite repeat in Paphiopedilum subgenus Parvisepalum, SatA, was identified and characterized using the RepeatExplorer pipeline in HiSeq Illumina reads from P. armeniacum (2n = 26). Reconstructed monomers were used to design a satellite-specific fluorescent in situ hybridization (FISH) probe. The data were also analysed within a phylogenetic framework built using the internal transcribed spacer (ITS) sequences of 45S nuclear ribosomal DNA. RESULTS SatA comprises c. 14.5% of the P. armeniacum genome and is specific to subgenus Parvisepalum. It is composed of four primary monomers that range from 230 to 359 bp and contains multiple inverted repeat regions with hairpin-loop motifs. A new karyotype of P. vietnamense (2n = 28) is presented and shows that the chromosome number in subgenus Parvisepalum is not conserved at 2n = 26, as previously reported. The physical locations of SatA sequences were visualised on the chromosomes of all seven Paphiopedilum species of subgenus Parvisepalum (2n = 26-28), together with the 5S and 45S rDNA loci using FISH. The SatA repeats were predominantly localisedin the centromeric, peri-centromeric and sub-telocentric chromosome regions, but the exact distribution pattern was species-specific. CONCLUSIONS We conclude that the newly discovered, highly abundant and rapidly evolving satellite sequence SatA is specific to Paphiopedilum subgenus Parvisepalum. SatA and rDNA chromosomal distributions are characteristic of species, and comparisons between species reveal that the distribution patterns generate a strong phylogenetic signal. We also conclude that the ancestral chromosome number of subgenus Parvisepalum and indeed of all Paphiopedilum could be either 2n = 26 or 28, if P. vietnamense is sister to all species in the subgenus as suggested by the ITS data.
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Affiliation(s)
- Yung-I Lee
- Biology Department, National Museum of Natural Science, No 1, Kuan-Chien Rd, 40453 Taichung, Taiwan, Republic of China
- Department of Life Sciences, National Chung Hsing University, 40227 Taichung, Taiwan, Republic of China
| | - Jing Wei Yap
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS UK
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB UK
- Forest Research Institute Malaysia (FRIM), 52109 Kepong, Selangor Darul Ehsan Malaysia
| | - Shairul Izan
- Plant Breeding, Wageningen University & Research, P.O. Box 386, NL-6700 AJ Wageningen, The Netherlands
- Department of Crop Science, Faculty of Agriculture, University Putra Malaysia (UPM) Serdang, Serdang, Selangor Malaysia
| | - Ilia J. Leitch
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB UK
| | - Michael F. Fay
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB UK
- School of Plant Biology, University of Western Australia, Crawley, WA 6009 Australia
| | - Yi-Ching Lee
- Biology Department, National Museum of Natural Science, No 1, Kuan-Chien Rd, 40453 Taichung, Taiwan, Republic of China
| | - Oriane Hidalgo
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB UK
| | - Steven Dodsworth
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB UK
| | - Marinus J. M. Smulders
- Plant Breeding, Wageningen University & Research, P.O. Box 386, NL-6700 AJ Wageningen, The Netherlands
| | - Barbara Gravendeel
- Endless Forms Group, Naturalis Biodiversity Center, Vondellaan 55, 2332 AA Leiden, The Netherlands
- Faculty of Science and Technology, University of Applied Sciences Leiden, Zernikedreef 11, 2333 CK Leiden, The Netherlands
- Institute Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Andrew R. Leitch
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS UK
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91
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Liu Q, Chang S, Hartman GL, Domier LL. Assembly and annotation of a draft genome sequence for Glycine latifolia, a perennial wild relative of soybean. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 95:71-85. [PMID: 29671916 DOI: 10.1111/tpj.13931] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 03/12/2018] [Accepted: 03/22/2018] [Indexed: 05/14/2023]
Abstract
Glycine latifolia (Benth.) Newell & Hymowitz (2n = 40), one of the 27 wild perennial relatives of soybean, possesses genetic diversity and agronomically favorable traits that are lacking in soybean. Here, we report the 939-Mb draft genome assembly of G. latifolia (PI 559298) using exclusively linked-reads sequenced from a single Chromium library. We organized scaffolds into 20 chromosome-scale pseudomolecules utilizing two genetic maps and the Glycine max (L.) Merr. genome sequence. High copy numbers of putative 91-bp centromere-specific tandem repeats were observed in consecutive blocks within predicted pericentromeric regions on several pseudomolecules. No 92-bp putative centromeric repeats, which are abundant in G. max, were detected in G. latifolia or Glycine tomentella. Annotation of the assembled genome and subsequent filtering yielded a high confidence gene set of 54 475 protein-coding loci. In comparative analysis with five legume species, genes related to defense responses were significantly overrepresented in Glycine-specific orthologous gene families. A total of 304 putative nucleotide-binding site (NBS)-leucine-rich-repeat (LRR) genes were identified in this genome assembly. Different from other legume species, we observed a scarcity of TIR-NBS-LRR genes in G. latifolia. The G. latifolia genome was also predicted to contain genes encoding 367 LRR-receptor-like kinases, a family of proteins involved in basal defense responses and responses to abiotic stress. The genome sequence and annotation of G. latifolia provides a valuable source of alternative alleles and novel genes to facilitate soybean improvement. This study also highlights the efficacy and cost-effectiveness of the application of Chromium linked-reads in diploid plant genome de novo assembly.
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Affiliation(s)
- Qiong Liu
- Department of Crop Sciences, University of Illinois, Urbana, IL, 61801, USA
| | - Sungyul Chang
- Department of Crop Sciences, University of Illinois, Urbana, IL, 61801, USA
| | - Glen L Hartman
- Department of Crop Sciences, University of Illinois, Urbana, IL, 61801, USA
- USDA ARS, Urbana, IL, 61801, USA
| | - Leslie L Domier
- Department of Crop Sciences, University of Illinois, Urbana, IL, 61801, USA
- USDA ARS, Urbana, IL, 61801, USA
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92
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Ávila Robledillo L, Koblížková A, Novák P, Böttinger K, Vrbová I, Neumann P, Schubert I, Macas J. Satellite DNA in Vicia faba is characterized by remarkable diversity in its sequence composition, association with centromeres, and replication timing. Sci Rep 2018; 8:5838. [PMID: 29643436 PMCID: PMC5895790 DOI: 10.1038/s41598-018-24196-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 03/28/2018] [Indexed: 11/17/2022] Open
Abstract
Satellite DNA, a class of repetitive sequences forming long arrays of tandemly repeated units, represents substantial portions of many plant genomes yet remains poorly characterized due to various methodological obstacles. Here we show that the genome of the field bean (Vicia faba, 2n = 12), a long-established model for cytogenetic studies in plants, contains a diverse set of satellite repeats, most of which remained concealed until their present investigation. Using next-generation sequencing combined with novel bioinformatics tools, we reconstructed consensus sequences of 23 novel satellite repeats representing 0.008–2.700% of the genome and mapped their distribution on chromosomes. We found that in addition to typical satellites with monomers hundreds of nucleotides long, V. faba contains a large number of satellite repeats with unusually long monomers (687–2033 bp), which are predominantly localized in pericentromeric regions. Using chromatin immunoprecipitation with CenH3 antibody, we revealed an extraordinary diversity of centromeric satellites, consisting of seven repeats with chromosome-specific distribution. We also found that in spite of their different nucleotide sequences, all centromeric repeats are replicated during mid-S phase, while most other satellites are replicated in the first part of late S phase, followed by a single family of FokI repeats representing the latest replicating chromatin.
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Affiliation(s)
- Laura Ávila Robledillo
- Biology Centre of the Czech Academy of Sciences, Institute of Plant Molecular Biology, České Budějovice, 37005, Czech Republic.,University of South Bohemia, Faculty of Science, České Budějovice, 37005, Czech Republic
| | - Andrea Koblížková
- Biology Centre of the Czech Academy of Sciences, Institute of Plant Molecular Biology, České Budějovice, 37005, Czech Republic
| | - Petr Novák
- Biology Centre of the Czech Academy of Sciences, Institute of Plant Molecular Biology, České Budějovice, 37005, Czech Republic
| | - Katharina Böttinger
- Biology Centre of the Czech Academy of Sciences, Institute of Plant Molecular Biology, České Budějovice, 37005, Czech Republic.,University of South Bohemia, Faculty of Science, České Budějovice, 37005, Czech Republic
| | - Iva Vrbová
- Biology Centre of the Czech Academy of Sciences, Institute of Plant Molecular Biology, České Budějovice, 37005, Czech Republic
| | - Pavel Neumann
- Biology Centre of the Czech Academy of Sciences, Institute of Plant Molecular Biology, České Budějovice, 37005, Czech Republic
| | - Ingo Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Gatersleben, Stadt Seeland, Germany
| | - Jiří Macas
- Biology Centre of the Czech Academy of Sciences, Institute of Plant Molecular Biology, České Budějovice, 37005, Czech Republic.
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93
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94
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High-throughput analysis unveils a highly shared satellite DNA library among three species of fish genus Astyanax. Sci Rep 2017; 7:12726. [PMID: 29018237 PMCID: PMC5635008 DOI: 10.1038/s41598-017-12939-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 09/20/2017] [Indexed: 01/08/2023] Open
Abstract
The high-throughput analysis of satellite DNA (satDNA) content, by means of Illumina sequencing, unveiled 45 satDNA families in the genome of Astyanax paranae, with repeat unit length (RUL) ranging from 6 to 365 bp and marked predominance of short satellites (median length = 59 bp). The analysis of chromosomal location of 35 satDNAs in A. paranae, A. fasciatus and A. bockmanni revealed that most satellites are shared between the three species and show highly similar patterns of chromosome distribution. The high similarity in satellite DNA content between these species is most likely due to their recent common descent. Among the few differences found, the ApaSat44-21 satellite was present only on the B chromosome of A. paranae, but not on the A or B chromosomes of the two other species. Likewise, the ApaSat20-18 satellite was B-specific in A. paranae but was however present on A and B chromosomes of A. fasciatus and A. bockmanni. The isochromosome nature of B chromosomes in these species was evidenced by the symmetric location of many satDNAs on both B chromosome arms, and the lower symmetry observed in the A. fasciatus BfMa chromosome suggests that it is older than those analyzed in A. paranae and A. bockmanni.
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95
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Yang S, Qin X, Cheng C, Li Z, Lou Q, Li J, Chen J. Organization and evolution of four differentially amplified tandem repeats in the Cucumis hystrix genome. PLANTA 2017; 246:749-761. [PMID: 28668977 DOI: 10.1007/s00425-017-2716-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 05/29/2017] [Indexed: 05/18/2023]
Abstract
Three subtelomeric satellites and one interstitial 5S rDNA were characterized in Cucumis hystrix, and the pericentromeric signals of two C. hystrix subtelomeric satellites along C. sativus chromosomes supported the hypothesis of chromosome fusion in Cucumis. Tandem repeats are chromosome structural fractions consisting of highly repetitive sequences organized in large tandem arrays in most eukaryotes. Differentiation of tandem repeats directly affects the chromosome structure, which contributes to species formation and evolution. Cucumis hystrix (2n = 2x = 24) is the only wild Cucumis species grouped into the same subgenus with C. sativus (2n = 2x = 14), hence its phylogenetic position confers a vital role for C. hystrix to understand the chromosome evolution in Cucumis. However, our knowledge of C. hystrix tandem repeats is insufficient for a detailed understanding of the chromosome evolution in Cucumis. Based on de novo tandem repeat characterization using bioinformatics and in situ hybridization (ISH), we identified and characterized four differentially amplified tandem repeats, Cucumis hystrix satellite 1-3 (CuhySat1-CuhySat3) located at the subtelomeric regions of all chromosomes, and Cucumis hystrix 5S (Cuhy5S) located at the interstitial regions of one single chromosome pair. Comparative ISH mapping using CuhySat1-3 and Cuhy5S revealed high homology of tandem repeats between C. hystrix and C. sativus. Intriguingly, we found signal distribution variations of CuhySat2 and CuhySat3 on C. sativus chromosomes. In comparison to their subtelomeric signal distribution on C. hystrix chromosomes, CuhySat3 showed a pericentromeric signal distribution and CuhySat2 showed both subtelomeric and pericentromeric signal distributions on C. sativus chromosomes. This detailed characterization of four C. hystrix tandem repeats significantly widens our knowledge of the C. hystrix chromosome structure, and the observed signal distribution variations will be helpful for understanding the chromosome evolution of Cucumis.
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Affiliation(s)
- Shuqiong Yang
- State Key Lab of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaodong Qin
- State Key Lab of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Chunyan Cheng
- State Key Lab of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ziang Li
- State Key Lab of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qunfeng Lou
- State Key Lab of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ji Li
- State Key Lab of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jinfeng Chen
- State Key Lab of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
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96
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Garrido-Ramos MA. Satellite DNA: An Evolving Topic. Genes (Basel) 2017; 8:genes8090230. [PMID: 28926993 PMCID: PMC5615363 DOI: 10.3390/genes8090230] [Citation(s) in RCA: 227] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 09/12/2017] [Accepted: 09/13/2017] [Indexed: 12/22/2022] Open
Abstract
Satellite DNA represents one of the most fascinating parts of the repetitive fraction of the eukaryotic genome. Since the discovery of highly repetitive tandem DNA in the 1960s, a lot of literature has extensively covered various topics related to the structure, organization, function, and evolution of such sequences. Today, with the advent of genomic tools, the study of satellite DNA has regained a great interest. Thus, Next-Generation Sequencing (NGS), together with high-throughput in silico analysis of the information contained in NGS reads, has revolutionized the analysis of the repetitive fraction of the eukaryotic genomes. The whole of the historical and current approaches to the topic gives us a broad view of the function and evolution of satellite DNA and its role in chromosomal evolution. Currently, we have extensive information on the molecular, chromosomal, biological, and population factors that affect the evolutionary fate of satellite DNA, knowledge that gives rise to a series of hypotheses that get on well with each other about the origin, spreading, and evolution of satellite DNA. In this paper, I review these hypotheses from a methodological, conceptual, and historical perspective and frame them in the context of chromosomal organization and evolution.
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Affiliation(s)
- Manuel A Garrido-Ramos
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain.
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97
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Utsunomia R, Ruiz-Ruano FJ, Silva DMZA, Serrano ÉA, Rosa IF, Scudeler PES, Hashimoto DT, Oliveira C, Camacho JPM, Foresti F. A Glimpse into the Satellite DNA Library in Characidae Fish (Teleostei, Characiformes). Front Genet 2017; 8:103. [PMID: 28855916 PMCID: PMC5557728 DOI: 10.3389/fgene.2017.00103] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 07/26/2017] [Indexed: 01/21/2023] Open
Abstract
Satellite DNA (satDNA) is an abundant fraction of repetitive DNA in eukaryotic genomes and plays an important role in genome organization and evolution. In general, satDNA sequences follow a concerted evolutionary pattern through the intragenomic homogenization of different repeat units. In addition, the satDNA library hypothesis predicts that related species share a series of satDNA variants descended from a common ancestor species, with differential amplification of different satDNA variants. The finding of a same satDNA family in species belonging to different genera within Characidae fish provided the opportunity to test both concerted evolution and library hypotheses. For this purpose, we analyzed here sequence variation and abundance of this satDNA family in ten species, by a combination of next generation sequencing (NGS), PCR and Sanger sequencing, and fluorescence in situ hybridization (FISH). We found extensive between-species variation for the number and size of pericentromeric FISH signals. At genomic level, the analysis of 1000s of DNA sequences obtained by Illumina sequencing and PCR amplification allowed defining 150 haplotypes which were linked in a common minimum spanning tree, where different patterns of concerted evolution were apparent. This also provided a glimpse into the satDNA library of this group of species. In consistency with the library hypothesis, different variants for this satDNA showed high differences in abundance between species, from highly abundant to simply relictual variants.
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Affiliation(s)
- Ricardo Utsunomia
- Department of Morphology, Institute of Biosciences, São Paulo State UniversityBotucatu, Brazil
| | | | - Duílio M Z A Silva
- Department of Morphology, Institute of Biosciences, São Paulo State UniversityBotucatu, Brazil
| | - Érica A Serrano
- Department of Morphology, Institute of Biosciences, São Paulo State UniversityBotucatu, Brazil
| | - Ivana F Rosa
- Department of Morphology, Institute of Biosciences, São Paulo State UniversityBotucatu, Brazil
| | - Patrícia E S Scudeler
- Department of Morphology, Institute of Biosciences, São Paulo State UniversityBotucatu, Brazil
| | | | - Claudio Oliveira
- Department of Morphology, Institute of Biosciences, São Paulo State UniversityBotucatu, Brazil
| | - Juan Pedro M Camacho
- Departamento de Genética, Facultad de Ciencias, Universidad de GranadaGranada, Spain
| | - Fausto Foresti
- Department of Morphology, Institute of Biosciences, São Paulo State UniversityBotucatu, Brazil
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98
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Novák P, Ávila Robledillo L, Koblížková A, Vrbová I, Neumann P, Macas J. TAREAN: a computational tool for identification and characterization of satellite DNA from unassembled short reads. Nucleic Acids Res 2017. [PMID: 28402514 DOI: 10.1093/nar/gkx257.] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Satellite DNA is one of the major classes of repetitive DNA, characterized by tandemly arranged repeat copies that form contiguous arrays up to megabases in length. This type of genomic organization makes satellite DNA difficult to assemble, which hampers characterization of satellite sequences by computational analysis of genomic contigs. Here, we present tandem repeat analyzer (TAREAN), a novel computational pipeline that circumvents this problem by detecting satellite repeats directly from unassembled short reads. The pipeline first employs graph-based sequence clustering to identify groups of reads that represent repetitive elements. Putative satellite repeats are subsequently detected by the presence of circular structures in their cluster graphs. Consensus sequences of repeat monomers are then reconstructed from the most frequent k-mers obtained by decomposing read sequences from corresponding clusters. The pipeline performance was successfully validated by analyzing low-pass genome sequencing data from five plant species where satellite DNA was previously experimentally characterized. Moreover, novel satellite repeats were predicted for the genome of Vicia faba and three of these repeats were verified by detecting their sequences on metaphase chromosomes using fluorescence in situ hybridization.
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Affiliation(s)
- Petr Novák
- Institute of Plant Molecular Biology, Biology Centre CAS, Ceské Budejovice CZ-37005, Czech Republic
| | - Laura Ávila Robledillo
- Institute of Plant Molecular Biology, Biology Centre CAS, Ceské Budejovice CZ-37005, Czech Republic
| | - Andrea Koblížková
- Institute of Plant Molecular Biology, Biology Centre CAS, Ceské Budejovice CZ-37005, Czech Republic
| | - Iva Vrbová
- Institute of Plant Molecular Biology, Biology Centre CAS, Ceské Budejovice CZ-37005, Czech Republic
| | - Pavel Neumann
- Institute of Plant Molecular Biology, Biology Centre CAS, Ceské Budejovice CZ-37005, Czech Republic
| | - Jirí Macas
- Institute of Plant Molecular Biology, Biology Centre CAS, Ceské Budejovice CZ-37005, Czech Republic
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99
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Novák P, Ávila Robledillo L, Koblížková A, Vrbová I, Neumann P, Macas J. TAREAN: a computational tool for identification and characterization of satellite DNA from unassembled short reads. Nucleic Acids Res 2017; 45:e111. [PMID: 28402514 PMCID: PMC5499541 DOI: 10.1093/nar/gkx257] [Citation(s) in RCA: 174] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 03/23/2017] [Accepted: 04/04/2017] [Indexed: 12/21/2022] Open
Abstract
Satellite DNA is one of the major classes of repetitive DNA, characterized by tandemly arranged repeat copies that form contiguous arrays up to megabases in length. This type of genomic organization makes satellite DNA difficult to assemble, which hampers characterization of satellite sequences by computational analysis of genomic contigs. Here, we present tandem repeat analyzer (TAREAN), a novel computational pipeline that circumvents this problem by detecting satellite repeats directly from unassembled short reads. The pipeline first employs graph-based sequence clustering to identify groups of reads that represent repetitive elements. Putative satellite repeats are subsequently detected by the presence of circular structures in their cluster graphs. Consensus sequences of repeat monomers are then reconstructed from the most frequent k-mers obtained by decomposing read sequences from corresponding clusters. The pipeline performance was successfully validated by analyzing low-pass genome sequencing data from five plant species where satellite DNA was previously experimentally characterized. Moreover, novel satellite repeats were predicted for the genome of Vicia faba and three of these repeats were verified by detecting their sequences on metaphase chromosomes using fluorescence in situ hybridization.
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Affiliation(s)
- Petr Novák
- Institute of Plant Molecular Biology, Biology Centre CAS, Ceské Budejovice CZ-37005, Czech Republic
| | - Laura Ávila Robledillo
- Institute of Plant Molecular Biology, Biology Centre CAS, Ceské Budejovice CZ-37005, Czech Republic
| | - Andrea Koblížková
- Institute of Plant Molecular Biology, Biology Centre CAS, Ceské Budejovice CZ-37005, Czech Republic
| | - Iva Vrbová
- Institute of Plant Molecular Biology, Biology Centre CAS, Ceské Budejovice CZ-37005, Czech Republic
| | - Pavel Neumann
- Institute of Plant Molecular Biology, Biology Centre CAS, Ceské Budejovice CZ-37005, Czech Republic
| | - Jirí Macas
- Institute of Plant Molecular Biology, Biology Centre CAS, Ceské Budejovice CZ-37005, Czech Republic
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100
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Verde I, Jenkins J, Dondini L, Micali S, Pagliarani G, Vendramin E, Paris R, Aramini V, Gazza L, Rossini L, Bassi D, Troggio M, Shu S, Grimwood J, Tartarini S, Dettori MT, Schmutz J. The Peach v2.0 release: high-resolution linkage mapping and deep resequencing improve chromosome-scale assembly and contiguity. BMC Genomics 2017. [PMID: 28284188 DOI: 10.1186/s12864-017-3606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023] Open
Abstract
BACKGROUND The availability of the peach genome sequence has fostered relevant research in peach and related Prunus species enabling the identification of genes underlying important horticultural traits as well as the development of advanced tools for genetic and genomic analyses. The first release of the peach genome (Peach v1.0) represented a high-quality WGS (Whole Genome Shotgun) chromosome-scale assembly with high contiguity (contig L50 214.2 kb), large portions of mapped sequences (96%) and high base accuracy (99.96%). The aim of this work was to improve the quality of the first assembly by increasing the portion of mapped and oriented sequences, correcting misassemblies and improving the contiguity and base accuracy using high-throughput linkage mapping and deep resequencing approaches. RESULTS Four linkage maps with 3,576 molecular markers were used to improve the portion of mapped and oriented sequences (from 96.0% and 85.6% of Peach v1.0 to 99.2% and 98.2% of v2.0, respectively) and enabled a more detailed identification of discernible misassemblies (10.4 Mb in total). The deep resequencing approach fixed 859 homozygous SNPs (Single Nucleotide Polymorphisms) and 1347 homozygous indels. Moreover, the assembled NGS contigs enabled the closing of 212 gaps with an improvement in the contig L50 of 19.2%. CONCLUSIONS The improved high quality peach genome assembly (Peach v2.0) represents a valuable tool for the analysis of the genetic diversity, domestication, and as a vehicle for genetic improvement of peach and related Prunus species. Moreover, the important phylogenetic position of peach and the absence of recent whole genome duplication (WGD) events make peach a pivotal species for comparative genomics studies aiming at elucidating plant speciation and diversification processes.
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Affiliation(s)
- Ignazio Verde
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA), Centro di Ricerca per la Frutticoltura, 00134, Rome, Italy.
| | - Jerry Jenkins
- HudsonAlpha Institute of Biotechnology, Huntsville, AL, USA
| | - Luca Dondini
- Department of Agricultural Sciences (DipSA), University of Bologna, Bologna, Italy
| | - Sabrina Micali
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA), Centro di Ricerca per la Frutticoltura, 00134, Rome, Italy
| | - Giulia Pagliarani
- Department of Agricultural Sciences (DipSA), University of Bologna, Bologna, Italy
| | - Elisa Vendramin
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA), Centro di Ricerca per la Frutticoltura, 00134, Rome, Italy
| | - Roberta Paris
- Department of Agricultural Sciences (DipSA), University of Bologna, Bologna, Italy
- Present address: Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA), Centre of Research for Industrial Crops, 40128, Bologna, Italy
| | - Valeria Aramini
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA), Centro di Ricerca per la Frutticoltura, 00134, Rome, Italy
| | - Laura Gazza
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA), Centro di Ricerca per la Frutticoltura, 00134, Rome, Italy
- Present address: Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA), Research Unit for Cereal Quality, Rome, Italy
| | - Laura Rossini
- Department of Agricultural and Environmental Sciences (DISAA), University of Milan, Milan, Italy
- Parco Tecnologico Padano, Via Einstein, 26900, Lodi, Italy
| | - Daniele Bassi
- Department of Agricultural and Environmental Sciences (DISAA), University of Milan, Milan, Italy
| | - Michela Troggio
- Research and Innovation Centre, Fondazione Edmund Mach (FEM), 38010, San Michele all'Adige, TN, Italy
| | - Shengqiang Shu
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Jane Grimwood
- HudsonAlpha Institute of Biotechnology, Huntsville, AL, USA
| | - Stefano Tartarini
- Department of Agricultural Sciences (DipSA), University of Bologna, Bologna, Italy
| | - Maria Teresa Dettori
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA), Centro di Ricerca per la Frutticoltura, 00134, Rome, Italy
| | - Jeremy Schmutz
- HudsonAlpha Institute of Biotechnology, Huntsville, AL, USA
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
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